(Press-News.org) GRAND RAPIDS, Mich. (Jan. 2, 2025) — A multi-institutional team of scientists has developed a free, publicly accessible resource to aid in classification of patient tumor samples based on distinct molecular features identified by The Cancer Genome Atlas (TCGA) Network.
The resource comprises classifier models that can accelerate the design of cancer subtype-specific test kits for use in clinical trials and cancer diagnosis. This is an important advance because tumors belonging to different subtypes may vary in their response to cancer therapies.
The resource is the first of its kind to bridge the gap between TCGA’s immense data library and clinical implementation.
A paper describing the tools published online today in Cancer Cell.
“TCGA defined molecular subtypes for each major type of cancer. With this resource, we aimed to provide the clinical and scientific communities with the tools to assign a newly diagnosed tumor to one of these established subtypes,” said Peter W. Laird, Ph.D., the Peter and Emajean Cook Endowed Chair in Epigenetics at Van Andel Institute and the study’s lead corresponding author. “Our new resource will be a powerful asset for creating clinical assays based on the diverse molecular variations between cancers.”
TCGA was a decade-long, National Cancer Institute-led effort to create detailed molecular maps of 33 cancer types. Unlike traditional approaches that define cancers based on the organ or tissue in which they arise, TCGA identified nuanced genomic, epigenomic, proteomic and transcriptomic characteristics that more precisely describe cancer subtypes.
Andrew D. Cherniack, Ph.D., of the Broad Institute of MIT and Harvard and Kyle Ellrott, Ph.D., of the Knight Cancer Institute at Oregon Health & Science University also are corresponding authors of the paper, which represents a collaborative effort between scientists from more than a dozen research organizations.
“Since many TCGA molecular subtypes were generated using hundreds or thousands of features from multiple data types, scientists and physicians have asked us for help subtyping their samples,” Cherniack said. “Our resource greatly simplifies this process.”
The team created the new resource by leveraging data from 8,791 TCGA cancer samples that represented 26 cancer cohorts and 106 cancer subtypes. They then used existing machine learning tools to develop and test nearly half a million models across six categories — gene expression, DNA methylation, miRNA, copy number, mutation calls and multi-omics — and selected those that performed best for inclusion in the online resource.
In total, the resource contains 737 ready-to-use models, which represent the top models from each of the 26 cancer cohorts, the five training algorithms and six data types.
“A major element of this effort was working to ensure that these models could be deployed by other groups onto new datasets,” Ellrott said. “All too often this type of work is difficult to replicate or apply to new samples.”
The resource may be accessed at https://github.com/NCICCGPO/gdan-tmp-models.
Co-first authors of the study include Christopher K. Wong of University of California, Santa Cruz, Christina Yau of University of California, San Francisco, and Buck Institute for Research on Aging, Mauro A. A. Castro of the Federal University of Paraná, Jordan E. Lee of Oregon Health and Science University, Brian J. Karlberg of Oregon Health and Science University, Jasleen K. Grewal of BC Cancer, Vincenzo Lagani of JADBio Gnosis DA and Ilia State University, and Bahar Tercan of the Institute for Systems Biology.
Other authors include Verena Friedl, Vladislav Uzunangelov and Joshua M. Stewart of University of California, Santa Cruz; Toshinori Hinoue of Van Andel Institute; Lindsay Westlake and Xavier Loinaz of the Broad Institute of MIT and Harvard; Ina Felau, Peggy I. Wang, Anab Kemal, Samantha J. Cesar-Johnson and Jean C. Zenklusen of the National Cancer Institute; Ilya Shmulevich of the Institute for Systems Biology; Alexander J. Lazar of the University of Texas MD Anderson Cancer Center; Ioannis Tsamardinos of JADBio Gnosis DA and University of Crete; Katherine A. Hoadley of Lineberger Comprehensive Cancer Center at University of North Carolina at Chapel Hill; The Cancer Genome Atlas Analysis Network; A. Gordon Robertson of BC Cancer; Theo A. Knijnenburg of the Institute for Systems Biology; and Christopher C. Benz of Buck Institute for Research on Aging.
Research reported in this publication was supported by the National Cancer Institute of the National Institutes of Health under award nos. U24CA264029 (Cherniack), U24CA264023 (Laird), U24CA264007 (Ellrott), U24CA264021 (Hoadley) and U24CA264009 (Stewart and Benz). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or other funders.
###
ABOUT VAN ANDEL INSTITUTE
Van Andel Institute (VAI) is committed to improving the health and enhancing the lives of current and future generations through cutting-edge biomedical research and innovative educational offerings. Established in Grand Rapids, Michigan, in 1996 by the Van Andel family, VAI is now home to more than 500 scientists, educators and support staff, who work with a growing number of national and international collaborators to foster discovery. The Institute’s scientists study the origins of cancer, Parkinson’s and other diseases and translate their findings into breakthrough prevention and treatment strategies. Our educators develop inquiry-based approaches for K–12 education to help students and teachers prepare the next generation of problem-solvers, while our Graduate School offers a rigorous, research-intensive Ph.D. program in molecular and cellular biology. Learn more at vai.org.
END
NEW YORK, NY--New work by Columbia researchers has turned a textbook principle of genetics on its head and revealed why some people who carry disease-causing genes experience no symptoms.
Every biology student learns that each cell in our body (except sperm and eggs) contains two copies of each gene, one from each parent, and each copy plays an equal part in the cell.
The new study shows that some cells are often biased when it comes to some genes and inactivate one parent’s copy. The phenomenon was discovered about a decade ago, but ...
AURORA, Colo. (Jan. 2, 2025) - Researchers at the University of Colorado Anschutz Medical Campus have discovered that some CAR-T cells engineered to fight cancer and other conditions carry the memory of past encounters with bacteria, viruses and other antigens within them, a finding that may allow scientists to manufacture the cells in more precise and targeted ways.
The study, published today in the journal Nature Immunology, focused on chimeric antigen receptor (CAR)-T cells, an effective therapy against ...
UNIVERSITY PARK, Pa. — When it comes to deciding where they’re going to get their next meal, different species of bees may be attracted to different flower traits, according to a study led by researchers at Penn State and published in PNAS Nexus.
The study focused on two species of solitary bees: the horned-face bee, which helps pollinate crops like apples and blueberries, and the alfalfa leafcutting bee, which pollinates alfalfa.
The researchers found that the horned-face bees tended to prefer plants with a large number of flowers — for them, quantity was most important. ...
A new study by investigators from Mass General Brigham uncovers how a novel immunotherapy prevents squamous cell carcinoma, with benefits lasting five years after treatment. This therapy is the first to activate specific components of the adaptive immune system, particularly CD4+ T helper cells, which are not known to be involved in traditional cancer treatments. This work highlights the potential for similar immunotherapies to prevent other cancers throughout the body. Results are published in the Journal of Clinical Investigation.
“One of the unique challenges with squamous cell carcinoma is that individuals who develop it are at an increased risk of developing multiple new ...
When children receive their second measles-mumps-rubella vaccine, around the time they start kindergarten, they gain protection against all three viruses for all or most of their lives. Yet the effectiveness of an influenza vaccine given in October starts to wane by the following spring.
Scientists have long been stymied by why some vaccines can coax the body to produce antibodies for decades, while others last mere months. Now, a study led by researchers at Stanford Medicine has shown that variation in vaccine durability can, in part, be pinned on a surprising type ...
Researchers at the University of Pittsburgh have developed a nasal swab test for kids that diagnoses specific asthma subtype, or endotype. This non-invasive approach could help clinicians prescribe medications more precisely and pave the way for research toward better treatments for lesser-studied asthma types, which have been difficult to diagnose accurately until now.
Published today in JAMA, the findings are based on data from three independent U.S.-based studies that focused on Puerto Rican and African American youths, who have higher rates of asthma and are more likely to die from the disease than their non-Hispanic white counterparts.
“Asthma ...
About The Study: Most study participants could not extract basic information—including whether they have cancer—from standard prostate cancer pathology reports but were able to understand this diagnostic information from the patient-centered pathology reports (PCPRs). Also, they discriminated between risk levels (i.e., lower levels of perceived worry in the low-risk condition) with PCPRs compared with standard reports. Hospital systems should consider including PCPRs with standard pathology reports to improve patient understanding.
Corresponding ...
About The Study: This case-control study found that individuals with more advanced breast cancer at diagnosis were more likely to have prevalent cardiovascular disease. This finding may be specific to hormone receptor–positive and ERBB2-negative (formerly HER2) disease. Future studies are needed to confirm these findings and investigate interventions to improve patient outcomes, including personalized cancer screening.
Corresponding Author: To contact the corresponding author, Kevin T. Nead, MD, MPhil, email ktnead@mdanderson.org.
To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/
(doi:10.1001/jamanetworkopen.2024.52890)
Editor’s ...
PITTSBURGH, Jan. 2, 2025 – University of Pittsburgh researchers uncovered a surprising link between Alzheimer’s disease and herpes simplex virus-1 (HSV-1), suggesting that viral infections may play a role in the disease. The study results are published today in Cell Reports.
The study also revealed how tau protein, often viewed as harmful in Alzheimer’s, might initially protect the brain from the virus but contribute to brain damage later. These findings could lead to new treatments targeting infections and the brain’s immune response.
“Our study challenges ...
HOUSTON ― Cardiovascular disease (CVD) and cancer are the two leading causes of death in the U.S. According to researchers from The University of Texas MD Anderson Cancer Center, patients diagnosed with late-stage or metastatic breast cancer have a statistically significant increased risk of pre-diagnosis CVD compared to those with early-stage cancer at diagnosis.
The study, published today in JAMA Network Open, found those with advanced breast cancer at diagnosis were 10% more likely to have had pre-existing ...
