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.

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.

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.

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 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.

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.

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.

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. 

Proteogenomic analysis may offer new insight into matching cancer patients with an effective therapy for their particular cancer. A new study identifies three molecular subtypes in head and neck squamous cell carcinoma (HNSCC) that could be used to better determine appropriate treatment. The research led by Baylor College of Medicine, Johns Hopkins University and the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) is published in the journal Cancer Cell.

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.