News and Announcements

Researchers from the National Institute of Health’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) and collaborating institutions have developed a novel protein expression-based stemness index (PROTsi) to evaluate oncogenic dedifferentiation in cancer. Their work, published in Cell Genomics, aims to quantify stem-like features in cancer which are closely linked to aggressive tumor behavior, resistance to therapies, and poor patient outcomes.…

A new pan-cancer study from the National Institute of Health’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) explores how inherited genetic variants shape protein function in cancer. Using a method called precision peptidomics, CPTAC researchers mapped over 337,000 coding germline variants to peptides detected in tumor samples and normal adjacent tissues across ten cancer types. Their work, published in Cell, has revealed how these variants might alter protein structure, allele-specific expression, post-translational modifications, and ultimately contribute to oncogenesis…

National Institutes of Health CPTAC researchers have uncovered new insights into tumor therapeutic resistance, heterogeneity, and immune evasion. Their work, published in Nature, leveraged several cutting-edge technologies, including spatial transcriptomics, single-nucleus RNA sequencing, and multiplexed imaging, to map the tumor microenvironment in unprecedented detail to understand how cells interact and how their location affects their behavior.…

The following is the eighth entry in a Q&A series highlighting selected Clinical Proteomic Tumor Analysis Consortium (CPTAC) researchers and their work. Join us as we discuss proteomic aspirations, the value of mentoring in science, and progress in multiple myeloma with Kiran Kumar Mangalaparthi, Ph.D., a Postdoctoral Researcher at Mayo Clinic in Rochester, Minnesota.…

Data analysis in proteogenomics has taken a marked step forward with the introduction of a new bioinformatics platform, Multiomics2Targets. This platform, developed by CPTAC researchers at the Icahn School of Medicine at Mount Sinai and published in Cell Reports Methods, integrates transcriptomics, proteomics, and phosphoproteomics data to identify potential therapeutic targets and is capable of generating detailed reports automatically. A companion protocol article describing how to use the system was also recently published in STAR Protocols.

CPTAC researchers from the University of Michigan and researchers from Monash University, Australia have developed a new software tool to complement the widely used FragPipe computational proteomics platform. FragPipe-Analyst (FP-A) is designed to streamline downstream statistical analysis and data visualization, simplifying the exploration of dense proteomics datasets.…

The following is the seventh entry in a Q&A series highlighting selected Clinical Proteomic Tumor Analysis Consortium (CPTAC) researchers and their work. Join us as we discuss metabolomics, collaboration, and the future of the field with Jennifer Kyle, PhD, a Staff Scientist at Pacific Northwest National Laboratory.…

A single-arm phase 2 clinical trial conducted by researchers from the University of Pittsburgh, UPMC Hillman Cancer Center and the National Cancer Institute (NCI), tested a new treatment approach for high-risk, resectable melanoma. The trial measured proteins with tests developed by the NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC)…

Large-scale datasets generated via high-throughput sequencing and multi-omics technologies are shaping how researchers uncover features of cancer biology. The National Cancer Institute's (NCI) Proteomic Data Commons (PDC), a component of the Cancer Research...

Single-cell proteomics (SCP) is enabling researchers to understand cancer progression, immune response, developmental pathways, and more all at the cellular level. Historically, SCP has represented a considerable challenge for researchers due to low amounts of proteins within a single cell and the,...

The National Cancer Institute's Proteomic Data Commons (PDC) launched in 2020, part of the National Cancer Institute's Cancer Research Data Commons (CRDC) data ecosystem, is the largest public repository of comprehensive tumor proteomic datasets, housing diverse data types such as proteome,...

Cancer immunotherapies hold promise for inducing durable responses across cancer types, yet their effectiveness varies significantly among patients. In an effort to deepen our understanding of the mechanisms underlying response and resistance to immunotherapy, CPTAC researchers from the Fred...

The following is the sixth entry in a Q&A series highlighting selected Clinical Proteomic Tumor Analysis Consortium (CPTAC) researchers and their work. Join us as we discuss bioinformatics, proteogenomics, and research ethics with Fernanda Martins Rodrigues, PhD, a post-doctoral research...

Despite improvements in detection and therapy, the prognosis for high-grade glioma (HGG) remains poor. Prior research has studied disease progression in HGG, but our understanding of how and why the disease recurs so often (>90% of patients within two years for the most aggressive HGG) remains...

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has performed proteogenomic characterization for over 1,000 primary tumors spanning 10 cancer types: breast invasive carcinoma (BRCA), clear cell renal cell carcinoma (CCRCC), colon adenocarcinoma (COAD), glioblastoma (GBM), head and neck...

The following is the fifth entry in a Q&A series highlighting selected Clinical Proteomic Tumor Analysis Consortium (CPTAC) researchers and their work. Join us as we discuss multiple facets of glycoproteomics research with Tung-Shing Mamie Lih, PhD, an associate researcher at Johns Hopkins...

In a recent study aiming to address knowledge gaps in non-clear cell renal cell carcinoma (non-ccRCC), researchers from the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) conducted an integrated multi-omic analysis of 48 non-ccRCC cases along with a previously...

The following is the fourth entry in a Q&A series highlighting selected Clinical Proteomic Tumor Analysis Consortium (CPTAC) researchers and their work. Join us as we discuss multiple facets of proteogenomics research with Yifat Geffen, PhD, a postdoctoral researcher at the Broad Institute of MIT...

Glioblastoma (GBM) is an aggressive brain tumor with poor prognosis despite advancements in treatment and diagnosis. Tumor recurrence, developing in most patients (>90%), poses a major challenge due to tumor heterogeneity and limited understanding of post-treatment evolution. Previous studies have...

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) recently held its Scientific Investigator Meeting in Portland, Oregon at the Oregon Health & Science University campus. The meeting featured key scientific and programmatic updates spanning multiple cancer types presented by consortium...

The following is the third entry in a new Q&A series highlighting selected Clinical Proteomic Tumor Analysis Consortium (CPTAC) researchers and their work. Join us as we discuss multiple facets of proteomics research with Nicole Tignor, PhD, Assistant Professor at the Icahn School of Medicine at...

Small cell lung cancer (SCLC) is an aggressive form of lung malignancy with historically poor prognoses and limited options for targeted treatment. The low availability of suitable biospecimens has also hampered large molecular characterization efforts.

The tumor microenvironment (TME) is a complex network which plays a crucial role in cancer progression and treatment responses. In a recently published Pan Cancer analysis, the Clinical Proteomic Tumor Analysis...

Acute Myeloid Leukemia (AML) is a hematologic malignancy characterized by the rapid proliferation of abnormal myeloid cells in the bone marrow and blood. AML is known for its heterogeneity, presenting challenges in treatment and predicting patient outcomes.