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Addendum Free access | 10.1172/jci.insight.98457

Subtyping sub-Saharan esophageal squamous cell carcinoma by comprehensive molecular analysis

Wenjin Liu, Jeff M. Snell, William R. Jeck, Katherine A. Hoadley, Matthew D. Wilkerson, Joel S. Parker, Nirali Patel, Yohannie B. Mlombe, Gift Mulima, N. George Liomba, Lindsey L. Wolf, Carol G. Shores, Satish Gopal, and Norman E. Sharpless

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Published November 16, 2017 - More info

Published in Volume 2, Issue 22 on November 16, 2017
JCI Insight. 2017;2(22):e98457. https://doi.org/10.1172/jci.insight.98457.
Copyright © 2017, American Society for Clinical Investigation
Published November 16, 2017 - Version history
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Related article:

Subtyping sub-Saharan esophageal squamous cell carcinoma by comprehensive molecular analysis
Wenjin Liu, … , Satish Gopal, Norman E. Sharpless
Wenjin Liu, … , Satish Gopal, Norman E. Sharpless
A comprehensive DNA and RNA analysis of esophageal squamous cell carcinoma from resource-poor Malawi, where incidence is 20-fold higher than western countries.
Research Article Genetics Oncology

Subtyping sub-Saharan esophageal squamous cell carcinoma by comprehensive molecular analysis

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Abstract

Esophageal squamous cell carcinoma (ESCC) is endemic in regions of sub-Saharan Africa (SSA), where it is the third most common cancer. Here, we describe whole-exome tumor/normal sequencing and RNA transcriptomic analysis of 59 patients with ESCC in Malawi. We observed similar genetic aberrations as reported in Asian and North American cohorts, including mutations of TP53, CDKN2A, NFE2L2, CHEK2, NOTCH1, FAT1, and FBXW7. Analyses for nonhuman sequences did not reveal evidence for infection with HPV or other occult pathogens. Mutational signature analysis revealed common signatures associated with aging, cytidine deaminase activity (APOBEC), and a third signature of unknown origin, but signatures of inhaled tobacco use, aflatoxin and mismatch repair were notably absent. Based on RNA expression analysis, ESCC could be divided into 3 distinct subtypes, which were distinguished by their expression of cell cycle and neural transcripts. This study demonstrates discrete subtypes of ESCC in SSA, and suggests that the endemic nature of this disease reflects exposure to a carcinogen other than tobacco and oncogenic viruses.

Authors

Wenjin Liu, Jeff M. Snell, William R. Jeck, Katherine A. Hoadley, Matthew D. Wilkerson, Joel S. Parker, Nirali Patel, Yohannie B. Mlombe, Gift Mulima, N. George Liomba, Lindsey L. Wolf, Carol G. Shores, Satish Gopal, Norman E. Sharpless

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Original citation: JCI Insight. 2016;1(16):e88755. https://doi.org/10.1172/jci.insight.88755

Citation for this addendum: JCI Insight. 2017;2(22):e95978. https://doi.org/10.1172/jci.insight.98457

Whole exome sequencing and RNA sequencing data for this study have been deposited in the NCBI’s Database of Genotypes and Phenotypes (dbGaP phs001448.v1.p1).

Footnotes

See the related article at Subtyping sub-Saharan esophageal squamous cell carcinoma by comprehensive molecular analysis.

Version history
  • Version 1 (November 16, 2017): Electronic publication
  • Version 2 (December 7, 2017): The subject has been updated to Addendum.

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