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Archive for June, 2012

A Protease for ‘Middle-down’ Proteomics

Author and Reporter: Ritu Saxena, Ph.D.

Neil Kelleher and his research team at Northwestern University have developed a method for enzymatic proteolysis large peptides for mass spectrometry–based proteomics using a protease OmpT. The method was published in a recent issue of the journal Nature. http://www.ncbi.nlm.nih.gov/pubmed/22706673

Proteomics is defined as the study of the structure and function of proteins. Proteomic technologies will play an important role in drug discovery, diagnostics and molecular medicine because is the link between genes, proteins and disease. As researchers study defective proteins that cause particular diseases, their findings will help develop new drugs that either alter the shape of a defective protein or mimic a missing one. http://www.ama-assn.org/ama/pub/physician-resources/medical-science/genetics-molecular-medicine/current-topics/proteomics.page Proteomics, although refers to the study of the structure and function of proteins, it is often specifically used for protein purification and mass spectrometry.

‘Bottom-up’ and ‘Top-down’ are the two main strategies for proteomic studies using mass spectrometry. In Bottom-up proteomics referred to as the more common method, proteins are broken down into smaller pieces through enzymatic digestion followed by characterization into amino acid sequences and post translational modifications prior to analysis by mass spectrometry. By identifying and sequencing these smaller pieces, researchers can then determine the identity of the protein they make up. In Top-down proteomics, on the other hand, the process of proteolysis is skipped and it focuses on complete characterization of intact proteins and their post-translational modifications (PTMs).

“Although both the top-down and bottom-up approaches continue to mature, they each have limitations. The tryptic peptides used in the bottom-up approach are the primary unit of measurement, but their relatively small size (typically ~8–25 residues long) leads to problems such as sample complex­ity, difficulties in assigning peptides to specific gene products rather than protein groups, and loss of single and combinato­rial PTM information. The top-down approach handles these issues by characterizing intact proteins, but its success declines in the high-mass region. Therefore, a hybrid approach based on 2–20 kDa peptides could unite positive aspects of both bottom-up and top-down proteomics” says Kelleher et al in the research article.

The hybrid approach, referred to as ‘middle-down’ proteomics would enable the analysis of complex mixtures pre-sorted by protein size. Previously research efforts ‘middle-down’ proteomics included exploring the restricted proteolysis with enzyme alternatives to Trypsin and chemical methods (such as microwave-assisted acid hydrolysis), However, these methods generated peptides that were marginally longer than those produced by trypsin digestion. For the current study, Kelleher adds “We established an OmpT-based middle-down platform to analyze complex mixtures pre-sorted by protein size. After inte­grating the data from the middle-down workflow that was applied to ~20–100-kDa proteins fractionated from the HeLa cell proteome, we identified 3,697 unique peptides (average size: 6.3 kDa) from 1,038 unique proteins (26% average sequence coverage) at an esti­mated 1% false discovery rate”.

OmpT, a protease derived from Escherichia coli K12 outer membrane belongs to the novel omptin protease family10 and is known to cleave between two consecutive basic amino acid residues (Lys/Arg-Lys/Arg). The authors developed OmpT into an efficient rea­gent to generate >2-kDa peptides for middle-down proteomics, thus, utilizing OmpT to achieve robust, yet restricted, proteolysis of a complex genome. http://www.ncbi.nlm.nih.gov/pubmed/22706673

Researcher Kelleher and his team have been in news earlier for their work on ‘top-down’ proteomics when his team developed a new method that could separate and identify thousands of protein molecules quickly. In the first large-scale demonstration of the top-down method, the researchers were able to identify more than 3,000 protein forms created from 1,043 genes from human HeLa cells. The study was published in last year in the October issue of the journal Nature. http://www.ncbi.nlm.nih.gov/pubmed?term=22037311

Thus, Kelleher and his group was able to demonstrate that OmpT-based proteomic approach has a robust and restricted proteolysis capacity making it an attractive option for mass-spectrometry-based analysis of primary structure of protein.

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The Relationship Between “Big Data” and Health Care – Value or Rubbish?

Author: Alan Fleischman, MBA      E-mail: a.fleischman@verizon.net

A blog (pathcareblog.com) entitled Why Big Data for Healthcare is Rubbish

http://pathcareblog.com/why-big-data-for-healthcare-is-rubbish/?goback=%2Eanb_1839273_*2_*1_*1_*1_*1_*1 takes direct aim at a recent report by the McKinsey Global Institute (Big Data: The Next Frontier for Innovation, Competition, and Productivity) http://www.mckinsey.com/insights/mgi/research/technology_and_innovation/big_data_the_next_frontier_for_innovation that projects substantial quantitative and qualitative benefits from implementing Big Data initiatives in health care.  Pathcare essentially states that McKinsey and Big Data ignore the two major stakeholders in healthcare – doctors and patients: “The study does not cite a single interview with a primary care physician or even a CEO of a healthcare organization that might support or validate their theories about big data value for healthcare. This is shoddy research, no matter how well packaged.” http://pathcareblog.com/why-big-data-for-healthcare-is-rubbish/?goback=%2Eanb_1839273_*2_*1_*1_*1_*1_*1

An article in Businessweek (The Health-Care Industry Turns to Big Data by Jordan Robertson, May 17, 2012) http://www.businessweek.com/articles/2012-05-17/the-health-care-industry-turns-to-big-data quotes benefits experienced by New York-Presbyterian Hospital from several data initiatives – including reducing “the rate of potentially fatal blood clots by about a third”, according to surgeon Nicholas Morrissey.  Morrisey is also working to develop a big data driven system to assess risk factors on new patients in the emergency room and the admission wards.  Along with hospitals, NSF and NIH have launched an initiative on Big Data to accelerate progress in biomedical research.

This article will not attempt to defend the research methodology utilized by McKinsey or the magnitude of the benefits projected, but it will defend the premise that medicine must improve its processes and procedures. Information systems are essential to this improvement and large amounts of data will need to be exchanged, integrated, and analyzed as a result. Evidence based medicine, effectiveness research, and performance assessments require the analysis of large amounts of data.  Like it or not, medicine is an industry with massive amounts of data, whether it is clinical, administrative, performance, or business.  Medicine can no longer function as a guild where senior craftsmen dispense tricks of the trade to apprentices and society grins and bears the results in terms of lives impacted and national treasure dispensed.  What is truly alarming to this author is the fact that healthcare has been so slow to adopt methods that have been proven effective in other industries – even low-tech methods.  This may explain the positive reception given to the use of simple checklists that have been advocated by the Institute for Healthcare Improvement and A. Gawandi in his book The Checklist Manifesto. http://gawande.com/the-checklist-manifesto  Checklists have been used in the airline industry since its inception.  Other industries have already demonstrated the benefits of Big Data over a substantial time frame – including finance, transportation, manufacturing, and retail. To be sure, I do not believe that Big Data is a cure-all for what ails medicine, nor do I believe that McKinsey advocated that viewpoint in its study.  However, it is one component on the road to improving a chaotic system.

The eye opening report by the Institute of Medicine on Medical Errors (To Err is Human: Building a Safer Health System, November 1999) http://www.iom.edu/~/media/Files/Report%20Files/1999/To-Err-is-Human/To%20Err%20is%20Human%201999%20%20report%20brief.pdf

estimated that as many as 98000 people die in hospitals each year as a result of preventable medical errors.  The costs in addition to loss of life are estimated to range from $17 billion to $29 billion each year.  One of the major conclusions from the Institute’s study was that faulty systems, processes, or conditions lead people to make mistakes or fail to prevent them.  The report clearly stated a need to address medicine from a systems perspective to decrease the alarming rate of medical errors.  A number of prominent physicians and healthcare organizations have advocated other approaches to improve the provision of healthcare – including changes to the basic organization of how primary care is dispensed (ACO, PCMH),  http://www.pcpcc.net/guide/better_to_best how hospitals fit into the provision of care, and how information systems can be utilized to improve both safety/quality and productivity /effectiveness.

Due to the impact of healthcare costs on our society and the slow rate of change in the industry, government policy makers have also been forced to take a more active role.  Thomas Lee and James Mongan of Partners HealthCare System in their book Chaos and Organization in Health Care http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid=11875 strongly advocate for this role and the importance of improving the healthcare information infrastructure.    In 2009 Congress passed the HITECH Act http://www.pwwemslaw.com/content.aspx?id=540 providing nearly $30 billion to address barrier to health IT adoption, $14.6 billion of which went to encourage adoption of electronic medical records.  Other funds were focused on developing Health Information Exchanges (HIE)  http://searchhealthit.techtarget.com/definition/Health-information-exchange-HIE toward the goal of making patient information available across all care delivery settings.  Bitton, Flier, and Jha (Health Information Technology in the Era of Care Delivery, To What End? JAMA,June 27,2012 – Vol 307,No. 24, P2593)

http://jama.jamanetwork.com/article.aspx?articleid=1199162 argue that the debate over whether health information and technology will save money and improve care is anachronistic.  They state flatly that information technology will be used in health care.  “Health IT is inevitable.  The question now is how best to do it”.

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Curator, Reporter: Aviral Vatsa, PhD, MBBS

Isolation of primary osteocytes from skeletally mature mice bones: A report on “Isolation and culture of primary osteocytes from the long bones of skeletally mature and aged mice” (BioTechniques 52:361-373 ( June 2012) doi 10.2144/0000113876)

A new study by Stern et al reports a technique where in the authors have isolated primary osteocytes from mature and aged mice.

Osteocytes are deeply embedded in the mineralised matrix of bone. They form the majority cell types of bone and play vital function in maintenance of bone homeostasis. However their study has been limited by their location in the bone and that they are terminally differentiated cells.

Osteocytes are the most abundant of the three bone cell types; however, the least is known about them. While their location deep within the bone matrix makes them ideally situated to sense bone strain, it also makes their observation and study in vivo difficult. Additionally, primary osteocytes, particularly those within the long bones of skeletally mature animals, have proven difficult to obtain and study ex vivo. Furthermore, once primary osteocytes are obtained, their study is often limited by their inability to proliferate as they are considered terminally differentiated cells. ”

As a result majority of the studies on osteocytes in vitro have used either cell lines and/or primary cells from new-born animals such as chicken, rat and mouse.

The MLO-Y4 cell line is well-characterized and represents the phenotype of early osteocytes ”

“Although the MLO-Y4 cell line is a very powerful tool for the study of osteocytes in vitro, there are known differences between primary osteocytes and the immortalized MLO-Y4 cell line. For example, MLO-Y4 cells express low to undetectable levels of Dentin matrix protein 1 (Dmp1) and Sclerostin (Sost), while osteocytes are known to express these genes in vivo .”

Primary osteocytes have most commonly been isolated from 16- or 18-day-old chick calvaria or from newborn through 4-day-old rat calvaria, 12-day-old mouse calvaria, and 3- to 4-week-old mouse calvaria and long bones.”

Studies utilizing these primary osteocytes can provide insight to the behavior of osteocytes during development but do not aid in the study of osteocytes from skeletally mature animals or enable the comparison between osteocytes isolated from skeletally mature but relatively young mice (4- to 6-month) and aged mice (>22-month-old).”

To circumvent the above mentioned limitations the authors utilised multi-step digestion technique. They subjected mouse long bone pieces (from 4-month old mouse and 22-month old mouse) to collagenase and EDTA alternatively for 25 minutes and collected the aspirate after each step for plating and culture of cells. (as described in the table, which has been taken from the study).

Table 1. Osteocyte isolation from murine long bone (courtesy: Stern et al)

They collected cells from nine such alternate steps in total and also the left over bone. These cells were then cultured for 7 days. Following parameters were tested to characterise the osteocytes.

  • E11/GP38 staining – early osteocyte specific protein
  • Alkaline Phosphatase (ALP) staining – indicator of osteoblastic state
  • COL 1 – major component of bone and produced by osteoblasts
  • Gene expression of E11, SOST, MEPE, Dmp1 – markers of osteogencity in different stages of osteogenesis
    • Osteoid osteocytes are known to express E11, Phex, and Mepe, while mineralizing osteocytes express Dmp1, and mature osteocytes encased in a mineralized matrix express Sost and Fgf23”

The authors were able to demonstrate that the isolated cells indeed expressed osteogenic markers. It was observed that cells isolated from later digestion steps (6-9) were more osteocyte like. This was also the case with the cells isolated from the left over bone pieces.

In this study, we were able to success fully isolate primary cells displaying several characteristics of osteocytes from the long bones of skeletally mature 4-month-old and 22-month-old mice through a process of sequential digestions and the use of a tissue homogenizer. From both the 4-month-old and 22-month-old mice, approximately 250,000 cells per osteocyte-enriched digestion (digestions 7–9) were obtained. These cells expressed E11/GP38 protein, and they lacked ALP and COL1A1 expression found in osteoblasts. Furthermore, several genes known to be expressed in osteocytes were also expressed in the cells obtained using our methodology. These include E11/gp38, Sost, Cox2, Mepe, Phex, and Dmp1.”

Limitations: 

As the authors pointed out, their study characterised the cells ensemble from separate digestion steps. This could lead to having a mixed population from each step.

The authors did not mention about the proliferation (or the absence of it) of the isolated cells. Since osteocytes are terminally differentiated cells, theoretically they should not proliferate. In addition when such primary cells are co-cultured with dividing cells, such as osteoblasts and fibroblasts in this case, the dividing population tends to over grow in culture leaving behind very few primary osteocytes. A detailed characterisation of these cells at different stages of digestion along with progressive time points will be very helpful.

Possibilities:

As authors claim, in future, this technique can help scientists to answer tricky questions about osteocytes such as comparing osteocytes from animals grouped on the basis of age, disease, bone characteristics, and therapies.

Reference: Isolation and culture of primary osteocytes from the long bones of skeletally mature and aged mice. BioTechniques 52:361-373 ( June 2012) doi 10.2144/0000113876 .

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Reported By: Dr. Venkat S. Karra

English: Emblem of the United Nations. Color i...

The United Nations is setting up an international scientific advisory board to guide the secretary-general on science matters, reports SciDevNet.

The plan for this council was announced at the UN Conference on Sustainable Development, or Rio+20 — the UN Environmental, Scientific and Cultural Organization will be taking the lead in setting the board up.

“The board will bring together eminent specialists from the natural sciences, the social and human sciences, and engineering, and representing diverse backgrounds and regions,” SciDevNet adds

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Resported By: Dr. Venkat S Karra

 

Combination Therapy to Starve Cancer Cells to Death.

via Combination Therapy to Starve Cancer Cells to Death.

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Curated by: Dr. Venkat S. Karra, Ph.D.

In our recent article we mentioned about the amyloidosis, most importantly the most common form of amlyodosis – Primary Amyloidosis (AL).

Primary amyloidosis (AL) is an acquired plasma cell disorder in which a monoclonal immunoglobulin light chain is produced in the bone marrow and usually found in the blood or urine. AL amyloidosis occasionally occurs with multiple myeloma. The amyloid fibrils in this type of amyloidosis are made up of immunoglobulin light chain proteins (kappa or lambda).

Amyloidosis can only be diagnosed by a positive biopsy (i.e., an identification of the amyloid deposits in a piece of tissue). Initial biopsies are most commonly obtained from the abdominal fat.

If amyloid is suspected in other organs, however, a biopsy may be needed from these specific areas. If amyloid is present in a tissue biopsy, further tests can be done to determine the type of the amyloid.

The Amyloid Treatment & Research Program (ATRP) at Boston Medical Center (BMC) is an international referral center that treats amyloidosis with stem cell transplantation.

Last week researchers at Mayo Clinic have used urinary exosomes as a non-invasive diagnostic tool that will offer a snapshot of what is occurring in kidney tissue.

Urinary exosomes are rapidly becoming a powerful tool in the study of renal disease.

English: Urinary system

Already proteomics studies are looking into ways of using urinary exosome to diagnose genetic diseases and characterize disease biomarkers.

The urinary exosomes are excreted from every renal epithelial cells (from the glomerular podocytes to the urinary epithelial cells lining the urinary drainage system) provides us with an opportunity to study proteins once were either difficult or impossible to reach.

With this understanding the researchers undertook this study to evaluate the possible differences among urinary exosomes from patients with different plasma cells dyscrasias. This study suggests that urinary exosomes may be an excellent non-invasive tool for identifying patients with AL amyloidosis because high molecular weight light chain oligomers were found only in patients with AL.

The oligomeric light chain species captured in the urinary exosomes may represent the initial steps of amyloidogenesis. The potential of urinary exosomes in AL is tremendous and deserves further studies. When combined with mass spectrometry and other proteomics techniques, urinary exosomes represent tremendous potential to increase our understanding of amyloidogenesis.

Authors believe that this is the first report of the use of urinary exosome in the study of patients with plasma cell dyscrasias, specifically patients with AL amyloidosis.

References:

1. Amyloidosis: http://pharmaceuticalintelligence.com/2012/06/04/amyloidosis/

2. Alzheimers Disease: http://pharmaceuticalintelligence.com/category/alzheimers-disease-2/

3. Prospects for urinary proteomics: exosomes as a source of urinary biomarkers

4. Source article: Differences in Immunoglobulin Light Chain Species Found in Urinary Exosomes in Light Chain Amyloidosis (AL)

5.  Exosomal Fetuin-A identified by proteomics: a novel urinary biomarker for detecting acute kidney injury.

 6. Characterization of PKD protein-positive exosome-like vesicles.

7. Large-scale proteomics and phosphoproteomics of urinary exosomes.

8. Proteomic analysis of urinary exosomes from patients of early IgA nephropathy and thin basement membrane nephropathy.

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Metabolic Disturbances Associated with Systemic Lupus Erythematosus.

via Metabolic Disturbances Associated with Systemic Lupus Erythematosus.

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Reporter: Aviva Lev-Ari, PhD, RN

The Price of Togetherness

Is togetherness the latest drug? Will touchy feeliness be the answer to the pharmaceutical industry’s crisis of productivity? Collaboration certainly isn’t anything new in the life sciences, but the nature and structure of partnerships is evolving to the point that many companies are now contemplating pooling their resources…and diluting their returns.

Certainly the past decade has been marked by more partnerships between industry and academia, where there has been an effort to find a win-win solution to academia’s funding deficits and pharma’s desire to get more helping hands in early innovation.

Out of this have grown “open-source” research efforts that use pharma’s financial backing to create or aggregate data any researcher can use. Sage Bionetworks, a three-year-old Seattle-based non-profit, offers a “commons” of pooled data and resources. Merck has contributed many human and mouse disease models for open consumption. Eli Lilly has opened up its doors to compounds created at academic labs through its PD2 and other Open Innovation Drug Discovery efforts. In 2008, GlaxoSmithKline released over 300 cell lines to the National Cancer Institute’s Cancer Bioinformatics Grid, open for academics to mine. The Structural Genomics Consortium is an open-access database of 3-D protein structures that counts Lilly, GSK, NovartisPfizer, and most recently Takeda among its members and financial backers.

While these kinds of open efforts come with a series of challenges concerning ownership, consent and disclosure, and many other issues, they exist because industry increasingly recognizes that biology is too complex for any one company, even a large one, to tackle on its own.

Major drug companies have also started to innovate the way they work with venture capitalists to help nurture early research. Johnson & Johnson announced back in January that it is partnering with Polaris Venture Partners to scout out and co-invest in biotech startups–presumably structuring deals such that venture backers can find an exit without relying on the lousy IPO market. And they’re hardly alone–as I highlighted a few months ago..

But now drug companies are starting to do the unthinkable–work directly with each other. They’ve taken baby steps in this direction before, often with a focus on emerging markets and diseases not viewed as critical profit-drivers. For example, 13 major drug companies joined the Bill and Melinda Gates Foundation earlier this year to combat tropical diseases. But rather than just contributing medicine, some of the companies– Abbott, Johnson & Johnson and Pfizer–are actually collaborating on research as part of the Drugs for Neglected Diseases Initiative. All the companies are sharing compound libraries.

That’s not entirely unprecedented, but companies that have wanted to work closely together in the past have formally launched joint ventures, like the HIV-focused ViiV Healthcare venture between Pfizer and GlaxoSmithKline.

Now these cooperative efforts are broadening. One announcement made at the recent Biotechnology Industry Organization (BIO)convention is the formation of a consortium for neuroscience research between seven companies including Biogen, Abbott Labs and Merck. The stakes a fairly small, at least money-wise–each company is only pledging $250,000 at this point. But it is symbolically important that they are sharing all the costs of basic research, as well as their expertise, to try to quickly and efficiently get R&D off the ground.

While some of this newfound camaraderie might be difficult for companies dreaming of developing blockbusters and keeping all the profits to themselves, there is a silver lining. The growing demand for drugs in emerging markets means that some of these collaboratively developed drugs may eventually reach much broader audiences–meaning larger populations over which to recoup development costs, bigger opportunities for rare disease indications, and acceptable profits even if prices are forced lower. That should be some consolation.

-Karl Thiel

http://www.biospace.com/news_story.aspx?NewsEntityId=264902&type=email&source=BE_062712

More by Karl Thiel

http://www.biospace.com/news_subject_all_results.aspx?CatagoryId=40094

Picturing US-Trained PhDs’ Paths

While the US National Institutes of Health Advisory Committee to the Director’s Biomedical Workforce Working Group issued a draft report this month, detailing data it collected as well as its recommendations for the federal agency, Sally Rockey really breaks it down at her NIH Office of Extramural Research blog. “I plan to highlight some of the specific data in future posts, but first, I’d like to discuss the outcome — the conceptual framework that presents a snapshot of the biomedical research workforce, incorporating the latest available data,” she says. And she does, in an infographic that follows the career paths of the 9,000 biomedical PhDs who graduated in the US in 2009. Seventy percent of them went on to do postdoctoral research, Rockey notes.

Down the line, “looking at the career paths taken by these US-trained biomedical PhDs, we can see that fewer than half end up in academia, either in research or in teaching, and only 23 percent of the total are in tenured or tenure-track positions,” she adds. “Many other people are conducting research, however, with 18 percent in industry and 6 percent in government.”

Overall, Rockey says, the non-academic biomedical workforce is huge. “If you’re a graduate student or postdoc looking at these numbers, particularly the proportion of people in industry and government settings, it makes sense to learn as much about these career paths as possible,” she writes at Rock Talk.

http://www.genomeweb.com/careers

NIH Advisory Committee to the Director’s Biomedical Workforce Working Group Issues Draft Report

 The US National Institutes of Health Advisory Committee to the Director’s Biomedical Workforce Working Group issued a draft report this week that summarizes data it has collected and includes recommendations “that can inform decisions about training the optimal number of people for the appropriate types of positions that will advance science and promote health,” it reads.In its report, the working group emphasizes the overall purpose of its research efforts and resulting recommendations, namely “to ensure future US competitiveness and innovation in biomedical research” through proper undergraduate, graduate, and postdoctoral training and to “attract and retain the best and most diverse scientists, engineers, and physicians from around the world,” as well as domestically.When it comes to graduate education, the working group suggests that NIH cap the total number of years a grad student can be supported by NIH funds, in order to encourage timely completion of PhD studies.As for graduate career training, the working group says that because around 30 percent of biomedical PhDs work in the biotech and pharmaceutical industries — in both research and non-research positions — “their transition would be more effective if their training was better aligned with the required skill-sets for these careers.” In addition, “institutions also could be encouraged to develop other degree programs — e.g. master’s degrees designed for specific science-oriented career outcomes, such as industry or public policy … as stand-alone programs or provide sound exit pathways for PhD students who do not wish to continue on the research career track,” the group continues.For PhDs who do wish to continue on with a postdoctoral fellowship, the working group suggests that NIH “create a pilot program for institutional postdoctoral offices to compete for funding to experiment in enriching and diversifying postdoctoral training,” and adjust the current stipends for the postdocs it supports to better reflect their years of training.In addition, the group recommends that NIH double the number of Pathway to Independence (K99/R00) awards it issues and shorten the eligibility period for applying to this program from five to three years of postdoc experience to encourage more PhDs to swiftly move into independent research positions. Likewise, the group suggests that NIH also double the number of NIH Director’s Early Independence awards “to facilitate the skip-the-postdoc career path for those who are ready immediately after graduate school.”More generally, the Biomedical Workforce Working Group recommends that institutions receiving NIH funds ramp up their efforts to collect information on career outcomes of the grad students and postdocs supported by federal research grants.

Finally, the group suggests that NIH create a permanent unit in the Office of the Director that would work with the extramural research community, the National Science Foundation, and the agency’s other institutes and centers “to coordinate data collection activities and provide ongoing analysis of the workforce and evaluation of NIH policies so that they better align with the workforce needs.”

http://www.genomeweb.com/nih-advisory-committee-directors-biomedical-workforce-working-group-issues-draft

Rock Talk

Helping connect you with the NIH perspective


So, What Does the Biomedical Research Workforce Look Like?

Posted on June 22, 2012 by Sally Rockey

Update 6/27/12: The full report is now posted on the ACD website.

As I blogged last week, and most of you have heard by now, a working group of the Advisory Committee to the NIH Director (ACD) that I co-chaired with Shirley Tilghman from Princeton just completed a study of the biomedical research workforce. We reported our findings to the ACD last Thursday (you can find a link to the videocasthere).

We gathered a lot of data during this study, which are included in the report (see the ACD site for the executive summary and instructions for obtaining a copy of the full report). The data also are posted on an accompanying website. I plan to highlight some of the specific data in future posts, but first, I’d like to discuss the outcome—the conceptual framework that presents a snapshot of the biomedical research workforce, incorporating the latest available data. The framework of the PhD workforce is presented below, and a companion framework for MDs and MD/PhDs in the biomedical research workforce can be seen in the report and on the website.

First, 9,000 biomedical PhDs graduated in the US in 2009 (including basic biomedical and clinical sciences), and 70% of these went on to do postdoctoral research. As we conducted our analysis, it became clear that there are few reliable data on the number of biomedical postdoctoral researchers in the US. We lack solid information on foreign-trained postdoctoral researchers, and many postdoctoral researchers change their title as they proceed through their training, complicating the data collection. That’s why the estimate of postdoctoral researchers ranges from 37,000 to 68,000.

Looking at the career paths taken by these US-trained biomedical PhDs, we can see that fewer than half end up in academia, either in research or in teaching, and only 23% of the total are in tenured or tenure-track positions. Many other people are conducting research, however, with 18% in industry and 6% in government.

The science related non-research box includes individuals working in industry, government, or other settings who do not conduct research but are part of the scientific enterprise. Many of the career paths represented by this box contribute to the scientific research enterprise and require graduate training in biomedical science. For example, program and review officers at NIH and managers in many biotechnology companies would be included in this group. This is my box too. It’s interesting to note the 18% included in this group is made up of PhDs employed in industry (13% of the total workforce), in government (2.5%), and in other settings (2.5%). This means that all individuals working in industry (research plus non-research occupations) represent about 30% of the workforce, and all those working in government represent about 9% (more than 10,000 individuals).

That leaves 13% in non-science related occupations and 2% unemployed (this does not include retirees or those who choose not to work). These are 2008 data, the latest available from the NSF Survey of Doctoral Recipients.

If you’re a graduate student or postdoc looking at these numbers, particularly the proportion of people in industry and government settings, it makes sense to learn as much about these career paths as possible. I’m very proud that we were able to develop this framework, as it seems that for the first time we have an idea of where domestically trained biomedical researchers are going. I was quite surprised by the idea that the majority of our trainees do not end up in academia. Did this surprise you?

diagram shows the flow of college graduates through graduate and postgraduate training and into the workforce

Notes on the figure

The main sources of the original data, from which the graphs in the report were made and these numbers were derived, come from three NSF surveys: the Survey of Graduate Students and Postdoctorates, the Survey of Earned Doctorates, and the Survey of Doctorate Recipients. You can see the specific sources of each number by clicking on the relevant box on the website.

The color of the numbers reflects our confidence in the accuracy of the data: high (green), medium (yellow), or low (red). For more details see colors. In this case, the red numbers in the post-training workforce box are accurate, but the color reflects the fact that we know almost nothing about the distribution of foreign-trained PhDs in the workforce, so the overall picture is an under-estimate.

The post-training workforce boxes are color coded, with light blue denoting those in research positions and academic teaching positions. The science related non-research box is colored dark blue to indicate that many of the careers represented in this box are closely related to the conduct of biomedical research.

http://nexus.od.nih.gov/all/2012/06/22/so-what-does-the-biomedical-research-workforce-look-like/

Live Chat: Are We Training Too Many Scientists?

by Jocelyn Kaiser on 27 June 2012, 8:30 AM |
Too many graduate students and postdocs chasing too few academic jobs has led to a dysfunctional biomedical research system. That’s the conclusion of a draft report on the biomedical workforce released this month by an advisory panel to the National Institutes of Health (NIH). The panel urged taking steps to shorten young scientists’ career paths, including capping how long graduate students can receive NIH support and better preparing them for non-academic careers. The report also encourages university labs to rely more on staff scientists rather than trainees.

But is it a good idea to tinker with the research system at a time when NIH funding is tighter than ever? And given that most biomedical Ph.D.s will find a job, are there really too many?

NIH Panel Urges Steps to Control Growth in Biomedical Research Trainees

by Jocelyn Kaiser on 14 June 2012, 5:50 PM |
A glut of trainees and a dearth of academic positions in the United States is creating a dysfunctional biomedical research system, an advisory group to the National Institutes of Health (NIH) concluded today. It urged several steps be taken to bring the problem under control. NIH should cap how many years it will support graduate students, pay postdoctoral researchers more, and encourage universities to fund staff scientist positions.

The changes may appear to make research labs less productive, but in the long run will result in “a more vibrant workforce,” said Shirley Tilghman, president of Princeton University and co-chair of the panel that delivered the draft report.

The widely anticipated report comes from a working group of the NIH Advisory Committee to the Director (ACD) co-led by NIH Deputy Director for Extramural Research Sally Rockey. The panel spent a year examining available data on the number and fate of biomedical researchers through different stages of their careers, focusing on the slow pace of advancement and the often-cited fact that the average age for an investigator winning the first independent grant from NIH is 42. (The panel’s economists abandoned a plan to model the workforce—there wasn’t time or sufficient data.)

 Live Chat: Are We Training Too Many Scientists? 

In the executive summary of their draft report, the panel found that a steep rise in U.S. biomedical Ph.D.s in the past decade, more foreign postdocs, and the aging of academic faculty members make it increasingly hard for young biomedical researchers to find academic jobs. Biomedical researchers are paid less than scientists in other fields, and the low pay and long training period may make the field unattractive to the best and brightest.

To address the problem, NIH needs to make some changes, the panel says. The agency should provide supplements to training grants that help students prepare for alternatives to academic careers, such as a master’s degree geared toward an industry position. It should cap how long a graduate student can receive NIH funding at 6 years (the average length of a biomedical Ph.D. including all funding is now 6.5 years, says Rockey). NIH should find ways to shift the funding source for graduate students, most of whom are now paid out of investigators’ grants, to training grants and fellowships. The reason: such programs provide higher quality training, and their graduates tend to be more successful than those funded from grants.

Postdoctoral researchers should also be supported to a greater extent by fellowships and training grants, the panel says. And postdoc stipends should be increased—starting with the entry level, now $39,264, which should rise to $42,000—and they should receive better benefits. “We think it is scandalous how [little] postdoctoral fellows are paid,” Tilghman said.

NIH should also encourage study sections to look favorably upon research projects that employ staff scientists, and institutions should create more of these positions. There is an “urban myth” that staff scientists are less productive than graduate students, Tilghman said. In fact, she said, graduate students are productive for a couple of years but are otherwise a “drain on the system.” Staff scientists, by contrast, are “often the glue that holds your lab together.”

Although the panel did not say the overall number of trainees should decline, the recommendations, if adopted, should make the growth in the number of trainees at least slow down because “we’re making it more expensive to have those individuals,” Tilghman said.

The recommendations drew concern from at least one ACD member. Biologist Robert Horvitz, of the Massachusetts Institute of Technology in Cambridge, questioned whether NIH should make “risky” changes to the system at a time when NIH is struggling with flat budgets and record-low success rates. “Some of this makes me very nervous,” he said. But Tilghman, who headed a National Research Council panel 14 years ago that she said came to “identical conclusions,” disagreed. “The only time it’s possible to make hard decisions … is actually during tough times,” she said.

NIH Director Francis Collins said he would like see some “experiments” before making “more systemically disruptive” changes to the funding system. But, he added, this time the Tilghman panel’s recommendations “will go somewhere. I promise you that.”

Tomorrow, ScienceInsider will post a story on another draft report presented later in the ACD meeting on diversity in the biomedical research workforce.

http://news.sciencemag.org/scienceinsider/2012/06/nih-panel-urges-steps-to-control.html

Can NIH Renovate the Biomedical Workforce?

By Michael Price

June 22, 2012

“The most effective training dollars that the NIH has to expend are those in their training grants.” —Shirley Tilghman

When molecular biologist and Princeton University President Shirley M. Tilghman first sounded the alarm about the need for major overhauls to the way the United States trains its biomedical workforce in the 1998 National Academies of Science report Trends in the Early Careers of Life Scientists, many of her proposals fell on deaf ears. Fourteen years later, Tilghman is arguing again for training reform, this time as chair of the National Institutes of Health (NIH) Biomedical Research Workforce Working Group.

Last week, Tilghman presented a draft of her group’s latest report to NIH’s Advisory Committee to the Director (ACD) at NIH headquarters in Bethesda, Maryland. In the report, the group calls on NIH to divert funding from research grants to training grants for graduate students, support more postdocs on training grants, increase pay and improve benefits for postdocs, and boost the prestige and remuneration of staff scientist positions in academic labs.

At the presentation, Tilghman and the other members of the working group argued that in its present state, the graduate training system at our nation’s universities and the workforce that graduates enter into are dysfunctional and unsustainable. At the root of that dysfunction, Tilghman said, is a mismatch between the training most graduate students receive and the careers most Ph.D. graduates end up in.

Shirley Tilghman

The number of academic jobs has shrunk dramatically compared to the number of new graduates. NIH estimates that 26% of biomedical Ph.D. recipients end up in tenure-track academic positions, down from 34% in 1993; meanwhile, the proportion of nontenure-track academic positions has remained constant. The growth in jobs for Ph.D. biomedical scientists, the working group concluded, is outside academia, so new graduates must be prepared to work in other roles: in industry, in government, or in positions tangentially related to their degrees, such as science writing or policy, Tilghman said.

Shifting funds toward training

How can universities prepare graduate students better for the careers they’re most likely to wind up in? One way, Tilghman said, would be for NIH to shift funding from R01 research grants, which currently support the majority of graduate students in biomedical sciences, to NIH training grants, which are peer-reviewed by NIH for their training-related virtues. The total number of graduate students supported by NIH, the report says, should remain constant.

While the number of graduate students supported by research grants has been higher than the number supported on training grants since the early 1980s, the gap steadily widened as NIH’s research budget grew—then shot up in the early 2000s when NIH’s budget doubled over 5 years (see graph below).

CREDIT: National Institutes of Health

Research grants are far and away the most common source of funding for graduate students today. Click here to enlarge image.

The report’s authors argue that many graduate students are ill-served by this approach because it limits the ability of NIH to hold principal investigators (PIs) accountable in their roles as mentors. Without oversight, Tilghman argued, it’s easy for PIs to see and treat their graduate students as laborers rather than scientists in training. If a larger proportion of the graduate student population were supported on training grants, she said, NIH could better monitor students’ training and ensure broader exposure to careers outside of academia—and better training in the skills needed to perform well in those careers.

The members of the working group “are, I think, unanimously of the view that the most effective training dollars that the NIH has to expend are those in their training grants,” Tilghman said. “Training grants are immensely effective at inducing good behavior on the part of graduate programs. … It is the only mechanism we have to really peer review the quality of graduate training.”

Robert Horvitz

Some members of the ACD weren’t buying it. Biologist Robert Horvitz of the Massachusetts Institute of Technology in Cambridge argued that shifting funding away from R01s takes away too much autonomy from PIs. “One wants to be sure that the principal investigators, who are supposed to be doing the research, continue to have enough flexibility to be able to support the research they want to do,” he said. Taking away that flexibility, he argued, could reduce research productivity.

Other ACD members, including Haile Debas, director of the University of California Global Health Institute in San Francisco, were more supportive of the recommendations. While such a shift would be bold, Debas said, “you can also do harm by doing nothing.” He proposed that NIH launch experiments to determine whether graduate students who get industry experience during their traineeships, for example, go on to have successful careers in industry.

Judith Bond, incoming president of the Federation of American Societies for Experimental Biology (FASEB) and a biochemist at Pennsylvania State University, Hershey, also disagrees with this recommendation, saying in an interview with Science Careers that “oversight of student training should be left to the universities, not the federal government.” Bond is not a member of the ACD.

Upping postdoc pay

The situation is equally grim, if not grimmer, for postdoctoral researchers, Tilghman and her colleagues argue in the report. The report recommends that more postdocs be supported by training grants and fewer by PIs’ research grants, with the total number of NIH-supported postdocs remaining constant or perhaps decreasing.

One way of reducing the number of postdocs—and decreasing the intense competition for jobs—would be to increase postdoc salaries from $39,264 to $42,000 and provide benefits equal to those of employees at their institutions, the report says. It also recommends that NIH mandate a 4% raise before the third year of postdoctoral work and a 6% raise before the seventh. The idea, Tilghman said, would be to motivate PIs to help their postdocs move as quickly as possible into jobs rather than toil away as a postdoc.

“One of the things the committee really grappled with is: To what degree are these [people] trainees … and to what extent are they worker bees who are the producers of the research in our lab?” Tilghman said. The working group felt strongly, she said, that emphasizing training is the best way to produce well-trained future PIs.

Cato Laurencin, an ACD member and CEO of the Connecticut Institute for Clinical and Translational Science in Farmington, agreed with the working group’s postdoc recommendations. “We’ve gotten into a mindset where postdocs last 5, 6, 7 years,” he said. “After 5 or 6 years of Ph.D. training, people are spending their careers in training. I am very concerned about that.”

Bond, too, agreed with the postdoc salary recommendation. “In general, FASEB is in favor of increasing postdoc salaries. … Postdocs are essential to work in the lab, and they should be paid a living wage,” she said.

But ACD member Horvitz was skeptical. The money to raise postdoc salaries “has to come from somewhere,” he said, and given NIH’s current budget woes, it might be impractical to raise postdoc pay. If PIs were forced to make do with fewer (but better paid) postdocs, he argued, lab productivity would probably decline.

Improving the staff scientist position

One way to provide more job opportunities for Ph.D. scientists would be to increase the number and stature of staff scientists in university labs. (See “A Hidden Academic Workforce.”) One way this could be accomplished would be to have universities shoulder a larger percentage of researcher salaries than most currently do, Tilghman said. That would make the positions more stable and less vulnerable to changes in NIH budgets and competitive grant renewals.

Those salaries should also be increased, the report argues, to be commensurate with the training levels of staff scientists and their value to the lab. If the number of postdocs drops as a result of raising postdoc salaries, staff scientists could fill the gap, which should help attract talented scientists to these positions.

Finally, Tilghman recommended that NIH award grants preferentially to PIs who employ staff scientists. “When I think about the tradeoff of a graduate student for a staff scientist who is already extremely well trained, who can work without constant supervision, who can really help train the younger people in the laboratory, … I actually think we’ll be more productive,” she said.

Tough times afford opportunity

Two of the key recommendations of the report—shifting funding away from R01s to create more training grants and increasing postdoc pay and benefits—met with resistance from members of the ACD. Yet Tilghman believes that these recommendations will gain more traction with NIH leadership than when she proposed similar reforms in 1998. Times are much tougher now, she said, which makes it easier to make larger changes. “The only time when it’s going to be possible to make hard decisions that would … have a long-term, beneficial effect on all the players in the biomedical workforce is … during tough times,” Tilghman said. “Doing nothing, in my view, is not an option.”

NIH Director Francis Collins said that the ACD appeared generally supportive of the report and that NIH would collect more data, build models, and run pilot programs so that they can better predict the impact of implementing the report’s recommendations. “I do think the NIH will want to take some action here,” he said. “I like the idea of doing some experiments to get some early indications of whether the interventions are achieving the goals that we hope for. It would be a very good thing before we do something more systematically disruptive in ways that we didn’t intend.”

Michael Price is a staff writer for Science Careers.http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/201206_22/caredit.a1200069

A Hidden Academic Workforce

 By Siri Carpenter

June 08, 2012

The staff scientist role is not just a boon for universities. It is also a career destination for some of the tens of thousands of highly trained researchers who wish to remain in or close to academic research—a cadre that’s far too large for the number of available faculty positions.

On university campuses, students, postdocs, and professors are so ubiquitous that it would be easy not to notice the other Ph.D.-level professional scientists—often dubbed staff scientists—who roam the halls. Some of them work as lab managers or project directors; others direct or help operate university core facilities. Despite their low profile, staff scientists are numerous and make a major contribution to their institutions.

At the University of Wisconsin (UW), Madison, between 700 and 800 members of the academic staff are Ph.D.-level scientists, estimates Heather Daniels, chair of the university’s Academic Staff Executive Committee. For comparison, the university has 2137 faculty members in all disciplines, with a number of staff scientists comparable to the number of science faculty members. The same may well be true at other, similar universities.

Many staff scientists write grants. In fact, UW Madison staff scientists brought in $120 million to the university last year, out of a total grant portfolio worth just over $1 billion. When you include grants on which staff scientists serve as co–principal investigators (co-PIs), that figure rises to $240 million.

The staff scientist role is not just a boon for universities. It is also a career destination for some of the tens of thousands of highly trained researchers who wish to remain in or close to academic research—a cadre that’s far too large for the number of available faculty positions.

Such positions typically pay better than postdocs and sometimes about as well as assistant professor positions. At UW Madison, the minimum starting salary for an academic staff scientist is $40,055. Unfortunately, there is no mechanism for annual merit-based increases, so staff scientists typically receive raises only when the state pay plan calls for an across-the-board increase. As a result, “the longer you’re here, the more your salary tends to fall behind,” Daniels says.

Most staff scientists are grant supported, a fact that, in addition to creating job insecurity, limits the ability of staff-scientist PIs to perpetuate their own careers. According to federal rules, researchers are not allowed to use time supported by federal grants to write grants. Government auditors have interpreted the rules to stipulate that grant-funded researchers are on the clock 100% of the time, Daniels says, even if they work much longer weeks than the 40-hour standard. So whenever a staff scientist’s salary comes entirely from federal grants, federal grant writing is effectively forbidden. The solution, usually, is to find non-federal money to pay part of that salary. “It’s been a struggle for a lot of universities,” she says, “to come up with non-grant dollars to give folks time to write grants. I think researchers are feeling really constrained by this.”

On the positive side, the role of staff scientist has several benefits. Staff scientists typically travel less, work fewer nights and weekends, spend less time writing grants, and have fewer administrative responsibilities than faculty members. They seldom have formal teaching responsibilities, which some staff scientists consider a perk. Much more than postdocs, staff scientists tend to have a hand in more than one scientific project at a time.

A nonfaculty career path can also provide geographic stability, notes Alexander Pico, a staff research scientist at the Gladstone Institutes, a group of research institutes closely affiliated with the University of California, San Francisco (UCSF). “If you go with the traditional route, you have to move a lot. You have to prove yourself as a Ph.D. student in one institution, then prove yourself in another as a postdoc, and then you’re expected to continue that as faculty, proving yourself in one environment after another before you get tenure,” Pico says. “The staff position is a little more stable. I really like the working culture at Gladstone, and I would really hate to have to leave just because it’s a convention in the career path.”

Here, we profile a sampling of staff scientists from two universities—UW Madison and UCSF—who have foregone the tenure track while remaining deeply rooted in university life.

Read Full Post »

Reported by: Dr. Venkat S. Karra, Ph.D

An interesting Interview by Dr. Miller with renowned OncoMeds on ASCO 2012 annual meeting:

American Society of Clinical Oncology

Kathy D. Miller, MD: Hello. I am Kathy Miller, Associate Professor of Medicine at the Indiana University School of Medicine in Indianapolis. I would like to welcome you to Medscape Oncology Insights, our annual wrap-up of the 2012 meeting of the American Society of Clinical Oncology (ASCO®). I am joined today by several of my colleagues: Dr. David Kerr, Professor of Cancer Medicine from the University of Oxford and former President of the European Society of Medical Oncology; Dr. Bruce Cheson, Deputy Chief of Hematology and Oncology, and Head of Hematology at the Georgetown University Hospital and Lombardi Comprehensive Cancer Center in Washington, DC; and last but not least, Dr. Maurie Markman, Vice President, Patient Oncology Services, and National Director for Medical Oncology, Cancer Treatment Centers of America, based in Philadelphia. Thank you all for joining us today.

Maurie, let’s start with you. When you think about highlights of this year’s ASCO® meeting for genitourinary (GU) and ovarian cancers, what are you taking home?

Ovarian Cancer: Clear Benefit With Bevacizumab

Maurie Markman, MD: There was a very interesting session, because of what was seen and what was not seen. The surprise for me was the randomized phase 3 trial[1] that looked at the question of bevacizumab plus chemotherapy vs chemotherapy alone in platinum-resistant ovarian cancer. Everyone would have predicted, on the basis of 30-plus years of research in this area, that it would be a negative trial, as all past trials have been. In fact, I was convinced it would be a negative trial because there were no press releases ahead of time. That usually tells you the story.

It turns out that the combination of bevacizumab and chemotherapy substantially improved progression-free survival in this setting — the first time this has ever been seen. I would suspect, however, that what most people take away from it is the fact that there was a tripling of the objective response rate, and clear evidence of patient benefit. This was very much a surprise; I don’t think anyone expected this.

The next question is going to be, what happens next? Is this drug going to receive regulatory approval on this basis? This is clearly an unmet need. That was a real positive.

On the other hand, one could argue that in contrast to other things that we will hear about, there is still no target of therapy in any of the gynecologic cancers. We haven’t found anything that would suggest an epidermal growth factor receptor (EGFR) mutation, or anything to suggest a KRAS mutation or anything that could point to where we need to go in this area. On the one hand, that is a very interesting finding, from the perspective of biology. But it is quite discouraging from the perspective of drug development.

Dr. Miller: The Cancer Genome Atlas (TCGA) data had to be discouraging. Essentially, every ovarian tumor is a different ovarian tumor.

Dr. Markman: Absolutely.

Dr. Miller: You have 10,000 rare diseases.

Dr. Markman: Other than p53, and we have known of that mutation for decades. It is universal, certainly in the high-grade cancers. But we don’t know how to deal with it. Other than that, the number of mutations found per tumor is enormous, and there are no patterns. So we have to do a lot of thinking. That is, the smart biologists have to do a lot of thinking.

Lymphoma: Chemotherapy? Enough Is Enough

Dr. Miller: Bruce, you spend a lot of your time focusing on the hematology side of malignancies. With the American Society of Hematology (ASH) and a whole separate meeting, sometimes it seems as though hematology doesn’t get as much attention at ASCO®. Was there any big news in the hematologic malignancies that people need to know about?

Bruce D. Cheson, MD: There were not. However, this has the potential to be an historic meeting, because we are going to finally learn that “enough is enough” with chemotherapy, and we are at that point.

We saw some very historic presentations. We saw rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP), vs rituximab, cyclophosphamide, vincristine, and prednisone (R-CVP), vs rituximab, fludarabine, and mitoxantrone (RFM) — where basically the only difference is in toxicity.[2]

Dr. Miller: “Pick your poison” — toxicity, but you will get to the same place.

Dr. Cheson: Yes. We also saw that R-bendamustine was better than R-CHOP,[3] but there are questions about the R-CHOP arm looking kind of lame. We were thinking, where are we going in follicular lymphoma?

Where we are going is what John Leonard and colleagues[4] presented in the relapse setting, and that’s biological agents. We have lots of those. We have lots of targeted agents. I predict that in the next year, instead of hearing more about R-CHOP and R-bendamustine, we are going to be hearing more about the GS-1101s; the PI3-kinase inhibitors; ibrutinib, the Bruton tyrosine kinase (BTK) inhibitor; and those drugs which we in the Cancer and Leukemia Group B (CLGB) (now Alliance) have been planning on combining with biological strategies. We are going to be trying to get rid of chemotherapy. This may be, hopefully, the last meeting we hear about regimen A vs regimen B. It’s kind of sickening.

We have the same situation in Hodgkin lymphoma — where we cure, depending on the stage, up to 90% of people, and at this meeting we see adriamycin, bleomycin, vinblastine, and dacarbazine (ABVD) vs bleomycin, etoposide, adriamycin, cyclophosphamide, vincristine, procarbazine, and prednisone (BEACOPP) again for about the fourth iteration. Lo and behold, there is no survival difference.

We saw lots of that, but now we have other drugs. We have brentuximab vedotin, which is an antibody/drug conjugate. It is anti-CD30, linked to auristatin, a tubulin poison, which in transplant-refractory patients had a 75% response rate. There weren’t any data at this meeting. The data on that drug were presented at ASH. But there are now trials incorporating brentuximab/vedotin, not only in second-line treatment, but we are now moving it up into front-line.

So, we have the tools; it’s just a question of being smart enough, and figuring out how to put them together in a coherent fashion, on the basis of scientific rationale. The most important thing I took away from this meeting is, enough is enough. You can pick your poison, as you put it. But don’t hold on to it for dear life, because there are new, very exciting drugs coming along that are being combined in a biological fashion.

Breast Cancer: Targeted Therapies Are Clear Winners

Dr. Miller: You might have snuck into a breast cancer session, because that is how I would summarize the breast cancer world this year as well. We saw adjuvant trials, metastatic trials, comparing one chemotherapy regimen with another. To summarize a lot of data, pick your third-generation adjuvant chemotherapy regimen and the toxicity will differ, depending on the drugs, but the efficacy doesn’t differ at all. In the metastatic setting, newer wasn’t better. It brought more toxicity, which then led to more dose reductions, which hampered efficacy.

So when we thought we were getting newer and better drugs, they didn’t actually do better for our patients. It sounded a little bit like ABVD vs BEACOPP in Hodgkin disease.

Dr. Cheson: We have to get rid of chemotherapy.

Dr. Miller: Targeted therapies, either with direct molecular targets or antibody/ drug conjugates, were the clear winners, with major improvements in efficacy and substantially less toxicity. I would be quite happy if I didn’t have to look at another basic chemotherapy study in breast cancer again. Was that the case in the gastrointestinal (GI) studies as well, David?

GI Phenotypes and 5 Daughters of Eve

David J. Kerr, MD: It was. We are seeing mildly disappointing and moderately good results. The big, well-designed study, REAL 3,[5] looking at the role of panitumumab with combination chemotherapy, had negative findings. Panitumumab seemed to do a bit worse, which was somewhat disappointing.

Some positives are coming out in colorectal cancer. The antiangiogenic therapies look as if they are here to stay. A nice randomized trial[6] looking at discontinuation or continuation of bevacizumab following progression in first-line chemotherapy shows that the bevacizumab follow-through has significant advantages, in terms of progression-free survival.

An interesting, clever, genetically designed drug, aflibercept, which is a vascular endothelial growth factor (VGEF) trap, showed very promising activity in second- line therapy.[7] So something is holding true there. We have a new drug, regorafenib, which is one of these oral multitargeted kinase inhibitors, that seems to have an important clinically useful role to play in third-line chemotherapy.

For me, the take-home message, in contradistinction to Maurie, is that we are starting to get a feel for the different molecular phenotypes for colorectal cancer. It looks as though there may be 5 daughters of Eve, and it needs to be confirmed. We need to internationalize what we are doing. It looks as though some patterns are starting to emerge that will allow us to make prognostic inferences, possibly treatment-wise, and so on. Things are starting to stack up for us, in terms of driver mutations, therapeutics, and providing the patient with better information, so this is somewhat luckier than the situation with ovarian just now.

How Do We Eliminate Chemotherapy?

Dr. Miller: When we look ahead, we would all love to get rid of chemotherapy. How do we do that? By understanding the biology, which is the easy answer. Bruce, you mentioned that we do tend to cling to our chemotherapy regimens. We have been having discussions about how to do this in breast cancer, and there is a great reluctance to give up the regimens that have gotten us to where we are.

Dr. Cheson: Reluctance from the doctor, but not from the patient.

Dr. Miller: So how do we move forward?

Dr. Cheson: There are a couple of ways. First is a better understanding of tumor biology. We have been sitting around doing what we do for so long. Now we have some tools, but we need to know how to apply them. At every clinical trial in CLGB (now Alliance), we have correlative science. We are doing natural killer (NK) cell numbers and functions. We are doing microarrays so that we can understand which regimen works in which patient. It may not be like your field (gynecologic cancer), where every patient has their own disease, which is what I get accused of saying in lymphoma all the time. I am glad someone else has that problem.

We have the drugs. We need to know how to put them together, but which patients should we target? Then, we need to figure out how to move them up front — such drugs as brentuximab, the Hodgkin drug, and anti-CD30, which in anaplastic large cell lymphoma has an 86% response rate in relapsed patients. In a good clinical trial, we need to take a risk and just do it. If a drug is 86% effective in the refractory setting, it is not going to be worse up front.

There are those who will say, “Well, the response may not last as long.” But there are several ways you can introduce these drugs in an up-front setting, such as window-of-opportunity studies, Or, you can first tack them on to some chemotherapy and then try and wean off the chemotherapy.

There are a number of ways to do it. You just have to do it. You have to take a risk and view it as a challenge. You have to say, “We have had enough of this; let’s move on.” We have the tools; let’s do it.

I-SPY: New Paradigm for Clinical Trials?

Dr. Miller: Maurie, you know I can’t resist, because this issue of clinical trials came up last year when we were talking about melanoma data, with striking activity reported by the BRAF investigators. Are you going to do those trials? Are you willing to take that risk?

Dr. Markman: Obviously, you have to look at the individual cancers. Consider the report that said breast cancer had 10 different cancers, maybe more. It is going to be harder and harder to do randomized trials in 10 subsets, even in a disease that is as common as breast cancer.

Dr. Miller: We are actually closer to your problem, where each patient is an individual disease, than to Bruce’s situation.

Dr. Markman: We do have to come up with a different clinical trial paradigm as we get to smaller subsets. Of course, the tsunami that many have predicted is here. It wasn’t part of the meeting directly, but a half-dozen or dozen companies are now offering whole-genome sequencing. We have to figure out how to use all these things. It may not be as simple as a particular molecular abnormality, but it may be, as many people are saying, particular systems.

For example, in the ovarian cancer area, there are BRCA1 and BRCA2, and there are some drugs that affect those mutations. But a very important study from last year looked at maintenance therapy in the second-line setting with olaparib[8] in tumors that were said to have a BRCA-ness profile. In other words, there is a molecular profile that is similar to that of BRCA1 and BRCA2, and in fact, it was a very positive trial, at least from the perspective of progression-free survival. You may not be able to find a particular molecular abnormality, but there may be patterns. And that may be (in our area, where you can’t find an abnormality) much more complicated than just finding a mutation. That may be the way forward in such diseases as ovarian cancer.

Dr. Cheson: Maybe I did wander into the breast meeting, but we need to reconsider how many phase 3 trials we want to do. The I-SPY concept is where we need to be going. You take a regimen that should work in a subset of patients, and you test that and see if it does. Then you can figure out who responded and who didn’t, doing various molecular techniques, and then you take the patients who responded and put them in one pile, and enrich that pile. You take the patients who didn’t respond, figure out why they didn’t respond, and retarget them. After a while, you have high response rates in this one, and you start to improve the outcome in the other one. We need to do this. There is no way around it. It’s coming.

I hate to say this, but I think maintenance is for losers, because if you are going to do right, you have to do it up front. Progression-free survival doesn’t necessarily correlate with overall survival. It is nice. You don’t see the doctor as often. But we need to do this right the first time. I thoroughly agree with you, Maurie — it is going to be a conglomerate of things, and that is why we have new, exciting drugs coming down the pipeline, such as these PI3-kinase mammalian target of rapamycin (mTOR) hybrid inhibitors. We need to block multiple pathways, because the tumors are damn smart. If you block one, it has all these other ways of getting around you.

More Fun With Something vs Nothing Trials

Dr. Kerr: Indeed, and that comes back to Maurie’s point about thinking in systems and programmatically. The answer to Kathy’s question — can we get rid of chemotherapy? — is no. But can we do better? Think about the huge focus that we have in trying to map biomarkers to the new drugs, often mechanistic. We are not doing enough with the conventional cytotoxic drugs that we have.

We could do a lot more. Genome-wide association studies, looking at patterns of toxicity, so that we can use polymorphisms to say “you get full dose of the drug, you get the reduced dose.” We could be using the tools of trade that we have much better. With the new platform technologies, we should be able select patients who do better with 5-fluorouracil (5-FU), with taxane, and so on.

Dr. Cheson: So, how do you study that in randomized trials?

Dr. Kerr: We are lucky in that we have been collecting material from the old days. Makes us something like Dickensian characters. We have hoarded a lot of material from something vs nothing-type trials, and that gives us the opportunity, in that large randomized setting, to develop some of these predictive markers for “yes or no 5-FU, yes or no taxane.” So, it is going back to our youths, when we did all that stuff.

Dr. Miller: That is how we made advances in breast cancer. The predecessors in my field collected tumors long before the technology that we now use to interrogate them was even a glint in someone’s eye. That may actually have a bigger global impact.

Dr. Kerr: I think so.

Dr. Miller: Although this is the American Society of Clinical Oncology, one third of our members are from outside the United States, one half of the attendees are from outside the United States, and most of the fabulous molecular things we have been talking about are not within reach of most patients globally. But some of our old things are cheap. Perhaps using them in a more intelligent way may actually have more benefit on a global scale.

A Question of Value

Dr. Kerr: Exactly. So you have segued into the concept of value. I was delighted to see the brief stance that ASCO® has taken toward value, and saying that there are some things that we do that don’t add value to the care of the patients that we look after. I am a huge fan of US medicine at its the very best, but there’s a lot of waste in what we do. The fact that ASCO® is trying to identify this — 17.5% of the gross domestic product (GDP) is being spent in health now — I thought that was fantastic. Yes, there is value out there, and we should seek it. We should mine old databases, fiddle with new drugs and old drugs, teach old drugs new tricks, and so on.

Dr. Cheson: Five years from now, you are going to look at this video, and you had a whole list of “mabs and mibs” that you are going to figure out and put together, and all of a sudden, FOLFOX, FOLFIRI will be “pffft.” You are going to be combining those biologic agents intelligently, and you are going to get rid of those chemotherapy drugs, I predict.

Dr. Miller: We are out of time for this year, but I am going to book you both for 5 years from now to see whose prediction of the future comes true, where the value lies, and where we can make improvements, because I’m not so sure that they are mutually exclusive. But that’s all from this year’s Medscape Oncology wrap-up of the Annual Oncology Society Meeting. Thank you again for joining me.

References

  1. Pujade-Lauraine E, Hilpert F, Weber B, et al. AURELIA: a randomized phase III trial evaluating bevacizumab (BEV) plus chemotherapy (CT) for platinum (PT)-resistant recurrent ovarian cancer (OC). Program and abstracts of the American Society of Clinical Oncology Annual Meeting and Exposition; June 1-5, 2012; Chicago, Illinois. Abstract LBA5002.
  2. Federico M, Luminari S, Dondi A, et al. R-CVP versus R-CHOP versus R-FM as first-line therapy for advanced-stage follicular lymphoma: Final results of FOLL05 trial from the Fondazione Italiana Linfomi (FIL). Program and abstracts of the American Society of Clinical Oncology Annual Meeting and Exposition; June 1-5, 2012; Chicago, Illinois. Abstract 8006.
  3. Rummel MJ, Niederle N, Maschmeyer G, et al. Bendamustine plus rituximab (B-R) versus CHOP plus rituximab (CHOP-R) as first-line treatment in patients with indolent and mantle cell lymphomas (MCL): updated results from the StiL NHL1 study. Program and abstracts of the American Society of Clinical Oncology Annual Meeting and Exposition; June 1-5, 2012; Chicago, Illinois. Abstract 3.
  4. Leonard J, Jung SH, Johnson JL, et al. CALGB 50401: a randomized trial of lenalidomide alone versus lenalidomide plus rituximab in patients with recurrent follicular lymphoma. Program and abstracts of the American Society of Clinical Oncology Annual Meeting and Exposition; June 1-5, 2012; Chicago, Illinois. Abstract 8000.
  5. Waddell TS, Chau I, Barbachano Y, et al. A randomized, multicenter trial of epirubicin, oxaliplatin, and capecitabine (EOC) plus panitumumab in advanced esophagogastric cancer (REAL3). Program and abstracts of the American Society of Clinical Oncology Annual Meeting and Exposition; June 1-5, 2012; Chicago, Illinois. Abstract LBA4000.
  6. Arnold D, Andre T, Bennouna J, et al. Bevacizumab (BEV) plus chemotherapy (CT) continued beyond first progression in patients with metastatic colorectal cancer (mCRC) previously treated with BEV plus CT: results of a randomized phase III intergroup study (TML study). Program and abstracts of the American Society of Clinical Oncology Annual Meeting and Exposition; June 1-5, 2012; Chicago, Illinois. Abstract CRA3503.
  7. Allegra CJ, Lakomy R, Tabernero J, et al. Effects of prior bevacizumab (B) use on outcomes from the VELOUR study: a phase III study of aflibercept (Afl) and FOLFIRI in patients (pts) with metastatic colorectal cancer (mCRC) after failure of an oxaliplatin regimen. Program and abstracts of the American Society of Clinical Oncology Annual Meeting and Exposition; June 1-5, 2012; Chicago, Illinois. Abstract 3505.
  8. Ledermann JA, Harter P, Gourley C, et al. Phase II randomized placebo-controlled study of olaparib (AZD2281) in patients with platinum-sensitive relapsed serous ovarian cancer (PSR SOC). Program and abstracts of the American Society of Clinical Oncology; June 3-7, 2011; Chicago, Illinois. Abstract 5003.

Source

Article(s) of Relevance:

I-SPY 2 Clinical Trial Design Promises to Accelerate FDA Approvals

Reported by: Dr. Venkat S. Karra, Ph.D

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Curated by: Dr. Venkat S. Karra, Ph.D

Auguste Deter. Alois Alzheimer's patient in No...

Nuerodegenertive disease – Alzheimer’s – is presumed to be caused by the accumulation of β-amyloid.

The diagnosis of Alzheimer’s disease focuses on

β-amyloid protein and

tau protein

Though much attention is on radiolabeled markers, imaging βamyloid is problematic because many cognitively normal elderly have large amounts of β-amyloid in their brain, and appear as “positives” in the imaging tests.

At the same time therapeutic approaches for Alzheimer’s disease have not been focused much on the process of producing a neurofibrillary tangle composed on tau protein.

Various brain sections showing tau protein

Various brain sections showing tau protein (Photo credit: WBUR)

Now the BUSM researchers identified a new group of proteins, termed RNA-binding proteins, which accumulate in the brains of patients with Alzheimer’s disease, and are present at much lower levels in subjects who are cognitively intact.

The researchers believe this work opens up novel approaches to diagnose and stage the likelihood of progression by quantifying the levels of these RNA-binding protein biomarkers that accumulate in the brains of Alzheimer patients.

The group found two different proteins, both of which show striking patterns of accumulation. “Proteins such as TIA-1 and TTP, accumulate in neurons that accumulate tau protein, and co-localize with neurofibrillary tangles. These proteins also bind to tau, and so might participate in the disease process,” explained senior author Benjamin Wolozin, MD, PhD, a professor in the departments of pharmacology and neurology at BUSM.

“A different RNA binding protein, G3BP, accumulates primarily in neurons that do not accumulate pathological tau protein.

This observation is striking because it shows that neurons lacking tau aggregates (and neurofibrillary tangles) are also affected by the disease process,” he added.

Wolozin’s group also pursued the observation that some of the RNA binding proteins bind to tau protein, and tested whether one of these proteins, TIA-1, might contribute to the disease process.

‘Stress’ induced aggregation of RNA-binding proteins

Previously, scientists like Tara Vanderweyde et. al., have demonstrated that TIA-1 spontaneously aggregates in response to stress as a normal part of the stress response. They examined the relationship between Stress Granules (SGs) and neuropathology in brain tissue from P301L Tau transgenic mice, as well as in cases of Alzheimer’s disease and FTDP-17.

Stress Granules (SGs) are ‘Stress’ induced aggregation of RNA-binding proteins.

The pattern of SG pathology differed dramatically based on the RNA-binding protein examined. SGs positive for T-cell intracellular antigen-1 (TIA-1) or tristetraprolin (TTP) initially did not co-localize with tau pathology, but then merge with tau inclusions as disease severity increases. In contrast, G3BP (ras GAP-binding protein) identifies a novel type of molecular pathology that shows increasing accumulation in neurons with increasing disease severity, but often is not associated with classic markers of tau pathology. TIA-1 and TTP both bind phospho-tau, and TIA-1 overexpression induces formation of inclusions containing phospho-tau. These data suggest that SG formation might stimulate tau pathophysiology.

Thus, study of RNA-binding proteins and SG biology highlights novel pathways interacting with the pathophysiology of AD.

With this understanding, Wolozin and his colleagues hypothesize that since TIA-1 binds tau, it might stimulate tau aggregation during the stress response. They introduced TIA-1 into neurons with tau protein, and subjected the neurons to stress. Consistent with their hypothesis, tau spontaneously aggregated in the presence of TIA-1, but not in the absence. Thus, the group has potentially identified an entirely novel mechanism to induce tau aggregates de novo.

In future work, the group hopes to use this novel finding to understand how neurofibrillary tangles for in Alzheimer’s disease and to screen for novel compounds that might inhibit the progression of Alzheimer’s disease.

They believe that it may open up novel approaches to diagnose and stage the progression likelihood of the disease in Alzheimer patients.

Curated by: Dr. Venkat S. Karra, Ph.D

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