Characterizing isoform switching events in esophageal adenocarcinoma

Yun Zhang; Katherine M. Weh; Connor L. Howard; Jean-Jack Riethoven; Jennifer L. Clarke; Kiran H. Lagisetty; Jules Lin; Rishindra M. Reddy; Andrew C. Chang; David G. Beer; Laura A. Kresty

Molecular Therapy: Nucleic Acids (Sep 2022)

Characterizing isoform switching events in esophageal adenocarcinoma

Yun Zhang,
Katherine M. Weh,
Connor L. Howard,
Jean-Jack Riethoven,
Jennifer L. Clarke,
Kiran H. Lagisetty,
Jules Lin,
Rishindra M. Reddy,
Andrew C. Chang,
David G. Beer,
Laura A. Kresty

Affiliations

Yun Zhang: Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
Katherine M. Weh: Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
Connor L. Howard: Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
Jean-Jack Riethoven: Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
Jennifer L. Clarke: Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
Kiran H. Lagisetty: Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
Jules Lin: Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
Rishindra M. Reddy: Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
Andrew C. Chang: Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
David G. Beer: Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
Laura A. Kresty: Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Corresponding author Laura A. Kresty, PhD, Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA.

Journal volume & issue: Vol. 29
pp. 749 – 768

Abstract

Read online

Isoform switching events with predicted functional consequences are common in many cancers, but characterization of switching events in esophageal adenocarcinoma (EAC) is lacking. Next-generation sequencing was used to detect levels of RNA transcripts and identify specific isoforms in treatment-naïve esophageal tissues ranging from premalignant Barrett’s esophagus (BE), BE with low- or high-grade dysplasia (BE.LGD, BE.HGD), and EAC. Samples were stratified by histopathology and TP53 mutation status, identifying significant isoform switching events with predicted functional consequences. Comparing BE.LGD with BE.HGD, a histopathology linked to cancer progression, isoform switching events were identified in 75 genes including KRAS, RNF128, and WRAP53. Stratification based on TP53 status increased the number of significant isoform switches to 135, suggesting switching events affect cellular functions based on TP53 mutation and tissue histopathology. Analysis of isoforms agnostic, exclusive, and shared with mutant TP53 revealed unique signatures including demethylation, lipid and retinoic acid metabolism, and glucuronidation, respectively. Nearly half of isoform switching events were identified without significant gene-level expression changes. Importantly, two TP53-interacting isoforms, RNF128 and WRAP53, were significantly linked to patient survival. Thus, analysis of isoform switching events may provide new insight for the identification of prognostic markers and inform new potential therapeutic targets for EAC.

Published in Molecular Therapy: Nucleic Acids

ISSN: 2162-2531 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Medicine: Therapeutics. Pharmacology
Website: https://www.cell.com/molecular-therapy-family/nucleic-acids/latest-content

About the journal

Abstract

Keywords