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Tan AC, Saw SP, Chen J, Lai GG, Oo HN, Takano A, Lau DP, Yeong JP, Tan GS, Lim KH, Skanderup AJ, Chan JW, Teh YL, Rajasekaran T, Jain A, Tan WL, Ng QS, Kanesvaran R, Lim WT, Ang MK, Tan DS. Clinical and Genomic Features of HER2 Exon 20 Insertion Mutations and Characterization of HER2 Expression by Immunohistochemistry in East Asian Non–Small-Cell Lung Cancer. JCO Precis Oncol 2022; 6:e2200278. [DOI: 10.1200/po.22.00278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PURPOSE HER2-altered non–small-cell lung cancer (NSCLC) represents a diverse subgroup, including mutations, amplifications, and overexpression. However, HER2 exon 20 insertion mutations are emerging as a distinct molecular subtype with expanding therapeutic options. We describe the molecular epidemiology and genomic features of HER2-altered NSCLC in an Asian tertiary cancer center. METHODS We identified patients with HER2-mutated NSCLC in our institutional database, collating clinicopathological features and treatment outcomes. The genomic landscape of human epidermal growth factor receptor 2 ( HER2)–mutated NSCLC was further evaluated using whole-exome sequencing (WES) data from combined local and publicly available data sets. HER2 amplification and overexpression as selection biomarkers in NSCLC were further interrogated using HER2 immunohistochemistry and correlations with WES and RNA sequencing data. RESULTS Among 1,252 patients with consecutive lung adenocarcinoma undergoing routine next-generation sequencing, the prevalence of HER2 mutations was 3.1%—exon 20 insertion mutations comprised 2.7%. We examined the clinicopathological features in 55 patients with HER2-mutated NSCLC comprising 40 exon 20 insertion and 15 nonexon 20 insertion mutations. The most common exon 20 insertion mutation was HER2Y772_A775dup in 30 (75%), followed by HER2G776delinsVC in five patients (13%). There were limited responses to HER2-directed therapies apart from trastuzumab-deruxtecan, and no responses were seen with immunotherapy monotherapy. Evaluating the genomics features of HER2 exon 20 insertion mutations using WES data revealed low tumor mutational burden (TMB), low incidence of cancer driver comutations, and a predominance of aging mutational signature—similar to EGFR-mutated tumors. In contrast, uncommon (or nonexon 20 insertion) HER2-mutated tumors resembled EGFR wild-type tumors with higher TMB, higher frequency of cancer driver comutations, and greater presence of smoking and APOBEC mutational signature. Finally, in evaluating HER2 immunohistochemistry in all lung adenocarcinoma, there was significant discordance comparing different scoring systems and poor correlation with HER2 RNA expression and HER2 amplification. CONCLUSION The incidence of HER2 mutations is 3.1% in East Asian nonsquamous NSCLC. HER2 exon 20 insertion–mutated tumors appear genomically distinct from uncommon (nonexon 20 insertion) HER2 mutations, the latter demonstrating higher TMB, co-occurring drivers, and predominant nonaging mutational signature. The therapeutic implications of the genomic and clinical features of HER2-mutated NSCLC warrant further investigation.
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Affiliation(s)
- Aaron C. Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Stephanie P.L. Saw
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Jianbin Chen
- Genome Institute of Singapore, Singapore, Singapore
| | - Gillianne G.Y. Lai
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Hlaing Nwe Oo
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Angela Takano
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Dawn P.X. Lau
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Joe P.S. Yeong
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Gek San Tan
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Kiat Hon Lim
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | | | - Johan W.K. Chan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Yi Lin Teh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Tanujaa Rajasekaran
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Amit Jain
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Wan Ling Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Quan Sing Ng
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Ravindran Kanesvaran
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Wan-Teck Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Mei-Kim Ang
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Daniel S.W. Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
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Chua KP, Teng YH, Tan AC, Takano A, Alvarez JJ, Nahar R, Rohatgi N, Lai GG, Aung ZW, Yeong JP, Lim KH, Naeini MM, Kassam I, Jain A, Tan WL, Gogna A, Too CW, Kanesvaran R, Ng QS, Ang MK, Rajasekaran T, Anantham D, Phua GC, Tan BS, Lee YY, Wang L, Teo AS, Khng AJ, Lim MJ, Suteja L, Toh CK, Lim WT, Iyer NG, Tam WL, Tan EH, Zhai W, Hillmer AM, Skanderup AJ, Tan DS. Integrative Profiling of T790M-Negative EGFR-Mutated NSCLC Reveals Pervasive Lineage Transition and Therapeutic Opportunities. Clin Cancer Res 2021; 27:5939-5950. [PMID: 34261696 PMCID: PMC9401458 DOI: 10.1158/1078-0432.ccr-20-4607] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/06/2021] [Accepted: 07/09/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE Despite the established role of EGFR tyrosine kinase inhibitors (TKIs) in EGFR-mutated NSCLC, drug resistance inevitably ensues, with a paucity of treatment options especially in EGFR T790M-negative resistance. EXPERIMENTAL DESIGN We performed whole-exome and transcriptome analysis of 59 patients with first- and second-generation EGFR TKI-resistant metastatic EGFR-mutated NSCLC to characterize and compare molecular alterations mediating resistance in T790M-positive (T790M+) and -negative (T790M-) disease. RESULTS Transcriptomic analysis revealed ubiquitous loss of adenocarcinoma lineage gene expression in T790M- tumors, orthogonally validated using multiplex IHC. There was enrichment of genomic features such as TP53 alterations, 3q chromosomal amplifications, whole-genome doubling and nonaging mutational signatures in T790M- tumors. Almost half of resistant tumors were further classified as immunehot, with clinical outcomes conditional on immune cell-infiltration state and T790M status. Finally, using a Bayesian statistical approach, we explored how T790M- and T790M+ disease might be predicted using comprehensive genomic and transcriptomic profiles of treatment-naïve patients. CONCLUSIONS Our results illustrate the interplay between genetic alterations, cell lineage plasticity, and immune microenvironment in shaping divergent TKI resistance and outcome trajectories in EGFR-mutated NSCLC. Genomic and transcriptomic profiling may facilitate the design of bespoke therapeutic approaches tailored to a tumor's adaptive potential.
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Affiliation(s)
- Khi Pin Chua
- Genome Institute of Singapore, Singapore, Singapore
| | - Yvonne H.F. Teng
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore.,Cancer Therapeutics Research Laboratory, National Cancer Center Singapore, Singapore, Singapore
| | - Aaron C. Tan
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore.,Duke-NUS Medical School Singapore, Singapore
| | - Angela Takano
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | | | - Rahul Nahar
- Genome Institute of Singapore, Singapore, Singapore
| | - Neha Rohatgi
- Genome Institute of Singapore, Singapore, Singapore
| | - Gillianne G.Y. Lai
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Zaw Win Aung
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Joe P.S. Yeong
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Kiat Hon Lim
- Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | | | | | - Amit Jain
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Wan Ling Tan
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Apoorva Gogna
- Department of Vascular and Interventional Radiology, Singapore General Hospital, Singapore, Singapore
| | - Chow Wei Too
- Department of Vascular and Interventional Radiology, Singapore General Hospital, Singapore, Singapore
| | - Ravindran Kanesvaran
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Quan Sing Ng
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Mei Kim Ang
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Tanujaa Rajasekaran
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Devanand Anantham
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Ghee Chee Phua
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Bien Soo Tan
- Department of Vascular and Interventional Radiology, Singapore General Hospital, Singapore, Singapore
| | - Yin Yeng Lee
- Genome Institute of Singapore, Singapore, Singapore
| | - Lanying Wang
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | | | | | - Ming Jie Lim
- Genome Institute of Singapore, Singapore, Singapore
| | - Lisda Suteja
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Chee Keong Toh
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Wan-Teck Lim
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore.,Duke-NUS Medical School Singapore, Singapore.,IMCB NCC MPI Singapore Oncogenome Laboratory, Institute of Molecular and Cell Biology, Singapore, Singapore
| | - N. Gopalakrishna Iyer
- Cancer Therapeutics Research Laboratory, National Cancer Center Singapore, Singapore, Singapore.,Duke-NUS Medical School Singapore, Singapore.,Division of Surgical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore, Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Eng-Huat Tan
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Weiwei Zhai
- Genome Institute of Singapore, Singapore, Singapore.,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Axel M. Hillmer
- Genome Institute of Singapore, Singapore, Singapore.,Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Anders J. Skanderup
- Genome Institute of Singapore, Singapore, Singapore.,Corresponding Authors: Daniel S.W. Tan, 11 Hospital Crescent, National Cancer Center Singapore, Singapore 169610. Phone: 656-436-8000; E-mail: ; and Anders J. Skanderup,
| | - Daniel S.W. Tan
- Genome Institute of Singapore, Singapore, Singapore.,Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore.,Cancer Therapeutics Research Laboratory, National Cancer Center Singapore, Singapore, Singapore.,Duke-NUS Medical School Singapore, Singapore.,Corresponding Authors: Daniel S.W. Tan, 11 Hospital Crescent, National Cancer Center Singapore, Singapore 169610. Phone: 656-436-8000; E-mail: ; and Anders J. Skanderup,
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