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The Human Melanoma Proteome Atlas: Proteogenomic Researchers Map Protein Expression in Malignant Melanoma

Earlier this year, a team from the European Cancer Moonshot Lund Center at Lund University published proteomics and corresponding proteogenomic integration studies for malignant melanomas (MM). The twin publications represent an effort to map protein levels in over 500 MM tumor samples (the MM500 study). By applying deep-learning based single-cell segmentation and phenotyping as well as proteogenomic characterization, the researchers successfully developed a novel Digital Melanoma Pathology.


CPTAC Researchers Produce a Highly Annotated, Publicly Accessible Database of Genes Associated with Platinum Resistance in Cancer

According to U.S. National Cancer Institute estimates, approximately 10–20% of all cancer patients will receive a platinum drug over the course of their treatment. Cisplatin, the first platinum-based anti-cancer therapy, was approved by the Food and Drug Administration (FDA) for treating testicular cancer in 1978; subsequently, more platinum formulations (i.e. carboplatin, oxaliplatin) were designed and approved to reduce side effects and bolster results.


Memorandum of Understanding signed by NCI, FDA and HRSA to bring cancer diagnostic devices closer to patients, particularly members of medically underserved and geographically isolated communities

On Friday, September 17, 2021, leadership from the National Cancer Institute (NCI), Food and Drug Administration (FDA), and Health Resources and Services Administration (HRSA) signed a Memorandum of Understanding (MOU) to support solutions for early cancer detection and diagnosis to improve patient outcomes, quality of life, and reduce health disparities among medically underserved, geographically isolated, and otherwise vulnerable populations.


Machine Learning Predicts Molecular Features of Endometrial Cancer with Exceptionally High Accuracy

The CPTAC research group led by Dr. David Fenyö at NYU Langone Medical Center has demonstrated the feasibility of a machine learning image processing tool designed to assist pathologists classifying endometrial cancer. Their customized multi-resolution deep convolutional neural network (CNN) model was able to provide information about patients’ histological subtypes, molecular subtypes, and mutation status rapidly and reliably from digitized H&E-stained pathological images.


Proteogenomics Provides New Insights into Pancreatic Ductal Adenocarcinoma

Despite advances in the efficacy and specificity of cancer treatments over the last decade, pancreatic cancer remains one of the leading causes of death worldwide. The most common type of pancreatic tumor, Pancreatic Ductal Adenocarcinoma (PDAC), has distinctly poor patient outcomes due to its aggressive progression and late symptom presentation.


A More Complete Molecular Picture of Lung Squamous Cell Carcinoma Comes into View

Lung cancer remains the leading cause of cancer-associated death in the United States and worldwide. Patients with a subtype called lung adenocarcinoma (LUAD) have benefited from the development of new targeted medicines, but the search for effective new therapies for another subtype called lung squamous cell carcinoma (LSCC) has largely come up short.


CPTAC Develops HER-2 Targeted Mass Spec Test (CLIA-certified)

In the era of precision medicine, human epidermal growth factor receptor 2 (HER2) is one of the important predictive and prognostic biomarkers in breast cancer. At present, conventional HER2-targeting therapies improve outcomes for patients with HER2-positive breast cancer, defined as tumors having HER2 protein overexpression or gene amplification. On the horizon, emerging HER2-targeting compounds are beginning to show benefit in some patients with neither HER2 protein overexpression nor ERBB2 gene amplification.


Study Finds Clues to Why Some Kidney Cancers Respond to Treatment While Others Do Not

Kidney cancer is the eighth most diagnosed cancer for both men and women in the United States, and about 76,000 new cases and nearly 14,000 deaths are expected in 2021. It is a category that includes many different kinds of cancer and is dominated by renal cell carcinoma.


AML Microenvironment Catalyzes a Step-wise Evolution to Gilteritinib Resistance

Adult acute myeloid leukemia (AML) is a cancer of the blood and bone marrow. It is characterized by an aberrant proliferation of immature myeloblasts that infiltrate the bone marrow and impair normal hematopoiesis. AML is the most common type of acute leukemia in adults and usually worsens quickly if left untreated. An estimated 20,240 people in the United States will be diagnosed with AML and 11,400 will die from this disease in 2021.


Multiplexed Assays to Monitor Your Oncogenic Growth Signaling Network

In the age of personalized cancer therapy, genetic sequencing technologies allow clinicians to rapidly pinpoint mutations likely involved in driving patient-specific tumorigenesis and disease progression. These oncogenic mutations lead to the aberrant activation of signaling pathways involved in cellular growth and division. Targeted therapeutics that inhibit specific components of these pathways often yield dramatic responses in patients whose cancers rely on them for sustained growth and survival. Unfortunately, tumor relapse is a common eventuality in these settings.


Data Sharing Policies: From Bermuda, to Fort Lauderdale, to Amsterdam, to Sydney

Advancements in science and health care are made possible through widespread access to results from cutting-edge research, enabling scientists to use and build on this knowledge. A critically important aspect of the success of the Human Genome Project was its approach to immediately release pre-publication primary sequence data.


UniProt Expands Collaboration With CPTAC

UniProt, the leading online protein reference library, has expanded its collaboration with the National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC). In addition to searching for a protein-of-interest in UniProt, which includes cross-reference links to the NCI CPTAC Assay Portal for fit-for-purpose targeted assays, users now have cross-reference links to the NCI CPTAC Antibody Portal for cancer-associated renewable antibodies.


CPTAC and FDA publish findings of a community effort to identify and correct mislabeled samples in multi-omics studies

In biomedical research, sample mislabeling or incorrect annotation has been a long-standing issue contributing to irreproducible results and invalid conclusions. These issues are particularly prevalent in large scale multi-omics studies, in which multiple different omics experiments are carried out at different time periods and/or in different labs and human errors can arise during sample transferring, sample tracking, large-scale data generation, and data sharing/management.


CPTAC Assists with CLSI C64: Advancing Quantitative Protein/Peptide Mass Spectrometry Tests Towards Medical Laboratories

Protein/Peptide mass spectrometry (MS) is an enabling technology that is ideally suited for precision diagnostics, due to its quantitative measurements that can be multiplexed and its ability to directly identify proteoforms. As a result, interest on the widespread implementation of quantitative protein MS tests transitioning into medical laboratories is growing. However, this adoption in medical laboratories faces hurdles, such as consensus guidelines and requirements that ensure accurate measurements.


The Next Horizon in Precision Oncology

Where is cancer research headed in the next decade? Scientists and oncologists at the National Cancer Institute share their thoughts on the NEXT HORIZON IN PRECISION ONCOLOGY - proteogenomics.


CPTAC Helps to Identify New Roles for TGFβ in the DNA Damage Response

TGFβ is a cytokine with many, often paradoxical, roles in cancer biology. Acting as a tumor suppressor, TGFβ exerts negative control on epithelial cell proliferation - a function that tumor cells must overcome in order to progress to malignant disease. On the other hand, TGFβ also acts as a pro-tumorigenic factor, promoting malignant phenotypes such as invasion, and exerting pro-tumor effects on components of the tumor microenvironment, such as suppression of anti-tumor immune responses.


CPTAC Researchers Expand the use of MSFragger to Search N- and O-linked Glycopeptides

CPTAC researchers out of the University of Michigan have hit another home run. The Nesvizhskii lab, developer of the FragPipe proteomics pipeline, has developed an extension of its MSFragger flagship software to now identify N- and O-linked glycopeptides. The study was recently published in Nature Methods. The new mode, MSFragger-Glyco, allows researchers to have the same ultrafast and sensitive search for glycopeptide spectrum matches, as with the original MSFragger software.


NCI’s International Cancer Proteogenome Consortium Welcomes Three New Member Institutions in the Global Fight Against Cancer

The National Cancer Institute (NCI) of the National Institutes of Health is pleased to announce the signing of two new memoranda of understanding (MOUs) for international cancer research and care, as well as new efforts in the emerging scientific area of proteogenomics for precision oncology. MOUs establish agreements to work together in clinical cancer research and in the development of standards and solutions for this science discipline being advanced by both organizations.


Aggressive Brain Tumor Mapped in Genetic, Molecular Detail

Glioblastoma is among the most aggressive and devastating of cancers. While rare compared with other cancers, it’s the most common type of brain cancer. Even with intensive therapy, relatively few patients survive longer than two years after diagnosis, and fewer than 10% of patients survive beyond five years. Despite extensive studies focused on genomic features of glioblastoma, relatively little progress has been made in improving treatment for patients with this deadly disease.


Dysregulation of Glycosylation in Prostate Cancer Cells Affect Extracellular Vesicle Proteome

Prostate cancer screening is typically done by evaluation of levels of prostate-specific antigens (PSA). Unfortunately, its effectiveness in stratifying low risk patients from those with aggressive (AG) prostate cancer is poor. Localized in the Golgi, α (1,6) fucosyltranferase (FUT8), a glycotransferase responsible for catalyzing the addition of fucose onto glycoprotein, has been previously shown to have a role in cell motility and invasiveness, and its over expression has been shown to associated with AG prostate cancer. 


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