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Well-Known Oncogenic Mutations ErbB2/Her2 May Also Play A Role in Leukemogenesis

Activating point mutations in ErbB/Her2 receptor tyrosine kinases have an infamous role in promoting oncogenesis across several different cancers, including breast and lung. Heterodimer activation of the ErbB2/ErbB3 oncogenic unit induces cancer cell proliferation via PI3K/AKT signaling pathways.


In Case You Missed It: CPTAC Junior Investigator Spotlight (Part 2)

In case you missed it, this final article (part 2 of 2) in the Investigator Spotlight Series, developed and written by Dr. Dawn Hayward, Office Clinical Cancer Proteomic Research (OCCPR) NCI Communications Fellow, highlights our up and coming Clinical Proteomic Tumor Analysis Consortium (CPTAC) researchers and their work. Part 2 features scientists from CPTAC’s Proteogenomic Data Analysis Centers (PGDACs). Find out more about the interesting and unique tools that are being developed and implemented by this up-and-coming crew of rising stars! Responses edited for length and clarity.


First Large-scale, Multicenter Proteogenomic Analysis Offers New Insights Into Pediatric Brain Tumor Biology

A comprehensive “proteogenomic” analysis of the proteins, genes, and RNA transcription involved in pediatric brain tumors has yielded a more complete understanding of these tumors, which are the leading cause of cancer-related deaths in children. The results could help physicians more accurately identify different types of tumors and methods for treating them.


Proteogenomics Enhances the Identification of Therapeutic Vulnerabilities in Breast Cancer

Researchers at Baylor College of Medicine, the Broad Institute of MIT and Harvard and other institutions have applied powerful proteogenomics approaches to better understand the biological complexity of breast cancer. With this approach, the researchers were able to propose more precise diagnostics for known treatment targets, identify new tumor susceptibilities for translation into treatments for aggressive tumors and implicate new mechanisms whereby breast cancers resist treatment.


Evaluating Biomarkers in Metastatic Breast Cancer Bone Biopsies Without Decalcification

In a recent publication in the journal Clinical Chemistry, CPTAC investigators from Fred Hutchinson Cancer Research Center described a robust technique for evaluating biomarker expression of key receptors in patients with breast cancer bone metastasis using non-decalcified bone biopsies in immuno multiple reaction monitoring mass spectroscopy (immuno-MRM-MS).


CPTAC Study Identifies Unique Linkage of Glycosylation to Ovarian Cancer

Protein glycosylation, the enzymatic process that attaches glycans or sugar molecules to proteins, plays a crucial role in cancer development processes, such as cell-cell adhesion, cell growth, ligand-receptor binding, and tumor metastasis. Aside from phosphorylation, other protein modifications have not been investigated in large-scale proteomic studies.


Improved BASIL Workflow Provides Precise and Robust Protein Profiling for Single-Cell Analysis

Almost 18 months ago, CPTAC researchers from the Integrative Omics Group at Pacific Northwest National Laboratory (PNNL), developed a stream-lined technique to increase the sensitivity of peptide phospho-group identification during mass spectral analysis. The solution, called the ‘boosting to amplify signal with isobaric labeling’ (BASIL), was developed to ‘see’ small spectrometric signals (typically...


In Case You Missed It: CPTAC Junior Investigator Spotlight (Part 1)

In case you missed it, this third article (part 1 of 2) in the Investigator Spotlight Series, developed and written by Dr. Dawn Hayward, Office Clinical Cancer Proteomic Research (OCCPR) NCI Communications Fellow, highlights our up and coming Clinical Proteomic Tumor Analysis Consortium (CPTAC) researchers and their work. Part I features scientists from CPTAC’s Proteomic Characterization Centers (PCC) and Proteomic Translational Research Centers (PTRC). Read on for how these young investigators are developing and implementing their unique tools! Responses edited for length and clarity.


New Proteogenomic Data Release for CPTAC Lung Squamous Cell Carcinoma Discovery Study!

Announcing our newest data release for the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Lung Squamous Cell Carcinoma (LSCC) Discovery study! Because LSCC accounts for about 30% of all lung cancers and has a ~20% 5-year survival rate, it’s imperative that cancer researchers learn more about the biology of this disease to find more effective treatments. CPTAC investigators have led this charge by examining tumor and normal adjacent tissue from 108 LSCC patients using multi-omics.


AutoRT - Using Peptide Retention Time Prediction to Accurately Determine Quality of Peptide Identification

In a recent issue of Nature Communications, Clinical Proteomics Tumor Analysis Consortium (CPTAC) researchers from Bing Zhang’s lab at Baylor College of Medicine describe a new bioinformatics software tool developed to evaluate the quality of variant peptide identifications. Using a deep learning algorithm, the software AutoRT, accurately predicts peptide retention time (that is the time points when peptides elute from the liquid chromatography column) based on its sequence.


The CPTAC Virtual Symposium - Sept 22, 2020

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) is pleased to announce its Virtual Scientific Symposium 2020, September 22nd, 2020. This year’s symposium will feature talks by leaders in the field of proteogenomics and will focus on CPTAC’s tumor characterization and translational studies for pediatric brain cancer, acute myeloid leukemia, and glycoproteomics – just to name a few!  


SBIR Proteomics Technologies Funding Announcement: Single-Cell Unbiased Discovery

The NCI’s Small Business Innovation Research (SBIR) Development Center has released a program solicitation (PHS 2021-1) which includes a new, Clinical Proteomic Tumor Analysis Consortium (CPTAC)-inspired grant. The announcement calls for the development of high-throughput, single-cell, unbiased discovery proteomic technologies. The goal of this opportunity is to advance our knowledge of cancer development and progression, and to enable robust cancer biomarker discovery and clinical application on a micro-scale. 


In Case You Missed It: CPTAC Investigator Spotlight on David Fenyö and Emily Kawaler

This article is the second in the Investigator Spotlight Series that was the brain child of Dr. Dawn Hayward, a NCI Communications Fellow at OCCPR, highlighting our CPTAC researchers and thier work. In case you missed it the first time, here she features CPTAC scientists Dr. David Fenyö and researcher Emily Kawaler!


CPTAC Investigators Establish Protein Level Prediction Model Using Crowdsourcing

Online on July 24th on Cell Systems, Clinical Proteomic Tumor Analysis Consortium (CPTAC) researchers shared the results of their first-ever, crowd-sourced NCI-CPTAC DREAM Proteogenomic Challenge. In this community-based, collaborative contest participants developed computational algorithms to predict protein abundance and phosphoprotein levels.

Focusing on the Issues


Fred Hutch Team Establishes a New CLIA Lab for Running Targeted-MS assays, Including a Novel CLIA-Approved HER2 Test

A major goal for NCI’s Cancer Proteomic Tumor Analysis Consortium (CPTAC) is to translate proteomic technologies into clinical use to improve treatment and diagnosis of cancer. Dr. Amanda Paulovich and team from the Fred Hutchinson Cancer Research Center (members of the CPTAC Consortium) have achieved an important milestone in this regard, by establishing a Clinical Laboratory Improvement Amendments (CLIA) - certified laboratory for running targeted proteomic assays based on multiple reaction monitoring (MRM) mass spectrometry (MS).


Lung Adenocarcinoma (LUAD) Discoveries from two NCI Proteomics Consortia

Two new studies released July 9th, 2020 in Cell unravel the biology of lung adenocarcinoma (LUAD) using a suite of molecular techniques that, combined, provide a more complete picture of the disease than ever before. Using a diverse cohort of smokers and non-smokers, male and female, from around the world, researchers from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and the International Cancer Proteogenome Consortium (ICPC) draw out a clearer understanding of LUAD tumor progression, identify biomarkers, and propose alternative therapeutic targets.


OCCPR Webinar: MSFragger

Join Dr. Alexey Nesvizhskii, Professor of Pathology and Computational Medicine & Bioinformatics at University of Michigan, as he speaks on our next OCCPR Webinar about his ultrafast MSFragger software. The webinar will take place on Wednesday, July 15th at 1pm - registration is free, but required.


In Case You Missed It: CPTAC Investigator Spotlight on Karin Rodland

The Investigator Spotlight Series was the brain child of Dr. Dawn Hayward, an NCI Communications Fellow at OCCPR, to highlight our CPTAC researchers and thier work. In case you missed it the first time, here she features CPTAC scientist Dr. Karin Rodland. Enjoy!


CPTAC At AACR Virtual Meeting II

We are so excited to be a part of the AACR Virtual Meeting II, June 22-24, 2020! Join us for our Clinical Proteomic Tumor Analysis Consortium (CPTAC) Educational Session: Resources and Data Dissemination Tuesday June 23rd, 3:00-5:00 p.m.


Proteomics 3 Ways – An Efficient Analysis of Global, Glyco-, and Phospho-Proteomics

In a new study published in Analytical Chemistry, we see another example of ingenuity by NCI’s Office of Cancer Clinical Proteomic Research (OCCPR) Clinical Proteomic Tumor Analysis Consortium (CPTAC) scientists. In an effort to optimize analytical output and conserve hard-to-obtain biospecimen samples, CPTAC researchers out of John Hopkins School of Medicine developed a new integrated workflow for multiplex analysis of global, glyco-, and phospho-proteomics. 


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