News Category: Scientific Coordination

Sage Bionetworks launches new coordination center with the National Cancer Institute to increase collaboration and resource sharing across the cancer biology community

Aims to improve interdisciplinary collaboration and increase diversity of early-stage investigators in cancer research

SEATTLE, NOVEMBER 15, 2022 – Sage Bionetworks is leading a new coordination center focused on collaboration, resource sharing, and outreach for the cancer research community across six programs funded by the National Institute of Health (NIH) / National Cancer Institute (NCI) Division of Cancer Biology (DCB).

Interdisciplinary communities of scientists convened by DCB are working on important questions in basic and translational cancer research. The Multi-Consortia Coordinating (MC2) Center for Cancer Biology, funded by DCB and hosted by Sage Bionetworks, breaks down existing silos and barriers that can hamper research collaboration. The MC2 Center works to motivate engagement and collaboration across consortia, support resource sharing, and disseminate knowledge among cancer biologists.

“Sage Bionetworks’ well-established Synapse platform, and the software ecosystem we’ve built on and around it, enables data and tool sharing and provides a solid foundation for the MC2 Center’s open science approach,” said James Eddy, Director of Architecture & Operations at Sage Bionetworks. “The MC2 Center facilitates research teams’ ability to collaborate and helps the broader cancer biology community find and use the resources these teams are generating.”

The MC2 Center aims to catalyze cancer research collaboration across disciplines and institutional boundaries. Sage Bionetworks and its project partners at Yale University, Colorado University Anschutz, Harvard Medical School, and the Carbone Cancer Center (CCC) and Institute for Clinical and Translational Research (ICTR) at the University of Wisconsin-Madison are learning and piloting methods and tools that support this goal.

The MC2 Center provides the perfect opportunity to build evidence-driven collaboration systems, learning through a “science of Team Science” approach about how to foster a culture of trust and openness in the cancer research community.

“Applying lessons from the field of the Science of Team Science to the development of the MC2 network allows us to provide targeted resources to build a community of researchers across these six successful programs,” said Betsy Rolland, Director of Team Science + Research Development at UWCCC and ICTR. “Our team will facilitate connections that provide researchers with even greater opportunities to collaborate on high-impact transformative research that, ultimately, will benefit cancer patients.”

Investing in the next generation of cancer biologists is also an important goal of the MC2 Center effort. Increased diversity and inclusion of investigators at the early stages of their careers throughout the infrastructure of MC2 Center – from steering committees to award programs – can create opportunities for researchers from historically marginalized communities to strengthen their career trajectories and meaningfully contribute to collaborative biomedical science.

“Discovery requires a diversity of perspectives and opportunities for many types of researchers to contribute to collective problem solving,” shares Julie Bletz, Director of Science Coordination at Sage Bionetworks. “At Sage Bionetworks, we believe finding ways to better support and integrate early-career investigators is a key element in creating a successful future for cancer biology research. Centering an inclusive and team-based approach can speed the translation of science into medicine.”

ABOUT SAGE BIONETWORKS
Sage Bionetworks (sagebionetworks.org) is a non-profit health research organization based in Seattle, Washington. Sage Bionetworks uses open practices that increase the reliability of scientific claims to speed the translation of science to medicine. Through its work, Sage Bionetworks supports responsible data sharing, objective evaluation of methods and results across researchers, and the empowerment of participants to be active partners in research.

MEDIA CONTACT:
Molly Michal, Team Soapbox
206-528-2550
molly@teamsoapbox.com

Sage Bionetworks awarded NIH grant to facilitate collaborative translation research on exceptional longevity

The Exceptional Longevity Data Management and Coordinating Center enables collaborations between researchers to identify what protective factors contribute to healthy aging past the century mark

SEATTLE, October 18, 2022 – A new National Institutes of Health (NIH) funded data management and coordination center (DMCC) will advance ongoing research on people living past 100 years old and the factors that contribute to their resilience and health.

The Exceptional Longevity (EL) DMCC brings together gerontology researchers, data scientists, and bioethicists in an open science approach to centralizing many sources of ongoing research into advanced age, and how our life spans and “health spans” – our period of good health and wellbeing – intersect.

The Exceptional Longevity Data Portal will be built on Sage Bionetworks’ Synapse platform, a technology platform that supports scientific collaborations centered around shared biomedical data sets under a robust data governance framework. The NIH’s ongoing Accelerating Medicines Partnership® Program for Alzheimer’s Disease (AMP® AD) is one example of where this tool is already in use to facilitate collaborative neurodegenerative disease and aging research through the AD Knowledge Portal.

“The EL DMCC will open a new frontier in research into aging, in which large-scale datasets are made widely accessible to accelerate discoveries that will benefit clinicians and patients grappling with age-related disease and decline,” explains Anna Greenwood, Director of Alzheimer’s Disease Translational Research at Sage Bionetworks. “Through the Data Portal, qualified researchers will have easier access to data that is rigorously managed. Ultimately, this team’s goal is to enable better science through greater collaboration and shared resources.”

EL researchers will have access to powerful computing capabilities through the connection of the Data Portal to a new Data Commons, being developed by Seven Bridges Genomics.

“Connecting researchers and helping them discover, explore, and analyze relevant datasets will help drive improvements for patients and their families,” said Jack DiGiovanna, General Manager at Seven Bridges. “We are excited to partner with Sage; integrating the Synapse Platform with CAVATICA to create a collaborative and interoperable research environment for longevity researchers.”

“High quality preventative medicine and improved quality of life are top goals of clinicians and their patients,” said Paola Sebastiani, Faculty Biostatistician at Tufts Medical Center and Professor of Medicine at Tufts University. “Integration of data from multiple studies of human longevity will help accelerate the translation of science on aging and exceptional longevity into useful clinical insights.”

The Exceptional Longevity Data Management and Coordinating Center is supported by the National Institute on Aging, part of the National Institutes of Health under grant number U24AG078753.

The content of this release is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

ABOUT SAGE BIONETWORKS

Sage Bionetworks (sagebionetworks.org) is a non-profit health research organization based in Seattle, Washington. Sage uses open practices that increase the reliability of scientific claims to speed the translation of science to medicine. Through its work, Sage supports responsible data sharing, objective evaluation of methods and results across researchers, and the empowerment of participants to be active partners in research.

MEDIA CONTACT:
Susan Ward, Team Soapbox
206-786-004
susan@teamsoapbox.com

Cancer Complexity Knowledge Portal Launched

The Cancer Complexity Knowledge Portal has officially launched. Funded by the National Cancer Institute Division of Cancer Biology, the portal enables researchers to submit multi-faceted queries related to the latest discoveries, data, tools, methods, and publications from three cancer research communities:

  • Cancer Systems Biology Consortium (CSBC), which aims to address the challenges of complexity in cancer research through a combination of experimental biology and computational modeling, multi-dimensional data analysis and systems engineering.
  • Physical Sciences in Oncology Network (PS-ON), which supports research programs that connect cancer biologists and oncologists with scientists from the fields of physics, mathematics, chemistry, and engineering to address some of the major questions and barriers in cancer research.
  • Cancer Tissue Engineering Collaborative (TEC), which supports the development and characterization of biomimetic tissue-engineered technologies.

Sage Bionetworks serves as the resource coordinating center for CSBC and PS-ON and developed and maintains the portal.

Sample queries:

Explore the Cancer Complexity Knowledge Portal

Sage Joins DAPI Project for Down Syndrome Research

NIH Award Funds Data Coordinating Center for Down Syndrome Research

The new initiative will fuel collaboration and discovery about the biology of Down syndrome and its co-occurring medical conditions

PARTNER PRESS RELEASE:

DENVER, Nov. 5, 2020 /PRNewswire/ — University of Colorado Anschutz Medical Campus announces scientists and data experts are joining forces to create the world’s first centralized platform for Down syndrome researchers to share, access, and analyze data. The goal of the new initiative, called the “Data Management and Portal for INCLUDE (DAPI) Project,” is to accelerate discoveries and advance medical care for individuals with Down syndrome. The National Institutes of Health (NIH) recently awarded a grant totaling $19.5M over five years to develop the center as part of the INCLUDE Project (INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE).

The DAPI Project is co-led by Dr. Adam Resnick, Director of the Center for Data Driven Discovery for Biomedicine (D3b) at Children’s Hospital of Philadelphia, Dr. Joaquin Espinosa, Executive Director of the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus, and Dr. Justin Guinney, Vice President of Computational Oncology at Sage Bionetworks. DAPI Project leaders will work closely with NIH INCLUDE Project staff to develop the center. This collaboration brings together strong expertise in Down syndrome research and open, data-driven science.

READ FULL PRESS RELEASE

Discovering Keys That Could Unlock Better Personalized Treatments to Destroy Cancer

International neoantigen initiative Tumor Neoantigen Selection Alliance (TESLA) identifies parameters for cancer vaccine or cell therapy advancement

 

SAN FRANCISCO – Neoantigens, tiny markers that arise from cancer mutations, flag cells as cancerous and could be the key to unlocking a new generation of immunotherapies. Targeting the “right” neoantigens – in a cancer vaccine or a cell therapy – has the promise to eliminate a patient’s cancer with minimal side effects. But hundreds of mutations can exist in a tumor, and only some can give rise to neoantigens that can trigger an immune response against cancer. The question is, which ones?

Scientists from an initiative launched by the Parker Institute for Cancer Immunotherapy (PICI) and the Cancer Research Institute called the Tumor Neoantigen Selection Alliance (TESLA) have discovered parameters to better predict which neoantigens can stimulate a cancer-killing effect. TESLA brings together a constellation of 36 top biotech, pharma, university and scientific nonprofit research teams. Their findings were published online today in Cell and could spawn a new generation of more effective, personalized cancer immunotherapies. Read full release…

Kristen Dang and Justin Guinney led the Sage Bionetworks team that collaborated on this study and paper.

AACR Project GENIE Serves As Hub and Harmonizer for Cancer Data

New data release highlights Sage’s key role in mapping data and enabling broader accessibility

 

FEATURED PROJECT

AACR Project GENIE (Genomics Evidence Neoplasia Information Exchange) launched in 2015 to serve as a registry for pan-cancer data from tens of thousands of patients treated at the eight participating institutions. The registry enables the mapping of cancer genomic data to clinical outcomes. Having patient data from AACR Project GENIE helps to improve clinical decision-making, especially for rare cancers and rare variants in common cancers.

Sage Bionetworks has served as the data hosting and integration hub, overseeing data ingestion and processing, and two data releases per year. Sage has contributed to the development of detailed data dictionaries and formats, and has deployed operating procedures that describe the workflow streams required of each institution as well as data processing pipelines to validate the data across the contributing centers.

Ensuring the cancer data is processed and standardized so researchers can easily access the breadth of information is a massive project. Over the course of 2019, this group has also been collaborating with teams at Memorial Sloan Kettering and the GDC to convert Project GENIE data from 44,756 cancer cases to be compatible with the National Cancer Institute’s Genomic Data Commons (GDC). (Read more about this impactful data release on the AACR blog.)

In an ideal world, there would be a single standard for clinical patient data. But there isn’t, so sharing cancer genomic data from one medical center to another is far from trivial. In this case, Sage’s Kristen Dang and Thomas Yu, and MSKCC’s Stacy Thomas oversaw the mapping of the data. It required programmatic and line-by-line review in order to convert the data for integration with GDC.

Sage values data accessibility and believes in breaking down barriers that can hinder crucial research. Preparing the initial data release for GDC came with challenges, but the process helped teams address some of the pain points, so future releases will be more streamlined.

UPCOMING DATA RELEASE

There will be an AACR Project GENIE data release in January 2020. Visit the data release log to stay current.

The Value of Team Science in Alzheimer’s Disease Research

Related News: Bringing Open Science to Drug Discovery for Alzheimer’s

The Sage Perspective

Silos in research are slowing us down. This isn’t a revelation, but it is a rallying call for many of us who hope to overcome barriers to advancing research, especially for a disease like Alzheimer’s.

In the study of Alzheimer’s, there has been a spectacular failure in the development of therapies. All the drugs that are allegedly disease-modifying have failed in late-stage clinical trials. The thinking around what causes the disease has not moved beyond a few hypotheses that have taken root.

This has occurred because the scientific community has fallen for the streetlight effect: We continue to expend resources to generate new data on hypotheses that have existing promising data because it is viewed as a safe bet. Given the repeated failure of clinical applications of these hypotheses (e.g. the Amyloid hypothesis), we face the stark reality that the true nature of the disease is a quagmire of uncertainty.

Fundamental shift

Yet there are rational strategies that have been successful in other domains such as finance that the community can use to mitigate that uncertainty. Instead of continuing to accrue data on what isn’t working, we ought to systematically explore the boundaries of our collective knowledge about Alzheimer’s Disease and balance the distribution of resources across low-, medium-, and high-risk ideas. This requires a fundamental shift in how we think about doing science, because no individual contributor can perform all of the tasks necessary to expand our collective knowledge in a meaningful manner.

There are so many silos that a lot of data, new ideas, and hypotheses don’t get shared. There also is some level of distrust in the community by researchers who want to guard proprietary information for the sake of a “magic bullet.” But there is no magic bullet. If we don’t collaborate strategically and diversify our research portfolio, we will continue to fail.

We are at a critical stage in Alzheimer’s Disease research where the community and individual researchers must put aside their individual reservations and work together. We have to let go of what’s not working and acknowledge that there are potentially other factors that affect how the disease behaves. It’s imperative that fresh ideas are given adequate space to succeed and to disrupt current structures to facilitate this exchange. We have to hedge our bets.

Radically open

At Sage, I lead a team that works across several programs that are identifying new drug targets to treat Alzheimer’s disease. There are many different academic institutions that are generating high-dimensional molecular data that can be used to try to identify new genes and pathways that could be fresh drug targets. We, in the spirit of open science, help orchestrate the analytic and data coordination efforts associated with that endeavor.

Our goal is to use a data-driven approach to better understand the underlying molecular mechanisms of the disease. It’s not something that any individual group would have the resources to do effectively. So it really requires a community-driven approach. Sage is positioned to conduct the scientific coordination that can help researchers work more effectively to get at these new ideas that might lead to a successful treatment.

Our primary project is AMP-AD (Accelerating Medicine Partnership in Alzheimer’s Disease), which is a public-private partnership supported by the National Institutes on Aging. We serve as a hub for all the data that’s being generated across the project. It’s a radically open model where all the data become open once they have gone through quality control. You don’t have any publication embargoes or restrictions on data use – aside from adhering to governance standards associated with sensitive human data.

We play a role in trying to increase the transparency of all the analyses that become available. We’re also building partnerships with academic investigators to streamline how we reach a consensus about what the data are telling us about the potential causes of this disease. We want to make sure that any conclusions are consistent across different research teams, because the more generalizable a solution is, the more likely it will lead to a successful treatment.

The long view

In addition to this scientific coordination work, my group is also performing original research on Alzheimer’s Disease. In all of our research, we operate under the same open model as all of our collaborators. Practicing this open approach in our own work is important at Sage. By holding ourselves to the same standard that we ask the community to live by, we can understand and work through any pain points. In this way, we hope to lead by example. At Sage, we do have the benefit of a culture and incentive structure that emphasize the long view versus, say, maximizing revenue in the short term. Being able to think on a longer time scale affords us the ability to make decisions that improve science more materially than if we were to focus on solo – and siloed – projects.

Any approach to tackling how science is done needs to be systematic in order to have long-lasting impact. For Alzheimer’s disease, we have an opportunity to improve how therapeutic development happens. Our vision and hope is that any future compounds that may result from open research we support would be achieved faster and more efficiently, and be made available in an affordable and equitable manner.

Being radically open and collaborative isn’t easy, but operating in a silo won’t get us far enough. We have to be more intentional about team science. Lives depend on it.

Sage’s Synapse Platform Key to Data Coordination for PsychENCODE Consortium

Image description: Cover image on the Dec. 14, 2018, issue of the journal Science features a neon illustration of a brain. The headline is 'Illuminating The Brain.'
COVER The human brain is the product of myriad molecular and genetic interactions. Here, a neon brain illustration represents individual genetic variability, some of which may lead to disease (denoted by dim or dark segments), as investigated by the PsychENCODE Consortium. This issue sheds light on neurogenetic and epigenetic variation in developing and adult neurotypical brains, as well as in schizophrenia, autism spectrum disorder, and bipolar disorder.
The journal Science today published a special issue, featuring a series of papers from the PsychENCODE consortium.
The PsychENCODE consortium is a NIMH-funded set of grants across 15 institutions that focus on generating genomic and epigenetic data from postmortem brain tissue of individuals diagnosed with neuropsychiatric disorders, developing brains, and cellular model systems. Consortia members share data and insights with each other and the greater research community. Sage Bionetworks, a nonprofit biomedical research and technology development organization founded in Seattle in 2009, functions as the data coordination center for the consortium, using its Synapse platform to share and release data to qualified investigators in the research community. 
 

Synapse tracks collaborative analysis across the PsychENCODE distributed teams, allowing each team to work on the same set of files and to broadcast their research findings in a transparent, reproducible manner. Synapse’s human data governance controls allow the distribution of sensitive human data directly to the broader research community. The PsychENCODE DCC at Sage Bionetworks is responsible for coordinating the upload of data to Synapse from each research project according to grant milestones, and for making the data available according to the Findable, Accessible, Interoperable, Reusable (FAIR) principle. 

Using Open Technology Platform to Help Develop Community Resource for Mobile Cognitive Tracking

New awards from the National Institute on Aging (NIA) will fund two independent projects to develop a suite of mobile cognitive tests that will be distributed via Sage’s technology platforms for integration into clinical research studies. Designing these remote cognitive assessments on a common technical platform provides a single point of entry for the broader community of researchers, who will be able to benefit from and contribute to the resource more rapidly and efficiently.

Remote cognitive assessments allow researchers to better understand the progression and variation in cognition in the context of daily living, an approach that is not possible with traditional tests performed in the clinic. Importantly, the research teams, led by investigators at Northwestern University and Penn State University are committed to developing the suite of tools on a common, open platform to enable an extensive and dynamic norming framework that will ensure that researchers understand the impact of context on test performance. This will be repeated across at least a half dozen research studies.

Dr. Richard Gerson, of Northwestern University, is leading a consortium of researchers from several institutions including Harvard University and University of California, San Francisco, in the development of the MobileToolbox library of iOS and Android cognitive assessments. Dr. Martin Silwinski, of Penn State University, is leading a second consortium of researchers from several institutions, including Washington University and University of Southern California, to develop accurate and more sensitive measurements for detecting subtle cognitive changes during preclinical states of neurological diseases, such as Alzheimer’s Disease.

Read news article from Penn State University

“By performing this work in the open domain, we create a dynamic resource to share cognitive tests in a manner where the community can independently evaluate their validation and norming criteria,” said Dr. Lara Mangravite, president, Sage Bionetworks. “In this way, clinical researchers will be able to easily identify and deploy cognitive tools that are optimally useful for their own research needs.”

New Research Tools Available in the Search for Therapies for Neurofibromatosis Type 1 (NF1)

New Research Tools Available in the Search for Therapies for Neurofibromatosis Type 1 (NF1) – A collaboration of the Neurofibromatosis Therapy Acceleration Program (NTAP), together with Sage Bionetworks, Johns Hopkins, NCATS and the University of Florida. Read the full article in Scientific Data (June 12, 2018).

 

Press release by Cathy Gara | published by NTAP

Plexiform neurofibromas affect up to 50 percent of people with neurofibromatosis type I (NF1), a rare disease of the nervous system for which there are no approved drug therapies.  NF1 has an incidence of 1/2600 – 1/3000 and arises from mutations in the NF1 gene whose protein, neurofibromin, is normally involved in suppressing cell division.  Without enough working neurofibromin, plexiform neurofibromas can form on nerves throughout the body.  These tumors often appear and grow rapidly throughout childhood. Although they are non-cancerous, their size and location can cause weakness, sensory abnormalities, deformity, and pain, and in some cases, turn malignant.

Plexiform neurofibromas involve several kinds of cells, but they are believed to arise from Schwann cells, a type of neural support cell, that are missing both copies of the NF1 gene.  As with all slow-growing, benign tumors, NF1 tumor cells are hard to grow in the laboratory, limiting the ability of scientists to test potential treatments in reproducible, well-characterized model systems.  In 2016, researchers at the University of Florida figured out how to continuously culture normal and NF1 patient-derived Schwann cells.

Now, a multi-institutional group of scientists from The Johns Hopkins University, the National Center for Advancing Translational Sciences (NCATS), the University of Florida, and Sage Bionetworks has created a new discovery tool.  They characterized, technically optimized and made publicly available a genetically diverse set of patient-derived Schwann cells with a range of NF1 mutations allowing the efficient testing of thousands of drug-cell combinations.  The cells of various NF1 backgrounds were then exposed to 1,912 cancer drugs that are in late stages of clinical development and with known protein targets to assess their ability to prevent the cells from dividing at various doses.  Testing drugs in cells with various patterns of NF1 mutations allows for precision in selecting drugs that are active against the specific cells that cause the tumors, but not bystander cells.

These advances are described in the manuscript “Pharmacological and genomic profiling of neurofibromatosis type 1 plexiform neurofibroma-derived Schwann cells,” published in Scientific Dataon June 12.  The results of this work set the stage for future experiments to: (1) test effective, already-approved drugs for plexiform neurofibromas and other “benign” tumors, (2) discover new pathway interactions that drive tumor growth, and (3) show how cells with different genetic signatures react to various drug combinations.

This work was a major initiative of the Neurofibromatosis Therapy Acceleration Program (NTAP) (www.n-tap.org) a research program based at the Johns Hopkins University School of Medicine.  Dr. Jaishri Blakeley, the Director of NTAP said, “the goal of this project was to create a reliable and fully characterized set of cell culture systems available to all researchers to encourage therapeutic discovery for neurofibromas and thereby fill a big gap in the research landscape.”  All of the data generated has been made openly available and can be accessed through http://www.synapse.org/pnfCellCulture and other sources outlined in the paper.  In addition, the cell culture systems generated are available via the biological materials resource and standards organization, ATCC (https://www.atcc.org).

About the Neurofibromatosis Therapy Acceleration Program (NTAP)

NTAP is a philanthropy driven research organization based at the Johns Hopkins University School of Medicine focused on accelerating the development of therapeutics for NF1 tumors by fostering collaboration, promoting the open and timely sharing of results, and streamlining research models.  The Johns Hopkins University and the University of Florida are academic institutions based in Baltimore, Maryland, and Gainesville, Florida, respectively.

About Sage Bionetworks

Sage Bionetworks is a nonprofit biomedical research organization, founded in 2009, with a vision to promote innovations in personalized medicine by enabling a community-based approach to scientific inquiries and discoveries. Sage Bionetworks strives to activate patients and to incentivize scientists, funders and researchers to work in fundamentally new ways in order to shape research, accelerate access to knowledge and transform human health. It is located on the campus of the Fred Hutchinson Cancer Research Center in Seattle, and is supported through a portfolio of philanthropic donations, competitive research grants, and commercial partnerships. More information is available at www.sagebase.org.

About NCATS

NCATS is a component of the National Institutes of Health (NIH) within the Department of Health and Human Services. NCATS conducts and supports research on the science and operation of translation — the process by which interventions to improve health are developed and implemented — to allow more treatments to get to more patients more quickly. For more information about how NCATS is improving health through smarter science, visit https://ncats.nih.gov. The NIH — the United States’ medical research agency — includes 27 institutes and centers and is the primary federal agency for conducting and supporting basic, clinical and translational medical research. It investigates the causes, treatments and cures for both common and rare diseases. For more information about the NIH and its programs, visit http://www.nih.gov.

For more information

Justin Guinney, PhD

Sage Bionetworks

206-928-8245

justin.guinney@sagebionetworks.org