Advanced mass spectrometry‐based multi‐omics technologies for exploring the pathogenesis of hepatocellular carcinoma

Abstract

Hepatocellular carcinoma (HCC) is one of the primary hepatic malignancies and is the third most common cause of cancer related death worldwide. Although a wealth of knowledge has been gained concerning the initiation and progression of HCC over the last half century, efforts to improve our understanding of its pathogenesis at a molecular level are still greatly needed, to enable clinicians to enhance the standards of the current diagnosis and treatment of HCC. In the post‐genome era, advanced mass spectrometry driven multi‐omics technologies (e.g., profiling of DNA damage adducts, RNA modification profiling, proteomics, and metabolomics) stand at the interface between chemistry and biology, and have yielded valuable outcomes from the study of a diversity of complicated diseases. Particularly, these technologies are being broadly used to dissect various biological aspects of HCC with the purpose of biomarker discovery, interrogating pathogenesis as well as for therapeutic discovery. This proof of knowledge‐based critical review aims at exploring the selected applications of those defined omics technologies in the HCC niche with an emphasis on translational applications driven by advanced mass spectrometry, toward the specific clinical use for HCC patients. This approach will enable the biomedical community, through both basic research and the clinical sciences, to enhance the applicability of mass spectrometry‐based omics technologies in dissecting the pathogenesis of HCC and could lead to novel therapeutic discoveries for HCC. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 35:331–349, 2016.

Responding to a Zoonotic Emergency with Multi-omics Research:Pentatrichomonas hominisHydrogenosomal Protein Characterization with Use of RNA Sequencing and Proteomics

“…In the postgenomics era, system-wide overview provided by multi-omics studies contributes valuable insights on algal research in biofuels development (Rai et al, 2016), veterinary medicine (Li et al, 2015), and systemic progression on pathogenesis in liver cancer research (Nie et al, 2016), respectively. Proteomics, as an important technique in multi-omics study, still has limitations, despite improvements that were made in the last decade.…”

Increasing Complexity to Simplify Clinical Care: High Resolution Mass Spectrometry as an Enabler of AI Guided Clinical and Therapeutic Monitoring

“…With the trend of increasing use of mass spectrometry in clinical care, MS based biomarkers are being validated for future incorporation into diagnostic criteria. Mass spectrometry has been used to study biomarker panels found in various cancers, [ 86–92 ] cystic fibrosis, [ 93 ] neurodegenerative diseases, [ 94,95 ] major depressive disorder, [ 96 ] nephrotic syndromes, [ 97 ] myocardial injury, [ 98 ] and even Fabry disease. [ 99 ] Some researchers provide a further push for this concept by coming up with innovative ways of using mass spectrometry data in clinical care.…”

Identification of protein abundance changes in biopsy-level hepatocellular carcinoma tissues using PCT-SWATH

“…The protein numbers identified per sample was slightly higher than those obtained from human kidney tissues 17 . 9 To evaluate the quantitative accuracy of the method, we computed the global Pearson correlation of the two technical replicates at the peptide level for all samples after removing missing values. The R 2 was 0.9729 ( Fig.…”

“…Better biomarkers are needed for HCC. The search for HCC biomarkers from clinical specimens using proteomics approaches has been focused mainly on blood samples 9,10 . Besides, some studies also investigated biological fluids including urine 11 and tissue interstitial fluid 12 .…”