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Archive for the ‘Infectious Disease & New Antibiotic Targets’ Category

From the Walter and Eliza Hall Institute of Medical Research: Hobbit and Blimp1 May Be Needed for Local Tissue Immune Response

Reporter: Stephen J Williams, PhD

 

Researchers uncover ‘local heroes’ of immune system

 

22 April 2016
Axel Kallies in the laboratory
Dr Axel Kallies and his team have identified genes that
control a molecular program to protect the body. 
Melbourne researchers have uncovered genes responsible for the way the body fights infection at the point of ‘invasion’ – whether it’s the skin, liver, lungs or the gut.

Research led by Dr Axel Kalliesand Dr Klaas van Gisbergen at the Walter and Eliza Hall Institute of Medical Research, and Dr Laura Mackay from the University of Melbourne at the Peter Doherty Institute for Infection and Immunity has identified the genes Hobit andBlimp1 and found that they control a universal molecular program responsible for placing immune cells at the ‘front lines’ of the body to fight infection and cancer.

The presence of these organ-residing cells, which differ strikingly from their counterparts circulating in the blood stream, is key to local protection against viruses and bacteria.

Walter and Eliza Hall Institute’s Dr Kallies said the human body was fighting disease-causing pathogens every minute of its life. Dr Kallies said identifying how immune cells remain in the part of the body where they are needed most was critical to developing better ways to protect us from infections such as malaria orHIV.

“Discovering these ‘local heroes’ and knowing how the localised immune response is established allows us to find ways to ensure the required cells are positioned where they are needed most,” Dr Kallies said.

“This research will help us understand how immune cells adapt, survive and respond within the organs they protect. This is critical to rid the body of pathogens even before they are established and may also have implications for understanding how the spread of cancer could be prevented.”

The Doherty Institute’s Dr Laura Mackay, who is also an associate investigator with the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, said the factors that control the ‘tissue-residency’ of immune cells – their ability to locally reside in different organs of the body – was previously unknown.

“These results have major implications for developing strategies to induce immune cells in tissues that protect against infectious diseases,” Dr Mackay said.

“It’s a crucial discovery for future vaccine strategies – Hobit and Blimp1 would be key to placing immune cells in the tissues, which we know are really important for protection.”

The findings have just been published in the journal Science.

This research was supported by the Victorian State Government Operational Infrastructure Support and the Australian Government National Health and Medical Research Council Independent Research Institute Infrastructure Support Scheme.

Further information:

Ebru Yaman
Media and Publications Manager
M: 0428 034 089
E: yaman.e@wehi.edu.au

Immune cell ‘survival’ gene key to better myeloma treatments

4 February 2013
Dr Victor Peperzak, Dr Ingela Vikstrom and Associate Professor David Tarlinton in a laboratory
Dr Victor Peperzak (left), Dr Ingela Vikstrom
(centre) and Associate Professor Tarlinton led a
research team that identified a gene that is
essential for survival of antibody-producing cells.
Scientists have identified the gene essential for survival of antibody-producing cells, a finding that could lead to better treatments for diseases where these cells are out of control, such as myeloma and chronic immune disorders.

The discovery that a gene calledMcl1 is critical for keeping this vital immune cell population alive was made by researchers at Melbourne’s Walter and Eliza Hall Institute. Associate Professor David Tarlinton, Dr Victor Peperzak and Dr Ingela Vikstrom from the institute’s Immunology division led the research, which was published today in Nature Immunology.

Antibody-producing cells, also known as plasma cells, live in the bone marrow and make antibodies that provide a person with long-term protection from viruses and bacteria, Associate Professor Tarlinton said. “Plasma cells are produced after vaccination or infection and are responsible for the immune ‘memory’ that can persist in humans for 70 or 80 years. In this study, we found that plasma cells critically rely on Mcl1 for their continued survival and, without it, they die within two days,” he said.

Dr Peperzak said the team was surprised to find that plasma cells used this as a ‘failsafe’ mechanism in controlling their survival. “One of the interesting things we found is that because plasma cells rapidly destroy Mcl-1 proteins within the cell yet depend on it for their survival, they need continuous external signals to tell them to produce more Mcl-1 protein,” Dr Peperzak said. “This keeps the plasma cells under tight control, with Mcl-1 acting like a timer that constantly counts down and, if not reset, instructs the cell to die.”

Plasma cells are vital to the immune response, but can be dangerous if not properly controlled, Associate Professor Tarlinton said. “As with any immune cell, plasma cells are really quite dangerous in many respects and need to be tightly controlled,” he said. “When they are out of control they continue to make antibodies that can be very damaging if there are too many. This happens in conditions such as myeloma – a cancer of plasma cells – and various forms of autoimmunity, such as systemic lupus erythamatosus or rheumatoid arthritis, where there are excessive levels of antibodies.”

Myeloma is a blood cancer that affects more than 1200 Australians each year, and is more common in people over 60. It is caused by the uncontrolled production of abnormal plasma cells in the bone marrow and the build up of damaging antibodies in the blood. Rheumatoid arthritis and lupus are autoimmune diseases in which the antibodies produced by plasma cells attack and destroy the body’s own tissues.

Associate Professor Tarlinton said that his hope was that the discovery could be used to develop new treatments for these conditions. “Myeloma in particular has a very poor prognosis, and is generally considered incurable,” Associate Professor Tarlinton said. “Now that we know Mcl1 is the one essential gene needed to keep plasma cells alive, we have begun ‘working backwards’ to identify all the critical molecules and signals needed to switch on Mcl1 and keep the cells alive. Our hope is that we will identify some point in the internal cell signalling pathway, or a critical external molecule, that could be blocked to stop Mcl-1 being produced by the cell. This would be an important new platform for diseases that currently have no specific or effective treatment, such as myeloma, or offer new treatment options for people who don’t respond well to existing treatments for diseases such as lupus or rheumatoid arthritis.”

This research was supported by the Australian National Health and Medical Research Council, Multiple Myeloma Research Foundation, European Molecular Biology Organization and the Victorian Government.

Read the article in Nature ImmunologyMcl-1 is essential for the survival of plasma cells.

Further information:

Liz Williams
Media and Publications Manager
P: +61 3 9345 2928
M: +61 405 279 095
E: williams@wehi.edu.au

Australian researchers find immune ‘kill switch’

as reported in http://www.abc.net.au/am/content/2012/s3649437.htm

Martin Cuddihy reported this story on Friday, December 7, 2012 08:12:00

TONY EASTLEY: For want of a better description we all apparently have an immune system ‘kill switch’.

Melbourne researchers have discovered why the body reacts the way it does when under stress from a severe infection.

They’ve found that the immune system switch destroys blood stem cells, and they’ve also discovered how to turn it off.

The discovery could mean a faster recovery rates from blood infections and from bouts of chemotherapy.

Martin Cuddihy reports.

MARTIN CUDDIHY: Worldwide, sepsis or blood poisoning is one of the leading causes of death in the intensive care units of hospitals.

When someone develops the condition the body goes into shock and blood stem cells start dying.

SETH MASTERS: You can think about it like suicide. The cells know that they should die to try and get rid of the infection but if the infection is overwhelming as it is with sepsis, then we need them to stay alive to help fight any infection.

MARTIN CUDDIHY: Dr Seth Masters from the Walter and Eliza Hall Institute in Melbourne is part of a research team that’s discovered the kill switch that tells cells when they should die.

Normally that’s a good thing, except when there’s a massive infection.

SETH MASTERS: You have to repopulate those immune cells somehow and these come from progenitor cells in the bone marrow and we think that this cell death pathway is something we can block to try and help the new cells regenerate to fight the infections better.

MARTIN CUDDIHY: So what does this cell receptor normally do?

SETH MASTERS: We are not entirely clear about that. We think that when a progenitor cell gets infected it’d be really bad if it stayed alive for too long cause it would pass that infection along to all of its daughters and sons.

So instead of staying infected, it just commits suicide and dies via this new pathway.

MARTIN CUDDIHY: Dr Masters is part of an international research team that’s found blocking a certain cell receptor stops blood cells from dying.

The researchers hope the discovery could lead to a treatment for sepsis and a way to help boost the immune system of cancer patients undergoing chemotherapy.

SETH MASTERS: I think that probably the most likely avenue where it could be of use is in trying to help recovery from chemotherapy. That’s a period during which we really need as many cells to mobilise out of the bone marrow into the periphery as possible to try and fight any potential infections that might be coming along.

And so we think that this cell death pathway might be stopping that from happening quickly and if we can inhibit it, we can make it go faster.

MARTIN CUDDIHY: Does that mean then that someone could be subjected to a more intense round of chemotherapy if this was to work and therefore you could boost their immune system following that round of chemo?

SETH MASTERS: Yeah, that does seem like a relatively attractive proposal. It is not something we have actually validated just yet but that would have to be on the cards if we can do some more research down those lines.

MARTIN CUDDIHY: The findings are published today in the medical journal Immunity.

TONY EASTLEY: Martin Cuddihy.

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New Class of Immune System Stimulants: Cyclic Di-Nucleotides (CDN): Shrink Tumors and bolster Vaccines, re-arm the Immune System’s Natural Killer Cells, which attack Cancer Cells and Virus-infected Cells

Reporter: Aviva Lev-Ari, PhD, RN

 

The Immunotherapeutics and Vaccine Research Initiative (IVRI), a UC Berkeley effort funded by Aduro Biotech, Inc.

The initiative was officially launched at an evening reception on March 24, the eve of a one-day symposium at UC Berkeley titled “Harnessing the Immune System to Fight Cancer and Infectious Diseases.” The symposium was jointly sponsored by UC Berkeley’s Henry Wheeler Center for Emerging and Neglected Diseases and Cancer Research Laboratory.

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Aduro Biotech helps launch new immunotherapy, vaccine effort

UC Berkeley cancer immunologists are teaming up with colleagues working on infectious disease to create a new Immunotherapeutics and Vaccine Research Initiative, fueled by $7.5 million in funding from Aduro Biotech Inc., a Berkeley company that develops immunotherapies for cancer and other diseases.

The Immunotherapeutics and Vaccine Research Initiative (IVRI), a UC Berkeley effort funded by Aduro Biotech, Inc.

Aduro’s three years of funding, with the potential for three more, will support work on some of today’s most promising techniques for stimulating the immune system to fight off cancer and infections. These may include investigating a new class of immune system stimulants called cyclic di-nucleotides, which have shown promise in shrinking tumors and bolstering vaccines against tuberculosis, and research that could help re-arm the immune system’s natural killer cells, which normally attack cancer cells and virus-infected cells, to better fight tumors.

“We’re increasingly finding that immune stimulants associated with disease-causing microbes work as cancer therapies, and conversely, that immunotherapies for cancer may have application in fighting infectious disease,” said IVRI director David Raulet, a professor and co-chair of the Department of Molecular and Cell Biology. “Bringing infectious disease and cancer researchers together in a synergistic research effort at UC Berkeley and Aduro Biotech is an exciting and unique idea, and could be where the next generation of therapies will come from.”

Aduro already uses some of UC Berkeley’s technology, including attenuated Listeria monocytogenes mutants and methods to engineer these bacteria to stimulate the immune system as vaccines for immunotherapy. This technology, pioneered by Dan Portnoy, a UC Berkeley professor who has joint appointments in the Department of Molecular and Cell Biology and the infectious diseases and vaccinology division of the School of Public Health, has been further refined by Aduro scientists and is now being employed in Phase IIB clinical trials for vaccines against pancreatic cancer and mesothelioma.

Stephen Isaacs

Stephen Isaacs, CEO of Aduro Biotech, at the launch of the IVRI on March 23. (Peg Skorpinski photos)

“Through this unique collaboration, there is tremendous opportunity to improve our understanding of the immune system’s potential to serve as an important weapon in treating cancer and infectious disease,” said Stephen T. Isaacs, chairman, president and CEO of Aduro Biotech. “By combining UC Berkeley’s leading research and academic resources with innovative technology platforms, such as those developed by Aduro, we are confident that this initiative will lead to an improved understanding of, and potential treatments for, some of the most devastating diseases.”

The initiative was officially launched at an evening reception on March 24, the eve of a one-day symposium at UC Berkeley titled “Harnessing the Immune System to Fight Cancer and Infectious Diseases.” The symposium was jointly sponsored by UC Berkeley’s Henry Wheeler Center for Emerging and Neglected Diseases and Cancer Research Laboratory.

Berkeley research revived cancer immunotherapy

Much of the excitement around combining these two areas — the immunology of cancer and the immunology of infectious disease — comes from the amazing success of immunotherapy against cancer, which started with the work of James Allison when he was a professor of immunology at UC Berkeley and director of the Cancer Research Laboratory from 1985 to 2004. Allison, now at the University of Texas MD Anderson Cancer Center, discovered a way to release a brake on the body’s immune response to cancer that has proved highly successful at unleashing the immune system to attack melanoma and is being tried against other types of cancer.

James Allison

James Allison, whose UC Berkeley work led to the renaissance of cancer immunotherapy.

Allison’s work revived attempts to rev up the immune system to fight cancer, and has led to many new avenues for creating cancer immune-therapies. In addition to Allison’s technique, which uses an antibody that blocks an immune suppressor called CTLA4, antibodies that block another immune suppressor, PD1, have been successful in treating melanoma, renal cancer and a type of lung cancer. Both CTLA4 and PD1 antibodies are now FDA-approved as cancer therapies.

Another promising avenue involves a protein in cells that responds to foreign DNA to launch an innate immune response — the first response of the body’s immune system. The protein, dubbed STING, is triggered by small molecules called cyclic di-nucleotides (CDN), and makes immune cells release interferon and other cytokines that activate disease-fighting T cells and stimulate the production of antibodies that together kill invading pathogens and destroy cancer cells. Listeria bacteria, for example, secrete a CDN directly into infected cells that activates STING.

Russell Vance, a UC Berkeley professor of molecular and cell biology and current head of the Cancer Research Laboratory, discovered several years ago that the chemical structure of these di-nucleotides is critical to their ability to work in humans. Aduro has since developed a CDN designed to work in humans and found that injecting it directly into a tumor in mice caused the tumor to shrink.

“It’s amazing how these discoveries made by infectious disease researchers have given us an exciting new approach to treat cancer,” Raulet said. “These really are areas that have a lot to say to each other.”

Another IVRI-affiliated researcher, Sarah Stanley, an assistant professor of public health, has found evidence that CDNs can help improve the imperfect vaccines we have today against tuberculosis.

Researchers at UC Berkeley will have access to Aduro’s novel technology platforms for research use, including its STING pathway activators, proprietary monoclonal antibodies and the engineered listeria bacteria, referred to as LADD (listeria attenuated double-deleted).

David Raulet

David Raulet, professor of molecular and cell biology and director of IVRI.

Raulet’s own research on natural killer or NK cells of the immune system has contributed to making these cells a new focus of cancer research. Revving up T cells is the goal of most immunotherapies today, but other immune cells, including NK cells, also attack tumors. As tumors advance, NK cells inside the tumors appear to become desensitized, he said. Recent research shows that some cytokines and other immune mediators Raulet discovered are able to “wake them up” and get them to resume their elimination of cancer cells.

“NK cell immunotherapies are very likely to be the next generation to complement T cell immunotherapies,” he predicted.

By focusing on fundamental scientific research to understand the immune system’s biochemical tools and signaling pathways, how the immune system recognizes invaders and how immune cells talk to one another, the IVRI has the potential to discover new ways to selectively target and cure many human diseases.

“The IVRI is a marriage of cancer immunotherapy and infectious disease immunology, where therapies in one area can be effective in the other, and observations in one can be applied to the other,” Raulet said. “It’s exciting to think that drugs tested first in diseases like cancer might have an impact on neglected diseases in the developing world, and that it can work in the other direction too.”

RELATED INFORMATION

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CRISPR/Cas9 and HIV1, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 2: CRISPR for Gene Editing and DNA Repair

CRISPR/Cas9 and HIV1

Larry H. Bernstein, MD, FCAP, Curator

LPBI

Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus

Hirotaka EbinaNaoko MisawaYuka Kanemura & Yoshio Koyanagi

Scientific Reports 2013; 2510(3)   http://dx.doi.org:/10.1038/srep02510

Even though highly active anti-retroviral therapy is able to keep HIV-1 replication under control, the virus can lie in a dormant state within the host genome, known as a latent reservoir, and poses a threat to re-emerge at any time. However, novel technologies aimed at disrupting HIV-1 provirus may be capable of eradicating viral genomes from infected individuals. In this study, we showed the potential of the CRISPR/Cas9 system to edit the HIV-1 genome and block its expression. When LTR-targeting CRISPR/Cas9 components were transfected into HIV-1 LTR expression-dormant and -inducible T cells, a significant loss of LTR-driven expression was observed after stimulation. Sequence analysis confirmed that this CRISPR/Cas9 system efficiently cleaved and mutated LTR target sites. More importantly, this system was also able to remove internal viral genes from the host cell chromosome. Our results suggest that the CRISPR/Cas9 system may be a useful tool for curing HIV-1 infection.

 

Integration of reverse transcribed viral DNA into the host cell genome is an essential step during the HIV-1 life cycle1. The integrated retroviral DNA is termed a provirus, which serves as the fundamental source of viral protein production. HIV-1 gene expression is regulated by LTR promoter and enhancer activities, where cellular transcription factors such as NF-κB, SP-1 and TBP bind to promote RNA polymerase II processivity. Subsequently, Tat protein is expressed from early double-spliced transcripts and binds to the trans activation response (TAR) region of HIV-1 RNA for its efficient elongation2.

Latent infection occurs when the HIV-1 provirus becomes transcriptionally inactive, resulting in a latent reservoir that has become the main obstacle in preventing viral eradication from HIV-1 infected individuals. However, the mechanisms of viral silencing and reactivation remain incompletely understood3. Previous studies have suggested that the position of the integration site strongly influences viral gene expression and may be one of the determinants of HIV-1 latency4. While highly active anti-retroviral therapy (HARRT) has dramatically decreased mortality from HIV-1 infection, there is currently no effective strategy to target the latent form of HIV-1 proviruses5.

Over the last decade, novel genome-editing methods that utilize artificial nucleases such as zinc finger nucleases (ZFNs)6 and transcription activator like-effector nucleases (TALENs)7 have been developed. These molecularly engineered nucleases recognize and cleave specific nucleotide sequences in target genomes for digestion, resulting in various mutations such as substitutions, deletions and insertions induced by host DNA repair machinery. These technologies have enabled the production of genome-manipulated animals in a wide range of species such as Drosophila8, Zebrafish9 and Rat10. However, ZFNs or TALENs remain somewhat difficult and time-consuming to design, develop, and empirically test in a cellular context11. Recently, a third genome-editing method was developed based on clustered regularly interspaced short palindromic repeat (CRISPR) systems. CRISPR systems were originally identified in bacteria and archaea12 as part of an adaptive immune system, dependent on a complex consisting of CRISPR RNAs (crRNAs) and CRISPR-associated (Cas) proteins to degrade complimentary sequences of invading viral and plasmid DNA. Mali et al. created a novel version of the genome-editing tool applicable to mammalian cells, termed the CRISPR/Cas9 system, which is based on modifications of the Streptococcus pyogenes type II CRISPR system in crRNA fused to trans-encoded tracrRNA13. This CRISPR/Cas9 system is composed of guide RNA (gRNA) and a human codon-optimized Cas9 nuclease that forms an RNA-protein complex to digest unique target sequences matching those of gRNA. The CRISPR/Cas9 system can be utilized by simple transfection of designed gRNA and a humanized Cas9 (hCas9) expression plasmid into target mammalian cells, making it a promising tool for various applications.

In this study, we tested the ability of the CRISPR/Cas9 system to suppress HIV-1 expression by editing HIV-1 integrated proviral DNA. Cas9 and gRNA, designed to target HIV-1 LTR, were transfected and significantly inhibited LTR-driven expression under the control of Tat. This LTR-targeted CRISPR/Cas9 system can also excise provirus from the cellular genome.

 

http://www.nature.com/article-assets/npg/srep/2013/130826/srep02510/images_hires/w926/srep02510-f2.jpg

CRISPR/Cas9 system can target the latent form of HIV-1 provirus in Jurkat cell

Because the putative latently infected cells are CD4+ T cells, we next tested the genome editing potential of the CRISPR/Cas9 system in these cells.

…..

 

In this study, we successfully disrupted the expression of HIV-1 provirus utilizing the CRISPR/Cas9 system (Fig. 1). Importantly, this disruption not only restricted transcriptionally active provirus, it also blocked the expression of latently integrated provirus (Fig. 3). Cas9 proteins are predicted to contain RuvC and HNH motifs15, which possess autonomous ssDNA cleavage activity. Interestingly, mutants lacking one of the motifs become nicking endonucleases16. It is plausible that the independent nicking activity of each domain may enhance efficient access to the heterochromatin state of latently integrated provirus. Another possibility is that Cas9 has a highly efficient target surveillance system similar to what has been previously reported for the Cas3 system17.

T6 gRNA that targeted the NF-κB binding site, also strongly suppressed the LTR promoter activity (Fig. 1). However, the effect was weaker than that of T5 gRNA. In this study we used an LTIG vector modified from the LTR of HIV-1 strain NL4-3 that possesses two adjacent NF-κB binding sites18. The T6 target site is at the end of the 5′ NF-κB binding site, meaning that mutations may not completely render transcription inactive since the 3′ NF-κB binding site may remain functional. On the other hand, T5 gRNA that targeted TAR, is profoundly effective in disrupting HIV-1 gene expression. The putative cleavage site was positioned at the neck of the stem loop region of TAR, which is critical for Cyclin T1-Tat-TAR ternary complex formation19. Therefore, the TAR sequence may be one of the best targets for blocking HIV-1 provirus expression. Target specificity of the CRISPR/Cas system is very high and a single mutation can disrupt targeting20, meaning that some provirus may escape from this genome-editing machinery if mutations arise in target sequences. However, given that the TAR region is relatively conserved and there is little variation among HIV-1 subtypes21, it could still be an appropriate target for the elimination of latently infected provirus.

Perhaps the most important finding in this study is that we could excise provirus from the host genome of HIV-1 infected cells, which may provide a ray of hope to eradicate HIV-1 from infected individuals. However, there are numerous hurdles that must be cleared before utilizing genome editing for HIV-1 eradication therapies such as gene therapy. First, the efficiency of genome-editing and/or proviral excision should be quantified in HIV infected primary cells, including latently infected CD4+ quiescent T cells. Second, an efficient delivery system must be developed. Fortunately, the CRISPR/Cas9 system has the advantage in size compared with TALENs22. Thus, the CRISPR system has the potential to be delivered by lentivirus vectors, whereas TALENs do not because of their large size and repeat sequences23. The final hurdle concerns possible off-target effects, which are pertinent concerns for all genome-editing strategies that may lead to nonspecific gene modification events. If Cas9 has off-target effects, then removal of the off-target activity may be the best approach before utilizing CRISPR/Cas system for anti-HIV treatment.

 

Elimination of HIV-1 Genomes from Human T-lymphoid Cells by CRISPR/Cas9 Gene Editing

Rafal KaminskiYilan ChenTracy FischerEllen TedaldiAlessandro Napoli,Yonggang ZhangJonathan KarnWenhui Hu & Kamel Khalili

Scientific Reports 6, Article number: 22555 (2016)   http://dx.doi.org:/10.1038/srep22555

 

We employed an RNA-guided CRISPR/Cas9 DNA editing system to precisely remove the entire HIV-1 genome spanning between 5′ and 3′ LTRs of integrated HIV-1 proviral DNA copies from latently infected human CD4+ T-cells. Comprehensive assessment of whole-genome sequencing of HIV-1 eradicated cells ruled out any off-target effects by our CRISPR/Cas9 technology that might compromise the integrity of the host genome and further showed no effect on several cell health indices including viability, cell cycle and apoptosis. Persistent co-expression of Cas9 and the specific targeting guide RNAs in HIV-1-eradicated T-cells protected them against new infection by HIV-1. Lentivirus-delivered CRISPR/Cas9 significantly diminished HIV-1 replication in infected primary CD4+ T-cell cultures and drastically reduced viral load in ex vivo culture of CD4+ T-cells obtained from HIV-1 infected patients. Thus, gene editing using CRISPR/Cas9 may provide a new therapeutic path for eliminating HIV-1 DNA from CD4+ T-cells and potentially serve as a novel and effective platform toward curing AIDS.

 

AIDS remains a major public health problem, as over 35 million people worldwide are HIV-1-infected and new infections continue at steady rate of greater than two million per year. Antiretroviral therapy (ART) effectively controls viremia in virtually all HIV-1 patients and partially restores the primary host cell (CD4+ T-cells), but fails to eliminate HIV-1 from latently-infected T-cells1,2. In latently-infected CD4+ T cells, integrated proviral DNA copies persist in a dormant state, but can be reactivated to produce replication-competent virus when T-cells are activated, resulting in rapid viral rebound upon interruption of antiretroviral treatment3,4,5,6,7,8. Therefore, most HIV-1-infected individuals, even those who respond very well to ART, must maintain life-long ART due to persistence of HIV-1-infected reservoir cells. During latency HIV infected cells produce little or no viral protein, thereby avoiding viral cytopathic effects and evading clearance by the host immune system. Because the resting CD4+ memory T-cell compartment9is thought to be the most prominent latently-infected cell pool, it is a key focus of research aimed at eradicating latent HIV-1 infection.

Recent efforts to eradicate HIV-1 from this cell population have used primarily a “shock and kill” approach, with the rationale that inducing HIV reactivation in CD4+ memory T-cells may trigger elimination of virus-producing cells by cytolysis or host immune responses. For example, epigenetic modification of chromatin structure is critical for establishing viral reactivation. Consequently, inhibition of histone deacetylase (HDAC) by Trichostatin A (TSA) and vorinostat (SAHA) led to reactivation of latent virus in cell lines10,11,12. Accordingly, other HDACi, including vorinostat, valproic acid, panobinostat and rombidepsin have been tested ex vivo and have led, in the best cases, to transient increases in viremia13,14. Similarly, protein kinase C agonists, can potently reactivate HIV either singly or in combination with HDACi15,16. However, there are multiple limitations of this approach: (i) since a large fraction of HIV genomes in this reservoir are non-functional, not all integrated provirus can produce replication-competent virus17; (ii) total numbers of CD4+ T cells reactivated from resting CD4+ T cell HIV-1 reservoirs, has been found by viral outgrowth assays to be much smaller than the numbers of cells infected, as detected by PCR-based assays, suggesting that not all cells within this reservoir are reactivated18; (iii) the cytotoxic T lymphocyte (CTL) immune response is not sufficiently robust to eliminate the reactivated infected cells19 and (iv) uninfected T-cells are not protected from HIV infection and can therefore sustain viral rebound.

These observations suggest that a cure strategy for HIV-1 infection should include methods that directly eliminate the proviral genome from the majority of HIV-1-positive cells, including CD4+ T-cells, and protect cells from future infection, with little or no harm to the host. The clustered, regularly-interspaced, short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) nuclease has wide utility for genome editing in a broad range of organisms including yeast, Drosophila, zebrafish, C. elegans, and mice, and has been applied in a broad range of in vivo and in vitro studies toward human diseases20,21,22,23,24. Recently we modified the CRISPR/Cas9 system to enable recognition of specific DNA sequences positioned within the HIV-1 promoter spanning the 5′ long terminal sequence (LTR)25,26. Using this modified system, we now demonstrate excision of integrated copies of the proviral DNA fragment from a latently HIV-1-infected human T-lymphoid cell line, completely eliminating HDAC inhibition-elicited viral production. Results of whole-genome sequencing and comprehensive bioinformatic analysis ruled out any genotoxicity to host cell DNA. Further, we found that lentivirally-delivered CRISPR/Cas9 reduces viral replication upon HIV-1 infection of primary cultured CD4+ T-cells. The results point toward this approach as a promising potential therapeutic avenue to eradicating HIV-1 from T reservoir cells of host patients, to prevent AIDS re-emergence.

 

Despite its remarkable therapeutic success and efficacy, ART treatment is unable to eradicate HIV-1 from infected patients who must therefore undergo life-long treatment. A new therapeutic strategy is thus needed in order to achieve permanent remission allowing patients to stop ART and reduce it’s attendant costs and potential long-term side effects. Our findings address key barriers to this goal, as we developed CRISPR/Cas9 techniques that eradicated integrated copies of HIV-1 from human CD4+ T-cells, inhibited HIV-1 infection in primary cultured human CD4+ T-cells, and suppressed viral replication ex vivo in peripheral blood mononuclear cells (PBMCs) and CD4+ T-cells of HIV-1+ patients. They also address a further key issue, providing evidence that such gene editing effectively impedes viral replication without causing genotoxicity to host DNA or eliciting destructive effects via host cell pathways. Prior studies using gene editing based on zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and CRISPR/Cas9 systems prompted much interest in their potential abilities to suppress viral infection, either by altering virus receptors or introducing mutations in the viral genome (for review see26,30). All these studies suggest that gene editing strategies can be engineered for targeting specific regions of the viral genome and once efficiently delivered to infected cells, their robust antiviral activity effectively suppresses viral replication. However, there are several important issues that require close attention including the careful design of the targeting strategy that achieves the highest levels of specificity and safety with optimum efficiency of editing.

In this study, due to the complexity associated with determination of the sites and numbers of randomly integrated proviral HIV-1 DNA in in vitro infected primary cell culture and the difficulty in full scale characterization of the InDel/Excision by Cas9/gRNAs in these cells, as a first step, we chose to use the clonal 2D10 cell line as a human T-cell latency model to establish: (i) the ability of Cas9/gRNA in removing the entire coding sequence of the integrated copies of the HIV-1 DNA using ultradeep whole genome sequencing and (ii) investigate its safely related to off-target effects and cell viability. Once these goals were accomplished, we shifted our attention to primary cell culture as well as patient samples to examine the efficiency of the CRISPR/Cas9 in affecting viral DNA load in a laboratory setting.

We found that CRISPR/Cas9 edited multiple copies of viral DNA scattered among the chromosomes. Combined treatment of latently-infected T cells with Cas9 plus gRNAs A and B that recognize specific DNA motifs within the LTR U3 region efficiently eliminated the entire viral DNA fragment spanning between the two LTRs. The remaining 5′ LTR and 3′ LTR cleavage sites by Cas9 and gRNA B in chromosome 1, and by Cas9 and gRNAs A and B in chromosome 16, were joined by host DNA repair at sites located precisely three nucleotides upstream of the PAM. Genome-wide assessment of CRISPR/Cas9-treated HIV-1-infected 2D10 cells clearly verified complete excision of the integrated copies of viral DNA from the second intron of RSBN1 and exon 2 of MSRB1 genes. To address the critical issue related to its specificity and potential off-target and adverse effects, we analyzed this comprehensively and at an unprecedented level of detail, by whole-genome sequencing and bioinformatic analyses. These revealed many naturally-occurring mutations in the genomes of control cells and gRNAs A- and B-mediated HIV-1 DNA eradication. The mutations discovered included naturally-occurring InDels, base excisions, and base substitutions, all of which are, more or less, expected in rapidly growing cells in culture, including Jurkat 2D10 cells. The critical issue is our discovery that none of these mutations resulted from our gene-editing system, as we identified no sequence identities with either gRNA A or B within 1200 nucleotides of any such mutation site. Further, our method of HIV-1 DNA excision had no adverse effects on proximal or distal cellular genes and showed no impact on cell viability, cell cycle progression or proliferation, and did not induce apoptosis, thus strongly supporting its safety at this translational phase, by all in vitromeasures assessed in cultured cells. We found that the expression levels of Cas9 and the gRNAs diminished after several passages and eventually disappeared, but as long as Cas9 and single or multiplex gRNAs were present, cells remained protected against new HIV-1infection.

Another key translational feasibility question we addressed is whether CRISPR/Cas9-mediated HIV-1 eradication can prevent or suppress HIV-1 infection in the most relevant human and patient target cell populations. We provide a critical new advance, by observing in PBMCs and CD4+ T-cells from HIV-1 infected patients that lentivirally-delivered Cas9/gRNAs A/B significantly decreased viral copy numbers and protein levels. Using primer sets directed within the LTR, we amplified and detected residual viral DNA fragments that were not completely deleted in these cells, yet were affected by Cas9/gRNAs and contained InDel mutants near the PAM sequence. These findings verified that CRISPR/Cas9 exerted efficacious antiviral activity in the PBMCs of HIV-1 patients. We also found that introducing Cas9/gRNAs A/B via lentiviral delivery into primary cultured human CD4+ HIV-1JRFL– or HIV-1NL4-3-infected T-cells significantly reduced viral copy numbers, corroborating earlier findings by us and others that stably-integrated HIV-1-directed Cas9 and gRNAs (distinct from our gRNAs A and B used presently) conferred resistance to HIV-1 infection in cell lines31,32. With the notion that CRISPR/Cas9 can target both integrated, as well as episomal DNA sequences, as evidenced by its editing ability of various human viruses as well as plasmid DNAs in either configuration31,32,33,34,35,36, it is likely that both the integrated as well as pre-integrated, free-floating intracellular HIV-1 DNA are edited by Cas9/gRNA.

As noted, during the course of our studies no ART was included prior to the treatment with CRISPR/Cas9 as our goal in this study was to determine the extent of viral suppression during the productive stage of viral infection. We observed a significant level of suppression suggesting that CRISPR/Cas9 may effectively disable expression of the functionally active integrated copies of HIV-1 DNA in the host chromosome. This notion is supported by our observations using 2D10 CD4+ T-cells where the latent copies of HIV-1 that are integrated in chromosomes 1 and 16 were effectively eliminated by CRISPR/Cas9. Our future studies are aimed to address the impact of CRISPR/Cas9 in in vitro infected CD4+ T-cells where the virus is controlled by ART and a cohort of naïve and ART-treated patient CD4+ T-cells. Results from these studies should determine whether or not, in the context of ART, the virus enters into the latent stage and remains responsive to CRISPR/Cas9. Of note, results from these ex vivo studies using ART treated patient PBMCs and CD4+ T-cells show that CRISPR/Cas9 effectively suppresses viral replication by introducing InDel mutations.

Our findings show comprehensively and conclusively that the entire coding sequence of host-integrated HIV-1 was eradicated in human 2D10 T cells, providing a strong first step of support for potential translatability of such a system to T-cell-directed HIV-1 therapies in patients. The complete absence of genomic and off-target functional effects in all assays also provides critical support for the promise of developing this approach for future therapeutic applications.

When evaluating a therapeutic strategy based on CRISPR/Cas9, it is critical to understand that not only will HIV-1 be eliminated from latently infected cells, but the majority of uninfected cells will become resistant to HIV infection. Thus, there is a high likelihood that rebounding viral infections will be contained by the resistant cells. Still, some formidable challenges remain before this type of strategy can be implemented. First, it will be important to maximize elimination of viral sequences from patients. This will require analysis of the HIV-1 quasi-species harbored by patients’ CD4+ T-cells and design of suitable, i.e. personalized CRISPRs. Second, improved delivery of CRISPR/Cas9 will be required to target the majority of circulating T-cells. In summary, our novel ex vivo findings that our lentiviral delivery-based approach reduced HIV-1 DNA copy numbers and protein levels in PBMCs of HIV-1 infected patients provides strong proof-of-concept evidence that CRISPR/Cas9 can be effectively utilized as part of HIV Cure strategies.

 

The therapeutic application of CRISPR/Cas9 technologies for HIV    PreviewFull text HTML   PDF

Sheena SaaymanabStuart A AlibKevin V MorrisacMarc S Weinberg*abd

Expert Opinion on Biological Therapy 2015;  15(6): 819-830    http://dx.doi.org:/10.1517/14712598.2015.1036736

Introduction: The use of antiretroviral therapy has led to a significant decrease in morbidity and mortality in HIV-infected individuals. Nevertheless, gene-based therapies represent a promising therapeutic paradigm for HIV-1, as they have the potential for sustained viral inhibition and reduced treatment interventions. One new method amendable to a gene-based therapy is the clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein-9 nuclease (Cas9) gene editing system.

Areas covered: CRISPR/Cas9 can be engineered to successfully modulate an array of disease-causing genetic elements. We discuss the diverse roles that CRISPR/Cas9 may play in targeting HIV and eradicating infection. The Cas9 nuclease coupled with one or more small guide RNAs can target the provirus to mediate excision of the integrated viral genome. Moreover, a modified nuclease-deficient Cas9 fused to transcription activation domains may induce targeted activation of proviral gene expression allowing for the purging of the latent reservoirs. These technologies can also be exploited to target host dependency factors such as the co-receptor CCR5, thus preventing cellular entry of the virus.

Expert opinion: The diversity of the CRISPR/Cas9 technologies offers great promise for targeting different stages of the viral life cycle, and have the capacity for mediating an effective and sustained genetic therapy against HIV.

Genetic therapy for HIV/AIDS

Ananthalakshmi PoluriMarc van Maanen & Richard E Sutton

Expert Opinion on Biological Therapy Sept 2003; 3(6):951-963

 

Towards a durable RNAi gene therapy for HIV-AIDS

Ben Berkhout & Olivier ter Brake

Expert Opinion on Biological Therapy  Feb 2009; 9(2): 161-170

 

 

 

 

 

 

 

 

Read Full Post »

Digital PCR

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

GEN Roundup: Digital PCR Advances Partition by Partition  

By Partitioning Samples Digital PCR Is Lowering Detection Limits and Enabling New Applications

GEN  Mar 1, 2016 (Vol. 36, No. 5)       http://www.genengnews.com/gen-articles/gen-roundup-digital-pcr-advances-partition-by-partition/5697

 

  • Digital PCR (dPCR) has generated intense interest because it is showing potential as a clinical diagnostics tool. It has already proven to be a useful technique for any application where extreme sensitivity or precise quantification is essential, such as identifying mutations or copy number variations in tumor cells, or examining gene expression at the single-cell level.

    GEN interviewed several dPCR experts to find out specifically why the technique is increasing in popularity. GEN also asked the experts to envision dPCR’s future capabilities.

  • GEN: What makes dPCR technology such a superior tool for discovery and diagnostic applications?

    Dr. Shelton The high levels of sensitivity, precision, and reproducibility in DNA and quantification are the major strengths of dPCR. The technology is robust where differences in primer efficiency or the presence of sample-specific PCR inhibitors are trivial to the final quantification through an end-point amplification reaction.

    This provides value to discovery as a trusted tool for validating potential biomarkers and hypotheses generated by broad profiling techniques such as microarrays or next-generation sequencing (NGS). In diagnostics applications, the reproducibility and rapid results of dPCR are critical for labs around the world to quickly compare and share data, especially for ultra-low detection of DNA where variability is high.

    Dr. Garner Digital PCR provides a precise direct counting approach for single molecule detection, thereby providing a straightforward process for the absolute quantification of nucleic acids in samples. One of the biggest advantages of using a system such as ours is its ability to do real-time reads on digital samples. When samples go through PCR, their results are recorded after each cycle.

    These results build a curve, and customers can analyze the data if something went wrong. If it isn’t a clean read—from either a contamination issue, primer-dimer issue, or off-target issue—the curve isn’t the classic PCR curve.

    Dr. Menezes Digital PCR allows absolute quantification of target concentration in samples without the need for standard curves. Obtaining consistent, precise, and absolute quantification with regular qPCR is dependent on standard curve generation and amplification efficiency calculations, which can introduce errors.

    Ms. Hibbs At MilliporeSigma Cell Design Studio, the implementation of dPCR has improved and accelerated the custom cell engineering workflow. After the application of zinc finger nuclease or CRISPR/Cas to create precise genetic modifications in mammalian cell lines, dPCR is used to characterize the expected frequency of homologous recombination and develop a screening strategy based on this expected frequency.

    In some cell lines, homologous recombination occurs at a low frequency. In such cases, dPCR is used to screen cell pools and subsequently identify rare clones having the desired mutation. Digital PCR is also used to accurately and expeditiously measure target gene copy number. It is used this way, for example, in polyploid cell lines.

    Dr. Price The ability to partition genomic samples to a level that enables robust detection of single target molecules is what sets dPCR apart as an innovative tool. Each partition (droplet in the case of the RainDrop System) operates as an individual PCR reaction, allowing for sensitive, reproducible, and precise quantification of nucleic acid molecules without the need for reference standards or endogenous controls.

    Partitioning also provides greater tolerance to PCR inhibitors compared to quantitative PCR (qPCR). In doing so, dPCR can remedy many shortcomings of qPCR by transforming the analog, exponential nature of PCR into a digital signal.

    Mr. Wakida Digital PCR is an ideal technology for detecting rare targets at concentrations of 0.1% or lower. By partitioning samples prior to PCR, exceptionally rare targets can be isolated into individual partitions and amplified.

    Digital PCR produces absolute quantitative results, so in some respects, it is easier than qPCR because it doesn’t require a standard curve, with the added advantages of being highly tolerant of inhibitors and being able to detect more minute fold changes. Absolute quantification is useful for generating reference standards, detecting viral load, and preparing NGS libraries.

  • GEN: In what field do you think dPCR will have the greatest impact in the future?

    Dr. Shelton dPCR will have a great impact on precision medicine, especially in liquid biopsy analysis. Cell-free DNA from bodily fluids such as urine or blood plasma can be analyzed quickly and cost-effectively using dPCR. For example, a rapid dPCR test can be performed to determine mutations present in a patient’s tumor and help drive treatment decisions.

    Iterative monitoring of disease states can also be achieved due to the relatively low cost of dPCR, providing faster response times when medications are failing. Gene editing will also be greatly impacted by dPCR. Digital PCR enables refinement and optimization of gene-editing tools and conditions. Digital PCR also serves as quality control of therapeutically modified cells and viral transfer vectors used in gene-therapy efforts.

    Dr. Garner The BioMark™ HD system combines dPCR with simultaneous real-time data for counting and validation. This capability is important for applications such as rare mutation detection, GMO quantitation, and aneuploidy detection—where false positives are intolerable and precision is paramount.

    Any field that requires precision and the ability to detect false positives is a likely target for Fluidigm’s dPCR. Suitable applications include detecting and quantifying cancer-causing genes in patients’ cells, viral RNA that infects bacteria, or fetal DNA in an expectant mother’s plasma.

    Dr. Menezes This technology is particularly useful for samples with low frequency sequences as, for example, those containing rare alleles, low levels of pathogen, or low levels of target gene expression. Teasing out fine differences in copy number variants is another area where this technology delivers more precise data.

    Ms. Hibbs Digital PCR overcomes limitations associated with low-abundance template material and quantification of rare mutations in a high background of wild-type DNA sequence. For this reason, dPCR is poised to have significant impacts in diverse clinical applications such as detection and quantification of rare mutations in liquid biopsies, detection of viral pathogens, and detection of copy number variation and mosaicism.

    Dr. Price Due to its high sensitivity, precision, and absolute quantification, the RainDrop dPCR has the potential to extend the range of nucleic acid analysis beyond the reach of other methods in a number of applications that could lend themselves to diagnostic, prognostic, and predictive applications. The precision of dPCR can be extremely useful in applications that require finer measures of fold change and rare variant detection.

    Digital PCR is suitable for addressing varied research and clinical challenges. These include the early detection of cancer, pathogen/viral detection and quantitation, copy number variation, rare mutation detection, fetal genetic screening, and predicting transplant rejection. Additional applications include gene expression analysis, microRNA analysis, and NGS library quantification.

    Mr. Wakida Digital PCR will have an impact on applications for detecting rare targets by enabling investigators to complement and extend their capabilities beyond traditionally employed methods. One such application is using dPCR to monitor rare targets in peripheral blood, as in liquid biopsies.

    The monitoring of peripheral blood by means of dPCR has been described in several peer-reviewed articles. In one such article, investigators considered the clinical value of Thermo’s QuantStudio™ 3D Digital PCR system for the detection of circulating DNA in metastatic colorectal cancer (Dig Liver Dis. 2015 Oct; 47(10): 884–90).

  • GEN: Is there a new technology on the horizon that will increase the speed and/or efficiency of dPCR?

    Dr. Shelton High-throughput sample analysis can be an issue with some dPCR systems. However, Bio-Rad’s Automated Droplet Generator allows labs to process 96 samples simultaneously, a capability that eliminates user-to-user variability and minimizes hands-on time.

    We also want users to get the most information from one sample. Therefore, we are focused on expanding the multiplexing capabilities of our system. In development at Bio-Rad are new technologies that increase the multiplexing capabilities without loss of specificity or accuracy in the downstream workflow.

    Dr. Garner Much of the industry direction seems to be in offering ever-higher resolution, or the ability to run more samples at the same resolution. Thus far, however, customers haven’t found commercial uses for these tools. Also, with increasing resolution and the search for even rarer mutations, the challenge of detecting false positives becomes an even bigger issue.

    Dr. Menezes Use of ZEN™ Double-Quenched Probes by IDT in digital PCR provides increased sensitivity and a lower limit of detection. Due to the second quencher, ZEN probes provide even lower background than traditional single-quenched probes. And this lower background enables increased sensitivity when analyzing samples with low copy number targets, where every droplet matters.

    Ms. Hibbs Quantification relies upon counting the number of positive partitions at the end point of the reaction. Accordingly, precision and resolution can be increased by increasing the number of partitions. We are now capable of analyzing on the order of millions of partitions per run, further extending the lower limit of detection. Additionally, the workflow is amenable to the integration of automation in order to increase throughput and standardize reaction set up.

    Dr. Price Although dPCR is still an emerging technology, there is tremendous interest in its potential clinical diagnostics applications. Enabling adoption of dPCR in the clinical lab requires addressing current gaps in workflow, cost, throughput, and turnaround time.

    Digital PCR technology has the potential for being improved significantly in two dimensions. First, one can address the problem of serially detecting positive versus negative partitions by leveraging lower-cost imaging detection technologies. Alternatively, one may capitalize on the small partition volumes to dramatically reduce the time to perform PCR. Ideally, the future will bring both capabilities to bear.

    Mr. Wakida Compared to qPCR, dPCR currently requires more hands-on time to set up experiments. We are investigating methods to address this.

 

PCR Shows Off Its Clinical Chops   

Thanks to Advances in Genomics, PCR Is Becoming More Common in Clinical Applications

  • Last May, Roche Molecular Systems announced that its cobas Liat Strep A assay received a CLIA waiver. This clinic-ready assay can detect Streptococcus pyogenes (group A ß-hemolytic streptococcus) DNA in throat swabs by targeting a segment of the S. pyogenes genome.

    Since its invention by Kary B. Mullis in 1985, the polymerase chain reaction (PCR) has become well established, even routine, in research laboratories. And now PCR is becoming more common in clinical applications, thanks to advances in genomics and the evolution of more sensitive quantitative PCR methodologies.

    Examples of clinical applications of PCR include point-of-care (POC) molecular tests for bacterial and viral detection, as well as mutation detection in liquid or tumor biopsies for patient stratification and treatment monitoring.
    Industry leaders recently participated in a CHI conference that was held in San Francisco. This conference—PCR for Molecular Medicine—encompassed research and clinical perspectives and emphasized advanced techniques and tools for effective disease diagnosis.
    To kick off the event, speakers shared their views on POC molecular tests. These tests, the speakers insisted, can provide significant value to healthcare only if they support timely decision making.
    Clinic-ready PCR platforms need to combine speed, ease of use, and accuracy. One such platform, the cobas Liat (“laboratory in a tube”), is manufactured by Roche Molecular Systems. The system employs nucleic acid purification and state-of-art PCR-based assay chemistry to enable POC sites to rapidly provide lab-quality results.
    The cobas Liat Strep A Assay detects Streptococcus pyogenes (group A β-hemolytic streptococcus) DNA by targeting a segment of the S. pyogenes genome. The operator transfers an aliquot of a throat swab sample in Amies medium into a cobas Liat Strep A Assay tube, scans the relevant tube and sample identification barcodes, and then inserts the tube into the analyzer for automated processing and result interpretation. No other operator intervention or interpretation is required. Results are ready in approximately 15 minutes.

    According to Shuqi Chen, Ph.D., vp of Point-of-Care R&D at Roche Molecular Systems, clinical studies of the cobas Liat Strep A Assay demonstrated 97.7% sensitivity when the test was used at CLIA-waived, intended-use sites, such as physicians’ offices. In comparison, rapid antigen tests and diagnostic culture have sensitivities of 70% and 81%, respectively (according to a 2009 study Tanz et al. in Pediatrics).

    The cobas Liat assay preserved the same ease-of-use and rapid turnaround as the rapid antigen tests. It addition, it provided significantly faster turnaround than the lab-based culture test, which can take 24–48 hours.

    A CLIA waiver was announced for the cobas Liat Strep A assay in May 2015. CLIA wavers have been submitted for cobas Liat flu assays, and Roche intends to extend the assay menu.

    POC tests are also moving into field applications. Coyote Bioscience has developed a novel method for one-step gene testing without nucleic acid extraction that can be as fast as 10 minutes from blood sample to result. Their portable devices for molecular diagnostics can be used as genetic biosensors to bring complex clinical testing directly to the patient.

    “Instead of sequential steps, reactions happen in parallel, significantly reducing analysis time. Buffer, enzyme, and temperature profiles are optimized to maximize sensitivity,” explained Sabrina Li, CEO, Coyote Bioscience. “Both RNA and DNA can be analyzed simultaneously from a drop of blood in the same reaction.”

    The first-generation Mini-8 system was used for Ebola detection in Africa where close to 600 samples were tested with 98.8% sensitivity. Recently in China, the Mini-8 system was applied in hospitals and small community clinics for hepatitis B and C and Bunia virus detection. The second-generation InstantGene system is currently being tested internally with clinical samples.

  • Digital PCR

    Conventional real-time PCR technology, while suited to the analysis of high-quality clinical samples, may effectively conceal amplification efficiency changes when sample quality is inconsistent. A more effective alternative, Bio-Rad suggests, is its droplet-digital PCR (ddPCR) technology, which can provide absolute quantification of target DNA or RNA, a critical advantage when samples are limited, degraded, or contain PCR inhibitors. The company says that of the half-dozen clinical trials that are using digital PCR, half rely on the Bio-Rad QX200 ddPCR system.

    Personalized cancer care requires ultra-sensitive detection and monitoring of actionable mutations from patient samples. The high sensitivity and precision of droplet-digital PCR (ddPCR) from Bio-Rad Laboratories offers critical advantages when clinical samples are limited, degraded, or contain PCR inhibitors.

    Typically, formalin-fixed and paraffin-embedded (FFPE) tissue samples are processed. FFPE samples work well for immunohistochemistry and protein analysis; however, the formalin fixation can damage nucleic acids and inhibit the PCR reaction. Samples may yield 100 ng of purified nucleic acid, but the actual amplifiable material is less than 1%, or 1 ng, in most cases.

    “Current qPCR technology depends on real-time fluorescence accumulation as the PCR is occurring, which can be an effective means of detecting and quantifying DNA targets in nondegraded samples,” commented Dawne Shelton, Ph.D., staff scientist, Digital Biology Center, Applications Development Group, Bio-Rad Laboratories. “Amplification efficiency is critical; if that amplification efficiency changes because of sample quality it is hidden in the qPCR methodology.”

    “In ddPCR, that is a big red flag,” Dr. Shelton continued. “It changes the format of how the data look immediately so you know the amount of inhibition and which samples are too inhibited to use.”

    Tissue types vary and contain different degrees of fat or other content that can also act as PCR inhibitors. In blood monitoring, the small circulating fragments of DNA are extremely degraded; in addition, food, supplements, or other compounds ingested by the patient may have an inhibitory effect.

    Clinical labs test for these variabilities and clean the blood, but remnant PCR inhibitors can remain. In ddPCR, a single template is partitioned into a droplet. If the droplet contains a good template, it produces a signal; otherwise, it does not—a simple yes or no answer.

    “Even if there is no PCR inhibition, most clinical samples yield very small amounts of nucleic acid,” Dr. Shelton added. “To make a secure decision using qPCR is difficult because you are in a gray zone at the very end of its linear range. ddPCR operates best with small sample amounts and provides good statistics for confidence in your results.”

    Currently, at least a half dozen clinical trials worldwide are using digital PCR, half of them are using the Bio-Rad QX200 Droplet Digital PCR system. Examples of studies include examining BCR-ABL monitoring in patients with chronic myelogenous leukemia (CML); identifying activating mutations in epidermal growth factor receptor (EGFR) for first-line therapy of new drugs in patients with lung cancer; and the monitoring of resistance mutations such as EFGR T790M in patients with non-small cell lung cancer (NSCLC).

    Clovis Oncology used a technology called BEAMing (Beads, Emulsions, Amplification, and Magnetics), a type of digital PCR for blood-based molecular testing, to perform EGFR testing on almost 250 patients in clinical trials. In BEAMing, individual EGFR gene copies from plasma are separated into individual water droplets in a water-in-oil emulsion. The gene copies are then amplified by PCR on magnetic beads.

    The beads are counted by flow cytometry using fluorescently labeled probes to distinguish mutant beads from wild-type. Because each bead can be traced to an individual EGFR molecule in the patient’s plasma, the method is highly quantitative.

    “BEAMing is particularly well-suited for the detection of known mutations in circulating tumor DNA. In this circumstance, the mutation of interest often occurs at low levels, perhaps only 1–2 copies per milliliter or even less, and in a high background of wild-type DNA that comes from normal tissue. BEAMing can detect one mutant molecule in a background of 5,000 wild-type molecules in clinical samples,” stated Andrew Allen, MRCP, Ph.D., chief medical officer, Clovis Oncology.

    In the studies, the EGFR-resistance mutation T790M could be identified in plasma 81% of the time that it was seen in the matched patient tumor biopsy. Additionally, about 10% of patients in the study had a T790M mutation in plasma that was not identified in tissue, presumably because of tumor heterogeneity. Another 5–10% of the patients did not provide an EGFR result, usually because the tissue biopsy had no tumor cells.

    In aggregate, these results suggest that plasma EGFR testing can be a valuable complement to tumor testing in the clinical management of NSCLC patients, and can provide an alternative when a biopsy is not available. Tumor biopsies may provide only limited tissue, if in fact any tissue is available, for molecular analysis. Also, mutations may be missed due to tumor heterogeneity. These mutations may be captured by sampling the blood, which acts as a reservoir for mutations from all parts of a patient’s tumor burden.

    In the last few years, a panoply of clinically actionable driver mutations have been identified for NSCLC, including mutations in EGFR, BRAF, and HER2, as well as ALK, ROS, and RET rearrangements. These driver mutations will migrate NSCLC molecular diagnostic testing in the next few years toward panel testing of relevant cancer genes using various digital technologies, including next-generation sequencing.

     

PCR Has a History of Amplifying Its Game

A GEN 35th Anniversary Retrospective

PCR Has a History of Amplifying Its Game

PCR is a fast and inexpensive technique used to amplify segments of DNA that continues to adapt and evolve for the demanding needs of molecular biology researchers. This diagram shows the basic principles of PCR amplification. [NHGRI]

  • The influence that the polymerase chain reaction (PCR) has had on modern molecular biology is nothing short of remarkable. This technique, which is akin to molecular photocopying, has been the centerpiece of everything from the OJ Simpson Trial to the completion of the Human Genome Project. Clinical laboratories use this DNA amplification method for infectious disease testing and tissue typing in organ transplantation. Most recently, with the explosion of the molecular diagnostics field and meteoric rise in the use of next-generation sequencing platforms, PCR has enhanced its standing as an essential pillar of genomic science.

    Let’s open the door to the past and take a look back around 35 years ago when GEN started reporting on the relatively new disciplines of genetic engineering and molecular biology. At that time, GEN was among the first to hear the buzz surrounding a new method to synthesize and amplify DNA in the laboratory. In reviewing the fascinating history of PCR, we will see how the molecular diagnostics field took shape and where it could be headed in the future.

  • Some Like It Hot

    The biological sciences rarely advance within a vacuum—rather they rely on previous discoveries to promote directly or indirectly our understanding. The contributions made by scientists in the field of molecular biology that contributed to the functional pieces of PCR were numerous and spread out over more than two decades.

    It began with H. Gobind Khorana’s advances in understanding the genetic code, leading to the use of synthetic DNA oligonucleotides, continued through Kjell Kleepe’s 1971 vision of a two-primer system for replicating DNA segments, to Fredrick Sanger’s method of DNA sequencing—a process that would win him the Nobel prize in 1980—which utilized DNA oligo primers, nucleotide precursors, and a DNA synthesis enzyme.

    All of the previous discoveries were essential to PCR’s birth, yet it would be an egregious mistake to begin a retrospective on PCR and not discuss the enzyme upon which the entire reaction hinges upon—DNA polymerase. In 1956, Nobel laureate Arthur Kornberg and his colleagues discovered DNA polymerase (Pol I), in Escherichia coli. Moreover, the researchers described the fundamental process by which the polymerase enzyme copies the base sequence of a DNA template strand. However, it would take biologists another 20 years to discover a version of DNA polymerase that was stable enough for use for any meaningful laboratory purposes.

    That discovery came in 1976 when a team of researchers from the University of Cincinnati described the activity of a DNA polymerase (Taq) they isolated from the extreme thermophile bacteria, Thermus aquaticus, which lives in hot springs and hydrothermal vents. The fact that this enzyme could withstand typical protein-denaturing temperatures and function optimally around 75–80°C fortuitously set the stage for the development of PCR.

    By 1983, all of the ingredients to bake the molecular cake were sitting in the biological cupboard waiting to be assembled in the proper order. At that time, Nobel laureate Kary Mullis was working as a scientist for the Cetus Corporation trying to perfect oligonucleotide synthesis. Mullis stumbled upon the idea of amplifying segments of DNA using multiple rounds of replication and the two primer system—essentially modifying and expanding upon Sanger’s sequencing reaction. Mullis discovered that the temperatures for each step (melting, annealing, and extension) in the reaction would need to be painstakingly controlled by hand. In addition, he realized that since the reactions were using a non-thermostable DNA polymerase, fresh enzyme would need to be “spiked in” after each successive cycle.

    Mullis’ hard work and persistence paid off as the reaction was successful at amplifying a particular segment of DNA that was flanked by two opposing nucleotide primer molecules. Two years later, the Cetus team presented their work at the annual meeting of the American Society for Human Genetics, and the first mention of the method was published in Science that same year; however, that article did not go into detail about the specifics of the newly developed PCR method—a paper that would be rejected by roughly 15 journals and would not be published until 1987.

    Although scientists were a bit slow on the uptake for the new method, the researchers at Cetus were developing ways to improve upon the original assay. In 1986, the scientists substituted the original heat-liable DNA polymerase for the temperature-resistant Taq polymerase, removing the need to spike in enzyme and dramatically reducing errors while increasing sensitivity. A year later, PerkinElmer launched their creation of a thermal cycler, allowing scientists to regulate the heating and cooling parts of the PCR reaction with greater efficiency.

    Extremely soon after the introduction of Taq and the launch of the thermal cycler, the PCR reaction exploded exponentially among research laboratories and not only vaulted molecular biology to the pinnacle of researcher interests, it also launched a molecular diagnostics revolution that continues today and shows no signs of slowing down.

  • Molecular Workhorse

    In the years since PCR first burst onto the scene, there have been a number of significant advancements to the technique that have widely improved the overall method. For example, in 1991, a new DNA polymerase from the hyperthermophilic bacteria Pyrococcus furiosus, or Pfu, was introduced as a high-fidelity alternative enzyme to Taq. Unlike Taq polymerase, Pfu has built in 3′ to 5′ exonuclease proofreading activity, which allows the enzyme to correct nucleotide incorporation errors on the fly—dramatically increasing base specificity, albeit at a reduced rate of amplification versusTaq.

    In 1995, two advancements were introduced to PCR users. The first, called antibody “hot-start” PCR, utilized an immunoglobulin molecule that is directed to the DNA polymerase and inhibits its activity until the first 95°C melt stage, denaturing the antibody and allowing the polymerase to become active. Although this process was effective in increasing the specificity of the PCR reaction, many researchers found that the technique was time consuming and often caused cross-contamination of samples.

    The second innovation introduced that year began another revolution for molecular biology and the PCR method. Real-time PCR, or quantitative PCR (qPCR), allowed researchers to quantitatively create DNA templates for PCR amplification from RNA transcripts through the use of the reverse-transcriptase enzyme and specifically incorporated fluorescent reporter dyes. The technique is still widely used by researchers to monitor gene expression extremely accurately. Over the past 20 years, many companies have spent many R&D dollars to create more accurate, higher throughput, and simple qPCR machines to meet researcher demands.

    With the advent of next-generation sequencing techniques—and the rise of techniques that started commanding the attention of more and more researchers—PCR machines and methods needed to evolve and modernize to keep pace. PCR remained the lynchpin in almost all the next-generation sequencing reactions that came along, but the traditional technique wasn’t nearly as precise as required.

    Digital PCR (dPCR) was introduced as a refinement of the conventional method, with the first real commercial system emerging around 2006. dPCR can be used to quantify directly and clonally amplify DNA or RNA.

    The apparatus carries out a single reaction within a sample. The sample, however, is separated into a large number of partitions. Moreover, the reaction is performed in each partition individually—allowing a more reliable measurement of nucleic acid content. Researchers often use this method for studying gene-sequence variations, such as copy number variants (CNV), point mutations, rare-sequence detection, and microRNA analysis, as well as for routine amplification of next-generation sequencing samples.

  • Future of PCR: Better, Faster, Stronger!

    It is almost impossible to envision a future laboratory setting that wouldn’t utilize PCR in some fashion, especially due to the heavy reliance of next-generation sequencing techniques for accurate PCR samples and at the very least using the method as a simple amplification tool for creating DNA fragments of interest.

    Yet there is at least one new next-generation sequencing technique that can identify native DNA sequences without an amplification step—nanopore sequencing. Although this technique has performed well in many preliminary trials, it is in its relative infancy. It will probably undergo additional development lasting several years before it approaches large-scale adoption by researchers. Even then, PCR has become so engrained into daily laboratory life that to try to phase out the technique would be like asking molecular biologists to give up their pipettes or restriction enzymes.

    Most PCR equipment manufacturers continue to seek ways to improve the speed and sensitivity of their thermal cyclers, while biologists continue to look toward ways to genetically engineer better DNA polymerase molecules with even greater fidelity than their naturally occurring cousins. Whatever the new advancements are, and wherever they lead the life sciences field, you can count on us at GEN to continue to provide our readers with detailed information for another 35 years … at least!

     

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Salmonella adaptive “switch”

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Molecular switch lets salmonella fight or evade immune system   

February 4, 2016   http://phys.org/news/2016-02-molecular-salmonella-evade-immune.html

 

 

http://cdn.phys.org/newman/csz/news/800/2016/salmonella.jpg

Salmonella forms a biofilm. Credit: CDC

 

Researchers at the University of Illinois at Chicago have discovered a molecular regulator that allows salmonella bacteria to switch from actively causing disease to lurking in a chronic but asymptomatic state called a biofilm.

http://phys.org/news/2016-02-molecular-salmonella-evade-immune.html#jCp

Their findings are published in the online journal, eLife.

Biofilms cling to surfaces in the body, such as the bronchial tubes or artificial joints, often without causing illness. But they can be a reservoir of bacteria that detach and cause disease or infect new hosts. The biofilms are resistant to host defenses and antibiotics because their tightly-packed structure exposes little surface area for drugs to reach. Many pathogenic bacteria are able to switch from an infectious to a dormant state as a strategy for survival inside their hosts.

 

Linda Kenney, professor of microbiology and immunology at the UIC College of Medicine and lead author of the study, had been studying how survive inside immune system cells called macrophages. These patrol the body and engulf viruses and bacteria they encounter. They encase their prey in a bubble called a vacuole that protects them from the invader until it can be destroyed.

Macrophages digest their quarry when the acidity inside the vacuole drops in response to the captive. But the bacteria have evolved a unique defense, enabling them to survive inside the vacuole and use the macrophage as a Trojan horse to travel elsewhere in the body undetected by other immune cells.

Kenney knew that a type of salmonella that causes typhoid fever in humans, called Salmonella typhi, and its mouse counterpart, Salmonella typhimurium, were able to survive inside macrophage vacuoles. She noticed that these bacteria did two things: inside the vacuole, they formed a kind of syringe – a long, hollow filament to inject the vacuole with a host of proteins that altered it. They also quickly assumed the same acidity of the vacuole.

“These two defenses, together, allow salmonella to survive and replicate in the harsh conditions of the vacuole,” Kenney said.

Further experiments revealed that sensing and mirroring the acidity, or pH, of the vacuole is what triggers salmonella to form the syringe.

“The syringe-forming and pH-adjusting genes are signaled to turn on by the lower pH inside the vacuole,” Kenney said. But these same salmonella, equipped to survive the hostile environment inside a macrophage vacuole, were also able to exist free in the body of the host—as biofilms.

“I wanted to know how Salmonella ‘decide’ between these two very different lifestyles,” Kenney said.

Studying S. typhimurium, Kenney discovered that the molecular switch is a bacterial molecule called SsrB. As the macrophage vacuole starts to acidify, SsrB is activated and it turns on the genes needed to form the syringe and adjust the pH. When salmonella lives outside the vacuole, where pH levels are neutral, SsrB instead turns on genes for sticky proteins in the membrane that help bacteria bind to one another to form biofilms.

Kenney said that many disease-causing salmonella evolved from harmless strains partly by acquiring new genes from other germs in a process called horizontal gene transfer.

“Salmonella acquired their pH-adjusting and syringe-forming genes in this way, as well as the switch that turns them on and off – SsrB,” she said. “The default mode, or its ancestral program, dictates that it make biofilms, cause no illness, and survive long enough to infect new hosts when the opportunity arises. The new genes allow it to survive the host’s main defense—the acidifying macrophage vacuole.”

Understanding how switch from the disease-causing state to the biofilm state could help scientists develop anticancer drugs that encourage the formation of biofilms on tumors, Kenney said.

“When salmonella forms biofilms on tumors, it releases TNF-alpha, a powerful anti-tumor molecule,” she said. “If we can better control the formation of biofilms, we can target them to tumors for cancer therapy.”

Explore further: Revealing camouflaged bacteria

More information: The horizontally-acquired response regulator SsrB drives a Salmonella lifestyle switch by relieving biofilm silencing, dx.doi.org/10.7554/eLife.10747 , elifesciences.org/content/5/e10747

The horizontally-acquired response regulator SsrB drives a Salmonella lifestyle switch by relieving biofilm silencing

 Stuti K Desai, 

A common strategy by which bacterial pathogens reside in humans is by shifting from a virulent lifestyle, (systemic infection), to a dormant carrier state. Two major serovars of Salmonella enterica, Typhi and Typhimurium, have evolved a two-component regulatory system to exist insideSalmonella-containing vacuoles in the macrophage, as well as to persist as asymptomatic biofilms in the gallbladder. Here we present evidence that SsrB, a transcriptional regulator encoded on the SPI-2 pathogenicity-island, determines the switch between these two lifestyles by controlling ancestral and horizontally-acquired genes. In the acidic macrophage vacuole, the kinase SsrA phosphorylates SsrB, and SsrB~P relieves silencing of virulence genes and activates their transcription. In the absence of SsrA, unphosphorylated SsrB directs transcription of factors required for biofilm formation specifically by activating csgD (agfD), the master biofilm regulator by disrupting the silenced, H-NS-bound promoter. Anti-silencing mechanisms thus control the switch between opposing lifestyles.

 

Introduction

Salmonella enterica serovar Typhimurium is a rod-shaped enteric bacterium which easily infects diverse hosts such as humans, cattle, poultry and reptiles through contaminated food or water, causing gastroenteritis. A human-restricted serovar of Salmonella enterica, serovar Typhi, causes typhoid fever and continues to be a dangerous pathogen throughout the world. Salmonella lives as a facultative pathogen in various natural and artificial environments as independent planktonic cells, cooperative swarms (Harshey and Matsuyama, 1994) or as multi-cellular communities called biofilms (see Steenackers et al., 2012 for a review). Upon successful invasion of host cells, Salmonella is phagocytosed by macrophages, where it resides in a modified vacuole in a self-nourishing niche called a Salmonella-Containing Vacuole (SCV). This intracellular lifestyle eventually adversely affects the host. Salmonella also resides as multi-cellular communities on intestinal epithelial cells (Boddicker et al., 2002), gallstones (Prouty et al., 2002) and tumors (Crull et al., 2011). It is believed that biofilms in the gall bladder are important for maintaining the carrier state, allowing Salmonella to persist (Crawford et al., 2010).

Each of these lifestyles of Salmonella are regulated by two-component regulatory systems (TCRS). TCRSs are comprised of a membrane-bound sensor histidine kinase and a cytoplasmic response regulator. The virulence genes of Salmonella are encoded on horizontally acquired AT-rich segments of the genome called Salmonella Pathogenecity Islands (SPIs), and are also tightly regulated by TCRSs. For example, the SsrA/B TCRS is essential for the activation of the SPI-2 regulon genes encoding a type-three secretory needle and effectors that are involved in formation of the SCV (Cirillo et al., 1998). Interestingly, the SsrA/B system itself is regulated by upstream two-component systems such as EnvZ/OmpR and PhoP/Q, which regulate gene expression in response to changes in osmolality, pH and the presence of anti-microbial peptides (Fields et al., 1989; Miller et al., 1989;Lee et al., 2000; Feng et al., 2003). The ssrA and ssrB genes are present on the SPI-2 pathogenecity island adjacent to each other and are regulated by a set of divergent promoters (Feng et al., 2003; Ochman et al., 1996). Under acidic pH and low osmolality, the ssrA and ssrB genes are transcriptionally activated by the binding of OmpR~P and PhoP~P to their promoters (Feng et al., 2003; Bijlsma and Groisman, 2005; Walthers and Kenney unpublished) whose levels are in turn regulated by the respective sensor kinases, EnvZ and PhoQ. SsrA is a tripartite membrane-bound histidine sensor kinase that undergoes a series of intra-molecular phosphorylation reactions before it transfers the phosphoryl group to the N-terminal aspartate residue of the response regulator, SsrB.

SsrB belongs to the NarL/FixJ family of transcriptional regulators that require phosphorylation-dependent dimerization to bind DNA. The X-ray crystal structure of NarL revealed that the C-terminal DNA binding domain was occluded by the N-terminus (Baikalov et al., 1996), and phosphorylation was predicted to relieve this inhibition. Full-length SsrB is unstable in solution, but an isolated C-terminal domain of SsrB, SsrBc, is capable of binding to the regulatory regions of nine genes belonging to the SPI-2 regulon, including ssrA and ssrB (Feng et al., 2004; Walthers et al., 2007) and activating transcription. A role for SsrB~P was identified by its dual function as a direct transcriptional activator and as an anti-silencer of H-NS-mediated repression (Walthers et al., 2007). The Histone like Nucleoid Structuring protein H-NS is involved in silencing many of the SPI-2 regulon genes in accordance with its role in binding to xenogenic AT-rich sequences and repressing their expression (Walthers et al., 2007; Navarre et al., 2006). H-NS binding to DNA leads to the formation of a stiff nucleoprotein filament which is essential in gene silencing (Lim et al., 2012; Liu et al., 2010; Amit et al., 2003; Winardhi et al., 2015). Moreover, relief of repression occurs due to the binding of SsrBc to this rigid H-NS-DNA complex (Walthers et al., 2011).

Salmonella reservoirs in host and non-host environments produce a three-dimensional extracellular matrix which consists of curli fimbriae, cellulose, proteins and extracellular DNA, to encase clusters of bacteria and form a mature biofilm. CsgD (AgfD) is the master regulator of biofilm formation (Gerstel et al., 2003); it is a LuxR family transcriptional activator that activates the expression of curli fimbriae encoded by csgDEFG/csgBAC operons (Collinson et al., 1996; Romling et al., 1998). CsgD also activates expression of adrA, increasing intracellular c-di-GMP levels, and activating the cellulose biosynthetic operon bcsABZC (Zogaj et al., 2001). Two other biofilm matrix components are also positively regulated by CsgD: BapA and the O-antigen capsule (Latasa et al., 2005; Gibson et al., 2006).

Transcriptional profiling of biofilms formed by S. Typhimurium SL1344 showed that many SPI-2 genes were down-regulated, yet SsrA was required for biofilms (Hamilton et al., 2009). This apparent paradox drove us to explore the underlying mechanism of biofilm formation. The role of SsrA/B in this process was of particular interest, since our previous comparison of SsrA and SsrB levels at neutral and acidic pH had shown that the expression of ssrA and ssrB was uncoupled (Feng et al., 2004).

We examined the ability of the wild type S. Typhimurium strain 14028s to form biofilms in the absence of ssrA and ssrB and found it to be dependent only on the expression of ssrB. We further showed that H-NS was a negative regulator of csgD. Surprisingly, the SsrB response regulator positively regulated the formation of biofilms by activating csgD expression in the absence of any phospho-donors. Moreover, AFM imaging revealed that unphosphorylated SsrB was able to bind to the csgD regulatory region and binding was sufficient to relieve H-NS-mediated repression and favor formation of S. Typhimurium biofilms.

As a result of these studies, we propose that SsrB, a pathogenicity island-2-encoded response regulator, sits at a pivotal position in governing Salmonella lifestyle fate: to either exist inside the host (in the SCV) as a promoter of virulence; or as a surface-attached multicellular biofilm, maintaining the carrier state. This switch is achieved merely by the ability of unphosphorylated SsrB to function as an anti-repressor of H-NS and the additional role of SsrB~P in activating SPI-2 transcription (Walthers et al., 2011).

 

eLife digest

Salmonella bacteria can infect a range of hosts, including humans and poultry, and cause sickness and diseases such as typhoid fever. Disease-causing Salmonella evolved from harmless bacteria in part by acquiring new genes from other organisms through a process called horizontal gene transfer. However, some strains of disease-causing Salmonella can also survive inside hosts as communities called biofilms without causing any illness to their hosts, who act as carriers of the disease and are able to pass their infection on to others.

So how do Salmonella bacteria ‘decide’ between these two lifestyles? Previous studies have uncovered a regulatory system that controls the decision in Salmonella, which is made up of two proteins called SsrA and SsrB. To trigger the disease-causing lifestyle, SsrA is activated and adds a phosphate group onto SsrB. This in turn causes SsrB to bind to and switch on disease-associated genes in the bacterium. However, it was less clear how the biofilm lifestyle was triggered.

Desai et al. now reveal that the phosphate-free form of SsrB – which was considered to be the inactive form of this protein – plays an important role in the formation of biofilms. Experiments involving an approach called atomic force microscopy showed that the unmodified SsrB acts to stop a major gene that controls biofilm formation from being switched off by a so-called repressor protein.

Salmonella acquired SsrB through horizontal gene transfer, and these findings show how this protein now acts as a molecular switch between disease-causing and biofilm-based lifestyles. SsrB protein is also involved in the decision to switch between these states, but how it does so remains a question for future work.

DOI:http://dx.doi.org/10.7554/eLife.10747.002

 

Figure 6.

https://elife-publishing-cdn.s3.amazonaws.com/10747/elife-10747-fig6-v1-480w.jpg

Figure 6.SsrB condenses H-NS bound csgD DNA.

(A) (i) AFM imaging in the presence of 600 nM H-NS shows a straight and rigid filament on csgD755. (ii) Addition of 600 nM SsrB to the H-NS bound csgD DNA resulted in areas of condensation (pink arrows; an ‘SsrB signature’) along with a few areas where the straight H-NS bound conformation persisted (yellow line; an ‘H-NS signature’); Scale bar = 200 nm as in Figure 5A. (B) A model for the mechanism of anti-silencing by SsrB at csgD wherein SsrB likely displaces H-NS from the ends of a stiffened nucleoprotein filament and relieves the blockade on the promoter for RNA polymerase to activate transcription. For details refer to (Winardhi et al., 2015).

 

Discussion

Pathogenic microbes constantly evolve novel means to counter the multitude of challenges posed by complex eukaryotic hosts. Successful acquisition and integeration of laterally acquired genes into the native genome of pathogens leads to novel capabilities enabling their survival in a wide range of environmental stresses. The present work demonstrates how the presence or absence of the horizontally acquired SsrA kinase controls post-translational modification of the transcription factor SsrB (i.e. phosphorylation at aspartate-56). This event controls the fate of Salmonella Typhimurium, resulting in either acute or chronic, but asymptomatic infection. A variation on two-component signaling in a similar lifestyle fate in Pseudomonas aeruginosa involved the presence or absence of the hybrid kinase RetS (Goodman et al., 2004).

SsrB sits at a pivotal decision point that determines Salmonella lifestyles

When the SsrA kinase is present and activated by acid stress, SsrB is phosphorylated and SsrB~P de-represses H-NS and activates transcription at SPI-2 and SPI-2 co-regulated genes, including: sifA(Walthers et al., 2011), ssaB, ssaM, sseA and ssaG (Walthers et al., 2007). In the absence of the SsrA kinase, SsrB is not phosphorylated, but it can counter H-NS silencing at csgD (Figure 4A–D andFigure 6A). SsrB binding and bending at the csgD promoter causes a sufficient change in the DNA secondary structure (Figure 5B,C) that likely enables access for RNA polymerase, stimulating csgDtranscription. It is interesting to note that SsrB is located on the SPI-2 pathogenicity island, and thus was acquired as Salmonella enterica diverged from Salmonella bongori. However, the capability to form biofilms is an ancestral trait, as phylogeny studies have shown that most of the natural or clinical isolates of Salmonella belonging to all the five sub-groups form rdar colonies (White and Surette, 2006). The SsrB response regulator can control two distinct lifestyle choices: the ability to assemble a type three secretory system and survive in the macrophage vacuole or the ability to form biofilms on gallstones in the gall bladder to establish the carrier state.

What then controls the presence or activation of the kinase SsrA? Our early experiments indicated that SsrA and SsrB were uncoupled from one another (i.e., SsrB was present in the absence of SsrA) and ssrA transcription was completely dependent on OmpR (Feng et al., 2004). The EnvZ/OmpR system is stimulated by a decrease in cytoplasmic pH when Salmonella enters the macrophage vacuole (Chakraborty et al., 2015). This may also be the stimulus for activating SsrA, since theSalmonella cytoplasm acidifies to pH 5.6 during infection and the cytoplasmic domain of EnvZ (EnvZc) was sufficient for signal transduction (Wang et al., 2012; Chakraborty et al., 2015). Previous reports also identified a role for PhoP in ssrA translation (Bijlsma and Groisman, 2005), which would further add to fluctuating SsrA levels. The present work describes a novel role for the unphosphorylated response regulator SsrB in de-repressing H-NS (Figure 6B). We show that under biofilm-inducing conditions, unphosphorylated SsrB is sufficient to activate the expression of csgD. There are only a few such examples of unphosphorylated response regulators playing a role in transcription such as DegU (Dahl et al., 1992) in Bacillus subtilis and RcsB (Latasa et al., 2012) in S.Typhimurium.

The importance of anti-silencing in gene regulation

In recent years, it has become apparent that H-NS silences pathogenicity island genes in Salmonella(Lucchini et al., 2006; Navarre et al., 2006; Walthers et al., 2007; 2011). Understanding how H-NS silences genes and how this silencing is relieved is an active area of research (Will et al., 2015;Winardhi et al., 2015). Because the anti-silencing style of gene regulation is indirect and does not rely on specific DNA interactions, searching for SsrB binding sites has not been informative in uncovering this type of regulation (Tomljenovic-Berube et al., 2010; Worley et al., 2000; Shea et al., 1996). Even a recent report in which the proteomes of wild type, hilA null (a transcriptional regulator of SPI-1 genes) and ssrB null were analyzed by SILAC and compared with an existing CHIP dataset failed to identify csgD as an SsrB-regulated locus (Brown et al., 2014), as sequence gazing alone does not help in identifying mechanisms of transcriptional regulation.

SsrB is well suited to this style of regulation, because it does not recognize a well-defined binding site (Feng et al., 2004; Walthers et al., 2007; Tomljenovic-Berube et al., 2010), it has a high non-specific binding component (Carroll et al., 2009) and it bends DNA upon binding (Carroll et al., 2009; Figure 6B, this work). Furthermore, previous microarray studies disrupted both ssrA and ssrB, which would not uncover a distinct role for SsrB in gene regulation under non SPI-2-inducing conditions in the absence of the SsrA kinase. It is worth mentioning here that in our AFM images, it was apparent that H-NS was still bound to some regions of the csgD promoter when SsrB condensed the DNA (Figure 6A(ii)). Thus, H-NS does not have to be completely stripped off the DNA for de-repression to occur, a finding that was also evident in our previous studies (Liu et al., 2010) and others (Will et al., 2014).

SsrB binds and bends DNA, resulting in highly curved DNA conformations. This DNA binding property of SsrB is distinct from H-NS, which forms rigid nucleoprotein filaments and thus straight DNA conformations (Figure 6A(i)). Bent DNA is therefore an energetically unfavorable substrate for H-NS binding, and a likely mechanism of SsrB-mediated anti-silencing of H-NS repressed genes. SsrB-dependent displacement of H-NS is more energetically favored to occur predominantly at the ends of H-NS-bound filaments, which requires disruption of fewer H-NS protein-protein interactions (Winardhi et al., 2015 and Figure 6B). In an equal mixture of H-NS and SsrB (Figure 6A(ii)), we do not see evidence of sharply bent filaments. This is expected because H-NS dissociation is likely restricted to the filament ends. Such events occur due to the cooperative nature of H-NS binding that results in a chain of linked H-NS proteins. Hence, H-NS displacement by SsrB likely occurs progressively from the filament end. This behavior has been observed in our single-molecule stretching experiments with H-NS filaments in the presence of SsrB. This ability of H-NS to re-orient on the DNA without being released would also promote its re-binding and silencing when SsrB or other anti-silencers are released (Figure 6B).

Structural homology does not indicate functional homology

Response regulators are grouped into subfamilies on the basis of the structures of their DNA binding domains. SsrB is in the NarL/FixJ subfamily, which possess a helix-turn-helix (HTH) motif in the C-terminus (Baikalov et al., 1996). NarL was the first full-length structure of a response regulator and it showed that the N-terminal phosphorylation domain physically blocked the recognition helix in the HTH motif (Maris et al., 2002). Thus, phosphorylation is required to relieve the inhibition of the N-terminus. In the results presented herein, it is apparent that SsrB has adapted to relieving H-NS-silencing and that phosphorylation is not required for this behavior, nor is it required for DNA binding (Figure 5B).

In summary, we showed that the response regulator SsrB is required for biofilm formation because it can de-repress H-NS at the csgD promoter (Figure 6B). This leads to the production of CsgD, the master regulator of biofilms. It is noteworthy that a laterally acquired gene product, SsrB, has evolved the job of regulating the levels of csgD, a transcriptional regulator encoded by the core genome. For this activity, phosphorylation of SsrB was not required, which is rare amongst response regulators. Furthermore, we identify H-NS as a repressor of csgD in Salmonella, instead of an activator (Gerstel et al., 2003). This unifies the regulation of CsgD by H-NS in E. coli (Ogasawara et al., 2010) and Salmonella. This work places SsrB at a unique decision point in the choice between lifestyles bySalmonella and makes it crucial for the entire gamut of pathogenesis, i.e., biofilms and virulence.

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Inflammatory Disorders: Articles published @ pharmaceuticalintelligence.com

Curators: Larry H. Bernstein, MD, FCAP and Aviva Lev-Ari, PhD, RN

This is a compilation of articles on Inflammatory Disorders that were published 

@ pharmaceuticalintelligence.com, since 4/2012 to date

There are published works that have not been included.  However, there is a substantial amount of material in the following categories:

  1. The systemic inflammatory response
    http://pharmaceuticalintelligence.com/2014/11/08/introduction-to-impairments-in-pathological-states-endocrine-disorders-stress-hypermetabolism-cancer/

    Summary and Perspectives: Impairments in Pathological States: Endocrine Disorders, Stress Hypermetabolism and Cancer

    Neutrophil Serine Proteases in Disease and Therapeutic Considerations

    What is the key method to harness Inflammation to close the doors for many complex diseases?

    Therapeutic Targets for Diabetes and Related Metabolic Disorders

    A Second Look at the Transthyretin Nutrition Inflammatory Conundrum

    Zebrafish Provide Insights Into Causes and Treatment of Human Diseases

    IBD: Immunomodulatory Effect of Retinoic Acid – IL-23/IL-17A axis correlates with the Nitric Oxide Pathway

    Role of Inflammation in Disease


    http://pharmaceuticalintelligence.com/2013/03/06/can-resolvins-suppress-acute-lung-injury/
    http://pharmaceuticalintelligence.com/2015/02/26/acute-lung-injury/

  2. sepsis
    http://pharmaceuticalintelligence.com/2012/10/20/nitric-oxide-and-sepsis-hemodynamic-collapse-and-the-search-for-therapeutic-options/
  3. vasculitis
    http://pharmaceuticalintelligence.com/2015/02/26/acute-lung-injury/

    The Molecular Biology of Renal Disorders: Nitric Oxide – Part III


    http://pharmaceuticalintelligence.com/2012/11/20/the-potential-for-nitric-oxide-donors-in-renal-function-disorders/

  4. neurodegenerative disease
    http://pharmaceuticalintelligence.com/2013/02/27/ustekinumab-new-drug-therapy-for-cognitive-decline-resulting-from-neuroinflammatory-cytokine-signaling-and-alzheimers-disease/

    Amyloid and Alzheimer’s Disease

    Alzheimer’s Disease – tau art thou, or amyloid

    Beyond tau and amyloid

    Remyelination of axon requires Gli1 inhibition

    Neurovascular pathways to neurodegeneration

    New Alzheimer’s Protein – AICD

    impairment of cognitive function and neurogenesis


    http://pharmaceuticalintelligence.com/2014/05/06/bwh-researchers-genetic-variations-can-influence-immune-cell-function-risk-factors-for-alzheimers-diseasedm-and-ms-later-in-life/

  5. cancer immunology
    http://pharmaceuticalintelligence.com/2013/04/12/innovations-in-tumor-immunology/

    Signaling of Immune Response in Colon Cancer

    Vaccines, Small Peptides, aptamers and Immunotherapy [9]

    Viruses, Vaccines and Immunotherapy

    Gene Expression and Adaptive Immune Resistance Mechanisms in Lymphoma

    The Delicate Connection: IDO (Indolamine 2, 3 dehydrogenase) and Cancer Immunology


  6. autoimmune diseases: rheumatoid arthritis, colitis, ileitis, …
    http://pharmaceuticalintelligence.com/2016/02/11/intestinal-inflammatory-pharmaceutics/
    http://pharmaceuticalintelligence.com/2016/01/07/two-new-drugs-for-inflammatory-bowel-syndrome-are-giving-patients-hope/
    http://pharmaceuticalintelligence.com/2015/12/16/contribution-to-inflammatory-bowel-disease-ibd-of-bacterial-overgrowth-in-gut-on-a-chip/

    Cytokines in IBD

    Autoimmune Inflammtory Bowel Diseases: Crohn’s Disease & Ulcerative Colitis: Potential Roles for Modulation of Interleukins 17 and 23 Signaling for Therapeutics

    Autoimmune Disease: Single Gene eliminates the Immune protein ISG15 resulting in inability to resolve Inflammation and fight Infections – Discovery @Rockefeller University

    Diarrheas – Bacterial and Nonbacterial

    Intestinal inflammatory pharmaceutics

    Biologics for Autoimmune Diseases – Cambridge Healthtech Institute’s Inaugural, May 5-6, 2014 | Seaport World Trade Center| Boston, MA

    Rheumatoid arthritis update


    http://pharmaceuticalintelligence.com/2013/08/04/the-delicate-connection-ido-indolamine-2-3-dehydrogenase-and-immunology/

    Confined Indolamine 2, 3 dioxygenase (IDO) Controls the Hemeostasis of Immune Responses for Good and Bad

    Tofacitinib, an Oral Janus Kinase Inhibitor, in Active Ulcerative Colitis

    Approach to Controlling Pathogenic Inflammation in Arthritis

    Rheumatoid Arthritis Risk


    http://pharmaceuticalintelligence.com/2012/07/08/the-mechanism-of-action-of-the-drug-acthar-for-systemic-lupus-erythematosus-sle/

  7. T cells in immunity
    http://pharmaceuticalintelligence.com/2015/09/07/t-cell-mediated-immune-responses-signaling-pathways-activated-by-tlrs/

    Allogeneic Stem Cell Transplantation [9.3]

    Graft-versus-Host Disease

    Autoimmune Disease: Single Gene eliminates the Immune protein ISG15 resulting in inability to resolve Inflammation and fight Infections – Discovery @Rockefeller University

    Immunity and Host Defense – A Bibliography of Research @Technion

    The Delicate Connection: IDO (Indolamine 2, 3 dehydrogenase) and Cancer Immunology

    Confined Indolamine 2, 3 dioxygenase (IDO) Controls the Hemeostasis of Immune Responses for Good and Bad


    http://pharmaceuticalintelligence.com/2013/04/14/immune-regulation-news/

Proteomics, metabolomics and diabetes

http://pharmaceuticalintelligence.com/2015/11/16/reducing-obesity-related-inflammation/

http://pharmaceuticalintelligence.com/2015/10/25/the-relationship-of-stress-hypermetabolism-to-essential-protein-needs/

http://pharmaceuticalintelligence.com/2015/10/24/the-relationship-of-s-amino-acids-to-marasmic-and-kwashiorkor-pem/

http://pharmaceuticalintelligence.com/2015/10/24/the-significant-burden-of-childhood-malnutrition-and-stunting/

http://pharmaceuticalintelligence.com/2015/04/14/protein-binding-protein-protein-interactions-therapeutic-implications-7-3/

http://pharmaceuticalintelligence.com/2015/03/07/transthyretin-and-the-stressful-condition/

http://pharmaceuticalintelligence.com/2015/02/13/neural-activity-regulating-endocrine-response/

http://pharmaceuticalintelligence.com/2015/01/31/proteomics/

http://pharmaceuticalintelligence.com/2015/01/17/proteins-an-evolutionary-record-of-diversity-and-adaptation/

http://pharmaceuticalintelligence.com/2014/11/01/summary-of-signaling-and-signaling-pathways/

http://pharmaceuticalintelligence.com/2014/10/31/complex-models-of-signaling-therapeutic-implications/

http://pharmaceuticalintelligence.com/2014/10/24/diabetes-mellitus/

http://pharmaceuticalintelligence.com/2014/10/16/metabolomics-summary-and-perspective/

http://pharmaceuticalintelligence.com/2014/10/14/metabolic-reactions-need-just-enough/

http://pharmaceuticalintelligence.com/2014/11/03/introduction-to-protein-synthesis-and-degradation/

http://pharmaceuticalintelligence.com/2015/09/25/proceedings-of-the-nyas/

http://pharmaceuticalintelligence.com/2014/10/31/complex-models-of-signaling-therapeutic-implications/

http://pharmaceuticalintelligence.com/2014/03/21/what-is-the-key-method-to-harness-inflammation-to-close-the-doors-for-many-complex-diseases/

http://pharmaceuticalintelligence.com/2013/03/05/irf-1-deficiency-skews-the-differentiation-of-dendritic-cells/

http://pharmaceuticalintelligence.com/2012/11/26/new-insights-on-no-donors/

http://pharmaceuticalintelligence.com/2012/11/20/the-potential-for-nitric-oxide-donors-in-renal-function-disorders/

 

 

 

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Concerns about Viruses

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

 

Zika: The Unexpected Pandemic

by Michael Smith

Sanjay Gupta, MD   Medscape     http://www.medpagetoday.com/InfectiousDisease/GeneralInfectiousDisease/55915

No one really saw Zika virus coming or cared much if it did.

In general, it has been regarded “clinically inconsequential,” Anthony Fauci, MD, director of the National Institute of Allergy and Infectious Diseases, told MedPage Today — so much so that it wasn’t even on a recent World Health Organization list of pathogens that need urgent research to prevent epidemics.

And — absent its apparent association with a spike in cases of microcephaly in Brazil — it probably still would be thought of as a minor nuisance, experts told MedPage Today.

But Zika virus illustrates a worrisome fact — the pace of emerging infectious diseases is both increasing and unpredictable.

Zika is a flavivirus, discovered in 1947, that is carried mainly by the mosquito Aedes aegypti. It causes a mild, self-limiting febrile illness in 20% to 25% of the people it infects; most people would never know they had it.

Until recently, it was pretty much confined to its ancestral home in Africa. Then in 2007 it was found in Micronesia and in 2013 ongoing transmission was documented in French Polynesia.

Early last year, it made its appearance in Brazil and it now appears to be established in 20 countries or territories in the Americas, including Puerto Rico.

Given that much of the region also has endemic dengue fever and chikungunya — with similar but more serious symptoms and also carried by A. aegypti — the appearance of Zika virus was originally just recorded with the notation that it would be nice to know more about these concurrent infections.

Then in September 2015, reports emerged of a spike in cases of microcephaly in the region of Brazil where the outbreak of Zika had been noted. It was an alarm bell, even though there’s still no definitive proof that Zika infection causes microcephaly.

“Microcephaly is obviously where the significant global public health concern is,” according to Michael Diamond, MD, PhD, of the Washington University School of Medicine in St. Louis.

But, he told MedPage Today, there have also been reports of a spike in Guillain-Barré syndrome during the Polynesian outbreak. Again, it’s an association with nothing to prove that Zika was responsible.

Still, there are now two clinical syndromes that have appeared at the same time as a Zika outbreak. It might be coincidence but health officials are urging precautions anyway.

And it’s yet another instance of a pathogen emerging from the shadows.

‘Emerging’ Pathogens?

The term “emerging diseases” is widely used but it’s often bit of a misnomer. Many such pathogens are bugs that have moved into new places, while a few are actually novel. In the latter group, put HIV, SARS and MERS. But Zika — like dengue, chikungunya, and West Nile virus — is a traveller.

Previously known or not, the list of such pathogens has grown in recent years. Consider a partial list: West Nile in 1999, SARS in 2002, the H1N1 pandemic influenza in 2009, MERS in 2012, Ebola in 2013, chikungunya in 2013.

And now Zika.

Is the apparent increase real? If so, what’s causing it? And what can we do?

The answers, experts told MedPage Today, are:

  • Yes, it’s probably a real phenomenon
  • It has multiple causes
  • And while there are steps we can take to minimize the effects — if we have the will and the cash — emerging diseases are going to be a continuing problem

“We’re definitely seeing more, there’s no question about it,” according to James LeDuc, PhD, director of the Galveston National Laboratory.

And it really shouldn’t be a surprise, he told MedPage Today: The National Academy of Sciences warned in 1992 that infectious disease had not been conquered and that — as a consequence of human activities — we were likely to see more and more pathogens spreading beyond their ancestral ranges.

The causes, that 1992 report said, include:

  • Increasing human populations, often pushing into new places and coming in contact with new pathogens
  • More and faster travel
  • Growing urbanization
  • Erosion of some traditional public health infrastructure, such as mosquito control programs

To those, we might have to add climate change, LeDuc said. For some of the mosquito-borne diseases especially, climate change might expand or move their ranges, as temperate regions become semi-tropical.

What propels Zika into the headlines is the link with birth defects. And however nuanced health officials try to be — it’s only an association, we still need more research, there might be other causes — just making the link creates fear.

“We’re still trying to figure out what’s going on with Zika and microcephaly,” commentedHeidi Brown, PhD, of the University of Arizona in Tucson. That’s going to take a lot of study and some time.

Put simply, an outbreak of disease needs three pro-conditions, Brown told MedPage Today: “You need the vector, you need the virus, and you need a human population that is susceptible.”

In the case of Zika, as well as dengue fever and chikungunya, the vector is A. aegypti, a mosquito that historically was implicated in the spread of yellow fever. In the early part of the last century, huge public health programs aimed to eradicate A. aegypti, with some success at reducing yellow fever.

But it’s the fate of successful public health programs to wither once they’ve achieved success and A. aegypti has made a comeback.

And, Brown said, A. aegypti is an “urban mosquito” — it likes to feed on people and to breed in the pools of standing water we all-too-often leave around our dwellings. The increasingly large cities of South and Central America, usually with slums where people can’t afford window screens or other protection against mosquito bites, offer a huge pool of targets.

Then an outbreak is just one plane ride away. “It’s very easy now for an infected person or an infected mosquito to move from one area to another,” Diamond said.

Of course, local conditions play an important role. Fauci told MedPage Today that it’s unlikely Zika will make huge inroads into the U.S. for two reasons. In the first place, most of the country has a severe enough winter to cause the mosquitoes to die off. And second, he said, “we can do vector control if we want to do vector control” — a capability that some other countries in the Americas don’t have.

Other experts noted that our cities are less densely populated than those in South and Central America and conditions are better — there’s air conditioning and household screens.

The same applies to other pathogens carried by A. aegypti, like dengue. But not every pathogen needs a mosquito. It’s still not clear what is the animal reservoir for Ebola, for instance, but in the recent epidemic, the vector was good old Homo sapiens. And other pathogens have intermediate hosts that don’t necessarily die off in the winter.

If the pathogens are likely to keep coming, what can we do? Slowing the pace and speed of travel is a nonstarter, we’re not going to stop living in cities, and our numbers, while growth is slowing, continue to rise.

In other words, the third of Brown’s triad — the pool of susceptible people — is going to remain.

That leaves the vector or the pathogen.

Mosquito Control

“Mosquitoes, in the end, don’t contribute much to society,” Diamond said, so A. aegypti is an obvious target if we want to prevent Zika, dengue, chikungunya, or yellow fever. And it’s something we know how to do, noted LeDuc, citing the mass eradication campaigns of the 20th century.

But that effort used “armies of people,” LeDuc noted. “That kind of commitment is just not economically feasible today,” he said.

On the other hand, the modern age has brought new tools. For instance, Australian researchers, focusing on dengue, think they can use Wolbachia, bacteria found in many insects, as a way to reduce the ability of A. aegypti to transmit viruses.

And the Brazilian city of Piracicaba is working with a British company, Oxitec, to release male mosquitoes genetically modified so their offspring don’t survive. The males don’t bite, so they can’t transmit disease, but if they outcompete normal males for mates, the net result would be a reduction in adult mosquitoes.

A similar program to prevent screwworm among livestock has been working in the U.S. since the 1950s, Brown said, so it’s not a pipe dream. But neither approach is a “silver bullet,” she said, and will need to be used in combination with other approaches.

Some approaches are decidedly low-tech. Eliminate sources of standing water. Wear insect repellent if you’re somewhere with mosquitoes. Ditto long sleeves and long pants. Put up bednets.

Those have the advantage that they work against all mosquito species, Diamond said, and therefore lots of pathogens.

No Help

A recurring theme in the story of emerging diseases is that there are no specific treatments and no vaccines. And if you think about it, that makes perfect sense — if we don’t know something is coming (because it’s emerging, after all), how can we have a vaccine or a therapy?

So consider the current Zika outbreak. Most people working in the field would not have predicted it for the next viral epidemic in the Americas and if they had would not have been especially worried.

“It took a lot of people by surprise and they were perhaps a little bit dismissive,” Brown said.

Other pathogens — Lassa fever, Rift Valley fever, Marburg, and MERS among them — might well have been higher on the priority list. Indeed, they are higher on the WHO’s blueprint for future research into epidemic prevention.

And who pays for the research? It’s not as if there is a huge commercial market for a vaccine or treatment for Zika, which in most cases causes mild or no illness. There might be a better market for other pathogens but how do you know where to focus?

The problem with vaccinology in this field, LeDuc said, is that vaccines generally have to be pathogen-specific and they are costly to develop. They’re also technically challenging; work on a dengue vaccine has been going on for years, he noted.

That said, Fauci commented, researchers on West Nile virus have developed a “platform” for a flavivirus vaccine that might be quickly adaptable to Zika. The issue then would be getting it through the regulatory hurdles and into the field — a long expensive process.

Even if a vaccine were available, how would it be used?

Writing with a colleague recently in the New England Journal of Medicine, Fauci noted that outbreaks are unpredictable, so vaccinating a population against a given pathogen would not be cost-effective, while stockpiling a vaccine for later deployment might be too slow to stop an epidemic.

And, of course, both approaches depend on knowing the pathogen is there or on its way.

The Ebola epidemic, which left thousands dead in West Africa, was missed for months because health officials in the region weren’t expecting it and didn’t recognize it when it arrived. In the case of Zika, the silent circulation of the virus in asymptomatic people makes it hard for surveillance systems to pick it up.

Then there’s treatment.

Broad-Spectrum Antivirals?

There is a specific therapy for just a handful of viruses, Diamond noted: hepatitis C, HIV, herpes simplex, and influenza. Such drugs are not easy to develop, especially in the throes of reacting to a crisis.

But LeDuc, for one, is “quite optimistic” that broad-spectrum antivirals can be developed. “The more we understand how pathogens cause disease,” he said, “the more we see common pathways” that might be avenues for intervention.

Once again, though, we run into the issue of getting drugs to people when they need it. Even if a Zika treatment were available, the vast majority of infected people would not take it because they would never know they were infected.

“One of the biggest challenges is diagnosis — and early diagnosis — so that we have a chance to intervene,” LeDuc said.

Mug’s Game

So what’s next?

Predicting the next outbreak is a mug’s game, as the case of Zika illustrates.

“There are many viruses that could emerge,” Diamond said, but whether they do or not depends on a host of variables, such things as the presence or absence of a vector and the titer needed to cause infection.

But the world could do better at being prepared, he said. “You can be reactionary or you can be proactive,” Diamond said.

The reactionary approach is to wait until something happens and then wheel out the fire trucks to put out the blaze. But we’d be better off, Diamond said, investing in “ways to make your house fireproof.”

Those investments would certainly include better surveillance, drugs, and vaccines, he said.

But first on the list, Diamond said, should be basic research on the nature of viruses so that we are “prepared to deal not just with the pandemic du jour but to really respond to any virus that comes up.”

 

HIV Growing Resistant to Common Treatment

Ryan Bushey, Associate Editor    http://www.dddmag.com/news/2016/01/hiv-growing-resistant-common-treatment

http://www.dddmag.com/sites/dddmag.com/files/ddd1601_HIV.jpg

Scientists from the University College London made a new discovery regarding the HIV virus.

The researchers learned the common HIV therapy tenofovir was less effective against certain strains of the pathogen after studying an estimated 2,000 patients, writes theBBC. Tenofovir is typically used in combination with other medication to suppress the growth of this infection.

A comparison was done between HIV patients in Africa versus those in Europe. Individuals in Africa were 60 percent more resistant to tenofovir whereas European patients experienced 20 percent more resistance.

Irregular dosing of the drug was partly to blame as well as sub-standard administration of the medication.

Lead author Dr. Ravi Gupta told the BBC, “If the right levels of the drug are not taken, as in they are too low or not regularly maintained, the virus can overcome the drug and become resistant.”

Gupta added that there should be a simultaneous global initiative and cash investment to improve facilities and disease monitoring in African countries.

 

Zika Update

The virus continues to spread as countries issue pregnancy advisories and drug firms pick up on vaccine development.

By Kerry Grens | January 28, 2016

As the mosquito-borne Zika virus has now spread to at least 23 countries in the Americas in recent months, the World Health Organization (WHO) is convening an emergency meeting on International Health Regulations Monday (February 1), Director-General Margaret Chan announced today (January 28).

Meanwhile, four countries—Ecuador, El Salvador, Jamaica, and Colombia—have asked women to delay getting pregnant for fear the virus can cause severe brain damage in fetuses. And some airlines have offered refund to pregnant travelers who booked trips to countries where Zika is circulating.

President Obama chimed in this week, calling for an acceleration of “research efforts to make available better diagnostic tests, to develop vaccines and therapeutics, and to ensure that all Americans have information about the Zika virus and steps they can take to better protect themselves from infection,” according to a White House statement.

There is currently no immunization or cure for Zika, but several pharmaceutical companies and academic labs have expressed interest in developing a vaccine. The University of Texas Medical Branch has already begun work on a Zika vaccine, which could be ready for testing in a year or two.

“What would take the longest time would be the process of passing it through the [US Food and Drug Administration] and other regulatory agencies to allow it for public use and that may take up to 10 to 12 years,” Nikos Vasilakis, who is working on the vaccine, told BBC News. His team is also advancing diagnostics that could help answer questions about the risks of fetal Zika exposure. (See “New Tests for Zika in the Works,” The Scientist, January 25, 2016.)

Sanofi, which has had a dengue shot recently approved in several countries, and GlaxoSmithKline have expressed interest in starting a vaccine program, while another firm, Inovio Pharmaceuticals, announcedMonday (January 25) it was beginning work on a Zika vaccine.

On Tuesday (January 26), the US Centers for Disease Control and Prevention (CDC) issued guidelines for screening babies whose mothers may have contracted Zika while pregnant. Infants should be tested for Zika if their mother tested positive or if they have microcephaly and their mothers were in a country with circulating virus while they were pregnant.

Microcephaly is not the only concern for exposed fetuses; these babies should also be screened for hearing and vision impairments, the CDC urged. “One rationale is we don’t know the spectrum of problems that perhaps are related to Zika virus, so we want to do a lot of screenings of infants out of an abundance of caution,” Cynthia Moore, the director of the CDC’s division of birth defects and developmental disabilities, told The New York Times. “We worry because other intrauterine infections may have some effects that last or show up after birth.”

Meanwhile, US health officials this week said a massive outbreak stateside is unlikely, given the geographic range of the mosquito species that transmit the virus and Americans’ housing conditions, with screens and air conditioning. “If you look at historically what we’ve seen, I think we can say that it’s a remote possibility and unlikely to happen,” Anthony Fauci, head of the National Institutes of Allergy and Infectious Disease, told NPR’s Shots.

 

Interim Guidelines for the Evaluation and Testing of Infants with Possible Congenital Zika Virus Infection — United States, 2016

The Lancet Infectious Diseases   JANUARY 28, 2016

Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study

Summary  
Background

Antiretroviral therapy (ART) is crucial for controlling HIV-1 infection through wide-scale treatment as prevention and pre-exposure prophylaxis (PrEP). Potent tenofovir disoproxil fumarate-containing regimens are increasingly used to treat and prevent HIV, although few data exist for frequency and risk factors of acquired drug resistance in regions hardest hit by the HIV pandemic. We aimed to do a global assessment of drug resistance after virological failure with first-line tenofovir-containing ART.

Methods

The TenoRes collaboration comprises adult HIV treatment cohorts and clinical trials of HIV drug resistance testing in Europe, Latin and North America, sub-Saharan Africa, and Asia. We extracted and harmonised data for patients undergoing genotypic resistance testing after virological failure with a first-line regimen containing tenofovir plus a cytosine analogue (lamivudine or emtricitabine) plus a non-nucleotide reverse-transcriptase inhibitor (NNRTI; efavirenz or nevirapine). We used an individual participant-level meta-analysis and multiple logistic regression to identify covariates associated with drug resistance. Our primary outcome was tenofovir resistance, defined as presence of K65R/N or K70E/G/Q mutations in the reverse transcriptase (RT) gene.   Findings

We included 1926 patients from 36 countries with treatment failure between 1998 and 2015. Prevalence of tenofovir resistance was highest in sub-Saharan Africa (370/654 [57%]). Pre-ART CD4 cell count was the covariate most strongly associated with the development of tenofovir resistance (odds ratio [OR] 1·50, 95% CI 1·27–1·77 for CD4 cell count <100 cells per μL). Use of lamivudine versus emtricitabine increased the risk of tenofovir resistance across regions (OR 1·48, 95% CI 1·20–1·82). Of 700 individuals with tenofovir resistance, 578 (83%) had cytosine analogue resistance (M184V/I mutation), 543 (78%) had major NNRTI resistance, and 457 (65%) had both. The mean plasma viral load at virological failure was similar in individuals with and without tenofovir resistance (145 700 copies per mL [SE 12 480] versus 133 900 copies per mL [SE 16 650; p=0·626]).

Interpretation

We recorded drug resistance in a high proportion of patients after virological failure on a tenofovir-containing first-line regimen across low-income and middle-income regions. Effective surveillance for transmission of drug resistance is crucial.

Introduction

More than 35 million people worldwide are living with HIV-1.1 There is no effective vaccine and therefore control of the HIV pandemic relies heavily on combination antiretroviral therapy (cART). WHO treatment guidelines for adult HIV-1 infection recommend the nucleotide reverse-transcriptase inhibitor (NRTI) tenofovir for first-line ART, in combination with lamivudine or emtricitabine and the non-nucleoside reverse-transcriptase inhibitor (NNRTI) efavirenz.2 Older NRTIs such as the thymidine analogue drugs are being replaced by tenofovir and the NNRTI nevirapine, although mentioned in WHO guidelines, is being phased out from first-line regimens.2

The global scale-up of cART has now reached 15 million treated individuals.1 The administration of cART at the time individuals with HIV-1 are initially diagnosed prevents immunological deterioration as early as possible and interrupts the spread of HIV-1 from newly diagnosed individuals.3 This strategy, referred to as treatment as prevention, is being studied especially in high-incidence regions and nearly always includes the use of first-line tenofovir-containing ART regimens. Likewise, the strategy of pre-exposure prophylaxis (PrEP) depends entirely on the administration of tenofovir or tenofovir and emtricitabine to uninfected individuals at high risk of HIV-1 infection.4

In individuals receiving tenofovir, HIV-1 develops phenotypically and clinically significant resistance usually as a result of one mutation at position 65 (lysine to arginine; K65R) in the reverse transcriptase (RT) gene.5 Data from clinical trials and cohorts in high-income settings using tenofovir combined with NNRTI have reported low prevalence of tenofovir resistance at viral failure,6, 7, 8 in stark contrast with reports from low-income and middle-income countries where prevalence seems to be much higher.9, 10 Similarly, high-level resistance to NNRTI and the cytosine analogue component (emtricitabine and lamivudine) arise through changes to one aminoacid, which suggests a low genetic barrier to resistance for these drugs as well. In view of the pivotal role of tenofovir-containing ART as both treatment and prophylaxis, and the striking potential for drug resistance, we did a global assessment of drug resistance after virological failure with first-line tenofovir-containing ART.

Research in context

Evidence before this study

We searched PubMed for studies of the prevalence of tenofovir resistance after failure of first-line antiretroviral therapy with efavirenz or nevirapine (non-nucleoside reverse-transcriptase inhibitors [NNRTIs]) in patients with HIV-1, published between January, 1999, and June, 2015, using the search terms “HIV” AND “tenofovir” AND “resistance”. We identified studies done in untreated adults (age >15 years) in which either efavirenz or nevirapine was combined with tenofovir and either emtricitabine or lamivudine as first line antiretroviral therapy. Several studies reported resistance data for tenofovir when the drug was started after initial use of stavudine or zidovudine; these studies were not reviewed further. We also excluded studies that reported tenofovir use without NNRTI because standard first-line antiretroviral therapy under a public health approach is based on NNRTI in adults.

We identified randomised controlled trials and a meta-analysis comparing NNRTI with protease inhibitors, in combination with tenofovir, which reported resistance data. Patients in high-income settings reported tenofovir resistance in 0–25% of virological failures and those in sub-Saharan Africa in 28–50%. The only other prospective study in sub-Saharan Africa was PASER-M, and was limited by few resistance data for patients given tenofovir plus NNRTI-based combination antiretroviral therapy (cART). The remaining studies were largely from South Africa and reported a wide range of prevalence (between 23% and 70%) of tenofovir resistance after virological failure. In west Africa, one study reported that 57% of virological failures were tenofovir resistant in a very small sample of 23 patients. Although aforementioned studies also reported NNRTI and cytosine analogue resistance, they were unable to quantify to what extent tenofovir resistance was a marker for high-level compromise of the regimen. We found no studies that specifically reported resistance data for patients given first-line tenofovir in east Africa. No study reported resistance data from more than one continent, and none seemed adequately powered to establish the effect of co-administered reverse-transcriptase inhibitors on the emergence of tenofovir resistance.

Added value of this study

This study reports the most comprehensive assessment of HIV-1 drug resistance after scale-up of first-line WHO recommended tenofovir-based antiretroviral regimens, showing that tenofovir resistance is surprisingly common in patients with treatment failure across many studies in all low-income regions. Importantly, these individuals also have notable resistance to other drugs in their regimen, leading to almost complete compromise of combination treatment. Challenging current perceptions in the specialty, our findings show that tenofovir resistant viruses have substantial transmission potential. Furthermore, our results show that viral strain affects tenofovir resistance in Europe but is not the main driver for resistance in viruses circulating in sub-Saharan Africa. Newly identified risk factors for resistance to tenofovir and NNRTI drugs include pre-treatment CD4 cell count (but not viral load) and co-administered antiretrovirals.

Implications of all the available evidence

Improvements in the quality of HIV care and viral load monitoring could mitigate the emergence and spread of tenofovir resistance, thereby prolonging the lifetime of tenofovir-containing regimens for both treatment and prophylaxis. Surveillance of tenofovir and NNRTI resistance should be a priority both in untreated and treated populations.

Methods …..

Results

The TenoRes collaboration included 1926 individuals from 36 countries (figure 1 and appendix).Table 1 summarises the median size and year of ART initiation for the cohorts comprising the collaboration. Viral load monitoring was done in about 50% of the cohorts including nearly all of cohorts from upper-income regions and from a small proportion of the cohorts in low-income and middle-income countries (appendix shows income status for each cohort; table 1).

 

http://www.thelancet.com/cms/attachment/2045482109/2056813674/gr1.sml

Figure 1

(A) Countries contributing data to resistance analysis and HIV-1 subtype distribution, (B) prevalence of drug resistance by mutation and by region

NNRTI=non-nucleotide reverse-transcriptase inhibitor. TDF=tenofovir disoproxil fumarate. *24% (n=462) of participants had tenofovir resistance when genotypes from viral load >1000 copies HIV-1 RNA per mL were considered.

 

Table 1

Characteristics of resistance studies included in analysis

Data are n, range, or n (%). cART=combination antiretroviral therapy.

*Multinational studies were treated as separate studies within each country.

 

The region-level pre-ART median CD4 cell count ranged from 44 to 104  cells per μL in sub-Saharan Africa, Asia, and Latin America (table 2). As expected, in north America pre-ART median CD4 cell count was 144 cells per μL and 190  cells per μL in Europe. The proportion of individuals using emtricitabine (vs lamivudine) and efavirenz (vs nevirapine) varied significantly by region. Emtricitabine was used significantly more than lamivudine in Europe, North America, and west and central Africa, and efavirenz was used significantly more than nevirapine in all regions apart from east and west and central Africa. The median duration of ART ranged from 11 to 26 months. Pre-treatment viral load ranged between 4·80 and 5·58 log copies per mL and was significantly higher in eastern and western and central Africa and Latin America than the other regions (table 2).

 

 

Table 2

Participant characteristics and details of antiretroviral therapy

Data are n (%) or median (IQR). TDF=tenofovir disoproxil fumarate.

 

Crude prevalence of tenofovir resistance in patients with treatment failure was highest in low-income and middle-income regions (figure 1). Prevalence of cytosine analogue resistance (M184V/I) was highest in sub-Saharan Africa and Latin America and lowest in western Europe. By contrast, resistance to NNRTI did not show this pattern (figure 1). Furthermore, the M184V/I mutation was less common than NNRTI resistance across all regions except in eastern Africa. Of the 700 patients with tenofovir resistance in the dataset, 457 (65%) had resistance to both remaining drugs. Participants with tenofovir resistant viruses were likely to be resistant to one or both accompanying drugs and therefore have profound compromise of their regimen, as compared with those without tenofovir resistance (figure 1).

Low baseline CD4 cell count was consistently associated with a higher prevalence of tenofovir resistance across regions. The pooled OR for tenofovir in individuals with a CD4 cell count of less than 100 cells per μL versus 100  cells per μL was 1·50 (95% CI 1·27–1·77; figure 2). By contrast, a high baseline viral load was only associated with a small, not significant increase in tenofovir resistance (OR for viral load ≥100 000 copies per mL vs <100 000 copies per mL was 1·17, 95% CI 0·94–1·44;appendix). We compared tenofovir resistance by use of co-administered antiretrovirals with tenofovir as first-line therapy. Use of lamivudine rather than emtricitabine (NRTIs) was associated with a higher prevalence of tenofovir resistance (OR 1·48, 95% CI 1·20–1·82), as was use of the NNRTI nevirapine rather than efavirenz (OR 1·46, 1·28–1·67; appendix). Subgroup analysis showed that as well as associations being consistent across regions, they were also generally similar across a range of study settings (appendix), although there was some evidence of a greater effect size of baseline CD4 when efavirenz was co-administered with tenofovir, as compared with nevirapine.

Figure 2

Pooled odds ratios for tenofovir resistance after viral failure for baseline CD4 cell count <100 vs≥100 × 106 cells per μL

TDF+ denotes presence of tenofovir resistance. TDF=tenofovir disoproxil fumarate.

 

When considering the effect of baseline CD4, baseline viral load (figure 3), and co-administered antiretrovirals (appendix) on cytosine analogue and NNRTI resistance, we noted that the magnitude of associations were smaller than those recorded for tenofovir resistance.

 

http://www.thelancet.com/cms/attachment/2045482109/2056813671/gr3.sml

Figure 3

Odds ratios for NNRTI resistance for (A) baseline CD4 cell count <100 vs ≥100 cells per μL, (B) viral load ≥100 000 vs <100 000 copies HIV-1 RNA per mL

NNRTI=non-nucleotide reverse-transcriptase inhibitor.

We also assessed the relation between viral subtype C on acquisition of tenofovir resistance. We restricted this analysis to western European studies in view of the consistent standard of care available in this region and relatively lower level of subtype diversity in other regions (figure 1A). We also limited the comparison to subtypes found in immigrant populations to minimise bias due to socioeconomic factors (thereby excluding subtype B infections mainly recorded in participants born in western Europe). Tenofovir resistance was higher in subtype C compared with non-C, non-B infections with a pooled OR of 2·44 (1·66–3·59).

As a sensitivity analysis we studied risk factors for tenofovir resistance using univariate (adjusted only for region) and multivariate logistic regression analyses (appendix). We noted a dose-response relationship for baseline CD4, which was not markedly altered by adjustment for baseline viral load, viral subtype, or type of co-administered drug used (appendix). Baseline viral load of 100 000 or more copies of HIV-1 RNA per mL was not significantly associated with tenofovir resistance (OR 1·31, 95% CI 0·91–1·91) and we noted no clear trend across increasing viral loads (appendix). Adjustment for several risk factors also had little effect on associations with tenofovir resistance of emtricitabine versus lamivudine and nevirapine versus efavirenz.

Finally, we compared the viral load at treatment failure in the presence and absence of tenofovir-associated mutations. The mean plasma viral load at treatment failure was not different in the presence or absence of tenofovir associated mutations (145 700 copies HIV RNA per mL [SE 12 480]vs 133 900 copies [SE 16 650]; p=0·626; figure 4 shows the within-study viral load by region). These results did not change when analysis was restricted to individuals who had evidence of the K65R mutation, either with or without M184V/I (appendix). Mutations at aminoacids K65 and M184 in the RT gene have been associated with suboptimum replication.13

http://www.thelancet.com/cms/attachment/2045482109/2056813672/gr4.sml

Figure 4

Boxplot of log viral load by presence (TDF-positive) or absence (TDF-negative) of tenofovir resistance at viral failure in studies with at least ten patients with TDF resistance and a viral load measurement at treatment failure

We restricted to studies with at least ten TDF-resistant mutations to help with graphical clarity, although the pattern of similar distributions of failure viral load in the presence or absence of TDF resistance was true for all studies. TDF=tenofovir disoproxil fumarate. Blue dots represent outliers.

 

Discussion

Our study has three main findings relating to the prevalence, risk factors for, and transmissibility of tenofovir resistance. First, we noted that levels of tenofovir resistance in individuals with viral failure ranged from 20% in Europe to more than 50% in sub-Saharan Africa. Second, a CD4 cell count of less than 100 cells per μL, treatment with nevirapine rather than efavirenz, and treatment with lamivudine rather than emtricitabine, were consistently associated with a 50% higher odds of tenofovir resistance in those with viral failure. Third, we noted that in patients with viral failure, viral loads were similar in the presence or absence of tenofovir resistance.

Our findings are important in view of the fact that following WHO recommendations,2 tenofovir is replacing thymidine analogues (zidovudine and stavudine) as part of the NRTI backbone in first-line regimens in resource-limited settings. Every drug in these regimens can be compromised by one aminoacid mutation, and the combination therapy is therefore potentially fragile. In view of the crucial role of tenofovir-containing ART in both treatment and prevention of new infections, restriction of drug resistance in high-burden settings is of paramount importance. Understanding how common tenofovir resistance is, and how and why it varies, is key to its prevention. Although our risk factors are only associated with a modest 50% increase in odds, this translates to a roughly 10% increase in resistance in those who fail when the overall tenofovir resistance prevalence is about 50% (as recorded in sub-Saharan Africa).

We hypothesise that the regional differences in tenofovir resistance are due to the frequency of viral load monitoring with close patient follow-up and feedback of results. For example, although viral load monitoring is not routinely done in most low-income and middle-income countries, in high-income countries viral load is tested three to four times per year with close patient follow-up and adherence support. Such an approach is likely to lead to earlier detection of viral failure, before selection of drug resistance mutations against tenofovir has occurred.14 This view is supported by the uncommon detection of drug resistance mutations in specimens with low viral load (400–1000 copies per mL) from patients given tenofovir in both high-income settings (figure 1; see higher prevalence of tenofovir resistance where viral load >1000 copies per mL is used as threshold in western Europe)15 and sub-Saharan Africa (Chunfu Yang, Centres for Disease Control, Atlanta, GA, USA, personal communication). Tenofovir resistance could be limited by viral load monitoring,16with rapid feedback to clinicians followed by adherence counselling to preserve first line, or switch to second line when this approach fails. Furthermore, pre-ART (baseline) resistance testing for key NNRTI mutations could potentially protect against tenofovir resistance by avoiding use of partly active treatment regimens. In our report, transmitted NNRTI resistance was low in the regions studied (<10%),17 and therefore not likely to be a major driver of wide variation in drug resistance across income settings.

Other factors that vary geographically could also affect success of ART and should be noted. Treatment failure is associated not only with drug resistance, but also side-effects. Efavirenz is associated with CNS side-effects such as sleep disturbance and is associated with treatment discontinuation.18 Furthermore, drug stock-outs and other indicators of quality of HIV services that have shown geographic variation would also predispose to treatment failure.19 The issue of regional variation in adherence levels has received considerable attention, with data from several studies suggesting that adherence is not worse in sub-Saharan Africa compared with North America.20, 21

With regards to increased tenofovir resistance in individuals with low baseline CD4 counts, this finding is consistent with results from the ACTG 5202 trial22 suggesting higher frequency of RT mutations in patients given ART with low CD4 cell counts, and offer a benefit of CD4 cell count measurement after diagnosis of HIV infection beyond establishing prophylaxis against opportunistic infections.23 Lamivudine warrants further study in first-line regimens in view of data presented in our study and the conflicting reports regarding virological efficacy of lamivudine versus emtricitabine.24,25, 26 Of note, the differences between lamivudine and emtricitabine might become less important in high-income regions where implementation of the second generation integrase inhibitor dolutegravir occurs, in view of the fact that this agent has not been associated with any cytosine analogue resistance at virological failure.27

Viral load has been associated with transmission risk.28 Despite evidence for diminished replication of tenofovir resistant viruses (containing the K65R mutation in the RT gene) in vitro, we noted similar viral loads in participants with and without tenofovir resistance. Therefore, there might be substantial potential for onward transmission to uninfected individuals,29 despite little evidence of K65R transmission up to now.30 This finding reinforces the need for drug resistance surveillance activities in both untreated and treated HIV-positive individuals.

There are several important limitations of our study. First, because we only included patients with virological failure related to existing study cohorts,1 our estimates of the prevalence of tenofovir resistance might not be representative in certain high-burden regions. Although this situation might have biased our findings on absolute prevalences of tenofovir resistance, it is unlikely to have affected associations with baseline CD4 or co-administered drugs. Second, we only included patients at failure so were unable to assess overall rates of tenofovir resistance in all patients starting first-line treatment. We used this method because many of the contributing studies had no clear denominator, especially those done in resource-limited settings. However, extensive WHO-led analysis reported that 15–35% (on treatment vs intention to treat) of patients in sub-Saharan Africa have virological failure by 12 months.31 Therefore, using a conservative 50% prevalence of tenofovir resistance at failure from our analysis, we suggest that it is likely that 7·5–17·5% of individuals given tenofovir plus cytosine analogue plus efavirenz will develop tenofovir resistance within 1 year of treatment initiation under present practices in sub-Saharan Africa.

Third, our findings on risk factors for tenofovir resistance were derived from an unadjusted meta-analysis involving very different study populations. Although this enhances the generalisability of results, it has the potential to lead to biased comparisons. However, we took measures to minimise biases. We exclusively used within-study and within-country comparisons for our primary analyses, thereby ensuring that comparisons were for participants undergoing similar treatment monitoring practices. We tested associations between risk factors and found that they were generally weak. For example, baseline CD4 cell count and viral load were only weakly associated with one another and neither was strongly associated with type of co-administered drug. Additionally, we undertook sensitivity analyses, which suggested that adjustment for other covariates had minimum effect on estimated associations. Lastly, our data tended to be consistent with previous studies—eg, our findings of higher resistance in subtype C patients are consistent with in-vitro data suggesting subtype C viruses are more susceptible to developing the K65R mutation.32

Fourth, despite our analysis being the largest drug resistance study ever undertaken after failure of first-line tenofovir-containing cART, patient numbers were somewhat limited by the slow uptake of tenofovir-based regimens in west and central Africa, eastern Europe, and Asia (in particular China and Russia), and information about baseline viral load in these settings was uncommon. As a result, European countries, Thailand, and South Africa contributed substantially to the analysis.

In summary, extensive drug resistance emerges in a high proportion of patients after virological failure on a tenofovir-containing first-line regimen across low-income and middle-income regions. Optimisation of treatment programmes and effective surveillance for transmission of drug resistance is therefore crucial.

Correspondence to: Dr Ravindra K Gupta, UCL, Department of Infection, London WC1E 6BT, UK ravindra.gupta@ucl.ac.uk

Cross-Reactive Ebola Antibodies

Human monoclonal antibodies induced during Ebola infection are able to neutralize related viral species, scientists show.

By Anna Azvolinsky | January 21, 2016

http://www.the-scientist.com//?articles.view/articleNo/45146/title/Cross-Reactive-Ebola-Antibodies/

 

http://www.the-scientist.com/images/News/January2016/620_Ebola%20Ab.jpg

Structure of Bundibugyo survivor antibodies (colors) bound to viral glycoproteinSCRIPPS RESEARCH INSTITUTE; CHARLES MURIN, ANDREW WARD

From blood samples of survivors of a 2007 Ebola outbreak in Uganda, researchers have isolated antibodies that are protective and can neutralize two other species of Ebolavirus, including ­­Zaire ebolavirus—the one responsible for the massive 2014 outbreak in West Africa. The binding specificities of these human monoclonal antibodies and their activity in animal models of Ebolavirus appeared today (January 21) in Cell.

“What is exciting is that the authors demonstrated that cross-reactive antibodies exist in survivors, and these antibodies are protective in animal models,”Larry Zeitlin, president of Mapp Biopharmaceutical, who was not involved in the current study but is collaborating with its authors as part of a National Institutes of Health (NIH)-funded project to develop and test vaccines and therapeutics against Ebolaviruses, told The Scientist in an email. “This gives real hope that a single product could be developed for treating all the Ebolavirus species.”

“This is a very good paper,” said Lisa Hensley, who has worked on the pathogenesis of viruses including Ebola and is associate director for science at the NIH’s Integrated Research Facility in Maryland. “Looking in people who survived Bundibugyo ebolavirus,” the species behind the 2007 outbreak, “brings our understanding of these viruses a step further. The study moved what we only knew anecdotally into convincing and strong data,” Hensley said.

Within the genus, there are currently three identified viral species that have caused deadly human outbreaks: Z. ebolavirus, B. ebolavirus, and Sudan ebolavirus.

Isolating peripheral blood B cells from seven survivors of B. ebolavirus, James Crowe, Jr., a viral immunologist and director of the Vanderbilt University Vaccine Center in Nashville, Tennessee, and his colleagues identified 90 antibodies that bound to the virus’s outer glycoprotein. Characterizing these human antibodies, the researchers found that 63 percent of them bound the glycoprotein of at least two of the three Ebolavirus species in vitro. Thirty-one (34 percent) of these antibodies were able to neutralize B. ebolavirus in an assay that is commonly used as a surrogate of an in vivo infection, and seven of these neutralized all three viral species, binding to one of three highly conserved regions of the glycoprotein.

The researchers found two different neutralizing antibodies, each used separately to treat Ebola-infected mice, effective. A single treatment with one of these antibodies successfully rescued Ebola-infected guinea pigs, while a combination of two antibodies resulted in complete protection of guinea pigs infected with Z. ebolavirus, the scientists showed.

“Protection against Ebola virus achieved in the guinea pig model is quite predictive of what can happen in humans, and in this model we can achieve protection,” said study coauthor Alexander Bukreyev, a virologist at the University of Texas Medical Branch in Galveston. “The key [result] is that the human immune system does produce protective antibodies. We just need to choose the right ones and give them at a high concentration.”

Crowe agreed. “Some of [the human antibodies] are extremely potent, some of the most potent antivirus antibodies ever isolated. Some of these antibodies possess the two major qualities you want to see in a therapeutic treatment—potent neutralization and breadth of activity against multiple Ebolavirus species.”

A recent study showed that serum isolated from Ebola survivors did not improve patient prognosis. But Mapp Biopharmaceutical’s cocktail of three mouse-derived, humanized monoclonal antibodies against Z. ebolavirus, ZMapp, was last year shown to be an effective treatment in Ebola-infected macaques. “Our goal for the second generation ZMapp product is a pan-Ebola virus antibody cocktail,” Zeitlin told The Scientist.The results of the present study, he added, “provides proof-of-concept for our effort.”

“The previously developed mouse monoclonal antibodies that were part of ZMapp were a solid start,” said Crowe. “But now, this study with antibodies from human survivors shows that we may have been underestimating the ability of antibodies to kill Ebola.”

The Ebola epitopes to which the cross-reactive antibodies bind will not only be helpful to develop new antibody cocktails as treatments but also point to a vaccine that could be used for multiple Ebola species. “This is the deeper implication of this work,” said Crowe.

Crowe, Bukreyev, and their colleagues are now isolating and analyzing antibodies against Z. ebolavirusstrains from the most recent outbreak. The researchers are also looking to combine the two types of therapies that have so far been shown to be most potent against Ebola, for a one-two punch: antibodies, which can neutralize already formed viral particles, and small interfering RNAs (siRNAs) that block viral replication.

The ultimate test will be whether the antibodies might be used in a protective vaccine or to treat people infected in the next outbreak. “That is everyone’s goal,” said Hensley. “What we do in animal models is nice, but how does it reflect what will happen in humans?”

A.I. Flyak et al., “Cross-reactive and potent neutralizing antibody responses in human survivors of natural Ebolavirus infection,” Cell, doi:10.1016/j.cell.2015.12.022, 2016.

 

 

 

 

Lung Cancer

http://www.cancernetwork.com/lung-cancer

The term “HER2-positive lung cancer” may actually refer to two distinct entities, according to a new study. HER2 mutations and HER2 amplifications were found in similar numbers of lung adenocarcinoma cases, but they did not occur in the same samples, suggesting HER2-targeted agents should differentiate between mutation and amplification.

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Neutrophil Serine Proteases in Disease and Therapeutic Considerations

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

SERPINB1 Regulates the activity of the neutrophil proteases elastase, cathepsin G, proteinase-3, chymase,
chymotrypsin, and kallikrein-3. Belongs to the serpin family. Ov-serpin subfamily. Note: This description may
include information from UniProtKB.
Chromosomal Location of Human Ortholog: 6p25
Cellular Component: extracellular space; membrane; cytoplasm
Molecular Function: serine-type endopeptidase inhibitor activity
Reference #:  P30740 (UniProtKB)
Alt. Names/Synonyms: anti-elastase; EI; ELANH2; ILEU; LEI; Leukocyte elastase inhibitor; M/NEI; MNEI; Monocyte/neutrophil elastase inhibitor; Peptidase inhibitor 2; PI-2; PI2; protease inhibitor 2 (anti-elastase), monocyte/neutrophil derived; serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 1; Serpin B1; serpin peptidase inhibitor, clade B (ovalbumin), member 1; SERPINB1
Gene Symbols: SERPINB1
Molecular weight: 42,742 Da
 

SERPIN PEPTIDASE INHIBITOR, CLADE B (OVALBUMIN), MEMBER 1; SERPINB1

Alternative titles; symbols
PROTEASE INHIBITOR 2, MONOCYTE/NEUTROPHIL DERIVED; ELANH2
ELASTASE INHIBITOR, MONOCYTE/NEUTROPHIL; EI
HGNC Approved Gene Symbol: SERPINB1
Cloning and Expression
Monocyte/neutrophil elastase inhibitor (EI) is a protein of approximately 42,000 Mr with serpin-like functional properties.
Remold-O’Donnell et al. (1992) cloned EI cDNA and identified 3 EI mRNA species of 1.5, 1.9, and 2.6 kb in monocyte-like cells
and no hybridizing mRNA in lymphoblastoid cells lacking detectable EI enzymatic activity. The cDNA open reading frame encoded
a 379-amino acid protein. Its sequence established EI as a member of the serpin superfamily. Sequence alignment indicated that
the reactive center P1 residue is cys-344, consistent with abrogation of elastase inhibitory activity by iodoacetamide and making
EI a naturally occurring cys-serpin.
 

 

Mapping

In the course of studying 4 closely linked genes encoding members of the ovalbumin family of serine proteinase inhibitors
(Ov-serpins) located on 18q21.3, Schneider et al. (1995) investigated the mapping of elastase inhibitor. They prepared PCR
primer sets of the gene, and by using the NIGMS monochromosomal somatic cell hybrid panel, showed that the EI gene maps
to chromosome 6.

By amplifying DNA of a somatic cell hybrid panel, Evans et al. (1995) unambiguously localized ELANH2 to chromosome 6.
With the use of a panel of radiation and somatic cell hybrids specific for chromosome 6, they refined the localization to
the short arm telomeric of D6S89, F13A (134570), and D6S202 at 6pter-p24.

http://www.phosphosite.org/getImageAction.do?id=27292293

 

 

REFERENCES
Evans, E., Cooley, J., Remold-O’Donnell, E. Characterization and chromosomal localization of ELANH2, the gene encoding human
monocyte/neutrophil elastase inhibitor. Genomics 28: 235-240, 1995. [PubMed: 8530031related citations] [Full Text]
Remold-O’Donnell, E., Chin, J., Alberts, M. Sequence and molecular characterization of human monocyte/neutrophil elastase inhibitor.
Proc. Nat. Acad. Sci. 89: 5635-5639, 1992. [PubMed: 1376927related citations][Full Text]
Schneider, S. S., Schick, C., Fish, K. E., Miller, E., Pena, J. C., Treter, S. D., Hui, S. M., Silverman, G. A. A serine proteinase inhibitor locus at
18q21.3 contains a tandem duplication of the human squamous cell carcinoma antigen gene. Proc. Nat. Acad. Sci. 92: 3147-3151, 1995.
[PubMed: 7724531,related citations] [Full Text]

 

Leukocyte elastase inhibitor (serpin B1) (IPR015557)

Short name: Serpin_B1

Family relationships

  • Serpin family (IPR000215)
    • Leukocyte elastase inhibitor (serpin B1) (IPR015557)

Description

Leukocyte elastase inhibitor is also known as serpin B1. Serpins (SERine Proteinase INhibitors) belong to MEROPS inhibitor family I4 (clan ID)
[PMID: 14705960].

Serpin B1 regulates the activity of neutrophil serine proteases such as elastase, cathepsin G and proteinase-3 and may play a regulatory role to
limit inflammatory damage due to proteases of cellular origin [PMID: 11747453]. It also functions as a potent intracellular inhibitor of granzyme
H [PMID: 23269243]. In mouse, four different homologues of human serpin B1 have been described [PMID: 12189154].

 

The neutrophil serine protease inhibitor SerpinB1 protects against inflammatory lung injury and morbidity in influenza virus infection

Dapeng Gong1,2, Charaf Benarafa1,2, Kevan L Hartshorn3 and Eileen Remold-O’Donnell1,2
J Immunol April 2009; 182(Meeting Abstract Supplement) 43.10
http://www.jimmunol.org/cgi/content/meeting_abstract/182/1_MeetingAbstracts/43.10

SerpinB1 is an efficient inhibitor of neutrophil serine proteases. SerpinB1-/- mice fail to clear bacterial lung infection with increased inflammation and neutrophil death. Here, we investigated the role of serpinB1 in influenza virus infection, where infiltrating neutrophils and monocytes facilitate virus clearance but can also cause tissue injury. Influenza virus (H3N2 A/Phil/82) infection caused greater and more protracted body weight loss in serpinB1-/- vs. WT mice (20% vs. 15%; nadir on day 4 vs. day 3). Increased morbidity was not associated with defective virus clearance. Cytokines (IFN, TNF, IL-17, IFN, G-CSF) and chemokines (MIP-1, KC, MIP-2) were increased in serpinB1-/- mice vs. WT on days 2-7 post-infection but not on day 1. In WT mice, histology indicated large infiltration of neutrophils peaking on day 1 and maximal airway injury on day 2 that resolved on day 3 coincident with the influx of monocytes/macrophages. In serpinB1-/- mice, neutrophils also peaked on day 1; epithelial injury was severe and sustained with accumulation of dead cells on day 2 and 3. Immunophenotyping of lung digests on day 2 and 3 showed delayed recruitment of monocytes, macrophages and DC in serpinB1-/- mice, but increase of activated CD4 (day 2-3) and CD8 (day 3) T cells. Our findings demonstrate that serpinB1 protects against morbidity and inflammatory lung injury associated with influenza infection.

 

The neutrophil serine protease inhibitor serpinb1 preserves lung defense functions in Pseudomonas aeruginosainfection

Charaf Benarafa 1 , 2 Gregory P. Priebe 3 , 4 , and Eileen Remold-O’Donnell 1 , 2
JEM July 30, 2007; 204(8): 1901-1909   http://dx.doi.org:/10.1084/jem.20070494

Neutrophil serine proteases (NSPs; elastase, cathepsin G, and proteinase-3) directly kill invading microbes. However, excess NSPs in the lungs play a central role in the pathology of inflammatory pulmonary disease. We show that serpinb1, an efficient inhibitor of the three NSPs, preserves cell and molecular components responsible for host defense against Pseudomonas aeruginosa. On infection, wild-type (WT) and serpinb1-deficient mice mount similar early responses, including robust production of cytokines and chemokines, recruitment of neutrophils, and initial containment of bacteria. However, serpinb1−/− mice have considerably increased mortality relative to WT mice in association with late-onset failed bacterial clearance. We found that serpinb1-deficient neutrophils recruited to the lungs have an intrinsic defect in survival accompanied by release of neutrophil protease activity, sustained inflammatory cytokine production, and proteolysis of the collectin surfactant protein–D (SP-D). Coadministration of recombinant SERPINB1 with the P. aeruginosa inoculum normalized bacterial clearance inserpinb1−/− mice. Thus, regulation of pulmonary innate immunity by serpinb1 is nonredundant and is required to protect two key components, the neutrophil and SP-D, from NSP damage during the host response to infection.

 

Neutrophils are the first and most abundant phagocytes mobilized to clear pathogenic bacteria during acute lung infection. Prominent among their antimicrobial weapons, neutrophils carry high concentrations of a unique set of serine proteases in their granules, including neu trophil elastase (NE), cathepsin G (CG), and proteinase-3. These neutrophil serine proteases (NSPs) are required to kill phagocytosed bacteria and fungi (12). Indeed, neutrophils lacking NE fail to kill phagocytosed pathogens, and mice deficient for NE and/or CG have increased mortality after infection with pulmonary pathogens (34). However, NSPs in the lung airspace can have a detrimental effect in severe inflammatory lung disease through degradation of host defense and matrix proteins (57). Thus, understanding of the mechanisms that regulate NSP actions during lung infections associated with neutrophilia will help identify strategies to balance host defense and prevent infection-induced tissue injury.

 

SERPINB1, also known as monocyte NE inhibitor (8), is an ancestral serpin super-family protein and one of the most efficient inhibitors of NE, CG, and proteinase-3 (910). SERPINB1 is broadly expressed and is at particularly high levels in the cytoplasm of neutrophils (1112). SERPINB1 has been found complexed to neutro phil proteases in lung fluids of cystic fibrosis patients and in a baboon model of bronchopulmonary dysplasia (1314). Although these studies suggest a role for SERPINB1 in regulating NSP activity, it is unclear whether these complexes reflect an important physiological role for SERPINB1 in the lung air space.

RESULTS

To define the physiological importance of SERPINB1 in shaping the outcome of bacterial lung infection, we generated mice deficient for serpinb1 (serpinb1−/−) by targeted mutagenesis in embryonic stem (ES) cells (Fig. 1, A–C). Crossings of heterozygous mice produced WT (+/+), heterozygous (+/−), and KO (−/−) mice for serpinb1 at expected Mendelian ratios (25% +/+, 51% +/−, and 24% −/−; n = 225; Fig. 1 D), indicating no embryonic lethality. Bone marrow neutrophils of serpinb1−/− mice lacked expression of the protein, whereas heterozygous serpinb1+/− mice had reduced levels compared with WT mice (Fig. 1 E). Importantly, levels of the cognate neutrophil proteases NE and CG, measured as antigenic units, were not altered by deletion of serpinb1 (Fig. 1 F). When maintained in a specific pathogen-free environment, serpinb1−/− mice did not differ from WT littermates in growth, litter size, or life span (followed up to 12 mo), and no gross or histopathological defects were observed at necropsy in 8-wk-old mice.

6–8-wk-old animals were intranasally inoculated with the nonmucoid Pseudomonas aeruginosa strain PAO1. Using two infection doses (3 × 106 and 7 × 106 CFU/mouse),serpinb1−/− mice had a significantly lower survival probability and a shorter median survival time compared with WT mice (Fig. 2 A). Further groups of infected mice were used to evaluate bacterial clearance. At 6 h after infection, the bacteria were similarly restricted in mice of the two genotypes, suggesting that the serpinb1−/− mice have a normal initial response to infection. At 24 h, the median bacterial count in the lungs of serpinb1−/− mice was five logs higher than that of the WT mice (P < 0.001), and the infection had spread systemically in serpinb1−/− mice but not in WT mice, as shown by high median CFU counts in the spleen (Fig. 2 B). Histological examination at 24 h after infection revealed abundant neutrophil infiltration in the lungs of both WT and serpinb1−/− mice, and consistent with the bacteriological findings, numerous foci of bacterial colonies and large areas of alveolar exudates were found in serpinb1−/− mice only (Fig. 2 C). When challenged with the mucoid P. aeruginosa clinical strain PA M57-15 isolated from a cystic fibrosis patient, WT mice cleared >99.9% of the inoculum within 24 h, whereas serpinb1-deficient mice failed to clear the infection (Fig. 2 D). Thus, the NSP inhibitor serpinb1 is essential for maximal protection against pneumonia induced by mucoid and nonmucoid strains of P. aeruginosa.

Figure 2.

Serpinb1−/− mice fail to clear P. aeruginosalung infection. (A) Kaplan-Meier survival curves of WT (+/+) and serpinb1-deficient (−/−) mice intranasally inoculated with nonmucoid P. aeruginosa strain PAO1. Increased mortality of serpinb1−/− mice was statistically significant (P = 0.03 at 3 × 106CFU/mouse; P < 0.0001 at 7 × 106CFU/mouse). (B) CFUs per milligram of lung (left) and splenic (right) tissue determined 6 and 24 h after inoculation with 3 × 106 CFUP. aeruginosa PAO1 in WT (+/+, filled circles) and serpinb1−/− (−/−, open circles) mice. Each symbol represents a value for an individual mouse. Differences between median values (horizontal lines) were analyzed by the Mann-Whitney U test. Data below the limit of detection (dotted line) are plotted as 0.5 CFU × dilution factor. (C) Lung sections stained with hematoxylin and eosin show bacterial colonies (arrowheads) and alveolar exudate in lungs of serpinb1−/− mice 24 h after infection with P. aeruginosa PAO1. Bars, 50 μm. (D) Total CFUs in the lung and spleen 24 h after inoculation with 2 × 108 CFU of the mucoid P. aeruginosa strain PA M57-15 in WT (+/+, filled circles) and serpinb1−/− (−/−, open circles) mice. Differences between median values (horizontal lines) were analyzed by the Mann-Whitney U test.

To verify specificity of the gene deletion, we tested whether delivering rSERPINB1 would correct the defective phenotype. Indeed, intranasal instillation of rSERPINB1 to serpinb1−/− mice at the time of inoculation significantly improved clearance of P. aeruginosa PAO1 from the lungs assessed at 24 h and reduced bacteremia compared with infectedserpinb1−/− mice that received PBS instead of the recombinant protein (Fig. S1 A, available at http://www.jem.org/cgi/content/full/jem.20070494/DC1). We have previously demonstrated that rSERPINB1 has no effect on the growth of P. aeruginosa in vitro (15) and does not induce bacterial aggrega tion (16). Also, rSERPINB1 mixed with PAO1 had no effect on adherence of the bacteria to human bronchial epithelial and corneal epithelial cell lines (unpublished data). Therefore, the improved bacterial clearance in treated serpinb1−/− mice is not related to a direct antibacterial role for rSERPINB1 but rather to reducing injury induced by excess neutrophil proteases. In addition, previous in vivo studies in WT rats showed that rSERPINB1 can protect against elastase-induced lung injury (17) and accelerate bacterial clearance two- to threefold in the Pseudomonas agar bead model (15).

Evidence of excess NSP action was examined in the lungs of infected serpinb1−/− mice by measuring surfactant protein–D (SP-D). SP-D, a multimeric collagenous C-type lectin produced by alveolar epithelial cells, is highly relevant as a host defense molecule, because it functions as an opsonin in microbial clearance (18) and acts on alveolar macrophages to regulate pro- and antiinflammatory cytokine production (19). SP-D is also relevant as an NSP target because it is degraded in vitro by trace levels of each of the NSPs (1620). SP-D levels in lung homogenates of WT and serpinb1−/− mice were similar 6 h after P. aeruginosa infection. At 24 h, SP-D levels were reduced in the lungs ofserpinb1−/− mice compared with WT mice, as indicated by immunoblots. A lower molecular mass band indicative of proteolytic degradation is also apparent (Fig. 3 A). Densitometry analysis of the 43-kD SP-D band relative to β-actin indicated that the reduction of SP-D level was statistically significant (+/+, 45 ± 6 [n = 8]; −/−, 10 ± 2 [n = 8]; P < 0.0001 according to the Student’s t test). Furthermore, rSERPINB1 treatment ofP. aeruginosa–infected serpinb1−/− mice partly prevented the degradation of SP-D in lung homogenates compared with nontreated mice (Fig. S1 B). As a further test of the impact of serpinb1 deletion on NSP activity, isolated neutrophils of serpinb1−/− mice were treated with LPS and FMLP and tested for their ability to cleave recombinant rat SP-D (rrSP-D) in vitro. The extent of rrSP-D cleavage by serpinb1−/− neutrophils was fourfold greater than by WT neutrophils, as determined by densitometry. The cleavage was specific for NSPs because it was abrogated by rSERPINB1 and diisopropyl fluorophosphate (Fig. 3 B). Collectively, these findings indicate a direct role for serpinb1 in regulating NSP activity released by neutrophils and in preserving SP-D, an important-host defense molecule.

Efficient clearance of P. aeruginosa infection requires an early cytokine and chemokine response coordinated by both resident alveolar macrophages and lung parenchymal cells (2122). The IL-8 homologue keratinocyte-derived chemokine (KC) and the cytokines TNF-α, IL-1β, and G-CSF were measured in cell-free bronchoalveolar (BAL) samples. Although the tested cytokines were undetectable in sham-infected mice of both genotypes (unpublished data), comparable induc tion of these cytokines was observed in BAL of WT and serpinb1−/− mice at 6 h after infection, demonstrating that there is no early defect in cytokine production in serpinb1−/− mice. At 24 h, levels of TNF-α, KC, and IL-1β were sustained or increased in serpinb1−/− mice and significantly higher than cytokine levels in WT mice. G-CSF levels at 24 h were elevated to a similar extent in BAL of WT and KO mice (Fig. 3 C). However, G-CSF levels were significantly higher in the serum of serpinb1−/− mice (WT, 336 ± 80 ng/ml; KO, 601 ± 13 ng/ml; n = 6 of each genotype; P < 0.01). In addition, serpinb1−/− mice that were treated at the time of infection with rSERPINB1 had cytokine levels in 24-h lung homogenates that were indistinguishable from those of infected WT mice (Fig. S1 C). The increased cytokine production in the lungs of infected serpinb1−/− mice may be caused by failed bacterial clearance but also by excess NSPs, which directly induce cytokine and neutrophil chemokine production in pulmonary parenchymal cells and alveolar macrophages (2324).

Neutrophil recruitment to the lungs was next examined as a pivotal event of the response to P. aeruginosa infection (25). Lung homogenates were assayed for the neutrophil-specific enzyme myeloperoxidase (MPO) to quantify marginating, interstitial, and alveolar neutrophils. Neutrophils in BAL fluid were directly counted as a measure of neutrophil accumulation in the alveolar and airway lumen. MPO in lung homo genates was undetectable in uninfected mice and was comparably increased in mice of both genotypes at 6 h, suggesting normal early serpinb1−/− neutrophil margination and migration into the interstitium. However, by 24 h after infection, MPO levels in lung homogenates remained high in WT mice but were significantly decreased in serpinb1−/− mice (Fig. 4 A). Importantly, the content of MPO per cell was the same for isolated neutrophils of WT andserpinb1−/− mice (+/+, 369 ± 33 mU/106 cells; −/−, 396 ± 27 mU/106 cells). The numbers of neutrophils in BAL were negligible in uninfected mice and were similarly increased in WT and serpinb1−/− mice at 6 h after infection. Neutrophil counts in BAL further increased at 24 h, but the mean BAL neutrophil numbers were significantly lower in serpinb1−/− mice compared with WT mice (Fig. 4 B). The evidence from the 6-h quantitation of MPO in homogenates and neutrophils in BAL strongly suggests that neutrophil recruitment is not defective in infected serpinb1−/− mice. Moreover, the high levels of cytokines and neutrophil chemoattractant KC in serpinb1−/− mice at 24 h (Fig. 3 C) also suggest that, potentially, more neutrophils should be recruited. Therefore, to examine neutrophil recruitment in serpinb1−/− mice, we used a noninfectious model in which neutrophils are mobilized to migrate to the lung after intranasal delivery of P. aeruginosa LPS. MPO levels in lung homogenate and neutrophil numbers in BAL were not statistically different in WT and serpinb1−/− mice 24 h after LPS instillation (Fig. 4, C and D). Furthermore, the number of circulating blood neutrophils and recruited peritoneal neutrophils after injection of sterile irritants glycogen and thioglycollate did not differ in WT and serpinb1−/− mice (unpublished data). Alveolar macrophage numbers were similar in uninfected mice of both genotypes (∼5 × 105 cells/mouse) and did not substantially change upon infection. Collectively, these findings show that neutrophil recruitment to the lungs in response to P. aeruginosa infection is not defective in serpinb1−/− mice, and therefore, the recovery of lower numbers of serpinb1−/− neutrophils at 24 h after infection suggests their decreased survival.

To examine the putative increased death of serpinb1−/− neutrophils in the lungs after P. aeruginosa infection, lung sections were analyzed by immunohistochemistry. Caspase-3–positive leukocytes were more relevant in the alveolar space of serpinb1−/− mice compared with WT mice at 24 h after infection, suggesting increased neutrophil apoptosis (Fig. 5 A). The positive cells were counted in 50 high power fields (hpf’s), and mean numbers of caspase-3–stained cells were increased in the lungs of serpinb1/− mice (1.8 ± 0.2 cells/hpf) compared with WT mice (0.4 ± 0.1 cells/hpf; P < 0.0001). To characterize neutrophils in the alveoli and airways, neutrophils in BAL were identified in flow cytometry by forward scatter (FSC) and side scatter and were stained with annexin V (AnV) and propidium iodide (PI). At 24 h after infection, the proportion of late apoptotic/necrotic neutrophils (AnV+PI+) was increased at the expense of viable neutrophils (AnVPI) in the BAL of serpinb1−/− mice compared with WT mice (Fig. 5 B). Neutrophil fragments in BAL were also identified in flow cytometry by low FSC (FSClow) within the neutrophil population defined by the neutrophil marker Gr-1. The number of neutrophil fragments (FSClow, Gr-1+) relative to intact neutrophils was increased two- to threefold at 24 h after infection for serpinb1−/− compared with WT mice (Fig. 5 C). Moreover, free MPO in BAL supernatants was increased in serpinb1−/− mice compared with WT mice at 24 h after infection, indicating increased PMN lysis or degranulation (Fig. 5 D).

Finally, we questioned whether the enhanced death of serpinb1−/− pulmonary neutrophils was a primary effect of gene deletion or a secondary effect caused by, for example, bacteria or components of inflammation. To address this, neutrophils were collected using the noninfectious LPS recruitment model and were cultured in vitro to allow for spontaneous cell death. After 24 h, the percentages of apoptotic and necrotic neutrophils evaluated by microscopy were increased in serpinb1−/− neutrophils compared with WT neutrophils (Fig. 6, A–C). A similar increase in apoptotic cells was observed using AnV/PI staining and measurements of hypodiploid DNA (unpublished data). Moreover, live cell numbers from serpinb1−/− mice remaining in culture after 24 h were significantly decreased compared with WT mice (Fig. 6 D). The in vitro findings indicate that enhanced death of pulmonary neutrophils of infected serpinb1−/− mice is at least in part a cell-autonomous defect likely mediated by unchecked NSP actions.

 

In this paper, we have demonstrated that serpinb1, an intracellular serpin family member, regulates the innate immune response and protects the host during lung bacterial infection. Serpinb1 is among the most potent inhibitors of NSPs and is carried at high levels within neutrophils. Serpinb1-deficient mice fail to clear P. aeruginosa PAO1 lung infection and succumb from systemic bacterial spreading. The defective immune function in serpinb1−/− mice stems at least in part from an increased rate of neutrophil necrosis, reducing the number of phagocytes and leading to increased NSP activity in the lungs with proteolysis of SP-D. In addition, serpinb1-deficient mice also have impaired clearance of the mucoid clinical strain PA M57-15. Interestingly, mucoid strains of P. aeruginosa are cleared with a very high efficiency from the lungs of WT and cystic fibrosis transmembrane conductance regulator–deficient mice (26). The phenotype of serpinb1−/− mice reproduces major pathologic features of human pulmonary diseases characterized by excessive inflammation, massive neutrophil recruitment to the air space, and destruction of cellular and molecular protective mechanisms. Importantly, serpinb1 deficiency may be helpful as an alternative or additional model of the inflammatory lung pathology of cystic fibrosis.

The present study documents a key protective role for serpinb1 in regulating NSP actions in the lung. This role has previously been attributed to the NSP inhibitors α1-antitrypsin and secretory leukocyte protease inhibitor, which are found in the airway and alveolar lining fluid (2728). However, patients with α1-antitrypsin deficiency do not present with pulmonary infection secondary to innate immune defects despite increased NSP activity that leads to reduced lung elasticity and emphysema. Moreover, there is so far no evidence that deficiency in secretory leukocyte protease inhibitor results in failure to clear pulmonary infection. Because synthesis and storage of NSPs in granules is an event that exclusively takes place in bone marrow promyelocytes (29), the regulation of NSPs in the lung relies entirely on NSP inhibitors. Thus, the extent of the innate immune defect inserpinb1−/− mice and the normalization of bacterial clearance with topical rSERPINB1 treatment indicate that serpinb1 is required to regulate NSP activity in the airway fluids and that, during acute lung infection associated with high neutrophilic recruitment, there is insufficient compensation by other NSP inhibitors. The devastating effects of NSPs when released in the lungs by degranulating and necrotic neutrophils are well documented in human pulmonary diseases (5630). Therefore, our findings clearly establish a physiological and nonredundant role for serpinb1 in regulating NSPs during pulmonary infection.

NSPs also cleave molecules involved in apoptotic cell clearance, including the surfactant protein SP-D and the phosphatidylserine receptor on macrophages (3132), thereby tipping the balance further toward a detrimental outcome. The increased numbers of leukocytes with active caspase-3 in the alveolar space of P. aeruginosa–infectedserpinb1−/− mice suggest that the removal of apoptotic cells may be inadequate during infection. SP-D has been shown to stimulate phagocytosis of P. aeruginosa by alveolar macrophages in vitro (33), and SP-D–deficient mice were found to have defective early (6-h) clearance of P. aeruginosa from the lung (34). Although the destruction of SP-D alone may not entirely account for the defective phenotype of serpinb1−/− mice, loss of SP-D likely diminishes bacterial clearance and removal of apop totic neutrophils.

Given that NSPs also mediate bacterial killing, why would NSP excess lead to a failed bacterial clearance? In the NE KO mice, the decreased killing activity of neutrophils is a direct consequence of the loss of the bactericidal activity of NE. The absence of an early bacterial clearance defect at 6 h after infection in serpinb1−/− mice suggests that there is initially normal bacterial killing. The current understanding is that the compartmentalization of the NSPs is crucial to the outcome of their actions: on the one hand, NSPs are protective when killing microbes within phagosomes, and on the other hand, extracellular NSPs destroy innate immune defense molecules such as lung collectins, immunoglobulins, and complement receptors. We have shown that the regulation of NSP activity is essential and that cytoplasmic serpinb1 provides this crucial shield. Neutrophils undergoing cell death gradually transition from apoptosis, characterized by a nonpermeable plasma membrane, to necrosis and lysis, where cellular and granule contents, including NSPs, are released. The increased pace of serpinb1−/− neutrophil cell death strongly suggests that unopposed NSPs may precipitate neutrophil demise and, therefore, reduce the neutrophil numbers leading to a late-onset innate immune defect. High levels of G-CSF, a prosurvival cytokine for neutrophils, also indicate that increased cell death is likely independent or downstream of G-CSF.

In conclusion, serpinb1 deficiency unleashes unbridled proteolytic activity during inflammation and thereby disables two critical components of the host response to bacterial infection, the neutrophil and the collectin SP-D. The phenotype of the infectedserpinb1-deficient mouse, characterized by a normal early antibacterial response that degenerates over time, highlights the delicate balance of protease–antiprotease systems that protect the host against its own defenses as well as invading microbes during infection-induced inflammation.

 

 

Proteinase 3 and neutrophil elastase enhance inflammation in mice by inactivating antiinflammatory progranulin

K Kessenbrock,1 LFröhlich,2 M Sixt,3 …., A Belaaouaj,5 J Ring,6,7 M Ollert,6 R Fässler,3 and DE. Jenne1
J Clin Invest. 2008 Jul 1; 118(7): 2438–2447.   http://dx.doi.org:/10.1172/JCI34694

Neutrophil granulocytes form the body’s first line of antibacterial defense, but they also contribute to tissue injury and noninfectious, chronic inflammation. Proteinase 3 (PR3) and neutrophil elastase (NE) are 2 abundant neutrophil serine proteases implicated in antimicrobial defense with overlapping and potentially redundant substrate specificity. Here, we unraveled a cooperative role for PR3 and NE in neutrophil activation and noninfectious inflammation in vivo, which we believe to be novel. Mice lacking both PR3 and NE demonstrated strongly diminished immune complex–mediated (IC-mediated) neutrophil infiltration in vivo as well as reduced activation of isolated neutrophils by ICs in vitro. In contrast, in mice lacking just NE, neutrophil recruitment to ICs was only marginally impaired. The defects in mice lacking both PR3 and NE were directly linked to the accumulation of antiinflammatory progranulin (PGRN). Both PR3 and NE cleaved PGRN in vitro and during neutrophil activation and inflammation in vivo. Local administration of recombinant PGRN potently inhibited neutrophilic inflammation in vivo, demonstrating that PGRN represents a crucial inflammation-suppressing mediator. We conclude that PR3 and NE enhance neutrophil-dependent inflammation by eliminating the local antiinflammatory activity of PGRN. Our results support the use of serine protease inhibitors as antiinflammatory agents.

 

Neutrophils belong to the body’s first line of cellular defense and respond quickly to tissue injury and invading microorganisms (1). In a variety of human diseases, like autoimmune disorders, infections, or hypersensitivity reactions, the underlying pathogenic mechanism is the formation of antigen-antibody complexes, so-called immune complexes (ICs), which trigger an inflammatory response by inducing the infiltration of neutrophils (2). The subsequent stimulation of neutrophils by C3b-opsonized ICs results in the generation of ROS and the release of intracellularly stored proteases leading to tissue damage and inflammation (3). It is therefore important to identify the mechanisms that control the activation of infiltrating neutrophils.

Neutrophils abundantly express a unique set of neutrophil serine proteases (NSPs), namely cathepsin G (CG), proteinase 3 (PR3; encoded by Prtn3), and neutrophil elastase (NE; encoded by Ela2), which are stored in the cytoplasmic, azurophilic granules. PR3 and NE are closely related enzymes, with overlapping and potentially redundant substrate specificities different from those of CG. All 3 NSPs are implicated in antimicrobial defense by degrading engulfed microorganisms inside the phagolysosomes of neutrophils (48). Among many other functions ascribed to these enzymes, PR3 and NE were also suggested to play a fundamental role in granulocyte development in the bone marrow (911).

While the vast majority of the enzymes is stored intracellularly, minor quantities of PR3 and NE are externalized early during neutrophil activation and remain bound to the cell surface, where they are protected against protease inhibitors (1213). These membrane presented proteases were suggested to act as path clearers for neutrophil migration by degrading components of the extracellular matrix (14). This notion has been addressed in a number of studies, which yielded conflicting results (1517). Thus, the role of PR3 and NE in leukocyte extravasation and interstitial migration still remains controversial.

Emerging data suggest that externalized NSPs can contribute to inflammatory processes in a more complex way than by simple proteolytic tissue degradation (18). For instance, recent observations using mice double-deficient for CG and NE indicate that pericellular CG enhances IC-mediated neutrophil activation and inflammation by modulating integrin clustering on the neutrophil cell surface (1920). Because to our knowledge no Prtn3–/– mice have previously been generated, the role of this NSP in inflammatory processes has not been deciphered. Moreover, NE-dependent functions that can be compensated by PR3 in Ela2–/–animals are still elusive.

One mechanism by which NSPs could upregulate the inflammatory response has recently been proposed. The ubiquitously expressed progranulin (PGRN) is a growth factor implicated in tissue regeneration, tumorigenesis, and inflammation (2123). PGRN was previously shown to directly inhibit adhesion-dependent neutrophil activation by suppressing the production of ROS and the release of neutrophil proteases in vitro (23). This antiinflammatory activity was degraded by NE-mediated proteolysis of PGRN to granulin (GRN) peptides (23). In contrast, GRN peptides may enhance inflammation (23) and have been detected in neutrophil-rich peritoneal exudates (24). In short, recent studies proposed PGRN as a regulator of the innate immune response, but the factors that control PGRN function are still poorly defined and its relevance to inflammation needs to be elucidated in vivo.

In the present study, we generated double-deficient Prtn3–/–Ela2–/– mice to investigate the role of these highly similar serine proteases in noninfectious neutrophilic inflammation. We established that PR3 and NE are required for acute inflammation in response to subcutaneous IC formation. The proteases were found to be directly involved in early neutrophil activation events, because isolated Prtn3–/–Ela2–/– neutrophils were poorly activated by ICs in vitro. These defects in Prtn3–/–Ela2–/– mice were accompanied by accumulation of PGRN. We demonstrated that PGRN represents a potent inflammation-suppressing factor that is cleaved by both PR3 and NE. Our data delineate what we believe to be a previously unknown proinflammatory role for PR3 and NE, which is accomplished via the local inactivation of antiinflammatory PGRN.

 

Generation of Prtn3–/–Ela2–/– mice.

To analyze the role of PR3 and NE in neutrophilic inflammation, we generated a Prtn3–/–Ela2–/– mouse line by targeted gene disruption in embryonic stem cells (see Supplemental Figure 1; supplemental material available online with this article; doi: 10.1172/JCI34694DS1). Positive recombination of the Prtn3/Ela2locus was proven by Southern blotting of embryonic stem cell clones (Figure ​(Figure1A).1A). Prtn3–/–Ela2–/– mice showed no expression of mRNA for PR3 and NE in bone marrow cells, as assessed by RT-PCR (Figure ​(Figure1B).1B). The successful elimination of PR3 and NE was confirmed at the level of proteolytic activity in neutrophil lysates using a PR3/NE-specific chromogenic substrate (Supplemental Figure 3) as well as by casein zymography (Figure ​(Figure1C).1C). The substantially reduced casein degradation by heterozygous neutrophils indicates gene-dosage dependence of PR3/NE activities. Furthermore, PR3 and NE deficiency was proven by Western blotting using cell lysates from bone marrow–derived neutrophils, while other enzymes stored in azurophilic granula, such as CG and myeloperoxidase (MPO), were normally detected (Figure ​(Figure1D).1D). Crossing of heterozygous Prtn3+/–Ela2+/– mice resulted in regular offspring of WT, heterozygous, and homozygous genotype according to the Mendelian ratio. Despite the absence of 2 abundant serine proteases, and in contrast to expectations based on previous reports (911), we found unchanged neutrophil morphology (Figure ​(Figure1E)1E) and regular neutrophil populations in the peripheral blood of the mutant mice, the latter as assessed via flow cytometry to determine the differentiation markers CD11b and Gr-1 (Figure ​(Figure1F)1F) (2526). Moreover, Prtn3–/–Ela2–/– mice demonstrated normal percentages of the leukocyte subpopulations in the peripheral blood, as determined by the Diff-Quick staining protocol and by hemocytometric counting (Supplemental Figure 2, A and B). Hence, the proteases are not crucially involved in granulopoiesis, and ablating PR3 and NE in the germ line represents a valid approach to assess their biological significance in vivo.

 

Figure 1

Generation and characterization of Prtn3–/–Ela2–/– mice.

PR3 and NE are dispensable for neutrophil extravasation and interstitial migration.

To examine neutrophil infiltration into the perivascular tissue, we applied phorbol esters (croton oil) to the mouse ears. At 4 h after stimulation, we assessed the neutrophil distribution in relation to the extravascular basement membrane (EBM) by immunofluorescence microscopy of fixed whole-mount specimens (Figure ​(Figure2A).2A). We found that Prtn3–/–Ela2–/– neutrophils transmigrated into the interstitium without retention at the EBM (Figure ​(Figure2B),2B), resulting in quantitatively normal and widespread neutrophil influx compared with WT mice (Figure ​(Figure2C).2C). Moreover, we analyzed chemotactic migration of isolated neutrophils through a 3-dimensional collagen meshwork in vitro (Supplemental Video 1) and found unhampered chemotaxis toward a C5a gradient, based on the directionality (Figure ​(Figure2D)2D) and velocity (Figure ​(Figure2E)2E) of Prtn3–/–Ela2–/–neutrophils. These findings led us to conclude that PR3 and NE are not principally required for neutrophil extravasation or interstitial migration.

 

Figure 2

PR3 and NE are not principally required for neutrophil extravasation and interstitial migration.

Reduced inflammatory response to ICs in Prtn3–/–Ela2–/– mice.

The formation of ICs represents an important trigger of neutrophil-dependent inflammation in many human diseases (2). To determine the role of PR3 and NE in this context, we induced a classic model of subcutaneous IC-mediated inflammation, namely the reverse passive Arthus reaction (RPA) (27). At 4 h after RPA induction, we assessed the cellular inflammatory infiltrates by histology using H&E-stained skin sections (Figure ​(Figure3A).3A). Neutrophils, which were additionally identified by Gr-1 immunohistochemistry, made up the vast majority of all cellular infiltrates (Figure ​(Figure3A).3A). We found that neutrophil infiltration to the sites of IC formation was severely diminished in Prtn3–/–Ela2–/– mice. Indeed, histological quantification revealed significantly reduced neutrophil influx in Prtn3–/–Ela2–/– mice compared with WT mice, while Ela2–/– mice showed marginally reduced neutrophil counts (Figure ​(Figure3B).3B). These results indicate that PR3 and NE fulfill an important proinflammatory function during IC-mediated inflammation.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430496/bin/JCI0834694.f3.jpg

Figure 3

Impaired inflammatory response to locally formed ICs inPrtn3–/–Ela2–/– mice.

(A) Representative photomicrographs of inflamed skin sections 4 h after IC formation. Neutrophils were identified morphologically (polymorphic nucleus) in H&E stainings and by Gr-1 staining (red). The cellular infiltrates were located to the adipose tissue next to the panniculus carnosus muscle (asterisks) and were primarily composed of neutrophil granulocytes. Scale bars: 200 μm. (B) Neutrophil infiltrates in lesions from Prtn3–/–Ela2–/– mice were significantly diminished compared with Ela2–/– mice and WT mice. Neutrophil influx in Ela2–/–mice was slightly, but not significantly, diminished compared with WT mice. Results are mean ± SEM infiltrated neutrophils per HPF. *P < 0.05.

PR3 and NE enhance neutrophil activation by ICs in vitro.

PR3 and NE enhance neutrophil activation by ICs in vitro.

Because PR3 and NE were required for the inflammatory response to IC (Figure ​(Figure3),3), but not to phorbol esters (Figure ​(Figure2),2), we considered the enzymes as enhancers of the neutrophil response to IC. We therefore assessed the oxidative burst using dihydrorhodamine as a readout for cellular activation of isolated, TNF-α–primed neutrophils in the presence of ICs in vitro. While both WT and Prtn3–/–Ela2–/– neutrophils showed a similar, approximately 20-min lag phase before the oxidative burst commenced, the ROS production over time was markedly reduced, by 30%–40%, in the absence of PR3 and NE (Figure ​(Figure4A).4A). In contrast, oxidative burst triggered by 25 nM PMA was not hindered in Prtn3–/–Ela2–/– neutrophils (Figure ​(Figure4B),4B), which indicated no general defect in producing ROS. We also performed a titration series ranging from 0.1 to 50 nM PMA and found no reduction in oxidative burst activity in Prtn3–/–Ela2–/– neutrophils at any PMA concentration used (Supplemental Figure 4). These data are consistent with our in vivo experiments showing that neutrophil influx to ICs was impaired (Figure ​(Figure3),3), whereas the inflammatory response to phorbol esters was normal (Figure ​(Figure2,2, A–C), in Prtn3–/–Ela2–/– mice. To compare neutrophil priming in WT and Prtn3–/–Ela2–/–neutrophils, we analyzed cell surface expression of CD11b after 30 min of incubation at various concentrations of TNF-α and found no difference (Supplemental Figure 5). Moreover, we observed normal neutrophil adhesion to IC-coated surfaces (Supplemental Figure 6A) and unaltered phagocytosis of opsonized, fluorescently labeled E. coli bacteria (Supplemental Figure 6, B and C) in the absence of both proteases. We therefore hypothesized that PR3 and NE enhance early events of adhesion-dependent neutrophil activation after TNF-α priming and binding of ICs. It is important to note that Ela2–/– neutrophils were previously shown to react normally in the same setup (20). Regarding the highly similar cleavage specificities of both proteases, we suggested that PR3 and NE complemented each other during the process of neutrophil activation and inflammation.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430496/bin/JCI0834694.f4.jpg

Figure 4

Impaired oxidative burst and PGRN degradation by IC-activatedPrtn3–/–Ela2–/– neutrophils.

Oxidative burst as the readout for neutrophil activation by ICs was measured over time. (A) While no difference was observed during the initial 20-min lag phase of the oxidative burst, Prtn3–/–Ela2–/– neutrophils exhibited diminished ROS production over time compared with WT neutrophils. (B) Bypassing receptor-mediated activation using 25 nM PMA restored the diminished oxidative burst of Prtn3–/–Ela2–/–neutrophils. Results are presented as normalized fluorescence in AU (relative to maximum fluorescence produced by WT cells). Data (mean ± SD) are representative of 3 independent experiments each conducted in triplicate. (C) Isolated mouse neutrophils were activated by ICs in vitro and tested for PGRN degradation by IB. In the cellular fraction, the PGRN (~80 kDa) signal was markedly increased in Prtn3–/–Ela2–/–cells compared with WT and Ela2–/– neutrophils. Intact PGRN was present in the supernatant (SN) of IC-activated Prtn3–/–Ela2–/–neutrophils only, not of WT or Ela2–/– cells. (D and E) Exogenous administration of 100 nM PGRN significantly reduced ROS production of neutrophils activated by ICs (D), but not when activated by PMA (E). Data (mean ± SD) are representative of 3 independent experiments each conducted in triplicate.

Antiinflammatory PGRN is degraded by PR3 and NE during IC-mediated neutrophil activation.

PGRN inhibits neutrophil activation by ICs in vitro.

Both PR3 and NE process PGRN in vitro.

Figure 5

PR3 and NE are major PGRN processing enzymes of neutrophils.

PGRN inhibits IC-mediated inflammation in vivo.

Figure 6

PGRN is a potent inhibitor of IC-stimulated inflammation in vivo.

PR3 and NE cleave PGRN during inflammation in vivo.

Finally, we aimed to demonstrate defective PGRN degradation in Prtn3–/–Ela2–/– mice during neutrophilic inflammation in vivo. For practical reasons, we harvested infiltrated neutrophils from the inflamed peritoneum 4 h after casein injection and subjected the lysates of these cells to anti-PGRN Western blot. Intact, inhibitory PGRN was detected in Prtn3–/–Ela2–/– neutrophils, but not in WT cells (Figure ​(Figure6D).6D). These data prove that neutrophilic inflammation is accompanied by proteolytic removal of antiinflammatory PGRN and that the process of PGRN degradation is essentially impaired in vivo in the absence of PR3 and NE.

 

Chronic inflammatory and autoimmune diseases are often perpetuated by continuous neutrophil infiltration and activation. According to the current view, the role of NSPs in these diseases is mainly associated with proteolytic tissue degradation after their release from activated or dying neutrophils. However, recent observations suggest that NSPs such as CG may contribute to noninfectious diseases in a more complex manner, namely as specific regulators of inflammation (18). Here, we demonstrate that PR3 and NE cooperatively fulfilled an important proinflammatory role during neutrophilic inflammation. PR3 and NE directly enhanced neutrophil activation by degrading oxidative burst–suppressing PGRN. These findings support the use of specific serine protease inhibitors as antiinflammatory agents.

Much attention has been paid to the degradation of extracellular matrix components by NSPs. We therefore expected that ablation of both PR3 and NE would cause impaired neutrophil extravasation and interstitial migration. Surprisingly, we found that the proteases were principally dispensable for these processes:Prtn3–/–Ela2–/– neutrophils migrated normally through a dense, 3-dimensional collagen matrix in vitro and demonstrated regular extravasation in vivo when phorbol esters were applied (Figure ​(Figure2).2). This finding is in agreement with recent reports that neutrophils preferentially and readily cross the EBM through regions of low matrix density in the absence of NE (28).

Conversely, we observed that PR3 and NE were required for the inflammatory response to locally formed ICs (Figure ​(Figure3).3). Even isolated Prtn3–/–Ela2–/– neutrophils were challenged in performing oxidative burst after IC stimulation in vitro (Figure ​(Figure4A),4A), showing that the proteases directly enhanced the activation of neutrophils also in the absence of extracellular matrix. However, when receptor-mediated signal transduction was bypassed by means of PMA, neutrophils from Prtn3–/–Ela2–/– mice performed normal oxidative burst (Figure ​(Figure4B),4B), indicating that the function of the phagocyte oxidase (phox) complex was not altered in the absence of PR3 and NE. These findings substantiate what we believe to be a novel paradigm: that all 3 serine proteases of azurophilic granules (CG, PR3, and NE), after their release in response to IC encounter, potentiate a positive autocrine feedback on neutrophil activation.

In contrast to CG, the highly related proteases PR3 and NE cooperate in the effacement of antiinflammatory PGRN, leading to enhanced neutrophil activation. Previous studies already demonstrated that PGRN is a potent inhibitor of the adhesion-dependent oxidative burst of neutrophils in vitro, which can be degraded by NE (23). Here, we showed that PR3 and NE play an equally important role in the regulation of PGRN function. Ela2–/– neutrophils were sufficiently able to degrade PGRN. Only in the absence of both PR3 and NE was PGRN degradation substantially impaired, resulting in the accumulation of antiinflammatory PGRN during neutrophil activation in vitro (Figure ​(Figure4C)4C) and neutrophilic inflammation in vivo (Figure ​(Figure6D).6D). Moreover, we provided in vivo evidence for the crucial role of PGRN as an inflammation-suppressing mediator, because administration of recombinant PGRN potently inhibited the neutrophil influx to sites of IC formation (Figure ​(Figure6,6, A–C). Hence, the cooperative degradation of PGRN by PR3 and NE is a decisive step for the establishment of neutrophilic inflammation.

The molecular mechanism of PGRN function is not yet completely understood, but it seems to interfere with integrin (CD11b/CD18) outside-in signaling by blocking the function of pyk2 and thus dampens adhesion-related oxidative burst even when added after the initial lag phase of oxidase activation (23). PGRN is produced by neutrophils and stored in highly mobile secretory granules (29). It was recently shown that PGRN can bind to heparan-sulfated proteoglycans (30), which are abundant components of the EBM and various cell surfaces, including those of neutrophils. Also, PR3 and NE are known to interact with heparan sulfates on the outer membrane of neutrophils, where the enzymes appear to be protected against protease inhibitors (121331). These circumstantial observations support the notion that PGRN cleavage by PR3 and NE takes place at the pericellular microenvironment of the neutrophil cell surface.

Impaired outside-in signaling most likely reduced the oxidative burst in Prtn3–/–Ela2–/– neutrophils adhering to ICs. In support of this hypothesis, we excluded an altered response to TNF-α priming (Supplemental Figure 5) as well as reduced adhesion to immobilized ICs and defective endocytosis of serum-opsonized E. coli in Prtn3–/–Ela2–/– neutrophils (Supplemental Figure 6). MPO content and processing was also unchanged in Prtn3–/–Ela2–/– neutrophils (Figure ​(Figure1D);1D); hence, the previously discussed inhibitory effect of MPO on phox activity (3233) does not appear to be stronger in neutrophils lacking PR3 and NE. Because there was no difference in the lag phase of the oxidative burst, initial IC-triggered receptor activation was probably not affected by either PRGN or PR3/NE. Our concept is consistent with all these observations and takes into account that PGRN unfolds its suppressing effects in the second phase, when additional membrane receptors, endogenous PGRN, and some PR3/NE from highly mobile intracellular pools are translocated to the cell surface. The decline and cessation of ROS production suggested to us that outside-in signaling was not sustained and that active oxidase complexes were no longer replenished in the absence of PR3 and NE. Our present findings, however, do not allow us to exclude other potential mechanisms, such as accelerated disassembly of the active oxidase complex.

 

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Proposed function of PR3 and NE in IC-mediated inflammation.

TNF-α–primed neutrophils extravasate from blood vessels, translocate PR3/NE to the cellular surface, and discharge PGRN to the pericellular environment (i). During transmigration of interstitial tissues (ii), neutrophil activation is initially suppressed by relatively high pericellular levels of antiinflammatory PGRN (green shading), which is also produced locally by keratinocytes and epithelial cells of the skin. Until IC depots are reached, neutrophil activation is inhibited by PGRN. Surface receptors (e.g., Mac-1) recognize ICs, which results in signal transduction (black dotted arrow) and activation of the phox. The molecular pathway of PGRN-mediated inhibition is not completely understood, but it may interfere with integrin signaling after IC encounter (green dotted line inside the cell). Adherence of neutrophils to ICs (iii) further increases pericellular PR3 and NE activity. PR3 and NE cooperatively degrade PGRN in the early stage of neutrophilic activation to facilitate optimal neutrophil activation (red shading), resulting in sustained integrin signaling (red arrow) and robust production of ROS by the phox system. Subsequently, neutrophils release ROS together with other proinflammatory mediators and chemotactic agents, thereby enhancing the recruitment of further neutrophils and establishing inflammation (iv). In the absence of PR3/NE, the switch from inflammation-suppressing (ii) to inflammation-enhancing (iii) conditions is substantially delayed, resulting in diminished inflammation in response to ICs (iv).

 

NSPs are strongly implicated as effector molecules in a large number of destructive diseases, such as emphysema or the autoimmune blistering skin disease bullous pemphigoid (143537). Normally, PR3/NE activity is tightly controlled by high plasma levels of α1-antitrypsin. This balance between proteases and protease inhibitors is disrupted in patients with genetic α1-antitrypsin deficiency, which represents a high risk factor for the development of emphysema and certain autoimmune disorders (38). The pathogenic effects of NSPs in these diseases have so far been associated with tissue destruction by the proteases after their release from dying neutrophils. Our findings showed that PR3 and NE were already involved in much earlier events of the inflammatory process, because the enzymes directly regulated cellular activation of infiltrating neutrophils by degrading inflammation-suppressing PGRN. This concept is further supported by previous studies showing increased inflammation in mice lacking serine protease inhibitors such as SERPINB1 or SLPI (3940). Blocking PR3/NE activity using specific inhibitors therefore represents a promising therapeutic strategy to treat chronic, noninfectious inflammation. Serine protease inhibitors as antiinflammatory agents can interfere with the disease process at 2 different stages, because they attenuate both early events of neutrophil activation and proteolytic tissue injury caused by released NSPs.

 

 

 

 

Editorial: Serine proteases, serpins, and neutropenia

David C. Dale

J Leuko Biol July 2011;  90(1): 3-4   http://dx.doi.org:/10.1189/jlb.1010592

Cyclic neutropenia and severe congenital neutropenia are autosomal-dominant diseases usually attributable to mutations in the gene for neutrophil elastase orELANE. Patients with these diseases are predisposed to recurrent and life-threatening infections [1]. Neutrophil elastase, the product of the ELANE gene, is a serine protease that is synthesized and packaged in the primary granules of neutrophils. These granules are formed at the promyelocytes stage of neutrophil development. Synthesis of mutant neutrophil elastase in promyelocytes triggers the unfolded protein response and a cascade of intracellular events, which culminates in death of neutrophil precursors through apoptosis [2]. This loss of cells causes the marrow abnormality often referred to as “maturation arrest” [34].

Neutrophil elastase is one of the serine proteases normally inhibited by serpinB1. In this issue of JLB, Benarafa and coauthors [5] present their intriguing studies of serpinB1 expression in human myeloid cells and their extensive investigations ofSERPINB1−/− mice. They observed that serpinB1 expression parallels protease expression. The peak of serpinB1 expression occurs in promyelocytes. Benarafa et al. [5] found that SERPINB1−/− mice have a deficiency of postmitotic neutrophils in the bone marrow. This change was accompanied by an increase in the plasma levels of G-CSF. The decreased supply of marrow neutrophils reduced the number of neutrophils that could be mobilized to an inflammatory site. Using colony-forming cell assays, they determined that the early myeloid progenitor pool was intact. Separate assays showed that maturing myeloid cells were being lost through accelerated apoptosis of maturing neutrophils in the marrow. The authors concluded that serpinB1 is required for maintenance of a healthy reserve of marrow neutrophils and a normal acute immune response [5].

This paper provides new and fascinating insights for understanding the mechanism for neutropenia. It also suggests opportunities to investigate potential therapies for patients with neutropenia and prompts several questions. As inhibition of the activity of intracellular serine proteases is the only known function of serpinB1, the findings reported by Benarafa et al. [5] suggest that uninhibited serine proteases perturbed neutrophil production severely. The SERPINB1−/− mice used in their work have accelerated apoptosis of myeloid cells, a finding suggesting that uninhibited serine proteases or mutant neutrophil elastase perturb myelopoiesis by similar mechanisms. It is now important to determine whether the defect in the SERPINB1−/− mice is, indeed, attributable to uninhibited activity of normal neutrophil elastase, other neutrophil proteases, or another mechanism. ″Double-knockout″ studies in mice deficient in neutrophil elastase and serpinB1 might provide an answer.

This report provides evidence regarding the intracellular mechanisms for the apoptosis of myeloid cells and indicates that other studies are ongoing. The key antiapoptotic proteins, Mcl-1, Bcl-XL, and A1/Bfl-I, are apparently not involved. A more precise understanding of the mechanisms of cell death is important for development of targeted therapies for neutropenia. It is also important to discover whether only cells of the neutrophil lineage are involved or whether monocytes are also affected. In cyclic and congenital neutropenia, patients failed to produce neutrophils, but they can produce monocytes; in fact, they overproduce monocytes and have significantly elevated blood monocyte counts. Neutropenia with monocytosis is probably attributable to differences in the expression of ELANE in the two lineages. Benarafa et al. [5] reported that human bone marrow monocytes contain substantially less serpinB1 than marrow neutrophils, suggesting that the expression of serpinB1 and the serine proteases are closely coordinated.

This report shows the importance of the marrow neutrophil reserves in the normal response to infections. Compared with humans, healthy mice are always neutropenic, but they have a bigger marrow neutrophil reserve, and their mature neutrophils in the marrow and blood look like human band neutrophils. These differences are well known, but they are critical for considering the clinical inferences that can be made from this report. For example, although theSERPINB1−/− mice were not neutropenic, human SERPINB1−/− might cause neutropenia because of physiological differences between the species. If some but not all mutations in SERPINB1 cause neutropenia, we might gain a better understanding about how serpinB1 normally inhibits the neutrophil’s serine proteases.

We do not know if some or all of the mutant neutrophil elastases can be inhibited by serpinB1. We do not know whether cyclic or congenital neutropenia are attributable to defects in this interaction. However, we do know that there are chemical inhibitors of neutrophil elastase that can abrogate apoptosis of myeloid cells in a cellular model for congenital neutropenia [6]. It would be interesting to see if these chemical inhibitors can replace the natural inhibitor and normalize neutrophil production in the SERPINB1−/− mice. This would provide evidence to support use of chemical protease inhibitors as a treatment for cyclic and congenital neutropenia.

Concerns with the use of G-CSF for the treatment of cyclic and congenital neutropenia are how and why some of these patients are at risk of developing leukemia. Are the SERPINB1−/− mice with a hyperproliferative marrow and high G-CSF levels also at risk of developing myeloid leukemia?

This is a very provocative paper, and much will be learned from further studies of the SERPINB1−/− mice.

 

SerpinB1 is critical for neutrophil survival through cell-autonomous inhibition of cathepsin G

Mathias Baumann1,2, Christine T. N. Pham3, and Charaf Benarafa1

Blood May 9, 2013; 121(19)   http://www.bloodjournal.org/content/121/19/3900

Key Points

  • Serine protease inhibitor serpinB1 protects neutrophils by inhibition of their own azurophil granule protease cathepsin G.
  • Granule permeabilization in neutrophils leads to cathepsin G–mediated death upstream and independent of apoptotic caspases.

Abstract

Bone marrow (BM) holds a large reserve of polymorphonuclear neutrophils (PMNs) that are rapidly mobilized to the circulation and tissues in response to danger signals. SerpinB1 is a potent inhibitor of neutrophil serine proteases neutrophil elastase (NE) and cathepsin G (CG). SerpinB1 deficiency (sB1−/−) results in a severe reduction of the BM PMN reserve and failure to clear bacterial infection. Using BM chimera, we found that serpinB1 deficiency in BM cells was necessary and sufficient to reproduce the BM neutropenia ofsB1−/− mice. Moreover, we showed that genetic deletion of CG, but not NE, fully rescued the BM neutropenia in sB1−/− mice. In mixed BM chimera and in vitro survival studies, we showed that CG modulates sB1−/− PMN survival through a cell-intrinsic pathway. In addition, membrane permeabilization by lysosomotropic agent L-leucyl-L-leucine methyl ester that allows cytosolic release of granule contents was sufficient to induce rapid PMN death through a CG-dependent pathway. CG-mediated PMN cytotoxicity was only partly blocked by caspase inhibition, suggesting that CG cleaves a distinct set of targets during apoptosis. In conclusion, we have unveiled a new cytotoxic function for the serine protease CG and showed that serpinB1 is critical for maintaining PMN survival by antagonizing intracellular CG activity.

Introduction

Polymorphonuclear neutrophil (PMN) granulocytes are essential components of the innate immune response to infection. PMNs are relatively short-lived leukocytes that originate from hematopoietic stem cells in the bone marrow (BM) in a process called granulopoiesis. Granulopoiesis proceeds through a proliferative phase followed by a maturation phase. After maturation, the BM retains a large reserve of mature PMNs, which includes over 90% of the mature PMNs in the body while only a small proportion (1%-5%) is in the blood.1,2 Even in noninflammatory conditions, granulopoiesis is remarkable as >1011 PMNs are produced daily in an adult human, only to be disposed of, largely unused, a few hours later.3 There is evidence that the majority of PMNs produced never reach circulation and die within the BM.4 Congenital or acquired forms of neutropenia are associated with the highest risks of bacterial and fungal infection,5 indicating a strong evolutionary pressure to maintain granulopoiesis at high levels and sustain a large mobilizable pool of PMNs in the BM.

In steady state, PMNs die by apoptosis, a form of programmed cell death that allows for the safe disposal of aging PMNs and their potentially toxic cargo. Like in other cells, caspases participate in the initiation, amplification, and execution steps of apoptosis in PMNs.6,7 Interestingly, noncaspase cysteine proteases calpain and cathepsin D were reported to induce PMN apoptosis through activation of caspases.811 In addition, PMNs carry a unique set of serine proteases (neutrophil serine proteases [NSPs]) including elastase (NE), cathepsin G (CG), and proteinase-3 (PR3) stored active in primary granules. There is strong evidence for a role of NSPs in killing pathogens and inducing tissue injury when released extracellularly.1214 In contrast, the function of NSPs in PMN homeostasis and cell death remains elusive. In particular, no defects in granulopoiesis or PMN homeostasis have been reported in mice deficient in cathepsin G (CG−/−),15 neutrophil elastase (NE−/−),16,17 or dipeptidylpeptidase I (DPPI−/−), which lack active NSPs.18 We have recently shown that mice lacking the serine protease inhibitor serpinB1 (sB1−/−) have reduced PMN survival in the lungs following Pseudomonas infection and that these mice have a profound reduction in mature PMN numbers in the BM.19,20SerpinB1, also known as monocyte NE inhibitor, is expressed at high levels in the cytoplasm of PMNs and is one of the most potent inhibitors of NE, CG, and PR3.21,22 In this study, we tested the hypothesis that serpinB1 promotes PMN survival by inhibiting 1 or several NSPs, and we discovered a novel regulatory pathway in PMN homeostasis in vivo.

 

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Figure 1

Defective PMN reserve in BM chimera depends on serpinB1 deficiency in the hematopoietic compartment. Flow cytometry analysis of major BM leukocyte subsets of lethally irradiated mice was performed 8 to 10 weeks after BM transfer. (A) Irradiated WT (CD45.1) mice were transferred with WT (●) or sB1−/− (○) BM cells. (B) Irradiated WT (●) andsB1−/− (○) mice both CD45.2 were transferred with WT (CD45.1) BM cells. Each circle represents leukocyte numbers for 1 mouse and horizontal line indicates the median. Median subsets numbers were compared by the Mann-Whitney test (*P < .05; ***P < .001).

CG regulates neutrophil numbers in the BM

Because serpinB1 is an efficient inhibitor of NE, CG, and PR3, we then examined PMN numbers in mice deficient in 1 or several NSPs in combination with serpinB1 deletion. As expected, sB1−/− mice had significantly reduced numbers and percentage of mature PMNs in the BM compared with WT and heterozygous sB1+/− mice. In addition, PMN numbers were normal in mice deficient in either DPPI, NE, or CG (Figure 2A). DPPI is not inhibited by serpinB1 but is required for the activation of all NSPs, and no NSP activity is detectable in DPPI−/− mice.18,23 PMN counts in DPPI−/−.sB1−/− BM were significantly higher than in sB1−/− BM, suggesting that 1 or several NSPs contribute to the PMN survival defect. To examine the role of NSPs in this process, we crossed several NSP-deficient strains with sB1−/− mice. We found that NE.CG.sB1−/− mice had normal PMN numbers indicating that these NSPs play a key role in the defective phenotype of sB1−/− PMNs (Figure 2A). Furthermore, CG.sB1−/− mice showed normal PMN numbers whereasNE.sB1−/− mice retained the BM neutropenia phenotype indicating that CG, but not NE, plays a significant role in the death of sB1−/− PMNs (Figure 2A). In addition, the double-deficient NE.sB1−/− mice had significantly lower BM myelocyte numbers than sB1−/− mice while the myelocyte numbers in singly deficient NE−/− and sB1−/− BM were normal (Figure 2B). These results suggest that NE may promote myeloid cell proliferation, an activity that is revealed only when serpinB1 is absent. This complex interaction between sB1 and NE requires further investigation. On the other hand, B-cell and monocyte numbers and relative percentage in the BM were largely similar in all genotypes (supplemental Figure 2). Total numbers of blood leukocytes, erythrocytes, and platelets were normal in mice deficient in NSPs and/or serpinB1 (supplemental Figure 3). PMN numbers in blood were normal insB1−/− mice in steady state and combined deficiency of NSPs did not significantly alter these numbers (Figure 2C). Taken together, our results indicate that serpinB1 likely sustains the survival of postmitotic PMNs through its interaction with CG.

Figure 2

PMN and myelocyte numbers in BM and blood of mice deficient in NSPs and serpinB1.

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CG-mediated PMN death proceeds independent of caspase activity

Figure 4

sB1−/− PMN death mediated by CG does not require caspase activity

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Granule membrane permeabilization induces CG-mediated death in PMNs

To test whether granule disruption contributes to the serpinB1-regulated CG-dependent cell death, BM cells were treated with the lysosomotropic agent LLME. LLME accumulates in lysosomes where the acyl transferase activity of DPPI generates hydrophobic (Leu-Leu)n-OMe polymers that induce lysosomal membrane permeabilization (LMP) and cytotoxicity in granule-bearing cells such as cytotoxic T lymphocytes, NK cells, and myeloid cells.29,30

Figure 5

LMP induces CG-mediated death in PMNs

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G-CSF therapy increases sB1−/− PMN numbers via enhanced granulopoiesis

G-CSF therapy is an effective long-term treatment in many cases of severe congenital neutropenia and it is also used to prevent chemotherapy-induced febrile neutropenia by enhancing PMN production. In addition, G-CSF delays neutrophil apoptosis by differentially regulating proapoptotic and antiapoptotic factors.10 To test whether G-CSF could rescue sB1−/− PMN survival defect, WT and sB1−/− mice were treated with therapeutic doses of G-CSF or saline for 5 days and BM and blood PMNs were analyzed 24 hours after the last injection. Total counts of myelocytes and PMNs were significantly increased in the BM of treated mice compared with their respective untreated genotype controls (Figure 6A-B). The increase in myelocyte numbers was identical in G-CSF–treated WT and sB1−/− mice, indicating that G-CSF–induced granulopoiesis proceeds normally in sB1−/−myeloid progenitors (Figure 6B).

Figure 6

In vivo G-CSF therapy increases PMN numbers in BM of sB1−/− mice.

 

SerpinB1 is a member of the clade B serpins, a subfamily composed of leaderless proteins with nucleocytoplasmic localization. Clade B serpins are often expressed in cells that also carry target proteases, which led to the hypothesis that intracellular serpins protect against misdirected granule proteases and/or protect bystander cells from released proteases.31 We previously reported that deficiency in serpinB1 is associated with reduced PMN survival in the BM and at inflammatory sites.19,20 The evidence presented here demonstrates that the cytoprotective function of serpinB1 in PMNs is based on the inhibition of granule protease CG. Deficiency in CG was sufficient to rescue the defect of sB1−/− mice as illustrated by normal PMN counts in the BM of double knockout CG.sB1−/− mice. We also showed that the protease-serpin interaction occurred within PMNs. Indeed, WT PMNs had a greater survival over sB1−/− PMNs in mixed BM chimera, whereas the survival of CG.sB1−/− PMNs was similar to WT PMNs after BM transfer. SerpinB1 is an ancestral clade B serpin with a conserved specificity determining reactive center loop in all vertebrates.32 Furthermore, human and mouse serpinB1 have the same specificity for chymotrypsin-like and elastase-like serine proteases.21,22 Likewise, human and mouse CG have identical substrate specificities and the phenotype of CG−/− murine PMN can be rescued by human CG.33 Therefore, it is highly likely that the antagonistic functions of CG and serpinB1 in cellular homeostasis observed in mice can be extended to other species.

Extracellular CG was previously reported to promote detachment-induced apoptosis (anoikis) in human and mouse cardiomyocytes.34 This activity is mediated through the shedding and transactivation of epidermal growth factor receptor and downregulation of focal adhesion signaling.35,36 In our study, exogenous human CG also induced PMN death in vitro but these effects were not enhanced in sB1−/− PMNs and the neutropenia associated with serpinB1 deficiency was principally cell intrinsic. How intracellular CG induces PMN death remains to be fully investigated. However, our studies provide some indications on the potential pathways. Like other NSPs, the expression of CG is transcriptionally restricted to the promyelocyte stage during PMN development and NSPs are then stored in active form in primary azurophil granules.37 Because serpinB1 is equally efficient at inhibiting NE, CG, and PR3, it was surprising that deletion of CG alone was sufficient to achieve a complete reversal of the PMN survival defect in CG.sB1−/− mice. A possible explanation would be that CG gains access to targets more readily than other granule proteases. There is evidence that binding to serglycin proteoglycans differs between NE and CG resulting in altered sorting of NE but not CG into granules of serglycin-deficient PMNs.38 Different interactions with granule matrix may thus contribute to differential release of CG from the granules compared with other NSPs. However, because sB1−/− PMNs have similar levels of CG and NE as WT PMNs20 and because LLME-induced granule permeabilization likely releases all granule contents equally, we favor an alternative interpretation where CG specifically targets essential cellular components that are not cleaved by the other serpinB1-inhibitable granule proteases. Upon granule permeabilization, we found that CG can induce cell death upstream of caspases as well as independent of caspases. CG was previously shown to activate caspase-7 in vitro and it functions at neutral pH, which is consistent with a physiological role in the nucleocytoplasmic environment.39 Cell death induced by lysosomal/granule membrane permeabilization has previously been linked to cysteine cathepsins in other cell types. However, these proteases appear to depend on caspase activation to trigger apoptosis and they function poorly at neutral pH, questioning their potential role as regulators of cell death.40 In contrast, CG-mediated cell death is not completely blocked by caspase inhibition, which is a property reminiscent of granzymes in cytotoxic T cells.41 In fact, CG is phylogenetically most closely related to serine proteases granzyme B and H.42 Granzymes have numerous nuclear, mitochondrial, and cytoplasmic target proteins leading to cell death41 and we anticipate that this may also be the case for CG.

……

G-CSF therapy is successfully used to treat most congenital and acquired neutropenia through increased granulopoiesis, mobilization from the BM, and increased survival of PMNs. Prosurvival effects of G-CSF include the upregulation of antiapoptotic Bcl-2 family members, which act upstream of the mitochondria and the activation of effector caspases. In sB1−/− mice, G-CSF levels in serum are fourfold higher than in WT mice in steady state and this is accompanied by an upregulation of the antiapoptotic Bcl-2 family member Mcl-1 in sB1−/− PMNs.19 Here, G-CSF therapy significantly increased granulopoiesis in both WT and sB1−/− mice. However, the PMN numbers in treated sB1−/− BM and blood were significantly lower than those of treated WT mice, indicating only a partial rescue of the survival defect. This is consistent with our findings that CG-mediated death can proceed independent of caspases and can thus bypass antiapoptotic effects mediated by G-CSF.

CG has largely been studied in association with antimicrobial and inflammatory functions due to its presence in PMNs.1214,49 In this context, we have previously shown that serpinB1 contributes to prevent increased mortality and morbidity associated with production of inflammatory cytokines upon infection with Pseudomonas aeruginosa and influenza A virus.20,50 In this study, we demonstrate that serpinB1 inhibition of the primary granule protease CG in PMNs is essential for PMN survival and this ultimately regulates PMN numbers in vivo. Our findings also extend the roles of CG from antimicrobial and immunoregulatory functions to a novel role in inducing cell death.

 

Neutrophil Elastase, Proteinase 3, and Cathepsin G as Therapeutic Targets in Human Diseases

Brice KorkmazMarshall S. HorwitzDieter E. Jenne and Francis Gauthier
Pharma Rev Dec 2010; 62(4):726-759  http://dx.doi.org:/10.1124/pr.110.002733

Polymorphonuclear neutrophils are the first cells recruited to inflammatory sites and form the earliest line of defense against invading microorganisms. Neutrophil elastase, proteinase 3, and cathepsin G are three hematopoietic serine proteases stored in large quantities in neutrophil cytoplasmic azurophilic granules. They act in combination with reactive oxygen species to help degrade engulfed microorganisms inside phagolysosomes. These proteases are also externalized in an active form during neutrophil activation at inflammatory sites, thus contributing to the regulation of inflammatory and immune responses. As multifunctional proteases, they also play a regulatory role in noninfectious inflammatory diseases. Mutations in the ELA2/ELANE gene, encoding neutrophil elastase, are the cause of human congenital neutropenia. Neutrophil membrane-bound proteinase 3 serves as an autoantigen in Wegener granulomatosis, a systemic autoimmune vasculitis. All three proteases are affected by mutations of the gene (CTSC) encoding dipeptidyl peptidase I, a protease required for activation of their proform before storage in cytoplasmic granules. Mutations of CTSC cause Papillon-Lefèvre syndrome. Because of their roles in host defense and disease, elastase, proteinase 3, and cathepsin G are of interest as potential therapeutic targets. In this review, we describe the physicochemical functions of these proteases, toward a goal of better delineating their role in human diseases and identifying new therapeutic strategies based on the modulation of their bioavailability and activity. We also describe how nonhuman primate experimental models could assist with testing the efficacy of proposed therapeutic strategies.

 

Human polymorphonuclear neutrophils represent 35 to 75% of the population of circulating leukocytes and are the most abundant type of white blood cell in mammals (Borregaard et al., 2005). They are classified as granulocytes because of their intracytoplasmic granule content and are characterized by a multilobular nucleus. Neutrophils develop from pluripotent stem cells in the bone marrow and are released into the bloodstream where they reach a concentration of 1.5 to 5 × 109 cells/liter. Their half-life in the circulation is only on the order of a few hours. They play an essential role in innate immune defense against invading pathogens and are among the primary mediators of inflammatory response. During the acute phase of inflammation, neutrophils are the first inflammatory cells to leave the vasculature, where they migrate toward sites of inflammation, following a gradient of inflammatory stimuli. They are responsible for short-term phagocytosis during the initial stages of infection (Borregaard and Cowland, 1997Hampton et al., 1998Segal, 2005). Neutrophils use complementary oxidative and nonoxidative pathways to defend the host against invading pathogens (Kobayashi et al., 2005).

The three serine proteases neutrophil elastase (NE1), proteinase 3 (PR3), and cathepsin G (CG) are major components of neutrophil azurophilic granules and participate in the nonoxidative pathway of intracellular and extracellular pathogen destruction. These neutrophil serine proteases (NSPs) act intracellularly within phagolysosomes to digest phagocytized microorganisms in combination with microbicidal peptides and the membrane-associated NADPH oxidase system, which produces reactive oxygen metabolites (Segal, 2005). An additional extracellular antimicrobial mechanism, neutrophil extracellular traps (NET), has been described that is made of a web-like structure of DNA secreted by activated neutrophils (Papayannopoulos and Zychlinsky, 2009) (Fig. 1). NETs are composed of chromatin bound to positively charged molecules, such as histones and NSPs, and serve as physical barriers that kill pathogens extracellularly, thus preventing further spreading. NET-associated NSPs participate in pathogen killing by degrading bacterial virulence factors extracellularly (Brinkmann et al., 2004;Papayannopoulos and Zychlinsky, 2009).

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Fig. 1.

Polymorphonuclear neutrophil. Quiescent (A) and chemically activated (B) neutrophils purified from peripheral blood. C, PMA-activated neutrophils embedded within NET and neutrophil spreading on insoluble elastin.

In addition to their involvement in pathogen destruction and the regulation of proinflammatory processes, NSPs are also involved in a variety of inflammatory human conditions, including chronic lung diseases (chronic obstructive pulmonary disease, cystic fibrosis, acute lung injury, and acute respiratory distress syndrome) (Lee and Downey, 2001Shapiro, 2002Moraes et al., 2003Owen, 2008b). In these disorders, accumulation and activation of neutrophils in the airways result in excessive secretion of active NSPs, thus causing lung matrix destruction and inflammation. NSPs are also involved in other human disorders as a consequence of gene mutations, altered cellular trafficking, or, for PR3, autoimmune disease. Mutations in the ELA2/ELANE gene encoding HNE are the cause of human cyclic neutropenia and severe congenital neutropenia (Horwitz et al., 19992007). Neutrophil membrane-bound proteinase 3 (mPR3) is the major target antigen of anti-neutrophil cytoplasmic autoantibodies (ANCA), which are associated with Wegener granulomatosis (Jenne et al., 1990). All three proteases are affected by mutation of the gene (CTSC) encoding dipeptidyl peptidase I (DPPI), which activates several granular hematopoietic serine proteases (Pham and Ley, 1999Adkison et al., 2002). Mutations of CTSC cause Papillon-Lefèvre syndrome and palmoplantar keratosis (Hart et al., 1999Toomes et al., 1999).

…….

Fully processed mature HNE, PR3, and CG isolated from azurophilic granules contain, respectively, 218 (Bode et al., 1986Sinha et al., 1987), 222 (Campanelli et al., 1990b), and 235 (Salvesen et al., 1987Hof et al., 1996) residues. They are present in several isoforms depending on their carbohydrate content, with apparent mass of 29 to 33 kDa upon SDS-polyacrylamide gel electrophoresis (Twumasi and Liener, 1977Watorek et al., 1993). HNE and PR3 display two sites of N-glycosylation, whereas CG possesses only one. NSPs are stored mainly in neutrophil azurophilic granules, but HNE is also localized in the nuclear envelope, as revealed by immunostaining and electron microscopy (Clark et al., 1980;Benson et al., 2003), whereas PR3 is also found in secretory vesicles (Witko-Sarsat et al., 1999a). Upon neutrophil activation, granular HNE, PR3, and CG are secreted extracellularly, although some molecules nevertheless remain at the cell surface (Owen and Campbell, 1999Owen, 2008a). The mechanism through which NSPs are sorted from the trans-Golgi network to the granules has not been completely defined, even though an intracellular proteoglycan, serglycin, has been identified as playing a role in elastase sorting and packaging into azurophilic granules (Niemann et al., 2007). Unlike HNE and CG, PR3 is constitutively expressed on the membranes of freshly isolated neutrophils (Csernok et al., 1990Halbwachs-Mecarelli et al., 1995). Stimulation of neutrophils at inflammatory sites triggers intracytoplasmic granules to translocate to the phagosomes and plasma membrane, thereby liberating their contents. The first step of the translocation to the target membrane depends on cytoskeleton remodeling and microtubule assembly (Burgoyne and Morgan, 2003). This is followed by a second step of granule tethering and docking, which are dependent on the sequential intervention of SNARE proteins (Jog et al., 2007).

…….

Exposure of neutrophils to cytokines (TNF-α), chemoattractants (platelet-activating factor, formyl-Met-Leu-Phe, or IL-8), or bacterial lipopolysaccharide leads to rapid granule translocation to the cell surface with secretion of HNE, PR3, and CG into the extracellular medium (Owen and Campbell, 1999). A fraction of secreted HNE, PR3, and CG is detected at the surface of activated neutrophils (Owen et al., 1995a1997Campbell et al., 2000). Resting purified neutrophils from peripheral blood express variable amounts of PR3 on their surface. A bimodal, apparently genetically determined, distribution has been observed with two populations of quiescent neutrophils that express or do not express the protease at their surface (Halbwachs-Mecarelli et al., 1995Schreiber et al., 2003). The percentage of mPR3-positive neutrophils ranges from 0 to 100% of the total neutrophil population within individuals. Furthermore, the percentage of mPR3-positive neutrophils remains stable over time and is not affected by neutrophil activation (Halbwachs-Mecarelli et al., 1995).

The mechanism through which HNE and CG are associated with the outer surface of the plasma membrane of neutrophils mainly involves electrostatic interactions with the sulfate groups of chondroitin sulfate- and heparan sulfate-containing proteoglycans (Campbell and Owen, 2007). These two proteases are released from neutrophil cell surfaces by high concentrations of salt (Owen et al., 1995b1997;Korkmaz et al., 2005a) and after treatment with chondroitinase ABC and heparinase (Campbell and Owen, 2007). Membrane PR3 is not solubilized by high salt concentrations, which means that its membrane association is not charge dependant (Witko-Sarsat et al., 1999aKorkmaz et al., 2009). Unlike HNE and CG, PR3 bears at its surface a hydrophobic patch formed by residues Phe166, Ile217, Trp218, Leu223, and Phe224 that is involved in membrane binding (Goldmann et al., 1999Hajjar et al., 2008) (Fig. 3B). Several membrane partners of PR3 have been identified, including CD16/FcγRIIIb (David et al., 2005Fridlich et al., 2006), phospholipid scramblase-1, a myristoylated membrane protein with translocase activity present in lipid rafts (Kantari et al., 2007), CD11b/CD18 (David et al., 2003), and human neutrophil antigen NB1/CD177 (von Vietinghoff et al., 2007Hu et al., 2009), a 58- to 64-kDa glycosyl-phosphatidylinositol anchored surface receptor belonging to the urokinase plasminogen activator receptor superfamily (Stroncek, 2007). NB1 shows a bimodal distribution that superimposes with that of PR3 on purified blood neutrophils (Bauer et al., 2007). Active, mature forms of PR3 but not pro-PR3 can bind to the surface of NB1-transfected human embryonic kidney 293 cells (von Vietinghoff et al., 2008) and Chinese hamster ovary cells (Korkmaz et al., 2008b). Interaction involves the hydrophobic patch of PR3 because specific amino acid substitutions disrupting this patch in the closely related gibbon PR3 prevent binding to NB1-transfected cells (Korkmaz et al., 2008b). Decreased interaction of pro-PR3 with NB1-transfected cells is explained by the topological changes affecting the activation domain containing the hydrophobic patch residues. Together, these results support the hydrophobic nature of PR3-membrane interaction.

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Roles in Inflammatory Process Regulation

NSPs are abundantly secreted into the extracellular environment upon neutrophil activation at inflammatory sites. A fraction of the released proteases remain bound in an active form on the external surface of the plasma membrane so that both soluble and membrane-bound NSPs are able to proteolytically regulate the activities of a variety of chemokines, cytokines, growth factors, and cell surface receptors. Secreted proteases also activate lymphocytes and cleave apoptotic and adhesion molecules (Bank and Ansorge, 2001Pham, 2006Meyer-Hoffert, 2009). Thus, they retain pro- and anti-inflammatory activities, resulting in a modulation of the immune response at sites of inflammation.

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Processing of Cytokines, Chemokines, and Growth Factors.

Processing and Activation of Cellular Receptors.

Induction of Apoptosis by Proteinase 3.

Physiological Inhibitors of Elastase, Proteinase 3, and Cathepsin G

During phagocytosis and neutrophil turnover, HNE, PR3, and CG are released into the extracellular space as active proteases. The proteolytic activity of HNE, PR3, and CG seems to be tightly regulated in the extracellular and pericellular space to avoid degradation of connective tissue proteins including elastin, collagen, and proteoglycans (Janoff, 1985). Protein inhibitors that belong to three main families, the serpins, the chelonianins, and the macroglobulins, ultimately control proteolytic activity of HNE, PR3, and CG activities. The individual contributions of these families depend on their tissue localization and that of their target proteases. The main characteristics of HNE, PR3, and CG physiological inhibitors are presented in Table 2.

 

Serine Protease Inhibitors

Serpins are the largest and most diverse family of protease inhibitors; more than 1000 members have been identified in human, plant, fungi, bacteria, archaea, and certain viruses (Silverman et al., 2001Mangan et al., 2008). They share a similar highly conserved tertiary structure and similar molecular weight of approximately 50 kDa. Human serpins belong to the first nine clades (A–I) of the 16 that have been described based on phylogenic relationships (Irving et al., 2000Silverman et al., 2001Mangan et al., 2008). For historical reasons, α1-protease inhibitor (α1-PI) was assigned to the first clade. Clade B, also known as the ov-serpin clan because of the similarity of its members to ovalbumin (a protein that belongs to the serpin family but lacks inhibitory activity), is the second largest clan in humans, with 15 members identified so far. Ov-serpin clan members are generally located in the cytoplasm and, to a lesser extent, on the cell surface and nucleus (Remold-O’Donnell, 1993).

Serpins play important regulatory functions in intracellular and extracellular proteolytic events, including blood coagulation, complement activation, fibrinolysis, cell migration, angiogenesis, and apoptosis (Potempa et al., 1994). Serpin dysfunction is known to contribute to diseases such as emphysema, thrombosis, angioedema, and cancer (Carrell and Lomas, 1997Lomas and Carrell, 2002). Most inhibitory serpins target trypsin-/chymotrypsin-like serine proteases, but some, termed “cross-class inhibitors,” have been shown to target cysteine proteases (Annand et al., 1999). The crystal structure of the prototype plasma inhibitor α1-PI revealed the archetype native serpin fold (Loebermann et al., 1984). All serpins typically have three β-sheets (termed A, B, and C) and eight or nine α-helices (hA–hI) arranged in a stressed configuration. The so-called reactive center loop (RCL) of inhibitory molecules determines specificity and forms the initial encounter complex with the target protease (Potempa et al., 1994Silverman et al., 2001). Serpins inhibit proteases by a suicide substrate inhibition mechanism. The protease initially recognizes the serpin as a potential substrate using residues of the reactive center loop and cleaves it between P1 and P1′ This cleavage allows insertion of the cleaved RCL into the β-sheet A of the serpin, dragging the protease with it and moving it over 71 Å to the distal end of the serpin to form a 1:1 stoichiometric covalent inhibitory complex (Huntington et al., 2000). Such cleavage generates a ∼4-kDa C-terminal fragment that remains noncovalently bound to the cleaved serpin. Displacement of the covalently attached active site serine residue from its catalytic partner histidine explains the loss of catalytic function in the covalent complex. The distortion of the catalytic site structure prevents the release of the protease from the complex, and the structural disorder induces its proteolytic inactivation (Huntington et al., 2000). Covalent complex formation between serpin and serine proteases triggers a number of conformational changes, particularly in the activation domain loops of the bound protease (Dementiev et al., 2006).

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Pathophysiology of Elastase, Proteinase 3 and Cathepsin G in Human Diseases

In many instances, the initiation and propagation of lung damage is a consequence of an exaggerated inappropriate inflammatory response, which includes the release of proteases and leukocyte-derived cytotoxic products (Owen, 2008b;Roghanian and Sallenave, 2008). Inflammation is a physiological protective response to injury or infection consisting of endothelial activation, leukocyte recruitment and activation, vasodilation, and increased vascular permeability. Although designed to curtail tissue injury and facilitate repair, the inflammatory response sometimes results in further injury and organ dysfunction. Inflammatory chronic lung diseases, chronic obstructive pulmonary disease, acute lung injury, acute respiratory distress syndrome, and cystic fibrosis are syndromes of severe pulmonary dysfunction resulting from a massive inflammatory response and affecting millions of people worldwide. The histological hallmark of these chronic inflammatory lung diseases is the accumulation of neutrophils in the microvasculature of the lung. Neutrophils are crucial to the innate immune response, and their activation leads to the release of multiple cytotoxic products, including reactive oxygen species and proteases (serine, cysteine, and metalloproteases). The physiological balance between proteases and antiproteases is required for the maintenance of the lung’s connective tissue, and an imbalance in favor of proteases results in lung injury (Umeki et al., 1988Tetley, 1993). A number of studies in animal and cell culture models have demonstrated a contribution of HNE and related NSPs to the development of chronic inflammatory lung diseases. Available preclinical and clinical data suggest that inhibition of NSP in lung diseases suppresses or attenuates the contribution of NSP to pathogenesis (Chughtai and O’Riordan, 2004Voynow et al., 2008Quinn et al., 2010). HNE could also participate in fibrotic lung remodeling by playing a focused role in the conversion of latent transforming growth factor-β into its biologically active form (Chua and Laurent, 2006Lungarella et al., 2008).

Anti-Neutrophil Cytoplasmic Autoantibody-Associated Vasculitides

ANCA-associated vasculitides encompasses a variety of diseases characterized by inflammation of blood vessels and by the presence of autoantibodies directed against neutrophil constituents. These autoantibodies are known as ANCAs (Kallenberg et al., 2006). In Wegener granulomatosis (WG), antibodies are mostly directed against PR3. WG is a relatively uncommon chronic inflammatory disorder first described in 1931 by Heinz Karl Ernst Klinger as a variant of polyarteritis nodosa (Klinger, 1931). In 1936, the German pathologist Friedrich Wegener described the disease as a distinct pathological entity (Wegener, 19361939). WG is characterized by necrotizing granulomatous inflammation and vasculitis of small vessels and can affect any organ (Fauci and Wolff, 1973Sarraf and Sneller, 2005). The most common sites of involvement are the upper and lower respiratory tract and the kidneys. WG affects approximately 1 in 20,000 people; it can occur in persons of any age but most often affects those aged 40 to 60 years (Walton, 1958Cotch et al., 1996). Approximately 90% of patients have cold or sinusitis symptoms that fail to respond to the usual therapeutic measures and that last considerably longer than the usual upper respiratory tract infection. Lung involvement occurs in approximately 85% of the patients. Other symptoms include nasal membrane ulcerations and crusting, saddle-nose deformity, inflammation of the ear with hearing problems, inflammation of the eye with sight problems, and cough (with or without hemoptysis).

Hereditary Neutropenias

Neutropenia is a hematological disorder characterized by an abnormally low number of neutrophils (Horwitz et al., 2007). The normal neutrophil count fluctuates across human populations and within individual patients in response to infection but typically lies in the range of 1.5 to 5 × 109 cells/liter. Neutropenia is categorized as severe when the cell count falls below 0.5 × 109 cells/liter. Hence, patients with neutropenia are more susceptible to bacterial infections and, without prompt medical attention, the condition may become life-threatening. Common causes of neutropenia include cancer chemotherapy, drug reactions, autoimmune diseases, and hereditary disorders (Berliner et al., 2004Schwartzberg, 2006).

Papillon-Lefèvre Syndrome

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New Strategies for Fighting Neutrophil Serine Protease-Related Human Diseases

Administration of therapeutic inhibitors to control unwanted proteolysis at inflammation sites has been tested as a therapy for a variety of inflammatory and infectious lung diseases (Chughtai and O’Riordan, 2004). Depending on the size and chemical nature of the inhibitors, they may be administered orally, intravenously, or by an aerosol route. Whatever the mode of administration, the access of therapeutic inhibitors to active proteases is often hampered by physicochemical constraints in the extravascular space and/or by the partitioning of proteases between soluble and solid phases.

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Concluding Remarks

NSPs were first recognized as protein-degrading enzymes but have now proven to be multifunctional components participating in a variety of pathophysiological processes. Thus, they appear as potential therapeutic targets for drugs that inhibit their active site or impair activation from their precursor. Overall, the available preclinical and clinical data suggest that inhibition of NSPs using therapeutic inhibitors would suppress or attenuate deleterious effects of inflammatory diseases, including lung diseases. Depending on the size and chemical nature of inhibitors, those may be administered orally, intravenously, or by aerosolization. But the results obtained until now have not been fully convincing because of the poor knowledge of the biological function of each protease, their spatiotemporal regulation during the course of the disease, the physicochemical constraints associated with inhibitor administration, or the use of animal models in which NSP regulation and specificity differ from those in human. Two different and complementary approaches may help bypass these putative problems. One is to target active proteases by inhibitors at the inflammatory site in animal models in which lung anatomy and physiology are close to those in human to allow in vitro and in vivo assays of human-directed drugs/inhibitors. The other is to prevent neutrophil accumulation at inflammatory sites by impairing production of proteolytically active NSPs using an inhibitor of their maturation protease, DPPI. Preventing neutrophil accumulation at the inflammatory sites by therapeutic inhibition of DPPI represents an original and novel approach, the exploration of which has just started (Méthot et al., 2008). Thus pharmacological inactivation of DPPI in human neutrophils could well reduce membrane binding of PR3 and, as a consequence, neutrophil priming by pathogenic auto-antibodies in WG. In addition, it has been recognized that the intracellular level of NSPs depends on their correct intracellular trafficking. In the future, pharmacological targeting of molecules specifically involved in the correct intracellular trafficking of each NSP could possibly regulate their production and activity, a feature that could be exploited as a therapeutic strategy for inflammatory diseases.

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antimicrobial evaluation of some novel bis-heterocyclic chalcones

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Synthesis and antimicrobial evaluation of some novel bis-heterocyclic chalcones from cyclic imides under microwave irradiation
Ravindra S. Dhivare1* and Shankarsing S. Rajput2
Chem Sci Rev Lett 2015; 4(15): 937-944     Article CS05204609    http://chesci.com/articles/csrl/v4i15/19_CS05204609.pdf

 

Synthesis of a new series of bis-heterocyclic chalcone derivatives has been reported. The condensation proceeded by the one pot reaction of N-phenyl succinimides and 4-hydroxy-3-methoxy benzaldehyde in presence of neutral alumina under microwave irradiation. The advantages of this method are high yield, shorter reaction time and simple workup procedure. Most of the synthesized compounds have shown moderate to significant antimicrobial activity against different microbial strains.

 

Chalcones and cyclic imides perform a significant title role in the heterocyclic synthesis containing oxygen, nitrogen and sulphur groups. Cyclic imides [1] like succinimides [2] [3] [4], maleimides [5], glutarimide [6], itaconimide[7] and phthalimides[8] showed the defensive antibacterial [9], antifungal activities. Cyclic imides exhibited the CNS anxiolytic and anti-depressive [10], brain metabolism [11], nephrotoxic [12], antiviral [13], anticonvulsant [14] electroshocks [15] , muscle relaxant [16], anti-mutagenic [17], analgesic [18], anxiety and depression [19], myeloperoxidase induction [20], antiproliferative [21], seedling growth [22] activities. The substituted heterocyclic imides were developed from cyclic anhydrides [23], formamide [24], trifluoroacetylation [25], triethylamine [26], hydroxylamine [27], thalidomide biotin [28] , pyrolidine triones [29] reagents and bis-heterocyclic analogs [30] by microwave synthesis. Bis-chalcones are the pioneer flavonoids of heterocycle ancestor containing carbon stuck between α, β- unsaturated aromatic rings and carbonyl carbons. These are prepared by the condensation [31] of the substituted ketones and aldehyde groups [32] [33]. The chalcone showed significant cytotoxic activities against antimicrobial [34] , cell line and breast cancer [35], anti-oxidant [36], bovine lens aldose reductase [37], tumor-genesis activities [38]. The chalcones are synthesized by utilizing a number of synthetic routes like solid phase Claisen-Schemdit, Cross-Aldol condensation, acid catalyst [39], coupling reaction [40], Knoevenagel condensation [41] and microwave assisted synthesis.

 

Preparation of substituted bis-heterocyclic chalcones: The N-substituted Phenylpyrrolidine-2, 5-diones or N-phenyl succinimides are conventionally synthesized by succinic anhydride and substituted anilines. Then afforded succinimides were employed for the preparation of bis-chalcone derivatives by microwave synthesis. The experimental method of conventional to microwave synthesis is schematically represented in figure 1

Figure 1 Experimental design of conventional to microwave method

General Procedure for the Synthesis of N-phenyl-pyrrolidine-2, 5-dione or N-Phenyl Succinimides

To accomplish the work succinic anhydride (0.1 moles) benzene was added and heated under reflux with constant stirring for 15 to 20 min till the solution becomes clear. Into this solution the primary aromatic amines (0.2 moles) in 5 ml benzene was slowly poured with constant stirring for 15- 20 min till the solution becomes homogenized. On the vaporization of benzene amorphous powder of 3-(N-phenyl) propanoic acid was obtained. Further the mixture of 3- (N-phenyl) propanoic acid and acetyl chloride (0.9 moles) was reflux for 15-20 min by thoroughly evolution of HCl fumes. The reaction mixture was cooled at room temp the solid product was obtained and recrystallized by ethanol as shown in the scheme 1

General procedure for the synthesis of bis-chalcones derived from N-phenyl succinimides

The bis-chalcones (6a-j) derivatives were synthesized by the mixture of 0.1 moles of N-phenyl succinimides (4a-j) and 0.2 mole of 4-hydroxy-3-methoxy benzaldehyde in 2 gm of neutral Al2O3 under microwave supported solvent free condition on 640W power for 5-8 min. The developed compounds were recrystallized from ethanol (Scheme 2)

 

Chemistry: The starting compounds of bis-chalcones 6a-j were prepared by the reaction of substituted N-phenyl-pyrrolidine-2, 5- dione 4a-j using 4-hydroxy-3-methoxy benzaldehyde. The series of 3,4-bis(4-hydroxy-3-methoxy benzylidene)-Nphenylpyrrolidine-2,5-diones 6a-j were synthesized in reasonable yields by the microwave irradiation of cyclic imides 4a-j with vanillin in presence of neutral alumina in solvent free condition. The structure of bis-chalcones was confirmed by IR, 1H NMR and elemental analysis.

Antimicrobial activities (4a-j and 6a-j): All the synthesized compounds 4a-j and 6a-j were screened for their antibacterial activity against gram positive bacteria Bacillus subtilis (MCMB-310) and gram negative bacteria Escherichia coli (MCMB-301) using DMF solvent as shown in the graph -1. And antifungal activities against Candida albicans (NCIM-3471) and Aspergillus niger (NCIM- 545) strains using DMSO solvent revealed in the graph – 2. All the results of the synthesized compounds were carried out by the triplicate format N=3 with Mean ± SD. The statistical significance was carried out by one way ANOVA and confirmed by Dunnett multiple comparisons test performed the standard drugs against synthesized compounds. P value < 0.05 was considered as statistically significant remarked by *p<0.05, **p<0.01, ***p<0.001 compared to standard groups. The calculated data were tabulated (not shown).

Table 1 Antimicrobial activities of Bis-chalcones      Bacillus subtilis, Escherichia coli, Candida albicans, Aspergillus niger

Graph 1 Antibacterial activities of 4a-j and 6a-j (B.S. and E.C.) Mean±SD

Graph 2 Antifungal activities of 4a-j and 6a-j (C.A. and A.N.) Mean±SD

 

Conclusion An entire new series of bis-heterocyclic chalcones containing 4-hydroxy-3-methoxy benzylidene nucleus have been synthesized in one pot and facile manner from cyclic imides in good yield. A good number of the synthesized bischalcone 6a-j showed noticeable synergistic antifungal activities against Candida albicans and Aspergillus niger fungal strains.

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novel Schiff base metal complexes

Larry H. Bernstein, MD, FCAP, Curator

LPBI

 

Synthesis and Characterisation of some novel Schiff base metal complexes: Spectral, XRD, Photoluminescence and Antimicrobial Studies
Rajendran Jayalakshmi and Rangappan Rajavel*  – Department of chemistry, Periyar University, Salem-636 011, Tamil Nadu, India

Chem Sci Rev Lett 2015; 4(15); 851-859        Article CS072046073        http://chesci.com/articles/csrl/v4i15/11_CS072046073.pdf

Schiff base ligands are potentially capable of forming stable complexes with most transition metal ions, which act as model compounds for biologically important species. Cu (II), Co (II), Ni (II) and Mn (II) Schiff base metal complexes was prepared by the condensation of benzil and 2,6-diamino pyridine in 1:1 molar ratio. The chemical structures of the Schiff base ligand and its metal complexes were confirmed by various spectroscopic studies like IR, UV-VIS, 1H NMR, TGA/DTA, Powder XRD, Molar conductance, and Photo luminescence. The free Schiff base ligand and its complexes have been tested for their antibacterial activity using disc diffusion method. From the biological studies, the complexes exhibit more activity than the ligand.

 

Metal-chelate Schiff base complexes have continued to play the role of one of the most important stereo chemical models in main group and transition metal coordination chemistry due to their preparative accessibility, diversity and structural variability(Garnovskii.,1993). Schiff bases have gained importance because of physiological and pharmacological activities associated with them. Schiff base metal complexes have ability to reversibly bind oxygen in epoxidation reactions [1], biological activity [2-4], catalytic activity in hydrogenation of olefins [5, 6] non-linear optical materials and [7] and photochromic properties [8]. The Schiff base complexes were also used as drugs and they possess a wide variety of antimicrobial activity against bacteria, fungi and it also inhibits the growth of certain type of tumours [9, 10]. The symmetric nature of a number of homo dinuclear transition metal derived metallobiosites and of the ability of the individual metal ions to have quite distinct roles in the functioning of the metalloenzyme concerned has led to a search for symmetrical dinucleating ligands which will give binuclear complexes capable of acting as models for the metallobiosites [11, 12]. 2, 6-Diamino-pyridine is a mediumproduction-volume chemical used as a pharmaceutical intermediate and a hair dye coupler in oxidation/permanent formulations. Although mutagenic activity has been reported, here in the present work we report the formation of Schiff base ligand from the condensation of 2, 6-diamino pyridine with benzil and the complexation with metal ions to form potentially active macrocyclic binuclear Schiff base metal complexes.

 

Synthesis of Ligand ((6E)-N2-((E)-2-(6-aminopyridin-2-ylimino)-1, 2-diphenylethyidine) pyridine-2, 6-diamine) The Schiff base ligand ((6E)-N2-((E)-2-(6-aminopyridin-2-ylimino)-1,2-diphenylethylidine)pyridine-2,6-diamine) were prepared by the drop wise addition of a solution of 2,6-diaminopyridine (0.22 g, 2 mmol) in ethanol (20 ml) to a stirred solution of benzil (0. 21 g, 1 mmol) in ethanol (20 ml). After the addition was completed, the mixture was condensed for 3 h at 900C. A brown precipitate solution was formed. The solution was kept for slow evaporation. The formed brown precipitate was filtered and washed with ethanol and then dried in air. Yield: 0.44 g (53%). Anal Calcd. For C24H20N6: C-73.45, H-5.14, and N-21.41. Found: C-73.38, H- 5.09, and N-21.40.

 

Synthesis of Schiff base metal complexes ([M2 (L) 2].4(OAc)) The macrocyclic binuclear Schiff base metal complexes (Cu(II), Ni(II), Co(II) and Mn(II)) were prepared by the condensation of 20 ml DMF solution of synthesized ligand (2mmol) adding to the constant stirring of 20 ml of ethanolic solution of metal salt (2 mmol M (where M = Cu2+, Ni2+, Co2+, Mn2+)) which was boiled for 3 hour under reflux. The coloured solution was formed. It was kept for slow evaporation and then collected the precipitate. It was filtered and washed with ethanol and then dried in vacuum.

 

The resultant macro cyclic Schiff metal complexes were colored powders, and stable for a long time in the open atmosphere. The analytical data and some of the physical properties of the Schiff base ligands and their binuclear metal complexes were summarized. All the metal complexes were sparingly soluble in general organic solvents, and soluble in DMF and DMSO, but insoluble in H2O, EtOH and MeOH. From the molar conductivity data, we clearly found the metal complexes were electrolytic in nature. The structural studies of the ligand and their complexes were done by spectroscopic methods.

Molar conductance The molar conductivity measurements commonly employed in the determination of the geometrical structure of inorganic compounds at infinite dilution. The molar conductance of binuclear Schiff base complexes was dissolved in DMSO and recorded (10-3M molar conductivity solution) at room temperature (Table 1). The complexes showed the range of molar conductance (127-134 ohm1 cm2mol1 ). From these values, we concluded that the complexes were electrolytic in nature. From the molar conductance, we concluded that the anions were outside the coordination sphere and not bonded to the metal ion therefore, these complexes may be formulated as [M2L2]4Z where, Z = acetate ion.

Table 1    Molar conductance and magnetic moment data of Schiff base binuclear metal complexes

S.No    Compounds                   Solvent      Molar conductance            Type of electrolyte        Magnetic moment            Geometry
Λm (ohm1 cm2 mol-1 )                                                          μ eff  B.M

1. [Cu2(L)2]4(OCOCH3)        DMSO                      132                                    1 :2  electrolyte                          1.74
2. [CO2(L)2]4(OCOCH3)      DMSO                      127                                     1 : 2 electrolyte                          4.83
3. [Ni2(L)2]4(OCOCH3)       DMSO                      134                                     1 : 2 electrolyte                          2.91
4. [Mn2(L)2]4(OCOCH3)     DMSO                     129                                      1 : 2 electrolyte                          5.82                          Octahedral 

 

IR Spectra of the free ligand and their binuclear metal complexes Vibrational spectra provide valuable information regarding the nature of functional group attached to the metal ion in the complexes. The IR spectra of the complexes show very similar spectra to one another. These spectra indicates the replacement of Ѵ(NH2) and Ѵ(C=O) of the starting materials with Ѵ(C=N) which suggest the occurs of the condensation reaction between amine and carbonyl groups [13]. Selected vibration bands of ligands and their metal complexes are given in Table 2. From the IR spectral analysis, the assignment of the important bands was made and recorded. In order to give a conclusive idea about the structure of the metal complexes, the IR bands of metal complexes were compared with free Schiff base ligand. The appearance of a strong, broad band at 3177 cm−1 in the spectra of the free ligands was assigned to ν (NH2). The IR band was shifted in the region (3063–3198 cm -1 ) shows the involvement of primary amine nitrogen atom coordinate to the metal ion for all the Schiff base metal complexes (Ray et al., 2009) after the complexation. The appearance of the band at 1629 cm -1 which may be assigned to the azomethine group Ѵ(C=N) vibration, indicate the condensation of the amino group of 2,6-diamino pyridine with the carbonyl group of benzil and formation of the proposed Schiff base. The IR spectra of all metal complexes show significant changes compared to free Schiff base ligand. After Complexation, the positions of the Ѵ(C=N) were shifted in the range (1660-1667cm1 ) indicates the participation of the azomethine group in complex formation (Singh et al., 2010). The position of an N – atom of the azomethine group and group of the pyridine ring in coordination is further supported by the presence of new bands in the range from 470–495cm-1which is assignable to (M-N) vibration. From the spectroscopic behaviour of metal complexes of pyridine, after the complexation the ring deformation found at 797 cm-1 and 711 cm−1. It was clearly indicate that the free pyridine is shifted to higher frequencies [14], and the coordination takes place via the pyridine nitrogen, as previously reported for pyridine complexes [15]. Therefore, this shift is clearly indicates the participation of pyridine in complex formation. The appearance of band range from 1660 cm−1 to 1438 cm−1 were due to symmetric stretching frequency and asymmetric stretching frequency of acetate ion. This clearly indicates that the acetate ions were coordinated outside of the coordination sphere.

Table 2 IR spectral data (cm-1 ) of the Schiff base (L) and their binuclear metal complexes

1H NMR spectrum of ligand and its macro cyclic binuclear metal complexes The 1H NMR data of the Schiff base (L) and the metal complexes were recorded in DMSO-d6 (Table 3). Assignment of 1H NMR signals were made according to their reported results for 2,6-diaminopyridine and its complexes [16-20]. The 1H-NMR spectra of ligand and its metal complexes show different peaks in the range 6.99-7.94 ppm corresponding to H3, H4, and H5 protons indicate unsymmetrical binding of the ligand to M (II) complexes. In the 1H NMR spectrum of M (II) complexes, singlet signal of the pyridine-NH2 (s, 3.1 to 3.7 ppm) and multiplet signals of aromatic protons (m, 6.72 to 7.94 ppm) of Schiff base (L) shifted compared to the starting material which suggests coordination through nitrogen atom of the azomethine group. For the metal complexes, a single sharp signal is appeared (region from 2.1 – 2.6 ppm) in the 1H NMR spectrum, suggest that the acetate ion is present in the outside coordination sphere of the metal complexes.

Table 3 1H NMR spectrum of ligand and its macro cyclic binuclear metal complexes

Electronic absorption spectra and magnetic moment measurements The electronic spectrum of the Schiff base ligand in DMSO (Table 4), the absorption band observed at 274 nm were assigned to π→π* transition and the band at 386 nm were assigned due to n→π* transition associated with the azomethine chromophore (-C=N).The absorption bands of the complexes are shift to longer wave numbers compared to that of the ligand [21]. For [M2 (L) 2]4(OCOCH3) complexes, the electronic absorption band occurs at 468-474 nm due to charge transfer from ligand to metal ion (LMCT). The obtained Cu (II) complexes exhibits a band at 652 nm assigned to 2Eg → 2T2g transition which is in conformity with octahedral geometry around the Cu (II) ion (Patil et al., 2010; Lever, 1968). The obtained magnetic moment value (µeff) for Cu(II)complex is 1.89 BM indicating that magnetic exchange occurs between the two copper sites and also supports octahedral geometry of Cu(II) complex [22]. The electronic absorption spectra of Co (II) complexes showed a band at 648 nm corresponding to 4T1g(F)→4A2g(F) transition and also the obtained magnetic moment value is 4.84 BM which confirm the octahedral geometry of the complex [23]. For the Ni (II) complex, it has the 3.06 BM magnetic moment value and the electronic spectrum showed a band at 645nm corresponding to 3A2g (F) →3T1g (F) transition which is consistent with the octahedral geometry of the complex. The Mn (II) binuclear complex shows bands at 633 nm corresponds to 6A1g→4T2g (4G) transitions and 5.82 BM magnetic value were compatible to an octahedral geometry of the ligand around manganese (II) ion [24].

Table 4 Electronic Spectral data of Schiff base ligand and their macro cyclic binuclear metal complexes

Compounds                    Electronic absorption spectra (nm)          Magnetic moment             Geometry of
π→π*   n→π*   L→M   d-d                          value(µeff)BM                  the complex
(nm)   (nm)      (nm)  (nm)
C12H12N6 (ligand)             274        342          –            –                                                                                       –
[Cu2(L)2]4(OCOCH3)      268       340        474     652                                1.89
[CO2(L)2]4(OCOCH3)     266        338        468    648                               4.84
[Ni2(L)2]4(OCOCH3)      256        339        471      645                               3.06                                        Octahedral
[Mn2(L)2]4(OCOCH3)   261         341         474     636                                5.82

 

TGA and DTA studies By using TGA and DTA analysis the thermal stability of the complexes were explained. The observation thermogram and curves (Table 5, Figure 2) were obtained at a heating rate of 100C/min over a temperature range of 40–7300C. The complex was stable up to 1600C and its decomposition started at this temperature. In the thermal decomposition process of the Cu (II) complex proceeds two steps of the mass losses corresponded to acetate, and NH2 leaving in the first, and second stages of the decomposition. The decomposition of the Cu (II) are irreversible. The Cobalt complexes were stable up to 2000C and its decomposition started at this temperature. The Cobalt (II) complex was decomposed in two steps with the temperature ranges from 200-470˚C corresponding to the loss of acetate and NH2 respectively. The Ni (II) complexes were stable up to 180oC and its decomposition started at this temperature. In the decomposition process of the Ni(II) complex, the estimated mass loss of the first step 6.85(6.91) corresponded to the loss of four acetate group and the second stage the liberation of four NH2 unit respectively, shown in table 6. The decomposition of the Nickel complex was irreversible. The thermal decomposition of the Manganese complex was stable up to 1700C and its decomposition started at this temperature. Thereafter, they start the decomposition process of the Mn (II) complex and weight loss observed in the temperature range 170-4600C, the mass loses corresponded to four acetate and four NH2 leaving in the first and second stages of the decomposition. The decomposition of the Mn (II) complexes are irreversible. The amount of acetate and NH2 groups stoichiometrically corresponding to the weight losses are given in the proposal chemical formulas of complexes.

Powder XRD Analysis Synthesized Schiff base metal (II) complexes were subjected to Powder X-ray diffractograms in the range (2ɵ = 10– 600 ) were shown in (Figure 3). Among the metal complexes Ni (II) complex shows well defined crystalline sharp peak which indicate the sample were crystalline nature. The appearance of crystallinity in the Schiff base metal complexes is due to the inherent crystalline nature of the metallic compounds. The average grain size (dXRD) of the Ni (II) complex is 32 nm which was calculated by using Scherer’s formula (Dhanaraj and Nair, 2009a,b) suggesting that the Ni(II) complex are nanocrystalline.

Table 5 Thermo gravimetric data of metal complexes

Figure 2 DTA/TGA Curve for metal complexes

Figure 3 Powder X-ray diffractogram for Ni complex

 

Fluorescence spectra The Schiff base and its binuclear metal complexes were analysed by the photoluminescence emission spectra (Figure 4) and recorded in DMSO at room temperature. Comparing with Schiff base ligand and its macro cyclic binuclear metal complexes, the metal complexes have strong fluorescence intensity than Schiff base. Among the metal complexes the Co (II) complex exhibited a strong fluorescence emission at 400 nm (Flourescence intensity 713) with excitation at 269 nm. The quenching of metal (II) complexes indicates that the ligand has a less potential photo active than metal (II) complexes.

Figure 4 Fluorescence spectra for all metal complexes

In vitro antimicrobial activity of Schiff base ligand and their metal complexes By using broth micro dilution procedures, the Schiff base ligand and their metal complexes were screened separately against for two Gram positive bacteria (Staphylococcus aureus and B. Subtilis), two Gram negative bacteria (E. Coli and S. typhi) and the fungi (A. fumigatus) for their antimicrobial activity. When the activity of Schiff base ligand and their metal complexes were increased by increasing the antimicrobial screening concentration (Table 6, Figure 5), because the concentration plays an important role in the zone of inhibition and the chelated metal complexes deactivate the various cellular enzyme [25]. Metal complexes show considerable antimicrobial activity even at low concentration and also more toxicity towards Gram-positive strains, Gram-negative strains and fungi compare with Schiff base ligand. The antimicrobial data shows that the copper complex noticed an excellent activity against bacteria and fungi than other metal complexes. The different antimicrobial activity of different metal complexes depends on the impermeability of the cell or the difference in ribosomes in microbial cell (Sengupta et al., 1998).

Table 6 Antimicrobial activity of Schiff base ligand and their metal complexes

Figure 5 Anti-Bacterial Activities of the Schiff Base and Its Binuclear Metal Complexes against Gram positive and negative Bacterias

Conclusion Macrocyclic binuclear metal (II) complexes was synthesized by using condensation method of a novel Schiff base ligand derived from 2, 6-diamino pyridine and benzil. The data which have been the physico chemical and spectral studies provides excellent structure and chemical composition of Schiff base and its metal complexes. The electronic absorption spectra, IR spectra and magnetic moment value reveals that the metal complexes were octahedral geometry and the Schiff base coordinated through six nitrogen atoms of azomethine group and pyridine ring. Powder XRD data reveals that the Ni(II) complex was nano crystalline structure. Based on the photo luminescence studies, we have confirmed the metal complexes were more potential photo active than Schiff base. The in vitro antimicrobial studies of metal (II) complexes showed better activity than Schiff base.

References

[1] Viswanathamurthi P, Natarajan K, Synth.React.Inorg.Met.-Org.Chem 2006; 36:415-418.

[2] Ren S, Wang R, Komastu K, Krause P.B, Zyrianov Y, Mckenna C. E, Csipke C, TokesZ. A, Lien E. J, J. Med. Chem 2002; 45: 410

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