Protein-gene Expression Nexus: Comprehensive characterization of human cancer cell lines with proteogenomic analysis

Hyung, Daejin; Baek, Min-Jeong; Lee, Jongkeun; Cho, Ju‐Yeon; Kim, Hyoun Sook; Park, Charny; Cho, Soo Young

doi:10.1016/j.csbj.2021.08.022

Cited by 5 publications

(3 citation statements)

References 53 publications

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“…Proteogenomics, the integration of genomics and proteomics, is an emerging technological development in the multi-omics field and has the potential to improve cancer characterization, diagnosis, and even advance cancer therapy( [37][38][39] ). Furthermore, such integration efforts are also being used to sequence antibody repertoires by MS 40 .…”

Section: Discussionmentioning

confidence: 99%

N-linked glycosylation of the M-protein variable region: Glycoproteogenomics reveals a new layer of personalized complexity in multiple myeloma

Langerhorst

Baerenfaenger

Kulkarni

et al. 2023

Preprint

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Multiple Myeloma (MM) is a plasma cell malignancy characterized by a monoclonal expansion of plasma cells that secrete a characteristic M-protein. This M-protein is crucial for diagnosis and monitoring of MM in the blood of patients. Recent evidence has emerged suggesting that N-glycosylation of the M-protein variable (Fab) region contributes to M-protein pathogenicity, and that it is a risk factor for disease progression of plasma cell disorders. Current methodologies lack the specificity to provide a site-specific glycoprofile of the Fab regions of M-proteins. Here, we introduce a novel glycoproteogenomics method that allows detailed M-protein glycoprofiling by integrating patient specific Fab region sequences (genomics) with glycoprofiling by glycoproteomics. Genomic analysis uncovered a more than two-fold increase in the Fab Light Chain N-glycosylation of M-proteins of patients with Multiple Myeloma compared to Fab Light Chain N-glycosylation of polyclonal antibodies from healthy individuals. Subsequent glycoproteogenomics analysis of 41 patients enrolled in the IFM 2009 clinical trial revealed that the majority of the Fab N-glycosylation sites were fully occupied with complex type glycans, distinguishable from Fc region glycans due to high levels of sialylation, fucosylation and bisecting structures. Together, glycoproteogenomics is a powerful tool to study de novo Fab N-glycosylation in plasma cell dyscrasias.

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Section: Discussionmentioning

confidence: 99%

N-linked glycosylation of the M-protein variable region: Glycoproteogenomics reveals a new layer of personalized complexity in multiple myeloma

Langerhorst

Baerenfaenger

Kulkarni

et al. 2023

Preprint

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“…Mani et al developed PANOPLYa cloud-based platform for automated and reproducible proteogenomic data analysis . The University of ALabama at Birmingham CANcer data analysis Portal (UALCAN) (https://ualcan.path.uab.edu/index.html) is a comprehensive, user-friendly, and interactive web resource for analyzing cancer -omic data (TCGA, MET500, CPTAC, and CBTTC). , PEN () presents a database that allows researchers to easily and extensively visualize and annotate changes such as somatic copy number alterations, transcriptomic differences, peptide expressions, and modifications . Peppy is a software tool designed to perform every necessary task of proteogenomic searches: generating a peptide database from a genome, tracking peptide loci, matching peptides to MS/MS spectra and assigning confidence values to those matches. , Peppy is available at .…”

Section: Swot Analysis Of Proteogenomics In Cancer Researchmentioning

confidence: 99%

“…218,219 PEN (http:// combio.snu.ac.kr/pen) presents a database that allows researchers to easily and extensively visualize and annotate changes such as somatic copy number alterations, transcriptomic differences, peptide expressions, and modifications. 220 Peppy is a software tool designed to perform every necessary task of proteogenomic searches: generating a peptide database from a genome, tracking peptide loci, matching peptides to MS/MS spectra and assigning confidence values to those matches. 221,222 Peppy is available at http://geneffects.…”

Section: ■ Swot Analysis Of Proteogenomics In Cancer Researchmentioning

confidence: 99%

Proteogenomics in Cancer: Then and Now

Wang,

Xu,

Lau

2023

J. Proteome Res.

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For years, the paths of sequencing technologies and mass spectrometry have occurred in isolation, with each developing its own unique culture and expertise. These two technologies are crucial for inspecting complementary aspects of the molecular phenotype across the central dogma. Integrative multiomics strives to bridge the analysis gap among different fields to complete more comprehensive mechanisms of life events and diseases. Proteogenomics is one integrated multiomics field. Here in this review, we mainly summarize and discuss three aspects: workflow of proteogenomics, proteogenomics applications in cancer research, and the SWOT (Strengths, Weaknesses, Opportunities, Threats) analysis of proteogenomics in cancer research. In conclusion, proteogenomics has a promising future as it clarifies the functional consequences of many unannotated genomic abnormalities or noncanonical variants and identifies driver genes and novel therapeutic targets across cancers, which would substantially accelerate the development of precision oncology.

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The role of proteomics in the multiplexed analysis of gene alterations in human cancer

Babu

Bhat

John

et al. 2021

Expert Review of Proteomics

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Protein-gene Expression Nexus: Comprehensive characterization of human cancer cell lines with proteogenomic analysis

Abstract: Graphical abstract

Cited by 5 publications

References 53 publications

N-linked glycosylation of the M-protein variable region: Glycoproteogenomics reveals a new layer of personalized complexity in multiple myeloma

N-linked glycosylation of the M-protein variable region: Glycoproteogenomics reveals a new layer of personalized complexity in multiple myeloma

Proteogenomics in Cancer: Then and Now

The role of proteomics in the multiplexed analysis of gene alterations in human cancer

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