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Archive for the ‘Small Molecules in Development of Therapeutic Drugs’ Category

Neural Networks in Alzheimer’s

Larry H. Bernstein, MD, FCAP, Curator

LPBI

SfN 2015 Recap: The Role of Synapses, Neural Networks in Alzheimer’s

Stephanie Guzowski, Editor

http://www.dddmag.com/articles/2015/11/sfn-2015-recap-role-synapses-neural-networks-alzheimers

http://www.dddmag.com/sites/dddmag.com/files/perineuronal%20nets_SfN.jpg

Perineuronal nets, shown in green, in three regions of the mouse brain. Credit: S.F. Palida et al.

Cognition and behavior rely on communication between individual neurons and extensive interactions between neural networks. But when synaptic dysfunction occurs, the results can be dire, leading to neurodegenerative symptoms in Alzheimer’s disease.

“The brain is the seed of our personal identity,” said Valina Dawson, Ph.D., director of neurogeneration and stem cell programs at Johns Hopkins University in Baltimore, Maryland. “It allows us to interact with our world but when things go wrong in the brain, it’s disastrous for the individual as well as the family.

“Our ability to treat these diseases is limited at the moment. We need new insight into what goes wrong.”

A lesser-known protein

Researchers, for years, have targeted amyloid beta (Aβ) in attempts to halt the progression of Alzheimer’s disease, and have recently, shown increased interest in the protein, tau.

But Paula Pousinha, Ph.D., at the French National Centre for Scientific Research, has focused her research on a lesser-known protein fragment: amyloid precursor protein intracellular domain (AICD). AICD is a fragment of amyloid precursor protein (APP), which is formed at the same time as Aβ in the brain. New evidence suggests that in addition to Aβ, AICD also disrupts communication between neurons during the progression of Alzheimer’s disease. Pousinha presented thesepublished findings at this year’s Society for Neuroscience (SfN) conference, which took place from October 17 to 21 in Chicago.

“Although AICD has been known for more than 10 years, it has been poorly studied,” said Pousinha.

Pousinha’s research team demonstrated that overexpressing AICD levels with AAV vector in rats’ brains “perturbs neuronal communication in the hippocampus,” a key structure necessary in forming memories and an area earliest affected in Alzheimer’s disease.

“In normal animals, if we apply to these neurons a high-frequency stimulation, afterward the neurons are stronger,” said Pousinha. “Neurons where we overexpressed AICD failed to have this potentization.”

Pousinha doesn’t negate the importance of Aβ in the development of neurodegenerative diseases. “Our study doesn’t exclude the pathological effects of Aβ,” she said. “We believe that Alzheimer’s disease is much more complex and has more than one candidate that has implications.

“It’s very important for the scientific community to understand the role of all these APP fragments of neuroinflammation — different pieces of the puzzle of how we can stop the disease progression.”

How do memories persist in the brain long term?

New research, also presented at this year’s SfN, has implications for understanding memory to develop treatments for Alzheimer’s disease and dementias. Sakina Palida, a graduate student at the University of California, San Diego found that localized modifications in the perineuronal net (PNN) at synapses could be a mechanism by which information is stably encoded and preserved in the brain over time.

“We still don’t understand how we stably encode and store memories in our brains for up to our entire lifetimes,” said Palida. The prevailing idea on how memories are maintained over time generally focus on postsynaptic proteins, said Palida. “But the problem with looking at intracellular synaptic proteins is that the majority turn over rapidly, of hours to at most a few days. So they’re very unstable.”

So, Palida and her team identified PNN as an ideal substrate for long-term memory. “Kind of like how you carve into stone — stone is a stable substrate — you retain the information regardless of what comes and goes over it.” They demonstrated that individual PNN proteins are highly stable, and that the PNN is locally degraded when synapses are strengthened.

And the team also demonstrated that mice lacking enzymes that degrade the PNN have deficient long-term, but not short-term, memory. “Which is a really exciting new result,” said Palida.

To track the PNN in live animals, Palida and her team fused a fluorescent protein to a small link protein in the PNN to allow tracking of PNN dynamics in real time. They also monitored PNN degradation in live cells after stimulating neurons with brain-derived neurotrophic factor (BDNF), a chemical secreted in the nervous system to enhance signaling — and observed localized degradation of the PNN at some newly formed synapses.

Crtl 1-Venus. Fusion of a fluorescent protein to small link proteins in the PNN allows tracking of PNN dynamics over time. Credit: S.F. Palida et al. Crtl1-Venus Neurons. Tracking PNN dynamics in live cells, in mouse brain tissue. Credit: S.F. Palida et al.

What’s next? “We’re currently making transgenic animals to express this protein, which would allow us to monitor PNN dynamics simultaneously with synaptic dynamics in a live animal brain, and really investigate this hypothesis further,” said Palida.

Increased APP intracellular domain (AICD) production perturbs synaptic signal integration via increased NMDAR function

*Paula A Pousinha1PubmedElisabeth Raymond1PubmedXavier Mouska1PubmedMichael Willem2PubmedHélène Marie1Pubmed

1660 Route de Lucioles, CNRS IPMC UMR 7275, Valbonne, France; 2Ludwig-Maximilians-University Munich, Munich, Germany

Alzheimer’s disease (AD) is a neurodegenerative disease that begins as mild short-term memory deficits and culminates in total loss of cognition and executive functions. The main culprit of the disease, resulting from Amyloid-Precursor Protein (APP) processing, has been thought to be amyloid-b peptide (Ab). However, despite the genetic and cell biological evidence that supports the amyloid cascade hypothesis, it is becoming clear that AD etiology is complex and that Ab alone is unable to account for all aspects of AD [Pimplikar et al. J Neurosci.30: 14946. 2010]. Gamma-secretase not only liberates Ab, but also its C-terminal intracellular counterpart called APP intracellular domain (AICD) [Passer. et al. JAlzheimers Dis.2: 289-301. 2000], which is known to also accumulate in AD patient’s brain [Ghosal et al. PNAS.106:18367. 2009], but surprisingly little is known about its functions in the hippocampus. To address this crucial issue, we increased AICD production in vivo in adult CA1 pyramidal neurons, mimicking the human pathological condition. Different ex-vivo electrophysiological and pharmacological approaches, including double- patch of neighbor neurons were used. We clearly demonstrate that in vivo AICD production increases synaptic NMDA receptor currents. This causes a frequency-dependent disruption of synaptic signal integration, leading to impaired long-term potentiation, which we were able to rescue by different pharmacological approaches. Our results provide convincing and entirely novel evidence that increased in vivo production of AICD is enough, per se, to cause synaptic dysfunction in CA1 hippocampal neurons.

131.21P2X2R-FE65 interaction induces synaptic failure and neuronal dyshomeostasis after treatments with soluble oligomers of amyloid beta peptide

300.15Early synaptic deficits in Alzheimer’s disease involve neuronal adenosine A2A receptors

215.08Homeostatic coupling between surface trafficking and cleavage of amyloid precursor protein

280.11A novel mechanism for lowering Abeta

383.22Impact of intracellular soluble oligomers of amyloid-β peptide on glutamatergic synaptic transmission

Society for Neuroscience Annual Meeting Showcases Strides in Brain Research

10/23/2015 – Stephanie Guzowski, Editor

CHICAGO – Nearly 30,000 researchers from more than 80 countries gathered this week at the annual Society for Neuroscience (SfN) meeting, the world’s largest conference focused on scientific discovery related to the brain and nervous system.

The 45th annual SfN meeting at McCormick Place convention center showcased more than 15,000 scientific presentations on advances in technologies and new research about brain structure, disease and treatments, and 517 exhibitors, according to event organizers.

Presentations covered a wide variety of topics including new technologies to study the brain, the science behind addiction, potential treatments for spinal cord injuries, and the role of synapses in neurological conditions.

Of particular focus was the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative, the large collaborative quest to develop technologies for a dynamic view of the brain. In early October, the National Institutes of Health announced its second round of funding to support goals, bringing the NIH investment to $85 million in fiscal year 2015.

Toxic Tau Could be Key to Alzheimer’s Treatment

01/06/2015 – Stephanie Guzowski, Editor

http://www.dddmag.com/articles/2015/01/toxic-tau-could-be-key-alzheimers-treatment

http://www.dddmag.com/sites/dddmag.com/files/tangles_Alz2.jpg

“But now, we know that tau is not simply a bystander but also a player,” Li said. “Both proteins work together to damage cell functions as the disease unfolds.”

Targeting tau

In the healthy brain, tau protein helps with the building and functioning of neurons. But when tau malfunctions, it creates abnormal clumps of protein fibers—neurofibrillary tangles—which spread rapidly throughout the brain. This highly toxic and altered form of the brain protein tau is called “tau oligomer.”

“There’s growing evidence that tau oligomers, not tau protein in general, are responsible for the development of neurodegenerative diseases, like Alzheimer’s,” said Julia Gerson, a graduate student in neuroscience at the University of Texas Medical Branch.

In Gerson’s research, which she presented at this year’s Society for Neuroscience meeting in Washington, D.C., Gerson and her team injected tau oligomers from people with Alzheimer’s into the brains of healthy mice. Subsequent testing revealed that the mice had developed memory loss.

“When we inject mice with tau oligomers, we see that they spend the same amount of time exploring a familiar object as an unfamiliar object,” said Gerson. “So they’re incapable of remembering that they’ve already seen this familiar object.”

What’s more, the molecules had multiplied throughout the animals’ brains. “This suggests that tau oligomers may spread from the injection site to other unaffected regions,” said Gerson.

Future treatments

Understanding tau’s connection to Alzheimer’s could have implications for potential therapies. “If we can stop the spread of these toxic tau oligomers, we may be capable of either preventing, or reversing, symptoms,” said Gerson. Gerson’s lab is currently investigating antibodies, which specifically fight tau oligomers.

Click to Enlarge. Normal brain vs. Alzheimer’s brain (Credit: Garrondo)

Erik Roberson, M.D., Ph.D., at the University of Alabama at Birmingham, and colleagues looked at how boosting the function of a specific type of neurotransmitter receptor, the NMDA receptor, provided benefit to people with the second most common type of dementia: frontotemporal dementia (FTD), a disease in which people experience rapid and dramatic changes in behavior, personality and social skills. People often quickly deteriorate and usually die about three years after diagnosis; there is also no effective treatment for FTD.

Since mutated tau impairs synapses—the connections between neurons—by reducing the size of NMDA receptors, “boosting the function of remaining NMDA receptors may help restore synaptic firing, and reverse behavioral abnormalities,” said Roberson.

Roberson’s, along with others’ work presented at the Society of Neuroscience meeting, focused on using animal models that mimic developing tau pathology. “These new mouse models, which contain both tau tangles and amyloid plaques” said Dr. Li, “offer the possibility of more accurately testing therapies directed at delaying the onset of amyloid beta plaques, tau accumulation and neuronal loss, all characteristic features of Alzheimer’s.”

Are clinical trials next?

Potentially, yes. “This arena of academic research has been ongoing for several years—it’s a younger area in terms of involvement of drug discovery,” said Sangram Sisodia, Ph.D., director of the Center for Molecular Neurobiology at the University of Chicago. “But I believe there is growing interest in pharma companies about targeting tau.

“The tau protein plays an incredibly complex role in the development of Alzheimer’s and other neurodegenerative diseases,” said Sisodia. “We are in the early stages of understanding that role, which will be crucial for developing effective preventions or treatments.”

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antibody-like proteins to awaken and destroy HIV holdouts

Larry H. Bernstein, MD, FCAP, Curator

LPBI

Two-Faced Proteins May Tackle HIV Reservoirs

Researchers design antibody-like proteins to awaken and destroy HIV holdouts.

By Amanda B. Keener | October 21, 2015

http://www.the-scientist.com//?articles.view/articleNo/44293/title/Two-Faced-Proteins-May-Tackle-HIV-Reservoirs/#.

For the millions of people living with HIV worldwide, a life-long commitment to antiretroviral drugs is a must. Without these drugs, reservoirs of HIV hiding within resting T cells throughout the body can easily resurge and cause disease. In a study published yesterday (October 20) in Nature Communications, researchers from the National Institute of Allergy and Infectious Diseases (NIAID) in Bethesda, Maryland, described a bispecific antibody-like protein that attacks those reservoirs by coaxing HIV out of hiding and targeting infected cells for destruction.

“In order to kill the [infected] cell, the cell has to be activated,” said study coauthor John Mascola, director of NIAID’s Vaccine Research Center. This is because HIV has a way of hiding out inside inactive CD4+ T cells where the virus adopts a dormant-like state known as latency. In this state, the virus is impervious to antiretroviral drugs as well as antibodies that might otherwise alert other immune cells to the virus’ presence inside an infected cell. “By definition, latently-infected cells don’t express virus proteins,” Oliver Schwartz, the head of the virus and immunity laboratory at the Pasteur Institute in Paris, who was not involved in the work, told The Scientist.

Mascola and his colleagues designed a protein that activates latently-infected T cells by targeting a protein found on the surface of all T cells called CD3. Engagement of CD3 signals infected CD4+ T cells to start dividing, which revamps HIV’s replication machinery causing the virus to make proteins that appear on the surface of the infected cell. Mascola’s team tested the protein, called VRC07-αCD3, on T cells donated by HIV patients on antiretroviral therapies. The researchers found that VRC07-αCD3 caused the T cells to display Env, indicating that latent virus had become reactivated.

In recent years, researchers have come up with a handful of approaches to activate latent HIV, such ashistone deacetylase inhibitors, which increase viral gene expression. VRC07-αCD3, however, doesn’t just activate latent HIV—it also binds Env on the surface of infected CD4+ T cells and tags the cells for killing by another sort of cell called CD8+ killer T cells. Using T cells in culture, Mascola’s team demonstrated that the CD3-binding region of the protein triggers killer CD8+ T cells to lyse CD4+ T cells expressing Env.

The NIAID study was preceded by one in The Journal of Clinical Investigation that described a similar protein with dual specificities for CD3 and Env, but with a slightly different structure. Both designs share features that allow the proteins to activate latent cells, tag Env, and activate and bring killer CD8+ T cells into close proximity of their infected targets.

The dual specificity for CD3 and Env also provides a layer of safety: it ensured the killer CD8+ T cells only acted in full force when HIV was present. “That was an encouraging part of the data,” Mascola said.

Schwartz said this feature potentially addresses the concern that nonspecific activation of large numbers of T cells could elicit a dangerous overactivation of the immune system called a cytokine storm.

Mascola and his colleagues tested the safety of VRC07-αCD3 in five HIV-infected Rhesus macaques by giving the animals six doses over the course of three weeks. The monkeys were also on antiretroviral drugs, and the virus remained undetectable throughout the treatment. Although the monkeys tolerated the drug well, VRC07-αCD3 did activate T cells and caused serum cytokine levels to increase. “So this type of treatment is not risk-free,” Caltech virologist Pamela Bjorkman, who was not involved in the work, wrote in an email to The Scientist.

Mascola said his group plans to continue testing VRC07-αCD3 in macaques and in humanized mice to work out a balance between T cell activation and HIV killing. However, neither model “really tells you what’s going to happen in people,” he said. “We’ll have to proceed slowly in the clinic.”

A. Pegu et al., “Activation and lysis of human CD4 cells latently infected with HIV-1,”Nature Communications, 6:8447 doi:10.1038/ncomms9447, 2015.

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New Topoisomerase Inhibitors in Clinical Trials

Curator: Stephen J. Williams, Ph.D.

Below is a great review of topoisomerase in cancer, approved inhibitors as well as some in clinical trials.

Biomolecules 2015, 5, 1652-1670; doi:10.3390/biom5031652

OPEN ACCESS

biomolecules

ISSN 2218-273X

www.mdpi.com/journal/biomolecules/

Review

Inhibition of Topoisomerase (DNA) I (TOP1): DNA Damage Repair and Anticancer Therapy

Yang Xu and Chengtao Her *

School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Mail Drop 64-7520, Pullman, WA 99164, USA; E-Mail: davidxy22@vetmed.wsu.edu

* Author to whom correspondence should be addressed; E-Mail: cher@wsu.edu; Tel.: +1-509-335-7537; Fax: +1-509-335-4159.

Academic Editors: Wolf-Dietrich Heyer, Thomas Helleday and Fumio Hanaoka Received: 22 May 2015 / Accepted: 14 July 2015 / Published: 22 July 2015

Abstract: Most chemotherapy regimens contain at least one DNA-damaging agent that preferentially affects the growth of cancer cells. This strategy takes advantage of the differences in cell proliferation between normal and cancer cells. Chemotherapeutic drugs are usually designed to target rapid-dividing cells because sustained proliferation is a common feature of cancer [1,2]. Rapid DNA replication is essential for highly proliferative cells, thus blocking of DNA replication will create numerous mutations and/or chromosome rearrangements—ultimately triggering cell death [3]. Along these lines, DNA topoisomerase inhibitors are of great interest because they help to maintain strand breaks generated by topoisomerases during replication. In this article, we discuss the characteristics of topoisomerase (DNA) I (TOP1) and its inhibitors, as well as the underlying DNA repair pathways and the use of TOP1 inhibitors in cancer therapy.

Biomolecules 2015, 5                                                                                                                           1653

  1. Type IB Topoisomerases and Inhibitors
    1.1. TOP1

DNA topoisomerases resolve topological constraints that may arise from DNA strand separation and are therefore important for transcription and replication [4]. There are six topoisomerases in humans, classified as Type IA, IB and IIA. Type IA topoisomerases TOP3a and TOP3b cleave one DNA strand to relax only negative supercoiling. In addition, TOP3a forms the BTR complex with BLM and RMI1/2, which plays a role in the dissolution of double-Holliday junctions [5]. Type IIA topoisomerases TOP2a and TOP2b generate double-strand breaks on one DNA molecule to allow the passing of other DNA strands [6]. Topoisomerases are attractive drug targets in cancer therapy. For example, the commonly used anticancer agents doxorubicin and etoposide (VP-16) are TOP2 inhibitors [7]. Type IB topoisomerases include the nuclear TOP1 and mitochondrial TOP1mt [4]. TOP1 initiates the DNA relaxation by nicking one DNA strand. It then forms a TOP1-DNA cleavage complex (TOP1cc) by covalently linked to the 3′-phosphate end via its tyrosine residue Y723 (3′-P-Y). Following the resolution of topological entanglements and the removal of TOP1, the 5′-hydroxyl end is realigned with the 3′-end for religation. Each nicking-closing cycle enables the relaxation of one DNA supercoiling (Figure 1).

Figure 1. A schematic representation of strand passages catalyzed by three types of topoisomerases (adapted from ref. [8]).

fig1topto

TOP1 is essential for embryonic development in mammals [9]. Although TOP1 plays an important role in the deconvolution of supercoils arising amid DNA replication, the precise steps involved with

Biomolecules 2015, 5                                                                                                                         1654

the recruitment of TOP1 to topological constraints remains to be revealed. It appears that in yeast TOP1 travels at a distance of 600 bp ahead of the replication fork [10] and remains associated with the GINS-MCM complex [11]. However, the yeast TOP1 is distinct from its human counterpart in that it has little effect on fork progression or the firing of replication origin [12]. In humans, TOP1 binds to the regions of the pre-replicative complex in cells during the M, early G1, and G1/S phases of the cell cycle to control the firing of replication origins [12]. This difference may explain why yeast cells are viable in the absence of TOP1. In addition, TOP1 also has functions in transcription that are independent of its role in resolving DNA topological entanglements. First, TOP1 is known to repress transcription by binding to TFIID [13]. Second, inhibition of TOP1 can cause the induction of c-Jun in leukemia cells, suggesting its additional role in the control of transcription [14]. Furthermore, TOP1 interacts with the splicing factor ASF/SF2 by which it promotes the maturation of RNA—through suppressing the formation of R-loops (RNA-DNA hybrids)—and prevents collision between transcription bubble and replication fork [15,16]. It appears that the levels of TOP1 have to be dynamically regulated. In B cells, TOP1 is reduced by activation-induced cytidine deaminase (AID) to facilitate class-switch recombination (CSR) and somatic hypermutation (SHM) [17,18]. Although TOP1mt is important for mitochondrial integrity and metabolism, mice lacking mitochondrial TOP1mt are viable and fertile but they are associated with increased negative supercoiling of mtDNA [19,20].

1.2. TOP1 Inhibitors

Stabilization of TOP1cc by topoisomerase poison is detrimental to cells due to the disruption of DNA uncoiling, increased strand breaks, and unstable RNA transcripts as well as incomplete DNA replication [21]. The TOP1 inhibitor camptothecin (CPT), first isolated from the Chinese tree Camptotheca acuminate, was clinically used for cancer treatment long before it was identified as a TOP1 inhibitor [22]. Due to side effects, CPT is no longer used clinically and it has been replaced by more effective and safer TOP1 inhibitors [23]. Currently, CPT derivatives topotecan (trade name: Hycamtin) and irinotecan (CPT-11, trade name: Camptosar) are routinely used to treat colorectal, ovarian and lung cancers, while a few other TOP1 inhibitors are being tested in clinical trials.

CPT is a 5-ring alkaloid that is active in its closed E-ring (lactone) form but it is inactive with an open E-ring (carboxylate) at physiological and alkaline pH [24]. Therefore, CPT is not effective for inhibiting TOP1mt due to a higher pH mitochondrial environment. The inactive form of CPT tends to bind to serum albumin, which might be a reason for its side effects. CPT is highly specific for TOP1 and the binding is of relatively low affinity and can be reversed after drug removal. These features make the action of CPT controllable [24], and in fact CPT is widely used in studies of replication-associated DNA damage response. There are a few CPT derivatives and non-CPT TOP1 inhibitors [4,8,24]. For example, CPT derivatives Diflomotecan and S39625 were designed to stabilize the E-ring. Irinotecan has the bis-piperidine side chain to increase its water solubility, but it also contributes to some side effects. Non-CPTs—such as indolocarbazoles, phenanthrolines (e.g., ARC-111) and indenoisoquinolines—refer to drugs that have no typical CPT E-ring structures but they can still specifically target TOP1 and bind irreversibly to TOP1cc. Some of the CPT derivatives (i.e., Gimatecan and Belotecan) and non-CPTs (i.e., NSC 725776 and NSC 724998) are presently tested in clinical trials [23].

Biomolecules 2015, 5                                                                                                                           1655

How does CPT trap TOP1cc? Analysis of the crystal structure and modeling suggest that CPT-TOP1-DNA forms a ternary complex to prevent the two DNA ends from religation [25–27]. Although it is still controversial on how CPT is intercalated into DNA, it seems that CPT traps TOP1cc with a thymine (T) at the -1 position and a guanine (G) at the +1 position on the scissile strand, and it is therefore sequence-specific [28]. Three amino acid residues of the TOP1 enzyme, R364, D533 and N722, combined with DNA bases, contribute to the stabilization of the ternary complex by forming hydrogen bonds and hydrophobic interactions. It is of note that several point mutations, including N722S, in Camptotheca acuminata TOP1 confer resistance to CPT [29]. Interestingly, the same amino acids also contribute to the inhibition of TOP1 by non-CPT drugs [24].

  1. Repair of TOP1 Poison-Induced DNA Lesions

As aforementioned, CPT-induced trapping of TOP1cc creates a single strand break with a free 5′-hydroxyl group, whereas the 3′-phosphate is connected to Y723 of TOP1 (3′-P-Y). At least two pathways contribute to the repair of DNA lesions created by TOP1 poison [30]. The tyrosyl-DNA-phosphodiesterase (TDP1) pathway starts with the ubiquitination and proteasome-mediated degradation of TOP1 in the CPT-TOP1-DNA complex to generate a 3′-P end linked to a short peptide [31]. TDP1 then cleaves the P-Y bond to release the 3′-P end; however, the 3′-P end cannot be directly ligated to the 5′-OH end because of the requirements of DNA ligases. The human polynucleotide kinase (PNKP) can process the DNA ends by functioning as both a 3′-phosphatase and a kinase to generate the required 3′-OH and 5′-P termini for direct ligation. The rest of the repair events can be best described by the single-strand break (SSB) repair pathway, which will be discussed below. Indeed, TDP1 and PNKP are tightly associated with the SSB repair machinery [32,33].

The endonuclease pathway requires multiple endonucleases to excise the DNA—usually at a few nucleotides away from the 3′-P-TOP1 end – on the scissile strand to release the DNA-TOP1 complex [30]. Initial studies were carried out to identify genes that functioned in CPT repair in the absence of TDP1 in yeast [34,35]. These studies led to the identification of RAD1-RAD10, SLX1-SLX4, MUS81-MMS4, MRE11-SAE2 as well as genes involved in recombination. The RAD1-RAD10 (human XPF/ERCC4-ERCC1) complex is a DNA structure-specific endonuclease that can act on 5′ overhang structures [36]. Interestingly, the cleavage site of XPF-ERCC1 is in the non-protruding DNA strand, about 3–4 nucleotides away from the 3′ end [36]. Therefore, trapped TOP1ccs can be removed by this endonuclease activity. Likewise, MUS81-MMS4 (human MUS81-EME1) can also cleave nicked duplex at the 5′ of the nick [37]. The SLX1-SLX4 endonuclease, although not tested on nicked duplexes, is able to process 3′ flap and other DNA structures [38,39]. In human cells, SLX4 also associates with XPF-ERCC1 and MUS81-EME1 endonucleases to process specific DNA intermediates [39,40]. Moreover, MRE11-RAD50 cleaves the 3′-P-Y bond and resects DNA to produce a 3′-OH end [41]. A direct role of SAE2 (human CtIP) in processing 3′-P-TOP1 is unknown, and its endonuclease activity appears to be limited to the 5′ flap or DNA “hairpin” structures [42,43]. Nonetheless, the endonuclease activity of CtIP is essential for processing CPT adducts [42]. In addition, like CtIP, the 5′ flap endonuclease RAD27 (human FEN1) seems to be unable to directly process 3′-P-TOP1 ends [44]. However, the gap endonuclease activity of FEN1 is important for processing stalled replication forks and CPT-induced adducts [45]. The role of FEN1 in SSB repair will be discussed further in the next section.

Biomolecules 2015, 5                                                                                                                           1656

During DNA replication, SSBs created by CPT are most likely converted to double-strand breaks (DSBs) by replication fork runoff. This conversion appears to be dependent on the proteolysis of TOP1 [46]. The repair of one-ended DSBs, as will be discussed in the next section, is largely dependent on homologous recombination (HR). However, low doses of CPT may also induce PARP1 and/or RAD51 dependent replication fork regression—generating no or few DSBs [47,48]. The regressed fork leads to the formation of a “chicken foot” DNA structure by newly synthesized strands [3,49,50]. The formation of regressed fork can be largely suppressed by ATR, EXO1, and DNA2 [51–53]. However, fork reversal can also be beneficial as it provides time for the repair of TOP1-induced DNA lesions by TDP1, thereby preventing DSB formation and the activation of error-prone non-homologous end-joining (NHEJ) [30].

  1. Pathways Involved in the Repair of CPT-Induced DNA Lesions

Normal cells use DNA damage response (DDR) pathways to maintain genomic stability [54]. As aforementioned, SSB and DSB repair mechanisms are the two major DDR pathways that repair TOP1-induced DNA lesions. Paradoxically, cancer cells exploit DDR pathways to accumulate necessary genomic alterations for promoting proliferation. Furthermore, altered DDR and apoptotic responses in cancer cells are the major obstacles to successful chemotherapy. Thus, the delineation of TOP1-related SSB and DSB repair mechanisms is of great importance for identifying drug targets that can selectively affect cancer cell survival.

3.1. Single-Strand Break (SSB) Repair

Trapping of TOP1cc results in a 3′-P-TOP1 end and a 5′-OH terminus. Because the two ends cannot be directly religated, the persisting SSB is likely to be detected by PARP1 in which activated PARP1 catalyzes the synthesis of poly(ADP-ribose) (PAR) chains for recruiting repair proteins [55]. This reaction can be rapidly reversed by PARG, which hydrolyzes the PAR chains. The PAR chains at the SSB sites are important for the recruitment of XRCC1 that functions as a loading dock for other SSB repair proteins including TDP1 and PNKP. TDP1 generates 3′-P and PNKP converts 3′-P to 3′-OH, and PNKP also converts 5′-OH to 5′-P, making ends compatible for religation with no base loss. The rejoining of the 3′-OH and 5′-P ends is mainly mediated by LIG3, in which XRCC1 mediates the recruitment of LIG3.

If the trapped TOP1cc intermediates are processed by endonucleases, the initial SSBs will be converted to 3′-OH and 5′-OH ends with a gap over a few nucleotides (in the case of XPF-ERCC1, the loss is in the range of 3–4 nt), leading to the activation of PARP1 and XRCC1 recruitment. Consequentially, Pol3 recruited by XRCC1 can catalyze the gap filling, and PCNA-Polö/E also plays a role in this process [55]. If the 5′-OH is not processed by PNKP, the 5′-flap resulted from gap filling is likely to be removed by FEN1, which explains why FEN1 deficiency also leads to an increased CPT sensitivity. The final ligation is catalyzed by LIG1 because of the presence of PCNA.

Biomolecules 2015, 5                                                                                                                           1657

3.2. Double-Strand Break (DSB) Repair

Successful DSB repair requires concerted actions of proteins involved in DNA damage signaling and repair [54]. To repair TOP1 poison-induced DNA lesions, ATR signaling is required due to the runoff of replication fork and the presence of long single-strand DNA (ssDNA) [56]. The full activation of ATR follows a “two-man” rule—the ssDNA-ATRIP-dependent recruitment of ATR kinase and the RAD17 clamp loader/9-1-1/TOPBP1 mediator loading at the ssDNA-dsDNA junction. ATR phosphorylates CHEK1 to harness cell cycle arrest. If one-ended DSB is formed, ATM will be activated through the action of the MRE11-RAD50-NBS1 (MRN) complex. ATM mainly phosphorylates CHEK2 to mediate cell cycle arrest. Both ATM and ATR are able to phosphorylate hundreds of proteins in response to DSB formation [57]. One remarkable substrate is the histone H2AX, which can be phosphorylated by both kinases to yield g-H2AX. It is conceived that the propagation of g-H2AX signaling along the chromatin facilitates MDC1 recruitment and BRCA1 signaling via the MDC1-RNF8-RNF168-RAP80 ubiquitin cascade—events that are essential for HR [58].

The repair of TOP1 poison-induced DNA lesions is in essence the repair of one-ended DSBs, which facilitates the restoration of replication forks to restart DNA replication. It is important to note that one-ended DSB repair occurs in the S phase and relies on HR rather than NHEJ [59]. The first step in HR is end resection to generate a 3′-overhang for homology searching. A TOP1 cleavage in the leading strand may require end resection by the MRN-CtIP-BRCA1 and BLM-EXO1-DNA2 complexes [60], whereas a cleavage in the lagging strand automatically forms a 3′-overhang. Rad51 then associates with the 3′-ssDNA to form a nucleofilament for strand invasion, which leads to the formation of a D-loop structure [61]. This process continues with DNA synthesis, branch migration and the resolution of Holliday junction structures to reconstitute a functional replication fork [62]. TOP1 poisons can also lead to the formation of two-ended DSB if two replication forks collide into each other at the site of SSB. The repair of this type of DSBs is not aimed for fork restoration and can be accomplished by the classical DSB repair mechanisms [61].

3.3. Genes Involved in CPT-Induced Damage Repair

A long list of genes, in which mutations confer sensitivity to CPT in yeast, chicken or mammalian cells, has been compiled [24,30,63]. With no surprise, many genes involved in SSB and DSB repair are on the list, such as PARP1, XRCC1, PNKP, TDP1 for SSB repair; MRN, ATM-CHK2, ATR-CHK1 for DSB signaling; BRCA1/2, XRCC2, XRCC3 for HR. Most recently, the hMSH5-FANCJ complex has also been implicated to play a role in CPT-induced DNA damage response and repair [64]. Mutations in the binding partners of these repair factors are also likely to sensitize cells to CPT treatment. For example, depletion of the MRN-binding partner hnRNPUL increases the sensitivity to CPT [65]; and deficiencies in ZRANB3 and SPIDR, binding partners of PCNA and RAD51, cause CPT hypersensitivity in cancer cells [66–68]. In addition, the two DNA helicases BLM and WRN have also been implicated in the repair of CPT-induced DNA lesions [69,70]. Early studies revealed that chicken BLM knockout cells and human BLM-deficient fibroblasts showed increased sensitivity to CPT [71,72]. On the contrary, mouse BLM knockout embryonic stem cells showed mild resistance to

Biomolecules 2015, 5                                                                                                                           1658

CPT [73]. This discrepancy is likely attributable to the complexity of CPT-induced DNA lesion repair as well as different treatment conditions and experimental systems.

Interstrand crosslinks (ICLs) resemble CPT-induced lesions in that they block both replication and transcription [74]. They may induce replication fork reversal and fork collapse, which require DNA incision for lesion processing and HR for repair. ICL repair is accomplished by the coordinated actions of 17 Fanconi anemia (FA) genes whose mutations contribute to FA in patients [75]. Depletion of FANCP/SLX4 or FANCQ/XPF causes cellular sensitivity to CPT because they form an endonuclease complex involved in the repair of trapped TOP1cc [38]. Likewise, depletion of FANCS/BRCA1, FANCD1/BRCA2, FANCN/PALB2 or FANCO/RAD51C sensitizes cells to CPT because of their involvement in HR [76]. Accordingly, depletion of the FA core complex except FANCM—involved in fork reversal—is not expected to increase CPT sensitivity because they are unable to recognize the trapped TOP1cc [76]. However, the roles of FANCI, D2, J and FAN1 in the process are elusive due to conflicting reports presumably reflecting different experimental systems [76–78]. For example, in a multicolor competition assay, loss of FANCI or FAN1 rendered cells sensitive to CPT treatment [77]. However, this observation could not be recapitulated in studies performed with FANCI-deficient lymphoblasts and FAN1-depleted HEK293 cells [76,79], indicating that the involvement of these two genes in CTP sensitivity might be cell type specific.

It is interesting to note that the MMS22L-TONSL complex plays a prominent role in mediating CPT sensitivity [80–83]. Depletion of this complex impairs RAD51 foci formation and triggers G2/M arrest, indicating that the MMS22L-TONSL complex participates in HR repair. Furthermore, this complex associates with MCM, FACT, ASF1 and histones. FACT and ASF1 are histone chaperones that function in H2A/H2B and H3/H4 chromatin assembly and disassembly, respectively [84]. They recycle parental histones from old DNA strands unwound by MCM and incorporate them into newly synthesized DNA strands. FACT and ASF1 also function in checkpoint signaling; therefore the involvement of MMS22L-TONSL in CPT response implies the existence of a close association between HR, DNA damage signaling and replication restart.

  1. TOP1 Inhibition in Cancer Treatment

The understanding of the function of TOP1 and the cellular effects of TOP1 inhibition has been a stepping-stone for the development of effective CPT derivatives in cancer therapy. Since TOP1 functions in normal and cancer cells, the use of low doses of TOP1 inhibitors are actively sought to treat cancers that heavily rely on the function of TOP1 for survival (e.g., highly malignant, rapid-dividing tumor cells). In fact, the FDA-approved CPT derivatives topotecan and irinotecan are currently used to treat ovarian and colorectal cancers, respectively [24].

Furthermore, the promising results from a Phase I trial have warranted further evaluation of the CPT derivative Diflomotecan in Phase II trials [85]. Other derivatives like Gimatecan, Lurtotecan and Exatecan are also being tested in clinical trials (Table 1). The non-CPT indolocarbazole BMS-250749 showed great anti-tumor activity against preclinical xenograft models [86], but no further evaluation beyond Phase I trials is presently available (Table 2). Another indolocarbazole compound Edotecarin has shown promising anti-tumor activity in xenograft models and it is now advanced to Phase II studies of patients with advanced solid tumors [87]. By contrast, Phenanthroline ARC-111 (topovale)

Biomolecules 2015, 5                                                                                                                             1659

was potently against human tumor xenografts and displayed anti-cancer activity in colon and Wilms’ tumors [88]; however, no result from Phase I clinical trials is available owing to profound bone marrow toxicity [89]. To date, indenoisoquinolines are the most promising non-CPT inhibitors in clinical trials. LMP400 (NSC 743400, indotecan) and LMP776 (NSC 725776, indimitecan) show significant anti-tumor activities in animal models and both are being evaluated in Phase I clinical trials for relapsed solid tumors and lymphomas [8,90].

Table 1. CPT derivatives in clinical trials [91].

Name                            Structure                     Clinical Trial            Malignancy        Reference

Biomolecules 2015, 5                                                                                                                           1660

Given the observation that CPT-mediated TOP1 inhibition provokes DNA repair activities, a synergistic effect is then anticipated on cancer cells by inhibition of TOP1 and downregulation of DNA repair activities. The rationale for this approach is to accelerate the accumulation of DNA breaks and trigger cellular apoptosis, probably through mitotic catastrophe [92]. Which DNA repair pathways can we exploit? Currently, the major interests are in SSB and DSB repair mechanisms. Indeed, PARP inhibitors can enhance the cytotoxicity of TOP1 inhibitors in cancer cell lines as well as in mouse models [93–96]. Phase I studies of combination therapy using PARP inhibitors veliparib or olaparib (FDA-approved) together with topotecan were carried out in patients with advanced solid tumors but showed some dose-dependent side effects [97,98]. TDP1 can be another potential target because it functions directly downstream of PARP1 in the repair of TOP1 poison-induced DNA lesions [99]. TDP1 inhibitors sensitize cells to CPT treatment in vitro [100,101], however in vivo evaluation is presently unavailable due to unsuitable properties of the compounds [102].

Table 2. Non-CPT derivatives in preclinical and clinical trials [91].

Name                       Structure               Clinical Trial            Malignancy             Reference

Indolocarbazoles
(Edotecarin,
BMS-250749)
Phase II

(Edotecarin, Pfizer)

Stomach, breast
neoplasms
Preclinical
(BMS-250749)
Anti-tumor activity
in preclinical
xenograft models
[86,87,103]
Phenanthridines
(ARC-111/topovale)
Anti-tumor activity

Preclinical                    in preclinical            [88,89,103]
xenograft models

Indenoisoquinolines
(LMP400, LMP776)
Phase I                              Lymphomas             [8,90,103]

DSB repair can be targeted by either inhibition of DSB signaling or inhibition of HR. ATM and ATR inhibitors can largely increase the sensitivity to CPT in cancer cells [104,105]. This can be explained by the fact that abrogation of the cell cycle arrest will allow cells with unreplicated or unrepaired chromosomes to enter mitosis thereby triggering mitotic catastrophe and cell death. Similarly, CHEK1 and CHEK2 inhibitors are tested in Phase I studies in combination with irinotecan [106,107]. Inhibitors that can directly block HR proteins are very limited [108]. This is partially attributed to the fact that HR genes are often mutated in cancer cells, thus diminishing the enthusiasm for developing HR inhibitors. One diterpenoid compound, however, was found to be able to inhibit the function of BRCA1 and render cytotoxicity in human prostate cancer cells [109]. Several RAD51 inhibitors have also been

Biomolecules 2015, 5                                                                                                                           1661

identified but have not been tested in cell lines [110]. Inhibition of BRCA1 and RAD51 can be also achieved indirectly by harnessing corresponding kinases [106]. Clearly, defective hMRE11 sensitizes colon cancer cells to CPT treatment [111]. Although MRE11-deficeint tumor xenografts failed to display significant growth inhibition by irinotecan alone, combining thymidine with irinotecan caused a dramatic growth delay [112].

TOP1 inhibitors might be also useful for treating cancers with BRCA1/2 mutations. The successful use of PARP inhibitors in treating BRCA1/2-deficient tumors has ignited a broad interest in searching for synthetic lethality among DNA damage response and repair genes [113,114]. In the PARP-BRCA1/2 example, the accumulation of SSBs by PARP inhibition would lead to the formation of DSBs during replication. In HR-deficient cells, DSBs can only be repaired by illegitimate (toxic) NHEJ—joining one-ended DSBs from different locations—leading to cell death [115,116]. However, resistance to PARP inhibitors can arise in BRCA1-deficient tumors during treatment from either genetic reversion of BRCA1 mutations or the loss of NHEJ [117–122]. Therefore, it would be beneficial to explore the possibility of developing a similar synthetic lethal strategy to use TOP1 inhibitors in the treatment of BRCA1/2-deficient tumors.

Figure 2. An overview of the effects of TOP1 inhibition is provided. Inhibitors and key DNA repair factors are highlighted.

Biomolecules 2015, 5                                                                                                                         1662

  1. Conclusions

Trapping of TOP1 by inhibitors generates SSBs and DSBs that are repaired by their corresponding repair pathways (Figure 2). Therefore, developing effective TOP1 inhibitors not only provides powerful tools to study DNA replication and repair but also establishes a foundation to devise new synthetic lethal strategies for efficient cancer treatments. The accumulation of DNA strand breaks (SSBs and DSBs) by TOP1 inhibition in HR-deficient tumor cells is expected to enhance cytotoxicity. However, increased DNA repair activities in cancer cells can make TOP1 inhibitors less effective, so silencing of repair pathways in conjunction with the use of TOP1 inhibitors offers an attractive new means for cancer control. Since each tumor is unique, it would be advantageous to identify the individualities of DNA repair pathways or biomarkers reflecting the changes of DNA repair activities in tumor cells [92,123]. This will make it possible to achieve better and predictable prognosis through tailored therapeutic regimens. Given that TOP1 is essential for transcription and DNA replication, future design of novel TOP1 inhibitors and combinational therapy strategies should aim to increase therapeutic efficacy of the inhibitors, thus reducing side effects.

Acknowledgments

The work in the Her laboratory is supported by the NIH grant GM084353.

Author Contributions

Yang Xu and Chengtao Her wrote and revised the article.

Conflicts of Interest

The authors declare that they have no conflicts of interest with the contents of this article.

Please see the following file for the referencesReferences for top paper

From a 2015 Clinical Cancer Research paper:

Phase 1 clinical pharmacology study of F14512, a new polyamine-vectorized anti-cancer drug, in naturally occurring canine lymphoma

Dominique Tierny1, Francois Serres1, Zacharie Segaoula1, Ingrid Bemelmans1, Emmanuel Bouchaert1,

Aurelie Petain2, Viviane Brel3, Stephane Couffin4, Thierry Marchal5, Laurent Nguyen6, Xavier Thuru7,

Pierre Ferre2, Nicolas Guilbaud8, and Bruno Gomes9,*

Abstract

Purpose: F14512 is a new topoisomerase II inhibitor containing a spermine moiety that facilitates selective uptake by tumor cells and increases topoisomerase II poisoning. F14512 is currently in Phase I/II clinical trial in patients with acute myeloid leukemia. The aim of this study was to investigate F14512 potential in a new clinical indication. Because of the many similarities between human and dog lymphomas, we sought to determine the tolerance, efficacy, PK/PD relationship of F14512 in this indication, and potential biomarkers that could be translated into human trials. Experimental design: Twenty-three dogs with stage III-IV naturally occurring lymphomas were enrolled in the Phase 1 dose-escalation trial which consisted of three cycles of F14512 intravenous injections. Endpoints included safety and therapeutic efficacy. Serial blood samples and tumor biopsies were obtained for PK/PD and biomarker studies. Results: Five dose levels were evaluated in order to determine the recommended dose. F14512 was well tolerated, with the expected dose-dependent hematological toxicity. F14512 induced an early decrease of tumoral lymph node cells, and a high response rate of 91% (21/23) with 10 complete responses, 11 partial responses, 1 stable disease and 1 progressive disease. Phosphorylation of histone H2AX was studied as a potential pharmacodynamic biomarker of F14512. Conclusions: This trial demonstrated that F14512 can be safely administered to dogs with lymphoma resulting in strong therapeutic efficacy. Additional evaluation of F14512 is needed to compare its efficacy with standards of care in dogs, and to translate biomarker and efficacy findings into clinical trials in humans.

AND From ASCO 2015 Annual Meeting

Survival impact of switching to different topoisomerase I or II inhibitors-based regimens (topo-I or topo-II) in extensive-disease small cell lung cancer (ED-SCLC): supplemental analysis from JCOG0509.

Abstract:

Background: The J0509 (phase III study for chemotherapy-naive ED-SCLC) demonstrated amrubicin plus cisplatin (AP) was inferior to irinotecan plus cisplatin (IP). However, median overall survival (OS) of both AP and IP (15 and 17 mo) was more favorable than those of previous trials (9-12 mo), probably because switching to different topo-I or topo-II in the second-line therapy, especially the use of topo-II in IP arm, was frequent. This analysis aimed to investigate whether observed survival benefit of IP arm can be explained by the treatment switching, and how post-protocol chemotherapy affected the result of J0509. Methods: Two analysis sets from J0509 were used: all randomized 283 pts and 250 pts who received post-protocol chemotherapy. One pt without initiation date of second-line therapy was excluded. A rank-preserving structural failure time (RPSFT) model was used to estimate “causal survival benefit” that would have been observed if all pts had been followed with the same type of regimen as randomized throughout the follow-up period. Additionally, to assess the survival impact of second-line use of topo-II, OS after initiating second-line therapy (OS2) was analyzed by multivariate Cox models. Results: %treatment switching in IP arm and AP arm was 65.2% (92/141) and 43.7% (62/142). By RPSFT model, estimated OS excluding the effect of the treatment switching was 2.7-fold longer in IP (topo-I) arm than AP (topo-II) arm. This causal survival benefit was stronger than the original report of J0509 (nearly 1.4-fold extension by Cox model), indicating that re-challenging topo-I in IP arm appeared beneficial. The multivariate Cox analysis for OS2 (n = 250) revealed second-line use of topo-II was detrimental (hazard ratio, 1.5; 95%CI, 1.1-2.1). Among sensitive relapsed pts in IP arm, OS2 was favorable in the following order: irinotecan-based regimen > the other topo-I > topo-II. Conclusions: IP remains the standard therapy. Re-challenging topo-I, especially irinotecan-based topo-I, seemed beneficial for IP-sensitive pts. This result should be confirmed in further investigations with large sample size. Clinical trial information: 000000720.

 

 

 

 

Below is actively recruiting clinical trials evaluating topoisomerase inhibitors. Shown are only a few trials for a complete list from CancerTrials.gov please see this link:

https://clinicaltrials.gov/ct2/results?term=topoisomerase+inhibitor&recr=Open#wrapper

A service of the U.S. National Institutes of Health

897 studies found for:    topoisomerase inhibitor | Open Studies

Include only open studies Exclude studies with Unknown status

Status Study
Recruiting A Study of Standard Treatment +/- Enoxaparin in Small Cell Lung Cancer

Condition: Small Cell Lung Cancer
Interventions: Drug: cisplatinum or carboplatin and e.g.etoposide.;   Drug: cisplatinum or carboplatin and e.g.etoposide+enoxaparin
Recruiting A Phase I Study of Indenoisoquinolines LMP400 and LMP776 in Adults With Relapsed Solid Tumors and Lymphomas

Conditions: Neoplasms;   Lymphoma
Interventions: Drug: LMP 400;   Drug: LMP 776
Recruiting A Dose-Ranging Study Evaluating the Efficacy, Safety, and Tolerability of GSK2140944 in the Treatment of Uncomplicated Urogenital Gonorrhea Caused by Neisseria Gonorrhoeae

Condition: Gonorrhea
Intervention: Drug: GSK2140944
Recruiting Selinexor in Combination With Irinotecan in Adenocarcinoma of Stomach and Distal Esophagus

Conditions: Esophageal Cancer;   Gastric Cancer
Interventions: Drug: Selinexor;   Drug: Irinotecan
Recruiting Multimodal Molecular Targeted Therapy to Treat Relapsed or Refractory High-risk Neuroblastoma

Condition: Neuroblastoma Recurrent
Interventions: Drug: Dasatinib;   Drug: Rapamycin;   Drug: Irinotecan;   Drug: Temozolomide
Unknown † Study of the Farnesyl Transferase Inhibitor, R115777, in Combination With Topotecan (NYU 99-32)

Condition: Cancer
Interventions: Drug: R115777 (farnesyl transferase inhibitor);   Drug: Topotecan
Recruiting Pegylated Irinotecan NKTR 102 in Treating Patients With Relapsed Small Cell Lung Cancer

Condition: Recurrent Small Cell Lung Carcinoma
Interventions: Other: Laboratory Biomarker Analysis;   Drug: Pegylated Irinotecan;   Other: Pharmacological Study
Recruiting Selinexor and Chemotherapy in Treating Patients With Relapsed or Refractory Acute Myeloid Leukemia

Conditions: Adult Acute Myeloid Leukemia With 11q23 (MLL) Abnormalities;   Adult Acute Myeloid Leukemia With Del(5q);   Adult Acute Myeloid Leukemia With Inv(16)(p13;q22);   Adult Acute Myeloid Leukemia With t(15;17)(q22;q12);   Adult Acute Myeloid Leukemia With t(16;16)(p13;q22);   Adult Acute Myeloid Leukemia With t(8;21)(q22;q22);   Recurrent Adult Acute Myeloid Leukemia;   Secondary Acute Myeloid Leukemia
Interventions: Drug: mitoxantrone hydrochloride;   Drug: etoposide;   Drug: cytarabine;   Drug: selinexor;   Other: laboratory biomarker analysis;   Other: pharmacological study
Recruiting WEE1 Inhibitor MK-1775 and Irinotecan Hydrochloride in Treating Younger Patients With Relapsed or Refractory Solid Tumors

Conditions: Childhood Solid Neoplasm;   Recurrent Childhood Medulloblastoma;   Recurrent Childhood Supratentorial Primitive Neuroectodermal Tumor;   Recurrent Neuroblastoma
Interventions: Drug: Irinotecan Hydrochloride;   Other: Laboratory Biomarker Analysis;   Other: Pharmacological Study;   Drug: WEE1 Inhibitor AZD1775
Recruiting PARP Inhibitor BMN-673 and Temozolomide or Irinotecan Hydrochloride in Treating Patients With Locally Advanced or Metastatic Solid Tumors

Conditions: Metastatic Cancer;   Unspecified Adult Solid Tumor
Interventions: Drug: PARP inhibitor BMN-673;   Drug: temozolomide;   Drug: irinotecan hydrochloride;   Other: pharmacological study;   Other: laboratory biomarker analysis
Recruiting A Phase II Multicenter, Randomized, Placebo Controlled, Double Blinded Clinical Study of KD018 as a Modulator of Irinotecan Chemotherapy in Patients With Metastatic Colorectal Cancer

Condition: Colorectal Neoplasms
Interventions: Drug: KD018;   Drug: Irinotecan;   Drug: Placebo
Recruiting The Efficacy of the 7 Days Tailored Therapy as 2nd Rescue Therapy for Eradication of H. Pylori Infection

Condition: Helicobacter Infection
Interventions: Procedure: H. pylori culture and antimicrobial susceptibility testing;   Drug: 14 days empirical bismuth quadruple therapy (Proton pump inhibitor);   Drug: Metronidazole;   Drug: Tetracycline;   Drug: tripotassium dicitrate bismuthate;   Drug: 7 days tailored therapy Proton Pump Inhibitor;   Drug: Moxifloxacin;   Drug: Amoxicillin
Recruiting G1T28 (CDK 4/6 Inhibitor) in Combination With Etoposide and Carboplatin in Extensive Stage Small Cell Lung Cancer (SCLC)

Condition: Small Cell Lung Cancer
Interventions: Drug: G1T28 + carboplatin/ etoposide;   Drug: Placebo + carboplatin/ etoposide
Recruiting Trial of Topotecan With VX-970, an ATR Kinase Inhibitor, in Small Cell Lung Cancer

Conditions: Carcinoma, Non-Small -Cell Lung;   Ovarian Neoplasms;   Small Cell Lung Carcinoma;   Uterine Cervical Neoplasms;   Carcinoma, Neuroendocrine
Interventions: Drug: Topotecan;   Drug: VX-970
Recruiting Prospective Analysis of UGT1A1 Promoter Polymorphism for Irinotecan Dose Escalation in Metastatic Colorectal Cancer Patients Treated With Bevacizumab Combined With FOLFIRI as the First-line Setting

Condition: Metastatic Colorectal Cancer
Interventions: Genetic: UGT1A1 genotyping (6,6);   Genetic: UGTIA1 genotyping (6,7);   Genetic: UGTIA1 genotyping (7,7);   Genetic: UGT1A1 non-genotyping;   Drug: bevacizumab (Avastin);   Drug: irinotecan;   Drug: Leucovorin;   Drug: 5-FU
Recruiting A Study of the Bruton’s Tyrosine Kinase Inhibitor, PCI-32765 (Ibrutinib), in Combination With Rituximab, Cyclophosphamide, Doxorubicin, Vincristine, and Prednisone in Patients With Newly Diagnosed Non-Germinal Center B-Cell Subtype of Diffuse Large B-Cell Lymphoma

Condition: Lymphoma
Interventions: Drug: Ibrutinib;   Drug: Placebo;   Drug: Rituximab;   Drug: Cyclophosphamide;   Drug: Doxorubicin;   Drug: Vincristine;   Drug: Prednisone (or equivalent)
Recruiting Irinotecan Combination Chemotherapy for Refractory or Relapsed Brain Tumor in Children and Adolescents

Condition: Brain Tumor
Intervention: Drug: Irinotecan combination chemotherapy
Recruiting A Study To Evaluate PF-04449913 With Chemotherapy In Patients With Acute Myeloid Leukemia or Myelodysplastic Syndrome

Condition: Acute Myeloid Leukemia
Interventions: Drug: PF-04449913;   Drug: Low dose ARA-C (LDAC);   Drug: Decitabine;   Drug: Daunorubicin;   Drug: Cytarabine
Recruiting Veliparib and Pegylated Liposomal Doxorubicin Hydrochloride in Treating Patients With Recurrent Ovarian Cancer, Fallopian Tube Cancer, or Primary Peritoneal Cancer or Metastatic Breast Cancer

Conditions: Estrogen Receptor Negative;   HER2/Neu Negative;   Male Breast Carcinoma;   Progesterone Receptor Negative;   Recurrent Breast Carcinoma;   Recurrent Fallopian Tube Carcinoma;   Recurrent Ovarian Carcinoma;   Recurrent Primary Peritoneal Carcinoma;   Stage IV Breast Cancer;   Triple-Negative Breast Carcinoma
Interventions: Other: Laboratory Biomarker Analysis;   Drug: Pegylated Liposomal Doxorubicin Hydrochloride;   Other: Pharmacological Study;   Drug: Veliparib
Recruiting A Study To Evaluate Ara-C and Idarubicin in Combination With the Selective Inhibitor Of Nuclear Export (SINE) Selinexor (KPT-330) in Patients With Relapsed Or Refractory AML

Condition: Acute Myeloid Leukemia (Relapsed/Refractory)
Interventions: Drug: Selinexor;   Drug: Idarubcin;   Drug: Cytarabine

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Targeted gene modification

Larry H Bernstein, MD, FCAP, Curator

Leaders in Pharmaceutical Intelligence

Article ID #183: Targeted gene modification. Published on 9/8/2015

WordCloud Image Produced by Adam Tubman

Series E. 2: 7.8

Mario R. Capecchi won a 2007 Nobel Prize for his work on targeted gene modification.

Born in Italy in 1937, scientist Mario R. Capecchi emigrated to the United States after World War II and later became a geneticist and professor. His groundbreaking work on targeted gene modification won him a Nobel Prize in 2007.

The Making of a Scientist II

In 1996, as a Kyoto Prize laureate, I was asked to write an autobiographical sketch of my early upbringing. Through this exercise, shared by all of the laureates, the hope was to uncover potential influences or experiences that may have been key to fostering the creative spirit within us. In my own case, what I saw was that, despite the complete absence of an early nurturing environment, the intrinsic drive to make a difference in our world is not easily quenched and that given an opportunity, early handicaps can be overcome and dreams achieved. This was intended as a message of hope for those who have struggled early in their lives. As I have previously noted, our ability to identify the genetic and environmental factors that contribute to talents such as creativity are too complex for us to currently predict. In the absence of such wisdom our only recourse is to provide all children with the opportunities to pursue their passions and dreams. Our understanding of human development is too meager to allow us to predict the next Beethoven, Modigliani, or Martin Luther King.

The content of the autobiographical sketch was based on my own memories, on conversations with my aunt and uncle, who raised me once I arrived in the United States, and on conversations with my mother. Because of the added exposure resulting from the winning of the Nobel Prize, I have received letters from people who knew me in Italy during those formative early years. In addition members of the press have taken an interest in my story and have sought independent corroboration. An amazing and wonderful surprise is that they have discovered a half-sister of whom I was completely unaware. She is two years younger than I, and was given up for adoption before she was one year old. Most recently I had the opportunity to meet my half-sister. She was a very nice person, as a sister should be. I am grateful for all of these new sources of information and revelation. Where appropriate, I will weave the new information into this retelling of my story.

Autobiographical Sketch
I was born in Verona, Italy on October 6, 1937. Fascism, Nazism, and Communism were raging through the country. My mother, Lucy Ramberg, was a poet; my father, Luciano Capecchi, an officer in the Italian Air Force. This was a time of extremes, turmoil and juxtapositions of opposites. They had a passionate love affair, and my mother wisely chose not to marry him. This took a great deal of courage on her part. It embittered my father.

Capecchi's mother
Figure 1. A photograph of my mother, Lucy Ramberg, at age 19.

I have only a few pictures of my mother. She was a beautiful woman with a passion for languages and a flair for the dramatic (see Figure 1). This picture was taken when she was 19. She grew up, with her two brothers, in a villa in Florence, Italy. There were magnificent gardens, a nanny, gardeners, cooks, house cleaners, and private tutors for languages, literature, history, and the sciences. She was fluent in half a dozen languages. Her father, Walter Ramberg, was an archeologist specializing in Greek antiquities, born and trained in Germany. Her mother was a painter born and raised in Oregon, USA. In her late teens, my grandmother, Lucy Dodd, packed up her steamer trunks and sailed with her mother from Oregon to Florence, Italy, where they settled. My grandmother was determined to become a painter. This occurred near the end of the 19th century, a time when young women were not expected to set off on their own with strong ambitions of developing their own careers.

Painting
Figure 2. A painting done by my grandmother, Lucy Dodd Ramberg, of her three children, left to right, Edward, Lucy, and Walter. It was painted at their villa in Florence, Italy in 1913.
Painting
Figure 3. A painting by Lucy Dodd Ramberg of my mother, Lucy, and uncle Edward having tea at the villa in Florence, Italy (1913).

My grandmother became a very gifted painter. Let me share with you a couple of her paintings, which also illustrate the young lives of her children. These paintings are very large, approximately seven feet by five feet. The first painting (Figure 2) is the center panel of a triptych depicting my mother and her two brothers Walter and Edward (both of whom became physicists) surrounded by olive trees at the villa in Florence. The influence of the French impressionist painters is evident. The second painting (Figure 3) is of my mother, age 8, and her younger brother Edward, age 6, having a tea party, again at the villa in Florence. Their father, the German archeologist, was killed as a young man in World War I. My grandmother finished raising her three children on her own by painting, mostly portraits, and by converting the family villa into a finishing school for young women, primarily from the United States.

Chalet in Italy
Figure 4. A photograph of the chalet where my mother and I lived in Wolfgrübben just north of Bolzano, Italy. In the foreground is my mother, Lucy.

My mother’s love and passion was poetry. She published in German. She received her university training at the Sorbonne in Paris and was a lecturer at that university in literature and languages. At that time, she joined with a group of poets, known as the Bohemians, who were prominent for their open opposition to Fascism and Nazism. In 1937, my mother moved to the Tyrol, the Italian Alps. Figure 4 shows the chalet north of Bolzano, in Wolfgrübben, with my mother in the foreground. We lived in this chalet until I was 3½ years old. In the spring of 1941, German officers came to our chalet and arrested my mother. This is one of my earliest memories. My mother had taught me to speak both Italian and German, and I was quite aware of what was happening. I sensed that I would not see my mother again for many years, if ever. She was incarcerated as a political prisoner in Germany.

I have believed that her place of incarceration was Dachau. This was based on conversations with my uncle Edward, my mother’s younger brother. During World War II, my uncle lived in the United States. Throughout these war years, he made many attempts to locate where my mother was being held. The most reliable information indicated that the location was near Munich. Dachau is located near Munich and was built to hold political prisoners. My mother survived her captivity, but after the war, despite my prodding, she refused to talk about her war experiences.

Reporters from the Associated Press (AP) have found records that my mother was indeed a prisoner during the war in Germany. In fact, they have found records of German interest in my mother’s political activities preceding 1939. In that year, they had her arrested by the Italian authorities and jailed in Perugia and subsequently released. However, the AP reporters did not find records indicating that my mother was incarcerated in Dachau. Though Germans were noted for their meticulous record keeping, it would be difficult now to evaluate the accuracy of the existing war records, particularly for cases where data is missing. It is clear, however, that exactly where in Germany my mother was held has not yet been determined. Regardless of which prison camp was involved, her experiences were undoubtedly more horrific than mine. She had aged beyond recognition during those five years of internment. Following her release, though she lived until she was 82 years old, she never psychologically recovered from her wartime experiences.

My mother had anticipated her arrest by German authorities. Prior to their arrival, she had sold most of her possessions and gave the proceeds to an Italian peasant family in the Tyrol so that they could take care of me. I lived on their farm for one year. It was a very simple life. They grew their own wheat, harvested it, and took it to the miller to be ground. From the flour they made bread which they took to the baker to be baked. During this time, I spent most of my time with the women of the farm. In the late fall, the grapes were harvested by hand and put into enormous wooden vats. The children, including me, stripped, jumped into the vats and mashed the grapes with our feet. We became squealing masses of purple energy. I still remember the pungent odor and taste of the fresh grapes. Most recently, members of the Dolomiten Press have located this farm and I had the opportunity to visit it. It is still owned by the same family that occupied it when I was there. The old farm house has been taken down and a new one erected. However, the pictures of the old farm house, as well as the surrounding land are remarkably consistent with my memories.

World War II was now fully under way. The American and British forces had landed in Southern Italy and were proceeding northward. Bombings of northern Italian cities were a daily occurrence. As constant reminders of the war, curfews and blackouts were in effect every night; no lights were permitted. In the night we could hear the drone of presumed American and British reconnaissance planes which we nicknamed “Pepe.” One hot afternoon, American planes swooped down from the sky and began machine gunning the peasants in the fields. A senseless exercise. A bullet grazed my leg, fortunately not breaking any bones. I still have the scar, which, many years later my daughter proudly had me display to her third-grade class in Utah.

For reasons that have never been clear to me, my mother’s money ran out after one year and, at age 4½, I set off on my own. I headed south, sometimes living in the streets, sometimes joining gangs of other homeless children, sometimes living in orphanages, and most of the time being hungry. My recollections of those four years are vivid but not continuous, rather like a series of snapshots. Some of them are brutal beyond description, others more palatable.

There are records in the archives of Ritten, a region of the Southern Alps of Italy, that I left Bozen to go to Reggio Emilia on July 18, 1942. AP reporters exploring this history have suggested that my father came to the farm, picked me up, and that we went together to Reggio Emilia where he was living. I have no memory of his coming to the farm, nor of having travelled with him to Reggio Emilia. I have recently received a letter from a man who remembers me as the youngest member of his street gang operating in Bolzano, which is on the way to Reggio Emilia.

I did end up in Reggio Emilia, which is approximately 160 miles south of Bolzano. I knew that my father lived in Reggio Emilia and I have previously noted that I had lived with him a couple of times from 1942-1946, for a total period of approximately three weeks. The question has been raised why I didn’t live with him for a much longer period. The reason was that he was extremely abusive. Amidst all of the horrors of war, perhaps the most difficult for me to accept as a child was having a father who was brutal to me.

Recently, I have also received a very nice letter from the priest in Reggio Emilia who ran the orphanage in which I was eventually placed. I remember him because he was one of the very few men I encountered in Reggio Emilia who showed compassion for the children and took an interest in me. I am surprised, but pleased, that after all these years he still remembers me among the thousands of children he was responsible for over the years. Further, I believe I was at that orphanage for only several months, the first time in the fall of 1945, after which I ran away, followed by a second period, in the same orphanage, in the spring of 1946. But his memory is genuine, for he recounts incidents consistent with my memories that could only have been known through our common experience.

In the spring of 1945, Munich was liberated by the American troops. My mother had survived her captivity and set out to find me. In October 1946, she succeeded. As an example of her flair for the dramatic, she found me on my ninth birthday, and I am sure that this was by design. I did not recognize her. In five years she had aged a lifetime. I was in a hospital when she found me. All of the children in this hospital were there for the same reasons: malnutrition, typhoid, or both. The prospects for most of those children ever leaving that hospital were slim because they had no nourishing food. Our daily diet consisted of a bowl of chicory coffee and a small crust of old bread. I had been in that hospital in Reggio Emilia for what seemed like a year. Scores of beds lined the rooms and corridors of the hospital, one bed touching the next. There were no sheets or blankets. It was easier to clean without them. Our symptoms were monotonously the same. In the morning we awoke fairly lucid. The nurse, Sister Maria, would take our temperature. She promised me that if I could go through one day without a high fever, I could leave the hospital. She knew that without any clothes I was not likely to run away. By late morning, the high, burning fever would return and we would pass into oblivion. Consistent with the diagnosis of typhoid, many years later I received a typhoid/paratyphoid shot, went into shock, and passed out.

Edward Ramberg
Figure 5. A photograph of my uncle Edward Ramberg working in his laboratory at RCA Princeton, New Jersey.

The same day that my mother arrived at the hospital, she bought me a full set of new clothes, a Tyrolean outfit complete with a small cap with a feather in it. I still have the hat. We went to Rome to process papers, where I had my first bath in six years, and then on to Naples. My mother’s younger brother, Edward, had sent her money to buy two boat tickets to America. I was expecting to see roads paved with gold in America. As it turned out, I found much more: opportunities.

On arriving in America, my mother and I lived with my uncle and aunt, Edward and Sarah Ramberg. Edward, my mother’s younger brother was a brilliant physicist. He was a Ph.D. student in quantum mechanics with Arnold Sommerfeld and translated one of Sommerfeld’s major texts into English. Among Edward’s many contributions was his discovery of how to focus electrons, knowledge which he used in helping to build the first electron microscope at RCA. Edward’s books on electron optics have been published in many languages. During my visit to Japan to celebrate the Kyoto Prize, several Japanese physicists approached me to express how grateful they were for my uncle’s texts from which they learned electron optics. Another achievement, of which he was less proud was being a principal contributor to the development of both black and white and color television. While I grew up in his home, television was not allowed. Figure 5 shows a photograph of my uncle working in his laboratory.

My aunt and uncle were Quakers and they did not support violence as solutions to political problems anywhere in the world. During World War II, my uncle did alternative service rather than bear arms. He worked in a mental institution in New Hampshire, cleared swamps in the south, and was a guinea pig for the development of vaccines against tropical diseases. After the war he settled in a commune in Pennsylvania, called Bryn Gweled, which he helped found. People of all races and religious affiliations were welcomed in this community. It was a marvelous place for children: it contained thick woods for exploration and had communal activities of all kinds – painting, dance, theater, sports, electronics, and many sessions devoted to the discussion of the major religious philosophies of the world. Every week there were communal work parties, putting in roads, phone lines, and electrical lines, building a community center and so on.

The contrast between living primarily alone in the streets of Italy and living in an intensely cooperative and supportive community in Pennsylvania was enormous. Time was needed for healing and for erasing the images of war from my mind. I remember that for many years after coming to the United States I would go to sleep tossing and turning with such force that by morning the sheets were torn and the bed frame broken. This activity disturbed my aunt and uncle to the extent that Sarah would take me from one child psychologist or psychiatrist, to another. These professionals were not very helpful, but the support of the community was. The nightly activity eventually subsided. There may be lessons to be learned from such experiences for the treatment of the children from Darfur, the Congo, and now Kenya.

Sarah and Edward took on the challenge of converting me into a productive human being. This, I am sure, was a very formidable task. I had received little or no formal education or training for living in a social environment. Quakers do not believe in frills, but rather in a life of service. My aunt and uncle taught me by example. I was given few material goods, but every opportunity to develop my mind and soul. What I made of myself would be entirely up to me. The day after I arrived in America, I went to school. I started in the third grade in the Southampton public school system. Sarah also took on the task of teaching me to read, starting from the very beginning.

The first task was to learn English. I had a marvelous third grade teacher. She was patient and encouraging. The class was studying Holland, so I started participation in class functions by painting a huge mural on butcher block paper with tulips, windmills, children ice skating, children in Dutch costumes, and ships. It was a collage of activities and colors. This did not require verbal communication.

I was a good, but not serious, student in grade school and high school. Academics came easily to me. I attended an outstanding high school, George School, a Quaker school north of Philadelphia. The teachers were superb, challenging, enthusiastic, competent, and caring. They enjoyed teaching. The campus was also magnificent, particularly in the spring when the cherry and dogwood trees were bursting with blossoms. An emphasis on Quaker beliefs permeated all of the academic and sports programs. A favorite period for many, including me, was Quaker meeting, a time set aside for silent meditation, and taking stock of where we were going. My wife and I sent our daughter to George School for her own last two years in high school so that she might also benefit from the personal virtues it promotes, and we think she has.

Sports were very important to me at George School, and physical activity has remained an important activity for me to this day. I played varsity football, soccer, and baseball, and wrestled. I was particularly proficient at wrestling. I enjoyed the drama of a single opponent, as well as the physical and psychological challenges of the sport. After George School, I went to Antioch, a small liberal arts college in Ohio.

At Antioch College I became a serious student, converting to academics all of the energy I had previously devoted to sports. Coming from George School, I carried the charge of making this a better, more equitable world for all people. Most of the problems appeared to be political, so I started out at Antioch majoring in political science. However, I soon became disillusioned with political science since there appeared to be little science to this discipline, so I switched to the physical sciences – physics and chemistry. I found great pleasure in the simplicity and elegance of mathematics and classical physics. I took almost every mathematics, physics, and chemistry course offered at Antioch, including Boolean algebra and topology, electrodynamics, and physical chemistry.

Although I found physics and mathematics intellectually satisfying, it was becoming apparent that what I was learning came from the past. The newest physics that was taught at Antioch was quantum mechanics, a revolution that had occurred in the 1920’s and earlier. Also, many frontiers of experimental physics, particularly experimental particle physics, were requiring the use of larger and larger accelerators, which involved bigger and bigger teams of scientists and support groups to execute the experiments. I was looking for a science in which the individual investigator had a more intimate, hands-on involvement with the experiments. Fortunately, Antioch had an outstanding work-study program; one quarter we studied on campus, the next was spent working on jobs related to our fields of interest. The jobs, in my case laboratory jobs, were maintained all over the country, and every three months we packed up our bags and set off for a new city and a new work experience. So one quarter off I went to Boston and the Massachusetts Institute of Technology (MIT).

There I encountered molecular biology as the field was being born (late 1950’s). This was a new breed of science and scientist. Everything was new. There were no limitations. Enthusiasm permeated this field. Devotees from physics, chemistry, genetics, and biology joined its ranks. The common premises were that the most complex biological phenomena could, with persistence, be understood in molecular terms and that biological phenomena observed in simple organisms, such as viruses and bacteria, were mirrored in more complex ones. Implicit corollaries to this premise were that whatever was learned in one organism was likely to be directly relevant to others and that similar approaches could be used to study biological phenomena in many organisms. Genetics, along with molecular biology, became the principal means for dissecting complex biological phenomena into workable subunits. Soon all organisms came under the scrutiny of these approaches.

I became a product of the molecular biology revolution. The next generation. As an Antioch college undergraduate, I worked several quarters in Alex Rich’s laboratory at MIT. He was an x-ray crystallographer, with very broad interests in molecular biology. While at MIT I was also fortunate to be influenced bySalvador Luria, Cyrus Leventhal and Boris Magasanik, through courses, seminars, and personal discussions. At that time Sheldon Penman and Jim Darnell were also working in Alex Rich’s laboratory. When placed in the same room, these two were particularly boisterous, providing comic relief to the fast moving era.

After Antioch, I set off for what I perceived as the “Mecca” of molecular biology, Harvard University. I had interviewed with Professor James D. Watson, of “Watson and Crick” fame, and asked him where should I do my graduate studies. His reply was curt and to the point: “Here. You would be fucking crazy to go anywhere else.” The simplicity of the message was very persuasive.

James D. Watson
Figure 6. A photograph of James D. Watson.

James D. Watson had a profound influence on my career (see Figure 6). He was my mentor. He did not teach me how to do molecular biology; because of my Antioch job experiences, I had already become a proficient experimenter. Jim instead taught me the process of science – how to extract the questions in a field that are critical to it and at the same time approachable through current technology. As an individual, he personified molecular biology, and, as his students, we were its eager practitioners. His bravado encouraged self-confidence in those around him. His stark honesty made our quest for truth uncompromising. His sense of justice encouraged compassion. He taught us not to bother with small questions, for such pursuits were likely to produce small answers. At a critical time, when I was contemplating leaving Harvard as a faculty member and going to Utah, he, being familiar with my self-sufficiency, counseled me that I could do good science anywhere. The move turned out to be a good decision. In Utah I had the luxury to pursue long-term projects that were not readily possible at Harvard, which, in too many cases had become a bastion of short-term gratification.

Doing science in Jim’s laboratory was exhilarating. As a graduate student, I was provided with what appeared to be limitless resources. I could not be kept out of the laboratory. Ninety-hour weeks were common. The lab was filled with talented students, each working on his or her own set of projects. Represented was a mixture of genetics, molecular biology, and biochemistry. We were cracking the genetic code, determining how proteins were synthesized, and isolating and characterizing the enzymatic machinery required for transcription. At this time, Walter Gilbert was also working in Jim’s laboratory. He was then a member of the physics department, but had also been bitten by the molecular biology bug. Jim and Wally complemented each other brilliantly, because they approached science from very different perspectives. Jim was intuitive, biological; Wally quantitative, with a physicist’s perspective. They were both very competitive. As students, we received the benefit of both, but also their scrutiny. They were merciless, but fair. You had to have a tough hide, but you learned rigor, both with respect to your science and your presentations. Once you made it through Jim’s laboratory, the rest of the world seemed a piece of cake. It was excellent training. Despite the toughness, which at times was hard, Jim was extremely supportive. He also made sure that you, the student, received full credit for your work. Despite the fact that Jim was responsible for all of the resources needed to run his laboratory, if you did all of the work for a given paper, then you were the sole author on that paper. Among all of the laboratory heads in the world, I believe that Jim Watson was among very few in implementing this policy.

The summer before I started graduate school, Marshall Nirenberg had announced that polyU directs the synthesis of polyphenylalanine in a cell free protein synthesizing extract. That paper was a bombshell! I decided I would generate a cell-free extract capable of synthesizing real, functional proteins. Jim’s laboratory had started working on the RNA bacteriophage, R17. Its genome also served as messenger RNA to direct the synthesis of its viral proteins. That would be my message. The cell-free protein synthesizing extract worked beautifully. Authentic viral coat protein and replicase were shown to be synthesized in the extract1. Further, the coat protein was functional, it bound to a specific sequence of the R17 genome, thereby modulating the synthesis of the replicase. To this day, the high affinity of the viral coat protein for this RNA sequence is exploited as a general reporter system to track RNA trafficking within living cells and neuronal axons. In collaboration with Gary Gussin, also a graduate student in Jim’s laboratory, this system was used to determine the molecular mechanism of genetic suppression of nonsense mutations2. In collaboration with Jerry Adams, another graduate student in Jim’s laboratory, the system was also used to determine that initiation of the synthesis of all proteins in bacteria proceeded through the use of formyl-methionine-tRNA3,4. A similar mechanism is involved in the initiation of protein synthesis in all eukaryotic organisms. Finally, I used the same in vitro system to show that termination of protein synthesis unexpectedly utilized protein factors, rather than tRNA, to accomplish this end5,6. Jim Watson would later offer the very complimentary comment “that Capecchi accomplished more as a graduate student than most scientists accomplish in a lifetime.” It was, indeed, a productive time, but it wasn’t work; it was sheer joy.

While a graduate student in Jim’s laboratory, I was invited to become a junior fellow of the Society of Fellows at Harvard. Being a junior fellow was very special. The society’s membership, junior and senior fellows, represented a broad spectrum of disciplines; all the members were talented, and most of them were much more verbal than I. Social discourse centered around meals, prepared by an exquisite French chef and ending with fine brandy and Cuban cigars. Frequent guests at these dinners were the likes of Leonard Bernstein. Surreal maybe, but also very special.

Karl G. Lark
Figure 7. A photograph of Karl G. Lark.

From Jim’s laboratory, I joined the faculty in the Department of Biochemistry at Harvard Medical School, across the river in Boston. During my four years at Harvard Medical School I quickly rose through the ranks, but then, I unexpectedly decided to go to Utah. I was looking for something different. There were excellent scientists in the department I was in at Harvard Medical School, but the department was not built with synergy in mind. Each research group was an island onto itself. At that time, they were also unwilling to hire additional young faculty and thereby provide the department with a more youthful, energetic character. At the University of Utah, I would be joining a newly formed department that was being assembled by a very talented scientist and administrator, Karl G. Lark (Figure 7). He had excellent taste in scientists and a vision of assembling a faculty that would enjoy working together and striving together for excellence. I could be a participant in the growth of that department and help shape its character. Furthermore, the University’s administration, led then by President David P. Gardner, was in synchrony with this vision and a strong supporter. Gordon had already attracted Baldomero (Toto) Olivera, Martin Rechsteiner, Sandy Parkinson, and Larry Okun to Utah. After I arrived at Utah, we were able to bring to Utah such outstanding scientists as Ray Gesteland, John Roth, and Mary Beckerle. Utah also provided wide open space, an entirely new canvas upon which to create a new career (see Figures 8). These are views from one of the homes in Utah which I have shared with my wife, Laurie Fraser, and daughter, Misha. The air is clean, and I can look for long distances. The elements of nature are all around us. What a place to begin a new life!

Views
Figure 8. Views from one of our homes in Utah and a photograph of my wife, Laurie Fraser, and daughter, Misha, just after she was born. Misha is now graduating from the University of California, Santa Cruz as an arts major.
References
1. Capecchi, M. R. (1966). Cell-free protein synthesis programmed with R17 RNA: Identification of two phage proteins. J. Mol. Bol. 21:173–193.
2. Capecchi, M. R. and Gussin, G. N. (1965). Suppression in vitro: Identification of a serine-tRNA as a “Nonsense Suppressor.” Science 149:417–422.
3. Adams, J. M. and Capecchi, M. R. (1966). N-formylmethionine-tRNA as the initiator of protein syntheses. Proc. Natl. Acad. Sci. USA 55:147–155.
4. Capecchi, M. R. (1966). Initiation of E. coli proteins. Proc. Natl. Acad. Sci. USA 55:1517–1524.
5. Capecchi, M. R. (1967). Polypeptide chain termination in vitro: Isolation of a release factor. Proc. Natl. Acad. Sci. USA 58:1144–1151.
6. Capecchi, M. R. and Klein, H. A. (1970). Release factors mediating termination of complete proteins. Nature 26:1029–1033.

From Les Prix Nobel. The Nobel Prizes 2007, Editor Karl Grandin, [Nobel Foundation], Stockholm, 2008

This autobiography/biography was written at the time of the award and later published in the book series Les Prix Nobel/ Nobel Lectures/The Nobel Prizes. The information is sometimes updated with an addendum submitted by the Laureate.

Copyright © The Nobel Foundation 2007

Dr. Capecchi is a member of the National Academy of Sciences (1991) and the European Academy of Sciences (2002). He has won numerous awards, including the Bristol-Myers Squibb Award for Distinguished Achievement in Neuroscience Research (1992), the Gairdner Foundation International Award for Achievements in Medical Sciences (1993), the General Motors Corporation’s Alfred P. Sloan Jr. Prize for Outstanding Basic Science Contributions to Cancer Research (1994), the German Molecular Bioanalytics Prize, (1996), the Kyoto Prize in Basic Sciences (1996), the Franklin Medal for Advancing Our Knowledge of the Physical Sciences (1997), the Feodor Lynen Lectureship (1998), the Rosenblatt Prize for Excellence (1998), the Baxter Award for Distinguished Research in the Biomedical Sciences (1998), the Helen Lowe Bamberger Colby and John E. Bamberger Presidential Endowed Chair in the University of Utah Health Sciences Center (1999), lectureship in the Life Sciences for the Collège de France (2000), the Horace Mann Distinguished Alumni Award, Antioch College (2000), the Italian Premio Phoenix-Anni Verdi for Genetics Research Award (2000), the Spanish Jiménez-Diáz Prize (2001), the Pioneers of Progress Award (2001), the Albert Lasker Award for Basic Medical Research (2001), the National Medal of Science (2001), the John Scott Medal Award (2002), the Massry Prize (2002), the Pezcoller Foundation-AACR International Award for Cancer Research (2003), the Wolf Prize in Medicine (2002/03), the March of Dimes Prize in Developmental Biology (2005),and the Nobel Prize in Physiology and Medicine (2007) with Oliver Smithies and Martin Evans.

Research interests include: the molecular genetic analysis of early mouse development, neural development in mammals, production of murine models of human genetic diseases, gene therapy, homologous recombination and programmed genomic rearrangements in the mouse.

http://www.hhmi.org/news/making-scientist

Mario Capecchi received a Kyoto Prize from the Inamori Foundation in 1996. The lecture he delivered when he accepted the prize in Japan in November 1996 tells the story of his remarkable life. The text of the lecture has been edited for length.

Radoslav Bozov commented on Targeted gene modification

Targeted gene modification Larry H Bernstein, MD, FCAP, Curator Leaders in Pharmaceutical Intelligence Series E. 2: …

Larry, same thing, data redundancy of data mining issues, of what data is in reality of physics beyond nano space in time! Working on something that does not exits in space and time, but computable mass of ‘designed’ energy formulated systems: Hox gene does not exist: It is a piece of time we percive through some kind of imagination +1,

The data generated through m/z methods is space-time unaccurate! Guess what is double R doing here instead of double Y, wonder why miRNA are obejctive to polymer degradation process ??!! what are we really seeing is not what is really in there!

Score Expect Method Identities Positives Gaps
19.2 bits(38) 0.076 Composition-based stats. 8/17(47%) 10/17(58%) 0/17(0%)

Query 511 LTEDRRAFAARMAEIGE 527
LT DRR AR+ + E
Sbjct 38 LTRDRRYEVARLLNLTE 54

Breaking news about genomic engineering, T2DM and cancer treatments

Larry H. Bernstein, MD, FCAP, Curator

http://pharmaceuticalintelligence.com/2015/09/28/breaking-news-about-genomic-engineering-t2dm-and-cancer-treatments/

Read Full Post »

To understand what happens in the brain to cause mental illness

Larry H Bernstein, MD, FCAP, Curator

Leaders in Pharmaceutical Intelligence

Series E. 2; 5.10

https://bbrfoundation.org/research/basic-research

Fernando Sampaio Goes, M.D., a 2008 NARSAD Young Investigator at Johns Hopkins School of Medicine, and his colleagues took an alternative approach to the ongoing genome-wide association studies (GWAS) that hunt for these factors by scouring the complete genomes of tens of thousands of individuals. The team––which included 2005 Young InvestigatorDimitrios Avramopoulos, M.D., Ph.D.; 2000 Young Investigator, 2008 Independent Investigator, and BBRF Scientific Council member James B. Potash, M.D., M.P.H.; and 2004 Young Investigator Peter P. Zandi, Ph.D.––conceived the study to detect rare genetic variations that GWAS are not designed to find.

Rather than scanning entire genomes for depression-associated variations, Goes’s team narrowed its search to a set of genes in which they already suspected alterations might contribute to depression: those that encode proteins found at or near the junctions between neurons, where cell-to-cell communication takes place. Based on previous surveys of these synaptic proteins, the scientists chose 1,742 genes to include in their analysis.

They compared the protein-coding sequences of that set of genes in 259 people with major depression to the same set in 334 unaffected individuals. To increase the chance of finding relevant genetic factors, all the patients with depression were selected based on the criterion of early-onset, recurrent depression, which is suspected by some to be a more heritable form of the illness. (An important component of depression causation is environmental, and reflects the particular life circumstances of those affected, who may or may not be naturally resilient when faced with stress and other environmental factors.)

The team’s analysis pointed to two sets of genes in which variations were linked with major depression. One includes genes that control the growth of dendritic spines (tiny knob-like protrusions from a neuron’s surface that receive inputs from other neurons). Other research has suggested that the size, density, and shape of these structures may be involved in mood disorders and other mental illnesses. The second gene set includes genes linked with the entry of calcium into neurons, which regulates a variety of processes, including the release of message-propagating neurotransmitters. Variations within this gene set have also been linked to autism and epilepsy.

Researchers have identified unique characteristics of emotional processing in young people with post-traumatic stress disorder (PTSD), showing for the first time how that processing might be disrupted at different ages.

Publishing their findings online August 5th in Neuropsychopharmacology, were 2012 NARSAD Young Investigator grantee Ryan J. Herringa, M.D., Ph.D., of the University of Wisconsin School of Medicine and Public Health and Richard C. Wolf, a Ph.D. candidate at the university. Together they  looked at brain activity during an emotion-related task in children aged 8 to 18, both with and without PTSD. The children with PTSD had experienced trauma such as sexual abuse, the death of a loved one, a physical accident, or witnessing violence.

The children viewed emotionally “threatening” and “neutral” pictures. During this task, the researchers used imaging to measure activity in brain regions associated in PTSD with an increased fear response and sense of threat. These regions include the amygdala, important for processing emotions; the dorsal anterior cingulate cortex (dACC), which helps to gauge threat levels; and the medial portion of the prefrontal cortex (PFC), crucial for dialing back fear responses and putting perceived threats in context.

The researchers found higher threat-related dACC activity in youths with PTSD, as well as weaker connections between the amygdala and mPFC. The findings suggest these brain regions contribute to the difficulty young people with PTSD have in assessing perceptions of threat.  The study also found that amygdala-PFC connections followed a different developmental path for youths with PTSD. Whereas those connections were stronger at older ages in those without PTSD, the same connections grew weaker for children with PTSD as they aged. This may reflect a progressive weakening in the ability of the PFC to reduce fear.

In research reported June 17th in the journal Neuron, scientists have shown that a protein called CPEB3 is critical for the stabilization and storage of long-term memories in mice. Three-timeNARSAD Distinguished Investigator and BBRF Scientific Council member Eric Kandel, M.D., led the research. Also on the team is 2013 NARSAD Young Investigator Pierre Trifilieff, Ph.D.

CPEB3 is a “prion-like” protein. Prions––infectious, misshapen proteins best known for the devastation they cause––clump together and lead to brain damage in people and animals with mad cow disease and related conditions. Similar protein-clumping mechanisms may also contribute to neurodegenerative diseases including Alzheimer’s, Parkinson’s, and amyotrophic lateral sclerosis. (Curiously, certain proteins with prion-like properties have an important role in the healthy brain.)

The new finding extends previous work showing that prion-like proteins are vital for the stabilization of long-term term memory in sea slugs and fruit flies. Although further work is needed to understand whether the same mechanism is at work in humans, humans do produce a protein similar to the mouse protein CPEB3.

Memories are stored in the connections between neurons, and proteins play a role in the long-term storage of the information. But since proteins degrade over time, scientists had wondered how a memory can persist long after a new experience triggers neurons to make memory-specific proteins. Prion-like proteins, which are self-perpetuating because they can convert normal proteins to their own misshapen form, appear to be the answer.

Genetic studies have recently yielded large numbers of “hits” for genes that subtly increase or decrease risk for disorders, including for schizophrenia. However, there have been no hits for major depression, perhaps because the studies are not yet large enough or because depression is less heritable. Estimates put the heritability of major depression at around 50%, with the remaining contribution coming from environmental and experiential causes.

However, a new approach has paid off: a study published online July 15th at the journal Natureidentifies two genomic regions that harbor genes that increase risk of major depression. A multinational collaboration employed a strategy of narrowing the pool of subjects to women in China with the most severe and stubborn form of depression, with the hope that a more homogenous population would yield results.

In an accompanying News and Views, 2014 Lieber Prizewinner for Outstanding Achievement in Schizophrenia Research,Patrick Sullivan, M.D., of the University of North Carolina, writes, “This first identification of replicable, significant genome-wide associations for MDD is exceptional.”

Qi Xu, Ph.D., of Peking Union Medical College and Jun Wang, Ph.D., of BGI-Shenzhen, who led the China components of the study, along with Foundation Scientific Council Member Kenneth Kendler, M.D., of Virginia Commonwealth University and 2007 NARSAD Distinguished Investigator Grantee Jonathan Flint, M.D., of the University of Oxford in the United Kingdom focused exclusively on women with severe, recurrent depression (an average of more than five episodes), building a sample of 5,303 cases and 5,337 controls. The results were replicated in a separate group of 3,231 Chinese women with major depression and 3,186 mixed male/female controls.

“I think this paper is groundbreaking because it really demonstrates that we can make progress in reducing genetic heterogeneity by paying attention to key clinical indicators,” said three-time NARSAD Grantee, Francis McMahon, M.D., of the National Institute of Mental Health (NIMH), who was not an author on the paper.

A team based at the University of Edinburgh analyzed data from thousands of Scottish adults to see whether they had genetic mutations either linked with obesity or major depressive disorder. They tested for relationships between those genetic profiles, the presence of depression or other psychological distress, and body mass index, a measure used to determine obesity. A genetic predisposition for obesity more strongly predicted actual obesity among those adults who were also depressed.

The findings were reported June 30th in Translational Psychiatry by a team including 2008NARSAD Distinguished Investigator Grantee David J. Porteous, Ph.D., and 2010 Independent Investigator Andrew M. McIntosh, Ph.D.

The study results show people becoming obese in part because of their depression, rather than becoming depressed because they are already obese. The experience of depression may drive disordered eating habits. It may also trigger chemical responses in the body (such as the release of the stress hormone cortisol) that promote weight gain, the researchers hypothesize.

The team also found some degree of association between a genetic profile linked to obesity and current psychological distress, even among individuals who were not obese. Obesity-linked genes also more closely predicted actual obesity among people experiencing distress even if they were not diagnosed with depression. This indicates that psychological strain, and not just depression per se, contributes to obesity.

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Proteins that control neurotransmitter release

Author & Curator: Larry H. Bernstein, MD, FCAP

Richard H. Scheller, PhD

The sec6/8 Complex Is Located at Neurite Outgrowth and Axonal Synapse-Assembly Domains

Christopher D. Hazuka, Davide L. Foletti, Shu-Chan Hsu, Yun Kee, F. Woodward Hopf, and Richard H. Scheller
Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305-5428

The Journal of Neuroscience, February 15, 1999, 19(4):1324–1334   http://www.jneurosci.org/content/19/4/1324.full.pdf

The molecules that specify domains on the neuronal plasma membrane for the delivery and accumulation of vesicles during neurite outgrowth and synapse formation are unknown. We investigated the role of the sec6/8 complex, a set of proteins that specifies vesicle targeting sites in yeast and epithelial cells, in neuronal membrane trafficking. This complex was found in layers of developing rat brain undergoing synaptogenesis. In cultured hippocampal neurons, the sec6/8 complex was present in regions of ongoing membrane addition: the tips of growing neurites, filopodia, and growth cones. In young axons, the sec6/8 complex was also confined to periodic domains of the plasma membrane. The distribution of synaptotagmin, synapsin1, sec6, and FM1–43 labeling in cultured neurons suggested that the plasma membrane localization of the sec6/8 complex preceded the arrival of synaptic markers and was downregulated in mature synapses. We propose that the sec6/8 complex specifies sites for targeting vesicles at domains of neurite outgrowth and potential active zones during synaptogenesis. Key words: synaptogenesis; neurotransmission; secretion; exocytosis; synaptic vesicle; vesicle targeting

Targeting of vesicles to synaptic sites during development may use similar mechanisms as those involved in vesicle fusion underlying membrane outgrowth. Before contact with a postsynaptic target, axons possess mobile vesicle clusters bearing synaptotagmin, which fuse with the plasma membrane after stimulation (Matteoli et al., 1992; Kraszewski et al., 1995; Dai and Peng, 1996). Thus, growing axons must contain the molecular machinery required for constitutive exocytosis, endocytosis, and activitydependent vesicle release. However, it is unclear how vesicles become clustered at synapses. Although vesicle fusion in axons might occur anywhere along the plasma membrane, there must be membrane targets that signal the clustering of vesicles for synapse formation. Furthermore, it is unclear how sites of vesicle exocytosis are modified as the neuron forms stable contacts with postsynaptic partners.

Identification of a Novel Rab11/25 Binding Domain Present in Eferin and Rip Proteins

Rytis Prekeris*, Jason M. Davies*, and Richard H. Scheller#
JBC Papers in Press. Published on July 31, 2001 as Manuscript M106133200
http://www.jbc.org/content/early/2001/07/31/jbc.M106133200.full.pdf

Rab11, a low molecular weight GTP binding protein, has been shown to play a key role in a variety of cellular processes, including endosomal recycling, phagocytosis, and transport of secretory proteins from the TGN. In this study we describe a novel Rab11 effector, EF hands containing Rab11 interacting protein (eferin). In addition, we identify a 20 amino acid domain that is present at the C-terminus of eferin and other Rab11/25 interacting proteins, such as Rip11 and nRip11. Using biochemical techniques we demonstrate that this domain is necessary and sufficient for Rab11 binding in vitro and that it is required for localization of Rab11 effector proteins in vivo. The data suggest that various Rab effectors compete with each other for the binding to Rab11/25 possibly accounting for the diversity of Rab11 functions.

Members of the Rab/Ypt GTPase family have emerged as important regulators of vesicular trafficking (1). Rab proteins have been proposed to mediate a variety of functions, including vesicle translocation and docking at a specific fusion sites. Like all small GTPases, Rabs cycle between active (GTP bound) and inactive (GDP bound) conformations (2). In the GTP bound state, Rab proteins can bind a variety of downstream effector proteins, while GTP hydrolysis leads to a conformational change in the “switch” region that renders the Rab GTPase unrecognizable to its effector proteins (3,4). A key question in understanding the interactions between Rabs and their effectors concerns the mechanisms by which Rab GTPases specifically bind a diverse spectrum of effectors and how this is regulated by the common structural motif used as a GTP switch. Biochemical and genetic studies have identified several hypervariable regions that might be involved in determining Rab specificity, including N- and C-termini, as well as α3/β5 by guest on September 6, 2015 http://www.jbc.org/ Downloaded from loop (5,6). Indeed, the recently reported structure of Rab3a bound to a putative effector, rabphillin-3a, revealed that Rab3a/rabphillin-3a complex interacts through two main regions (7). The first consists of conformationally sensitive “switch” regions of Rab3a bound to the a1 helix and the C-terminal part of rabphillin-3a. The second involves the SGAWFF domain of rabphillin-3a which fits into a pocket formed by the three hypervariable complementary determining regions (CDRs) of Rab3a, corresponding to the N- and C-termini and α3/β5 loop. Thus, it appears that the hypervariable RabCDR are involved in determining the specificity of effector binding, while the conserved “switch” regions impart GTP dependency and binding. It remains to be determined, however, whether this paradigm also applies to other Rab/effector complexes. Rab11a, -11b, and -25 are closely related members of Rab GTPase family that have been implicated in regulating a variety of different post-Golgi trafficking pathways, such as protein recycling (8), phagocytosis (9), insulin-stimulated Glut4 insertion in the plasma membrane (10), and membrane trafficking from early endosomes to the transGolgi network (11). During the last few years several Rab11/25 interacting proteins have been identified, including Rab11BP/Rabphilin-11, Rip11, nRip11, and myosin Vb (12- 15). However, the mechanisms of their function, as well as molecular aspects of their interactions with Rab11, remain to be fully understood. In the present study, we report the identification of EF-hands containing Rab11/25 interacting protein (eferin). Furthermore, we characterized a Rab binding domain (RBD11) which is present at the Cterminus of eferin as well as other Rab11/25 binding proteins, such as Rip11 and nRip11. Using biochemical techniques we demonstrated that RBD11 is the region which encodes the specificity for Rab11/25, but is distinct from the region interacting with Rab “switch” domain, since its interactions with the Rab11/25 are not GTP-dependent.

The functional significance of the differences in Rip and eferin interactions with Rab11/25 remains to be determined. One possibility is that additional cellular factors can regulate the affinity of Rab11/25 binding to its effectors. Indeed, the recombinant full length Rip11 binds poorly to Rab11a in pull down and yeast-two hybrid assays as compared to full length endogenous Rip11 from cellular TX-100 extracts (data not shown). Furthermore, it has been previously shown that Rip11 can also interact with γSNAP and cytoskeleton (13,24). Thus, the interactions of Rips and eferin with different factors could be used as a means of differentially regulating Rab11/25 binding. Alternatively, the Rab11/25 binding motif in eferin and Rip11 might be conformationlly hidden and require activation before binding to Rab11/25. We have previously demonstrated that phosphorylation of Rip11 plays an important role in its trafficking (13). Thus, differential phosphorylation on Rab11/25 binding motifs could also play a role in regulating the binding of Rip11 and eferin to Rab GTPases. Despite to recent progress in understanding the roles of Rabs and their effectors in regulating membrane trafficking, we are only beginning to unravel the structural determinants of their function. Identification and characterization of the Rab11/25 binding regions in Rip and Eferin proteins will be of a crucial importance in understanding the molecular mechanisms involved in differential regulation of the variety of Rab11-dependent trafficking pathways.

J. Immunol. Methods
J Immunol Methods 2008 Mar 14;332(1-2):41-52. Epub 2008 Jan 14.
Genentech Inc., 1DNA Way, South San Francisco, California, 94080, United States. jagath@gene.com
Cysteines with reactive thiol groups are attractive tools for site-specific labeling of proteins. Engineering a reactive cysteine residue into proteins with multiple disulfide bonds is often a challenging task as it may interfere with structural and functional properties of the protein. Here we developed a phage display-based biochemical assay, PHESELECTOR (Phage ELISA for Selection of Reactive Thiols) to rapidly screen reactive thiol groups on antibody fragments without interfering with their antigen binding, using trastuzumab-Fab (hu4D5Fab) as a model system

Antibody-drug conjugates enhance the antitumor effects of antibodies and reduce adverse systemic effects of potent cytotoxic drugs. However, conventional drug conjugation strategies yield heterogenous conjugates with relatively narrow therapeutic index (maximum tolerated dose/curative dose). Using leads from our previously described phage display-based method to predict suitable conjugation sites, we engineered cysteine substitutions at positions on light and heavy chains that provide reactive thiol groups and do not perturb immunoglobulin folding and assembly, or alter antigen binding.

Neuron
Neuron 2008 Nov;60(3):400-1

Antibody drug conjugates (ADCs) combine the ideal properties of both antibodies and cytotoxic drugs by targeting potent drugs to the antigen-expressing tumor cells, thereby enhancing their antitumor activity. Successful ADC development for a given target antigen depends on optimization of antibody selection, linker stability, cytotoxic drug potency, and mode of linker-drug conjugation to the antibody. Here, we systematically examined the in vitro potency as well as in vivo preclinical efficacy and safety profiles of a heterogeneous preparation of conventional trastuzumab-mcc-DM1 (TMAb-mcc-DM1) ADC with that of a homogeneous engineered thio-trastuzumab-mpeo-DM1 (thioTMAb-mpeo-DM1) conjugate.

Sensory and signaling pathways are exquisitely organized in primary cilia. Bardet-Biedl syndrome (BBS) patients have compromised cilia and signaling. BBS proteins form the BBSome, which binds Rabin8, a guanine nucleotide exchange factor (GEF) activating the Rab8 GTPase, required for ciliary assembly.

The reactive thiol in cysteine is used for coupling maleimide linkers in the generation of antibody conjugates. To assess the impact of the conjugation site, we engineered cysteines into a therapeutic HER2/neu antibody at three sites differing in solvent accessibility and local charge. The highly solvent-accessible site rapidly lost conjugated thiol-reactive linkers in plasma owing to maleimide exchange with reactive thiols in albumin, free cysteine or glutathione.

The intracellular pathogenic bacterium Salmonella enterica serovar typhimurium (Salmonella) relies on acidification of the Salmonella-containing vacuole (SCV) for survival inside host cells. The transport and fusion of membrane-bound compartments in a cell is regulated by small GTPases, including Rac and members of the Rab GTPase family, and their effector proteins. However, the role of these components in survival of intracellular pathogens is not completely understood.

Nat. Med.
Nat Med 2013 Oct;19(10):1232-5
Genentech Research and Early Development, 1 DNA Way, San Francisco, California, USA.
MAbs
MAbs 2014 Jan-Feb;6(1):95-107
Multi-transmembrane proteins are especially difficult targets for antibody generation largely due to the challenge of producing a protein that maintains its native conformation in the absence of a stabilizing membrane. Here, we describe an immunization strategy that successfully resulted in the identification of monoclonal antibodies that bind specifically to extracellular epitopes of a 12 transmembrane protein, multi-drug resistant protein 4 (MRP4). These monoclonal antibodies were developed following hydrodynamic tail vein immunization with a cytomegalovirus (CMV) promoter-based plasmid expressing MRP4 cDNA and were characterized by flow cytometry.

Antibody-drug conjugates (ADCs) have a significant impact toward the treatment of cancer, as evidenced by the clinical activity of the recently approved ADCs, brentuximab vedotin for Hodgkin lymphoma and ado-trastuzumab emtansine (trastuzumab-MCC-DM1) for metastatic HER2+ breast cancer. DM1 is an analog of the natural product maytansine, a microtubule inhibitor that by itself has limited clinical activity and high systemic toxicity. However, by conjugation of DM1 to trastuzumab, the safety was improved and clinical activity was demonstrated.

Richard H Scheller, PhD

Published on 16 Sep 2014

The Keck School of Medicine of USC is the first medical school in the nation to host the Lasker Lectures, featuring recipients of the prestigious 2013 Albert Lasker Basic Medical Research Award. In this installment, Richard H. Scheller, PhD, executive vice president of Genentech research and early development, discusses breakthoughs in drug development that are turning the tide in the war against cancer.

https://www.youtube.com/watch?v=Fx54EVJMcxM

Kavli Prize 2015

Xenon Pharmaceuticals Appoints Dr. Richard H. Scheller to Its Board of Directors

Biopharmaceutical company Xenon Pharmaceuticals (NasdaqGM:XENE) reported on Monday the addition of Richard H. Scheller, PhD to its board of directors.

Most recently, Dr Scheller has served as chief science officer and head of Therapeutics at 23andMe.

Previously Dr Scheller was the executive vice president at Genentech Research and Early Development & a member of the Roche Corporate Executive Committee; chief scientific officer, executive vice president of Research and senior vice president of Research at Genentech; as well as a professor of Molecular and Cellular Physiology and of Biological Sciences at Stanford University Medical Center and an investigator of the Howard Hughes Medical Institute.

Dr Scheller is currently an adjunct professor in the Department of Biochemistry and Biophysics, School of Medicine at the University of California, San Francisco.

He has been a Director at Xenon Pharmaceuticals Inc. since March 16, 2015 and Medrio, Inc. since November 2012. He serves as a Member of the Medical and Scientific Review Board of Evotec (US), Inc. (Renovis Inc.). In 2014, he was named a trustee of Caltech. He served as a Member of Scientific Advisory Board of Intra-Cellular Therapies, Inc. and Rinat Neuroscience Corporation.

He served on numerous advisory boards including the National Advisory Mental Health Council of the National Institutes of Health. Dr. Scheller served as chairman of the Genentech Foundation’s board of directors. He is a globally recognized leader in biomedical research.

He has published over 200 papers in scientific journals, and worked in cell biology. He has received several additional awards for his work elucidating the molecular mechanisms governing neurotransmitter release, including the 2013 Albert Lasker Basic Medical Research Award, the 2014 California Institute of Technology’s Caltech Distinguished Alumni Award, the 2010 Kavli Prize in Neuroscience, and the 1997 U.S. National Academy of Sciences Award in Molecular Biology. He is a Fellow of the American Academy of Arts and Sciences. Dr. Scheller holds a Doctorate in Chemistry from the California Institute of Technology in 1980, where he was also a Postdoctoral Fellow, Division of Biology. He was also a Postdoctoral Fellow at Columbia University, College of Physicians & Surgeons. He has Bachelor’s Degree in Biochemistry in 1975 at the University of Wisconsin, Madison.

Education: 1971-1975 University of Wisconsin-Madison B.S. – Biochemistry with Honors 1975-1980 California Institute of Technology Ph.D. – Chemistry – Advisor: Eric H. Davidson 1980-1981 California Institute of Technology Postdoctoral Fellow-Division of Biology Advisor: Eric H. Davidson 1981-1982 Columbia University-College of Physicians & Surgeons Postdoctoral Fellow-Molecular Neurobiology Advisors: Richard Axel and Eric R. Kandel Industry Positions: 2001-2003 Senior Vice President – Research Genentech, Inc. 2003-2009 Executive Vice President – Research Genentech, Inc. 2008-2009 Chief Scientific Officer and Executive Vice President – Research Genentech, Inc. 2009- Executive Vice President – Genentech Research and Early Development (gRED) and Member of the Enlarged Roche Corporate Executive Committee Academic Appointments: 1982-1987 Assistant Professor, Department of Biological Sciences, Stanford University 1987-1990 Associate Professor, Department of Biological Sciences, Stanford University 1990-1993 Associate Professor, Department of Molecular and Cellular Physiology, Stanford University Associate Professor (by courtesy), Department of Biological Sciences, Stanford University

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CRISPR/Cas9 Finds Its Way As an Important Tool For Drug Discovery & Development

  UPDATED 6/11/2021

CRISPR Diagnostics: CRISPR-dx Comes of Age: Tool in Drug Development

The past five years has seen a rapid expansion of the ability of CRISPR based tools toward diagnostic testing. Recently, CRISPR has been used to detect SARS-CoV-2 in patients. An article in the journal Science describes the different classes of CRISPR diagnostics in use today .

Update near end of post

UPDATED 8/08/2020

Association to Causation: Using GWAS to Identify Druggable Targets

A Gen Webinar Thursday, August 6, 2020; 11:00am – 12:30pm EST

See at end of post

Curator: Stephen J. Williams, Ph.D.

 

2.1.2.1

CRISPR/Cas9 Finds Its Way As an Important Tool For Drug Discovery & Development, 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

The RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system can be used to facilitate efficient genome engineering in eukaryotic cells by simply specifying a 20-nt targeting sequence within its guide RNA.

CRISPR/Cas systems are part of the adaptive immune system of bacteria and archaea, protecting them against invading nucleic acids such as viruses by cleaving the foreign DNA in a sequence-dependent manner. Although CRISPR arrays were first identified in the Escherichia coli genome in 1987 (Ishino et al., 1987), their biological function was not understood until 2005, when it was shown that the spacers were homologous to viral and plasmid sequences suggesting a role in adaptive immunity (Bolotin et al., 2005; Mojica et al., 2005; Pourcel et al., 2005). Two years later, CRISPR arrays were confirmed to provide protection against invading viruses when combined with Cas genes (Barrangou et al., 2007). The mechanism of this immune system based on RNA-mediated DNA targeting was demonstrated shortly thereafter (Brouns et al., 2008; Deltcheva et al., 2011; Garneau et al., 2010; Marraffini and Sontheimer, 2008).

Jennifer Doudna, PhD Professor of Molecular and Cell Biology and Chemistry, University of California, Berkeley Investigator, Howard Hughes Medical Institute has recently received numerous awards and accolades for the discovery of CRISPR/Cas9 as a tool for mammalian genetic manipulation as well as her primary intended research target to understand bacterial resistance to viral infection.

A good post on the matter and Dr. Doudna can be seen below:

http://pharmaceuticalintelligence.com/2014/06/13/215-245-6132014-jennifer-doudna-the-biology-of-crisprs-from-genome-defense-to-genetic-engineering/

In Delineating a Role for CRISPR-Cas9 in Pharmaceutical Targeting inheritable metabolic disorders in which may benefit from a CRISPR-Cas9 mediated therapy is discussed. However this curation is meant to focus on CRISPR/CAS9 AS A TOOL IN PRECLINICAL DRUG DEVELOPMENT.

 

Three Areas of Importance of CRISPR/Cas9 as a TOOL in Preclinical Drug Discovery Include:

  1. Gene-Function Studies: CRISPR/CAS9 ability to DEFINE GENETIC LESION and INSERTION SITE
  2. CRISPR/CAS9 Use in Developing Models of Disease
  3. CRISPR/CAS9 Use as a Diagnostic Tool
  • Using CRISPR/Cas9 in PRECLINICAL TOXICOLOGY STUDIES

I.     Gene-Function Studies: CRISPR/CAS9 ability to DEFINE GENETIC LESION and INSERTION SITE

The advent of the first tools for manipulating genetic material (cloning, PCR, transgenic technology, and before microarray and other’omic methods) allowed scientists to probe novel, individual gene functions as well as their variants and mutants in a “one-gene-at-a time” process. In essence, a gene (or mutant gene) was sequenced, cloned into expression vectors and transfected into recipient cells where function was evaluated.

However, some of the experimental issues with this methodology involved

  • Most transfections experiments result in NON ISOGENIC cell lines – by definition the insertion of a transgene alters the genetic makeup of a cell line. Simple transfection experiments with one transgene compared to a “null” transfectant compares non-isogenic lines, possibly confusing the interpretation of gene-function studies. Therefore a common technique is to develop cell lines with inducible gene expression, thereby allowing the investigator to compare a gene’s effect in ISOGENIC cell lines.
  1. Use of CRSPR in Highthrough-put Screening of Genetic Function

A very nice presentation and summary of CRSPR’s use in determining gene function in a high-throughput manner can be found below

www.rna.uzh.ch/events/journalclub/20140429JCCaihong.pdf

  1. Determining Off-target Effects of Gene Therapy Simplified with CRSPR

In GUIDE-seq: First genome-wide method of detecting off-target DNA breaks induced by CRISPR-Cas nucleases (from This Journal’s series on Live Meeting Coverage) at a 2014 Koch lecture

Shengdar Q Tsai and J Keith Joung describe

“

an approach for global detection of DNA double-stranded breaks (DSBs) introduced by RGNs and potentially other nucleases. This method, called genome-wide, unbiased identification of DSBs enabled by sequencing (GUIDE-seq), relies on capture of double-stranded oligodeoxynucleotides into DSBs. Application of GUIDE-seq to 13 RGNs in two human cell lines revealed wide variability in RGN off-target activities and unappreciated characteristics of off-target sequences. The majority of identified sites were not detected by existing computational methods or chromatin immunoprecipitation sequencing (ChIP-seq). GUIDE-seq also identified RGN-independent genomic breakpoint ‘hotspots’.

SOURCE http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3117.html

“

II. CRISPR/Cas9 Use in Developing Models of Disease

 

  1. Developing Animal Tumor Models

In a post this year I discussed a talk at the recent 2015 AACR National Meeting on a laboratories ability to use CRISPR gene editing in-vivo to produce a hepatocarcinoma using viral delivery. The post can be seen here: Notes from Opening Plenary Session – The Genome and Beyond from the 2015 AACR Meeting in Philadelphia PA; Sunday April 19, 2015

1) In this talk Dr. Tyler Jacks discussed his use of CRSPR to generate a mouse model of liver tumor in an immunocompetent mouse. Some notes from this talk are given below

  1. B) Engineering Cancer Genomes: Tyler Jacks, Ph.D.; Director, Koch Institute for Integrative Cancer Research
  • Cancer GEM’s (genetically engineered mouse models of cancer) had moved from transgenics to defined oncogenes
  • Observation that p53 -/- mice develop spontaneous tumors (lymphomas)
  • then GEMs moved to Cre/Lox systems to generate mice with deletions however these tumor models require lots of animals, much time to create, expensive to keep;
  • figured can use CRSPR/Cas9 as rapid, inexpensive way to generate engineered mice and tumor models
  • he used CRSPR/Cas9 vectors targeting PTEN to introduce PTEN mutations in-vivo to hepatocytes; when they also introduced p53 mutations produced hemangiosarcomas; took ONLY THREE months to produce detectable tumors
  • also produced liver tumors by using CRSPR/Cas9 to introduce gain of function mutation in β-catenin

See an article describing this study by MIT News “A New Way To Model Cancer: New gene-editing technique allows scientists to more rapidly study the role of mutations in tumor development.”

The original research article can be found in the August 6, 2014 issue of Nature[1]

And see also on the Jacks Lab site under Research

2)     In the Upcoming Meeting New Frontiers in Gene Editing multiple uses of CRISPR technology is discussed in relation to gene knockout/function studies, tumor model development and

New Frontiers in Gene Editing

Session Spotlight:
BUILDING IN VIVO MODELS FOR DRUG DISCOVERY

Genome Editing Animal Models in Drug Discovery
Myung Shin, Ph.D., Senior Principal Scientist, Biology-Discovery, Genetics and Pharmacogenomics, Merck Research Laboratories

Recent advances in genome editing have greatly accelerated and expanded the ability to generate animal models. These tools allow generating mouse models in condensed timeline compared to that of conventional gene-targeting knock-out/knock-in strategies. Moreover, the genome editing methods have expanded the ability to generate animal models beyond mice. In this talk, we will discuss the application of ZFN and CRISPR to generate various animal models for drug discovery programs.

In vivo Cancer Modeling and Genetic Screening Using CRISPR/Cas9
Sidi Chen, Ph.D., Postdoctoral Fellow, Laboratories of Dr. Phillip A. Sharp and Dr. Feng Zhang, Koch Institute for Integrative Cancer Research at MIT and Broad Institute of Harvard and MIT

Here we describe a genome-wide CRISPR-Cas9-mediated loss-of-function screen in tumor growth and metastasis. We mutagenized a non-metastatic mouse cancer cell line using a genome-scale library. The mutant cell pool rapidly generates metastases when transplanted into immunocompromised mice. Enriched sgRNAs in lung metastases and late stage primary tumors were found to target a small set of genes, suggesting specific loss-of-function mutations drive tumor growth and metastasis.

FEATURED PRESENTATION: In vivo Chromosome Engineering Using CRISPR-Cas9
Andrea Ventura, M.D., Ph.D., Assistant Member, Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center

We will discuss our experience using somatic genome editing to engineer oncogenic chromosomal rearrangements in vivo. More specifically, we will present the results of our ongoing efforts aimed at modeling cancers driven by chromosomal rearrangements using viral mediated delivery of Crispr-Cas9 to adult animals.

RNAi and CRISPR/Cas9-Based in vivo Models for Drug Discovery
Christof Fellmann, Ph.D., Postdoctoral Fellow, Laboratory of Dr. Jennifer Doudna, Department of Molecular and Cell Biology, The University of California, Berkeley

Genetically engineered mouse models (GEMMs) are a powerful tool to study disease initiation, treatment response and relapse. By combining CRISPR/Cas9 and “Sensor” validated, tetracycline-regulated “miR-E” shRNA technology, we have developed a fast and scalable platform to generate RNAi GEMMs with reversible gene silencing capability. The synergy of CRISPR/Cas9 and RNAi enabled us to not only model disease pathogenesis, but also mimic drug therapy in mice, providing us capability to perform preclinical studies in vivo.

In vivo Genome Editing Using Staphylococcus aureus Cas9
Fei Ann Ran, Ph.D., Post-doctoral Fellow, Laboratory of Dr. Feng Zhang, Broad Institute and Junior Fellow, Harvard Society of Fellows

The RNA-guided Cas9 nuclease from the bacterial CRISPR/Cas system has been adapted as a powerful tool for facilitating targeted genome editing in eukaryotes. Recently, we have identified an additional small Cas9 nuclease from Staphylococcus aureus that can be packaged with its guide RNA into a single adeno-associated virus (AAV) vector for in vivo applications. We demonstrate the use of this system for effective gene modification in adult animals and further expand the Cas9 toolbox for in vivo genome editing.

OriGene, Making the Right Tools for CRISPR Research
Xuan Liu, Ph.D., Senior Director, Marketing, OriGene

CRISPR technology has quickly revolutionized the scientific community. Its simplicity has democratized the genome editing technology and enabled every lab to consider its utility in gene function research. As the largest tool box for gene functional research, OriGene created a large collection of CRISPR-related tools, including various all-in-one vectors for gRNA cloning, donor vector backbones, genome-wide knockout kits, AAVS1 insertion vectors, etc. OriGene’s high quality products will accelerate CRISPR research.

  1. Transgenic Animals : Custom Mouse and Rat Model Generation Service Using CRISPR/Cas9 by AppliedStem Cell Inc. (http://www.appliedstemcell.com/)

A critical component of producing transgenic animals is the ability of each successive generations to pass on the transgene. In her post on this site, A NEW ERA OF GENETIC MANIPULATION  Dr. Demet Sag discusses the molecular biology of Cas9 systems and their efficiency to cause point mutations which can be passed on to subsequent generations

“

This group developed a new technology for editing genes that can be transferable change to the next generation by combining microbial immune defense mechanism, CRISPR/Cas9 that is the latest ground breaking technology for translational genomics with gene therapy-like approach.

  • In short, this so-called “mutagenic chain reaction” (MCR) introduces a recessive mutation defined by CRISPR/Cas9 that lead into a high rate of transferable information to the next generation. They reported that when they crossed the female MCR offspring to wild type flies, the yellow phenotype observed more than 95 percent efficiency.

“

The advantage of CRISPR/Cas9 over ZFNs or TALENs is its scalability and multiplexibility in that multiple sites within the mammalian genome can be simultaneously modified, providing a robust, high-throughput approach for gene editing in mammalian cells.

Applied StemCell, Inc. offers various services related to animal models including conventional transgenic rats, and phenotype analysis using knock-in, knock-out strategies.

Further explanation of their use of CRSPR can be found at the site below:

http://pharmaceuticalintelligence.com/2014/10/29/gene-editing-at-crispr-speed-services-and-tools/

In addition, ReproCELL Inc., a Tokyo based stem cell company, uses CRSPR to develop

· Tailored disease model cells (hiPSC-Disease Model Cells)

  • 2 types of services
  • ReproUNUS™-g:human iPS cell derived functional cells involving gene editing by CRISPR/Cas9 system
  • eproUNUS™-p:patient derived iPS cell derived functional cells

III. Using CRISPR/Cas9 in PRECLINICAL TOXICOLOGY STUDIES

As of now it is unclear as to the strategy of pharma in how to use this technology for toxicology testing however a few companies have licensed the technology to use across their R&D platforms including

A recent paper used a sister technique TALEN to generate knock-in pigs which suggest that it would be possible to generate pigs with human transgenes, especially in human liver isozymes in orer to study hepatotoxicity of drugs.

Efficient bi-allelic gene knockout and site-specific knock-in mediated by TALENs in pigs

Jing Yao, Jiaojiao Huang, Tang Hai, Xianlong Wang, Guosong Qin, Hongyong Zhang, Rong Wu, Chunwei Cao, Jianzhong Jeff Xi, Zengqiang Yuan, Jianguo Zhao

Sci Rep. 2014; 4: 6926. Published online 2014 November 5. doi: 10.1038/srep06926

UPDATED 8/08/2020

Association to Causation: Using GWAS to Identify Druggable Targets

A Gen Webinar Thursday, August 6⋅11:00am – 12:30pm

This webinar is available at https://www.genengnews.com/resources/webinars/association-to-causation-using-gwas-to-identify-druggable-target/

Speakers:

Martin Kampmann, PhD

matinkampmann ucsf

Associate Professor
UCSF
Investigator
Chan Zuckerberg Biohub

Kevin Holden, PhD

kevinholdn sythego

Head of Science
Synthego

Abhi Saharia, PhD

abhisharia sythego

VP, Commercial Development
Synthego

Human genetics provides perhaps the single best opportunity to innovate and improve clinical success rates, through the identification of novel drug targets for complex disease. Even as correlation identifies multiple genetic variants associated with disease, it is challenging to conduct requisite functional studies to identify the causal variants, especially since most association signals map to non-coding regions of the genome.

Genetic editing technologies, such as CRISPR, have enabled the modeling of associated variants at their native loci, including non-coding loci, empowering the identification of underlying biological mechanisms of disease with potential causal genes. However, genome editing is largely manual today severely limiting scale, and forcing the use of rational filters to prioritize which variants to investigate functionally.

In this GEN webinar, we will discuss several strategies enabling large-scale functional investigation of disease-associated variants in a cost- and time-effective manner, including different types of pooled CRISPR-based screens and the development of a fully automated genome engineering platform. We will also review how optimization of genome engineering on this platform enables the engineering of disease-associated variants at scale in pluripotent cells.

  • They will be presenting on use of wide scale CRSPR screens to validate druggable targets
  • The presenters will also discuss new platforms for these wide scale screens

Martin Kampmann, PhD UCSF

  • Multiple genetic variants associated with disease
  • Big gap between accumulation of genetic variant information and functions of these variants
  • CRSPRi or CRSPa (siRNA coupled or enhancer coupled CRSPR guides)
  • Arrayed screens: multiplate guide RNAs and phenotype measured (phenotype can be morphology, complex biological systems like organoids or non autonomous functions
  • Using pooled screens and use of suitable cell model critical for this strategy
  • For example in iPSC vs. neurons has different expression patterns upon same CRSPR of UBA1
  • Advantage is using CRSPR to take iPSC from diseased variant patient to make a corrected isogenic control then introduce gRNAs and use modifier screens to determine phenotypes
  • Generated a platform called CRISPRbrain.org to do bioinformatics on various experiments with different guide RNAs (CRSPRs)

Abhi Saharia, PhD Syntheco

  • Target identification with CSRSPR at Scale
  • Nature medicine paper did GWAS and found 27 SNV associated with high risk disease and a rational filter focused on 1 SNV in noncoding region but why study a single variant and if studied all 27 would they have been able to identify a more representative druggable set?
  • Goal is to reduce or eliminate these rational filters
  • HALO (scalable RNA guide), ECLIPSE platform (automated generation of modified cell lines, BIOINFORMATIC platform (integrated informatics)
  • Syntheco uses an electroporation with ribonucleic proteins (RNP) to give highest efficiency and minimizes off target as complex is only in cells for a short period of time
  • They confirm they are doing single cell cloning by using automated microscopy to confirm single cell growth in each cloning well

Kevin Holden, Head of Science at Syntheco

  • Engineering iPSc genetically modified cells at scale
  • The closer you get to your target site the more efficient your CRSPR so a big factor when making guides, especially for knock-in CRSPR
  • Adding a small molecule non homologous end joining inhibitor increases efficiency to 95%
  • Cold shocking the cells also assists in homologous repair
  • Use cleavage resistant templates

III. CRISPR/CAS9 AS A DIAGNOSTIC TOOL

     In the journal Science, Omar Abudayyeh and Jonathan Gootenberg discuss how CRISPR-based diagnostic (CRISPR-dx) tools offer a solution, and multiple CRISPR-dx products for detection of the SARS-CoV-2 RNA genome have been authorized by the US Food and Drug Administration (FDA).  In addition they discuss the work by Jiao et al. in combining this technique to develop a rapid and sensitive SARS-CoV2 diagnostic test.

Omar O. Abudayyeh, Jonathan S. Gootenberg. Science  28 May 2021: CRISPR Diagnostics
Vol. 372, Issue 6545, pp. 914-915; DOI: 10.1126/science.abi9335

Summary

Although clinical diagnostics take many forms, nucleic acid–based testing has become the gold standard for sensitive detection of many diseases, including pathogenic infections. Quantitative polymerase chain reaction (qPCR) has been widely adopted for its ability to detect only a few DNA or RNA molecules that can unambiguously specify a particular disease. However, the complexity of this technique restricts application to laboratory settings. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has underscored the need for the development and deployment of nucleic acid tests that are economical, easily scaled, and capable of being run in low-resource settings, without sacrifices in speed, sensitivity or specificity. CRISPR-based diagnostic (CRISPR-dx) tools offer a solution, and multiple CRISPR-dx products for detection of the SARS-CoV-2 RNA genome have been authorized by the US Food and Drug Administration (FDA). On page 941 of this issue, Jiao et al. (1) describe a new CRISPR-based tool to distinguish several SARS-CoV-2 variants in a single reaction.

Although clinical diagnostics take many forms, nucleic acid–based testing has become the gold standard for sensitive detection of many diseases, including pathogenic infections. Quantitative polymerase chain reaction (qPCR) has been widely adopted for its ability to detect only a few DNA or RNA molecules that can unambiguously specify a particular disease. However, the complexity of this technique restricts application to laboratory settings. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has underscored the need for the development and deployment of nucleic acid tests that are economical, easily scaled, and capable of being run in low-resource settings, without sacrifices in speed, sensitivity or specificity. CRISPR-based diagnostic (CRISPR-dx) tools offer a solution, and multiple CRISPR-dx products for detection of the SARS-CoV-2 RNA genome have been authorized by the US Food and Drug Administration (FDA). On page 941 of this issue, Jiao et al. (1) describe a new CRISPR-based tool to distinguish several SARS-CoV-2 variants in a single reaction.

There are multiple types of CRISPR systems comprising basic components of a single protein or protein complex, which cuts a specific DNA or RNA target programmed by a complementary guide sequence in a CRISPR-associated RNA (crRNA). The type V and VI systems and the CRISPR-associated endonucleases Cas12 (2, 3) and Cas13 (4, 5) bind and cut DNA or RNA, respectively. Furthermore, upon recognizing a target DNA or RNA sequence, Cas12 and Cas13 proteins exhibit “collateral activity” whereby any DNA or RNA, respectively, in the sample is cleaved regardless of its nucleic acid sequence (4, 6). Thus, reporter DNAs or RNAs, which allow for visual or fluorescent detection upon cleavage, can be added to a sample to infer the presence or absence of specific DNA or RNA species (4–8).

Initial versions of CRISPR-dx utilizing Cas13 alone were sensitive to the low picomolar range, corresponding to a limit of detection of millions of molecules in a microliter sample. To improve sensitivity, preamplification methods, such as recombinase polymerase amplification (RPA), PCR, loop-mediated isothermal amplification (LAMP), or nucleic acid sequence–based amplification (NASBA), can be used with Cas12 or Cas13 to enable a limit of detection down to a single molecule (8). This preamplification approach, applicable to both Cas12 and Cas13 (6, 7), enabled a suite of detection methods and multiplexing up to four orthogonal targets (7). Additional developments expanded CRISPR-dx readouts beyond fluorescence, including lateral flow (7), colorimetric (9), and electronic or material responsive readouts (10), allowing for instrument-free approaches. In addition, post–collateral-cleavage amplification methods, such as the use of the CRISPR-associated enzyme Csm6, have been combined with Cas13 to further increase the speed of CRISPR-dx tests (7). As an alternative to collateral-cleavage–based detection, type III CRISPR systems, which involve large multiprotein complexes capable of targeting both DNA and RNA, have been used for SARS-CoV-2 detection through production of colorimetric or fluorometric readouts (11).

FDA-authorized CRISPR-dx tests are currently only for use in centralized labs, because the most common CRISPR detection protocols require fluid handling steps and two different incubations, precluding their immediate use at the point of care. Single-step formulations have been developed to overcome this limitation, and these “one-pot” versions of CRISPR-dx are simple to run, operate at a single temperature, and run without complex equipment, producing either fluorescence or lateral flow readouts. The programmability of CRISPR makes new diagnostic tests easier to develop, and within months of the release of the SARS-CoV-2 genome, many COVID-19–specific CRISPR tests were reported and distributed around the world.

The broader capability for Cas enzyme–enhanced nucleic acid binding or cleavage has led to several other detection modalities. Cas9-based methods for cleaving nucleic acids in solution for diagnostic purposes have been combined with other detection platforms, such as destruction of undesired amplicons for preparation of next-generation sequencing libraries (12), or selective removal of alleles for nucleotide-specific detection (13). Alternatively, the programmable cleavage event from the Cas nuclease can be used to initiate an amplification reaction (14). Cas9-based DNA targeting has also been used for nucleotide detection in combination with solid-state electronics, promising an amplification-free platform for detection. In this platform, called CRISPR-Chip, the Cas9 protein binds nucleotide targets of interest (often in the context of the native genome) to graphene transistors, where the presence of these targets alters either current or voltage (15). By utilizing additional Cas9 orthologs and specific guide designs, CRISPR-Chip approaches have been tuned for single–base-pair sensitivity (15). Because they are integrated with electronic readers, CRISPR-Chip platforms may allow facile point-of-care detection with handheld devices.

 

Different classes of CRISPR diagnostics. GRAPHIC: ERIN DANIEL


Jiao et al. use a distinct characteristic of type II CRISPR systems, which involve Cas9, to develop a new type of noncollateral based CRISPR detection. Unlike Cas12s and Cas13, Cas9-crRNA complex formation requires an additional RNA known as the trans-activating CRISPR RNA (tracrRNA). By sequencing RNAs bound to Cas9 from Campylobacter jejuni in its natural host, the authors identified unexpected crRNAs, called noncanonical crRNA (ncrRNA), that corresponded to endogenous transcripts. Upon investigation of this surprising observation, it became clear that the tracrRNA was capable of hybridizing to semi-complementary sequences from a variety of RNA sources, leading to biogenesis of ncrRNAs of various sizes. Recognizing that they could program tracrRNAs to target a transcript of interest, the authors generated a reprogrammed tracrRNA (Rptr) that could bind and cleave a desired transcript, converting a piece of that transcript into a functional guide RNA. By then creating fluorescent DNA sensors that would be cleaved by the Rptr and ncrRNAs, the sensing of RNA by Cas9 could be linked to a detectable readout. This platform, called LEOPARD (leveraging engineered tracrRNAs and on-target DNAs for parallel RNA detection), can be combined with gel-based readouts and enables multiplexed detection of several different sequences in a single reaction (see the figure).

Jiao et al. also combined LEOPARD with PCR in a multistep workflow to detect SARS-CoV-2 genomes from patients with COVID-19. Although more work is needed to integrate this Cas9-based detection modality into a single step with RPA or LAMP to create a portable and sensitive isothermal test, an advantage of this approach is the higher-order multiplexing that can be achieved, allowing multiple pathogens, diseases, or variants to be detected simultaneously. More work is also needed to combine this technology with extraction-free methods for better ease of use; alternative readouts to gel-based readouts, such as lateral flow and colorimetric readouts, would be beneficial for point-of-care detection.

In just 5 years, the CRISPR-dx field has rapidly expanded, growing from a set of peculiar molecular biology discoveries to multiple FDA-authorized COVID-19 tests and spanning four of the six major subtypes of CRISPR systems. Despite the tremendous promise of CRISPR-dx, substantial challenges remain to adapting these technologies for point-of-care and at-home settings. Simplification of the chemistries to operate as a single reaction in a matter of minutes would be revolutionary, especially if the reaction could be run at room temperature without any complex or expensive equipment. These improvements to CRISPR-dx assays can be achieved by identification or engineering of additional Cas enzymes with lower-temperature requirements, higher sensitivity, or faster kinetics, enabling rapid and simple amplification-free detection with single-molecule sensitivity.

Often overlooked is the necessity for a sample DNA or RNA preparation step that is simple enough to be added directly to the CRISPR reaction to maintain a simple workflow for point-of-care testing. In addition, higher-order multiplexing developments would allow for expansive testing menus and approach the possibility of testing for all known diseases. As these advancements are realized, innovative uses of CRISPR-dx will continue in areas such as surveillance, integration with biomaterials, and environmental monitoring. In future years, CRISPR-dx assays may become universal in the clinic and at home, reshaping how diseases are diagnosed.

References and Notes

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Other related articles on CRISPR/Cas9 were published in this Open Access Online Scientific Journal, include the following:

Search Results for ‘CRISPR’

Where is the most promising avenue to success in Pharmaceuticals with CRISPR-Cas9?

CRISPR/Cas9 genome editing tool for Staphylococcus aureus Cas9 complex (SaCas9) @ MIT’s Broad Institute

Delineating a Role for CRISPR-Cas9 in Pharmaceutical Targeting

Using CRISPR to investigate pancreatic cancer

Simple technology makes CRISPR gene editing cheaper

RNAi, CRISPR, and Gene Editing: Discussions on How To’s and Best Practices @14th Annual World Preclinical Congress June 10-12, 2015 | Westin Boston Waterfront | Boston, MA

CRISPR/Cas9: Contributions on Endoribonuclease Structure and Function, Role in Immunity and Applications in Genome Engineering

CRISPR-CAS editing brings cloning of woolly mammoth one step closer to reality

GUIDE-seq: First genome-wide method of detecting off-target DNA breaks induced by CRISPR-Cas nucleases

The Patents for CRISPR, the DNA editing technology as the Biggest Biotech Discovery of the Century

CRISPR: Applications for Autoimmune Diseases @UCSF

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Metabolic Genomics and Pharmaceutics, Vol. 1 of BioMed Series D available on Amazon Kindle

Metabolic Genomics and Pharmaceutics, Vol. 1 of BioMed Series D available on Amazon Kindle

Reporter: Stephen S Williams, PhD

Article ID #180: Metabolic Genomics and Pharmaceutics, Vol. 1 of BioMed Series D available on Amazon Kindle. Published on 8/15/2015

WordCloud Image Produced by Adam Tubman

Leaders in Pharmaceutical Business Intelligence would like to announce the First volume of their BioMedical E-Book Series D:

Metabolic Genomics & Pharmaceutics, Vol. I

SACHS FLYER 2014 Metabolomics SeriesDindividualred-page2

which is now available on Amazon Kindle at

http://www.amazon.com/dp/B012BB0ZF0.

This e-Book is a comprehensive review of recent Original Research on  METABOLOMICS and related opportunities for Targeted Therapy written by Experts, Authors, Writers. This is the first volume of the Series D: e-Books on BioMedicine – Metabolomics, Immunology, Infectious Diseases.  It is written for comprehension at the third year medical student level, or as a reference for licensing board exams, but it is also written for the education of a first time baccalaureate degree reader in the biological sciences.  Hopefully, it can be read with great interest by the undergraduate student who is undecided in the choice of a career. The results of Original Research are gaining value added for the e-Reader by the Methodology of Curation. The e-Book’s articles have been published on the Open Access Online Scientific Journal, since April 2012.  All new articles on this subject, will continue to be incorporated, as published with periodical updates.

We invite e-Readers to write an Article Reviews on Amazon for this e-Book on Amazon.

All forthcoming BioMed e-Book Titles can be viewed at:

http://pharmaceuticalintelligence.com/biomed-e-books/

Leaders in Pharmaceutical Business Intelligence, launched in April 2012 an Open Access Online Scientific Journal is a scientific, medical and business multi expert authoring environment in several domains of  life sciences, pharmaceutical, healthcare & medicine industries. The venture operates as an online scientific intellectual exchange at their website http://pharmaceuticalintelligence.com and for curation and reporting on frontiers in biomedical, biological sciences, healthcare economics, pharmacology, pharmaceuticals & medicine. In addition the venture publishes a Medical E-book Series available on Amazon’s Kindle platform.

Analyzing and sharing the vast and rapidly expanding volume of scientific knowledge has never been so crucial to innovation in the medical field. WE are addressing need of overcoming this scientific information overload by:

  • delivering curation and summary interpretations of latest findings and innovations on an open-access, Web 2.0 platform with future goals of providing primarily concept-driven search in the near future
  • providing a social platform for scientists and clinicians to enter into discussion using social media
  • compiling recent discoveries and issues in yearly-updated Medical E-book Series on Amazon’s mobile Kindle platform

This curation offers better organization and visibility to the critical information useful for the next innovations in academic, clinical, and industrial research by providing these hybrid networks.

Table of Contents for Metabolic Genomics & Pharmaceutics, Vol. I

Chapter 1: Metabolic Pathways

Chapter 2: Lipid Metabolism

Chapter 3: Cell Signaling

Chapter 4: Protein Synthesis and Degradation

Chapter 5: Sub-cellular Structure

Chapter 6: Proteomics

Chapter 7: Metabolomics

Chapter 8:  Impairments in Pathological States: Endocrine Disorders; Stress

                   Hypermetabolism and Cancer

Chapter 9: Genomic Expression in Health and Disease 

 

Summary 

Epilogue

 

 

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Cancer Biology and Genomics for Disease Diagnosis (Vol. I) Now Available for Amazon Kindle

Cancer Biology and Genomics for Disease Diagnosis (Vol. I) Now Available for Amazon Kindle

Reporter: Stephen J Williams, PhD

Article ID #179: Cancer Biology and Genomics for Disease Diagnosis (Vol. I) Now Available for Amazon Kindle. Published on 8/14/2015

WordCloud Image Produced by Adam Tubman

Leaders in Pharmaceutical Business Intelligence would like to announce the First volume of their BioMedical E-Book Series C: e-Books on Cancer & Oncology

Volume One: Cancer Biology and Genomics for Disease Diagnosis

CancerandOncologyseriesCcoverwhich is now available on Amazon Kindle at                          http://www.amazon.com/dp/B013RVYR2K.

This e-Book is a comprehensive review of recent Original Research on Cancer & Genomics including related opportunities for Targeted Therapy written by Experts, Authors, Writers. This ebook highlights some of the recent trends and discoveries in cancer research and cancer treatment, with particular attention how new technological and informatics advancements have ushered in paradigm shifts in how we think about, diagnose, and treat cancer. The results of Original Research are gaining value added for the e-Reader by the Methodology of Curation. The e-Book’s articles have been published on the Open Access Online Scientific Journal, since April 2012.  All new articles on this subject, will continue to be incorporated, as published with periodical updates.

We invite e-Readers to write an Article Reviews on Amazon for this e-Book on Amazon. All forthcoming BioMed e-Book Titles can be viewed at:

http://pharmaceuticalintelligence.com/biomed-e-books/

Leaders in Pharmaceutical Business Intelligence, launched in April 2012 an Open Access Online Scientific Journal is a scientific, medical and business multi expert authoring environment in several domains of  life sciences, pharmaceutical, healthcare & medicine industries. The venture operates as an online scientific intellectual exchange at their website http://pharmaceuticalintelligence.com and for curation and reporting on frontiers in biomedical, biological sciences, healthcare economics, pharmacology, pharmaceuticals & medicine. In addition the venture publishes a Medical E-book Series available on Amazon’s Kindle platform.

Analyzing and sharing the vast and rapidly expanding volume of scientific knowledge has never been so crucial to innovation in the medical field. WE are addressing need of overcoming this scientific information overload by:

  • delivering curation and summary interpretations of latest findings and innovations
  • on an open-access, Web 2.0 platform with future goals of providing primarily concept-driven search in the near future
  • providing a social platform for scientists and clinicians to enter into discussion using social media
  • compiling recent discoveries and issues in yearly-updated Medical E-book Series on Amazon’s mobile Kindle platform

This curation offers better organization and visibility to the critical information useful for the next innovations in academic, clinical, and industrial research by providing these hybrid networks.

Table of Contents for Cancer Biology and Genomics for Disease Diagnosis

Preface

Introduction  The evolution of cancer therapy and cancer research: How we got here?

Part I. Historical Perspective of Cancer Demographics, Etiology, and Progress in Research

Chapter 1:  The Occurrence of Cancer in World Populations

Chapter 2.  Rapid Scientific Advances Changes Our View on How Cancer Forms

Chapter 3:  A Genetic Basis and Genetic Complexity of Cancer Emerge

Chapter 4: How Epigenetic and Metabolic Factors Affect Tumor Growth

Chapter 5: Advances in Breast and Gastrointestinal Cancer Research Supports Hope for Cure

Part II. Advent of Translational Medicine, “omics”, and Personalized Medicine Ushers in New Paradigms in Cancer Treatment and Advances in Drug Development

Chapter 6:  Treatment Strategies

Chapter 7:  Personalized Medicine and Targeted Therapy

Part III.Translational Medicine, Genomics, and New Technologies Converge to Improve Early Detection

Chapter 8:  Diagnosis                                     

Chapter 9:  Detection

Chapter 10:  Biomarkers

Chapter 11:  Imaging In Cancer

Chapter 12: Nanotechnology Imparts New Advances in Cancer Treatment, Detection, &  Imaging                                 

Epilogue by Larry H. Bernstein, MD, FACP: Envisioning New Insights in Cancer Translational Biology

 

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Envisage-Wistar Partnership and Immunacel LLC Presents at PCCI

Reporter: Stephen J. Williams, PhD

The Pharmaceutical Consulting Consortium International (PCCI) June Meeting: Envisage-Wistar Partnership and Immunacel LLC

An early stage healthcare venture creation and management firm

Presenter: Vic Subbu, COO of Immunacel & Managing Partner of Envisage and Heather Steinman, VP of Business Development & Executive Director Tech Transfer Wistar Institute

Monday, June 8, 2015

Embassy Suites, Chesterbrook, Pennsylvania (directions)

Announcement from the PCCI website:

Much has been said lately about how to improve the tech transfer situation. Wistar is meeting this challenge. Immunacel is the first of a series of developmental challenges and the Envisage-Wistar partnership solution becomes the meat of the evening’s discussion.

The Wistar Institute is the nation’s first independent institution devoted to medical research and training. The Wistar Institute has evolved from its beginnings as an anatomical teaching museum to its present-day status as an international leader in basic biomedical research.

Envisage LLC is an early stage healthcare venture creation and management firm. By focusing on key healthcare segments, Envisage aims to identify and advance promising healthcare innovations into value-add ventures.

IMMUNACCEL LLC is a Wistar Institute spin-out focused on accelerating the development of immune-mediated treatments for cancer and other unmet medical needs:

MMUNACCEL’s 3-D cancer-immune cell organotypic culture system is a physiologically relevant culture system utilizing primary human cancer cells and cytotoxic T cells (CTL) generated from patient T-cells, amongst fibroblasts and collagen assembled in a 3-D organotypic model.

Other related articles on PCCI and Philadelphia Biotech were published in this Open Access Online Scientific Journal, include the following:

PCCI’s 7th Annual Roundtable “Crowdfunding for Life Sciences: A Bridge Over Troubled Waters?” May 12 2014 Embassy Suites Hotel, Chesterbrook PA 6:00-9:30 PM

Protecting Your Biotech IP and Market Strategy: Notes from Life Sciences Collaborative 2015 Meeting

The Vibrant Philly Biotech Scene: Focus on KannaLife Sciences and the Discipline and Potential of Pharmacognosy

The Vibrant Philly Biotech Scene: Focus on Computer-Aided Drug Design and Gfree Bio, LLC

The Vibrant Philly Biotech Scene: Focus on Vaccines and Philimmune, LLC

The Bioscience Crowdfunding Environment: The Bigger Better VC?

R&D Alliances between Big Pharma and Academic Research Centers: Pharma’s Realization that Internal R&D Groups alone aren’t enough

BIO Partnering: Intersection of Academic and Industry: BIO INTERNATIONAL CONVENTION June 23-26, 2014 | San Diego, CA

Diagnostics and Biomarkers: Novel Genomics Industry Trends vs Present Market Conditions and Historical Scientific Leaders Memoirs

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