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FDA and NIH Sign Memorandum of Understanding: Interagency Collaboration to Advance Proteogenomics Research

The National Cancer Institute (NCI) of the National Institutes of Health is pleased to announce the signing of a memorandum of understanding (MOU) bolstering its ongoing collaboration with the U.S. Food and Drug Administration (FDA). This MOU provides a framework that will enable and encourage the sharing of knowledge and support the formation of research teams to solve complex problems in the area of each agency’s mission, with a focus on the molecular characterization/classification of tumors.

Ex Vivo Drug Sensitivity Testing in AML: Improving Response Predictability Using Proteomic Measurements

Genetic heterogeneity amongst leukemic cells is a major contributor to low survival rates and poor clinical outcomes for patients with acute myeloid leukemia (AML). This diversity drives complex signaling pathways at the protein level which necessitate individualized treatment protocols for each patient. In order to improve patient outcomes, ex vivo drug sensitivity assays to predict patient-specific drug responses are being researched.

CPTAC Investigators Analyze Proteogenomic Markers of Chemotherapy Resistance and Response in Triple Negative Breast Cancer

CPTAC investigators from Baylor College of Medicine and the Broad Institute of MIT and Harvard in collaboration with oncologists at Washington University in St. Louis have identified biological markers in triple negative breast cancer (TNBC) that are associated with resistance to chemotherapy treatment.

Collaborating with Major International Partners - NCI Welcomes Renewed Commitments to the Cancer Moonshot with Australia, Canada, and Germany

The National Cancer Institute (NCI) of the National Institutes of Health is pleased to announce the renewal of partnerships with Australia, Canada, and Germany. These partnerships, through memoranda of understanding (MOUs) to the NCI Cancer Moonshot International Cancer Proteogenome Consortium (ICPC), affirms a commitment to accelerate our understanding of how proteins and genes (proteogenomics) contribute to an individual’s cancer and better inform patient care.

CPTAC Collaborates with the NIH Common Fund: Over 490 New Assays Released to the Public

CPTAC investigators from Washington University School of Medicine in St. Louis have developed new multiplexed assays for analyzing kinase proteins by parallel reaction monitoring mass spectrometry (PRM), a targeted form of mass spectrometry that enables highly sensitive and specific measurements. The set of new 408 assays corresponding to 234 unique proteins, present a new community resource for quantifying the proteins and phosphoproteins involved in kinase signaling.

NCI's CPTAC and PDC Recognized by FedHealthIT for Outstanding Commitment to Excellence and Innovation

This year, the 8th Annual FedHealthIT Innovation Awards recognized programs from the Department of Veterans Affairs, Military Health, Health and Human Services, and Centers for Medicare and Medicaid Services. These programs were carefully selected by their peers for their commitment to excellence, constant innovation, and producing results.

CellCarta Will Offer MRM-based Assay Services Using CPTAC Assays Developed at the Fred Hutchinson Cancer Center

In May, a leading provider of precision medicine laboratory services, CellCarta, acquired the commercial rights to the CPTAC-qualified antibody panels and assays developed by the Paulovich laboratory at Fred Hutchinson Cancer Center; they produce high-end multiplex quantitative immuno-MRM mass spectrophotometry-based assays for pharmaceutical and biotech industry partners.

  Dr. Amanda Paulovich

CPTAC Announces New PCC, PGDAC, and PTRC Teams

This month, the Office of Cancer Clinical Proteomics Research (OCCPR) at the National Cancer Institute (NCI), part of the National Institutes of Health, has reaffirmed its commitment to furthering proteogenomics research by announcing the next round of Proteome Characterization Center (PCC; RFA-CA-21-023), Proteogenomic Data Analysis Center (PGDAC; RFA-CA-21-024), and Proteogenomic Translational Research Center (PTRC; RFA-CA-21-025) teams.

NCI Welcomes Renewed Commitments to the Cancer Moonshot with Japan and the Republic of Korea

The National Cancer Institute (NCI) of the National Institutes of Health is pleased to announce the renewal of three separate collaborations with Japan and the Republic of Korea (ROK), affirming the two countries’ commitment to international cancer research and care, expanding efforts in the emerging area of proteogenomics, and the goals of the reignited Cancer Moonshot.

Proteogenomic Characterization of In vivo Protein Complexes via Chemical Cross-Linking and Mass Spectrometry

Protein complexes are a fundamental component of physiological and pathological processes. Despite organisms having a limited number of genes and therefore a finite number of proteins at their disposal, the number of possible combinations amongst these proteins is essentially inexhaustible; myriad protein complexes are constantly being assembled and disassembled at different physiology and pathological status in order to perform the complex and diverse biological functions.

Young Scientist Highlight: Aniket Dagar

The following is the transcript of an interview conducted to highlight promising undergraduate student researcher Aniket Dagar from University of Michigan. Aniket was recently awarded a meritorious poster award for the poster he presented at the 2022 American Association for Cancer Research (AACR) annual meeting titled “Discovery of a Candidate Prognostic Biomarker for Clear Cell Renal Cell Carcinoma based on Transcriptomic and Proteomic Analyses.”

CPTAC Glycoproteomic Researchers Develop "Peptide-First" Multi-Attribute Glycan Identification Method

Glycosylation is critical for a wide range of biological processes and is implicated in numerous diseases. Analysis of the glycoproteome has the potential to reveal a wealth of clinical insights, but the heterogeneity of glycosylation makes this analysis difficult. Because of the analytical challenges resulting from the inherent heterogeneity of glycosylation, analysis of the glycoproteome has generally lagged behind other omics fields. To deal with this, a rapid expansion of software tools is underway in this area.

Machine Learning-Derived Metrics Enable Computational Method Comparison in Phosphoproteomics Research

Protein phosphorylation dysregulation has been recognized as a key feature of several diseases, especially cancer. In recent years, phosphoproteomic research has revealed novel, effective biomarkers and drug targets for disease prognosis and treatment. Tandem mass spectrometry (MS/MS)-based phosphoproteomics provides a high-throughput method to study protein phosphorylation in complex biological samples. However, translating phosphoproteomic data into relevant biological and clinical insights relies on effective data analysis.

Proteogenomics Provides New Insights into Intrahepatic Cholangiocarcinoma

Intrahepatic cholangiocarcinoma (iCCA) is the second-most common primary liver tumor and has a low 5-year survival rate of 15%. Treatment of iCCA is particularly difficult due to its markedly aggressive progression, late symptom presentation, and early metastasis. In order to improve patient prognoses, it is critical to understand the pathogenesis of iCCA more deeply and identify novel molecular pathways that may serve as a theoretical foundation for personalized treatment of the disease.

CPTAC Researchers Identify CPT1A as a Potential Therapeutic Target in Platinum-Refractory, High-Grade Serous Ovarian Cancer Patients

At present, typical treatment for patients with high-grade serous ovarian cancer (HGSOC) is surgical debulking coupled with platinum-based chemotherapy. Despite the majority of HGSOCs being sensitive to platinum-based therapy initially, most become resistant over the course of treatment. The development of more efficacious therapies for platinum-resistant disease is an urgent clinical goal. In order to more effectively combat HGSOC, researchers are striving to identify predictive biomarkers of platinum response.

CPTAC Researchers Detect Fraud in Large-Scale Molecular Omics Datasets with Exceptional Accuracy Using Machine Learning

Modern computational tools for data collection and analysis have revolutionized how scientists are able to research and respond to problems. While the growing number of large, public data sets is a great boon for researchers, the accessibility of these resources can introduce quality and security risks. Data in the biological sciences is particularly vulnerable to fraud given its massive size, making it easier to hide manipulation. Inspired in part by techniques used to detect fraud in the financial sector, Dr.

CPTAC Researchers Develop a Novel, Targeted Mass Spectrometry Assay Panel that Enables Quantification of Immunomodulatory Proteins

Immunotherapies are revolutionizing modern cancer care, but at present, many technologies do not accurately quantify the myriad soluble proteins in the tumor microenvironment which impact immunity. This, in turn, contributes to the pervasiveness of patient resistance and immune-related adverse events. In order overcome these hurdles, it is necessary to design more refined protein quantification techniques that complement immunoassays for quantifying human proteins.