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Molecular Cancer
Published in: Molecular Cancer 1/2018

Open Access 01-12-2018 | Research

Proteogenomic characterization and comprehensive integrative genomic analysis of human colorectal cancer liver metastasis

Authors: Yu-Shui Ma, Tao Huang, Xiao-Ming Zhong, Hong-Wei Zhang, Xian-Ling Cong, Hong Xu, Gai-Xia Lu, Fei Yu, Shao-Bo Xue, Zhong-Wei Lv, Da Fu

Published in: Molecular Cancer | Issue 1/2018

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Abstract

Background

Proteogenomic characterization and integrative and comparative genomic analysis provide a functional context to annotate genomic abnormalities with prognostic value.

Methods

Here, we analyzed the proteomes and performed whole exome and transcriptome sequencing and single nucleotide polymorphism array profiling for 2 sets of triplet samples comprised of normal colorectal tissue, primary CRC tissue, and synchronous matched liver metastatic tissue.

Results

We identified 112 CNV-mRNA-protein correlated molecules, including up-regulated COL1A2 and BGN associated with prognosis, and four strongest hot spots (chromosomes X, 7, 16 and 1) driving global mRNA abundance variation in CRC liver metastasis. Two sites (DMRTB1R202H and PARP4V458I) were revealed to frequent mutate only in the liver metastatic cohort and displayed dysregulated protein abundance. Moreover, we confirmed that the mutated peptide number has potential prognosis value and somatic variants displayed increased protein abundance, including high MYH9 and CCT6A expression, with clinical significance.

Conclusions

Our proteogenomic characterization and integrative and comparative genomic analysis provides a new paradigm for understanding human colon and rectal cancer liver metastasis.

Trial registration

ClinicalTrials, NCT02917707. Registered 28 September 2016, https://​clinicaltrials.​gov/​ct2/​show/​NCT02917707.
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Metadata
Title
Proteogenomic characterization and comprehensive integrative genomic analysis of human colorectal cancer liver metastasis
Authors
Yu-Shui Ma
Tao Huang
Xiao-Ming Zhong
Hong-Wei Zhang
Xian-Ling Cong
Hong Xu
Gai-Xia Lu
Fei Yu
Shao-Bo Xue
Zhong-Wei Lv
Da Fu
Publication date
01-12-2018
Publisher
BioMed Central
Published in
Molecular Cancer / Issue 1/2018
Electronic ISSN: 1476-4598
DOI
https://doi.org/10.1186/s12943-018-0890-1

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