. 2021 Feb 2;34(5):108707.

doi: 10.1016/j.celrep.2021.108707.

Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway

Jian Carrot-Zhang¹, Xiaotong Yao², Siddhartha Devarakonda³, Aditya Deshpande², Jeffrey S Damrauer⁴, Tiago Chedraoui Silva⁵, Christopher K Wong⁶, Hyo Young Choi⁷, Ina Felau⁸, A Gordon Robertson⁹, Mauro A A Castro¹⁰, Lisui Bao¹¹, Esther Rheinbay¹², Eric Minwei Liu¹³, Tuan Trieu¹³, David Haan⁶, Christina Yau¹⁴, Toshinori Hinoue¹⁵, Yuexin Liu¹⁶, Ofer Shapira¹⁷, Kiran Kumar¹⁸, Karen L Mungall⁹, Hailei Zhang¹⁷, Jake June-Koo Lee¹⁹, Ashton Berger¹⁷, Galen F Gao¹⁷, Binyamin Zhitomirsky¹², Wen-Wei Liang²⁰, Meng Zhou¹, Sitapriya Moorthi²¹, Alice H Berger²¹, Eric A Collisson²², Michael C Zody²³, Li Ding²⁰, Andrew D Cherniack¹⁸, Gad Getz¹², Olivier Elemento²⁴, Christopher C Benz²⁵, Josh Stuart⁶, J C Zenklusen⁸, Rameen Beroukhim²⁶, Jason C Chang²⁷, Joshua D Campbell²⁸, D Neil Hayes⁷, Lixing Yang¹¹, Peter W Laird¹⁵, John N Weinstein¹⁶, David J Kwiatkowski²⁹, Ming S Tsao³⁰, William D Travis²⁷, Ekta Khurana¹³, Benjamin P Berman³¹, Katherine A Hoadley⁴, Nicolas Robine²³; TCGA Research Network; Matthew Meyerson³², Ramaswamy Govindan³³, Marcin Imielinski³⁴

Collaborators, Affiliations

Collaborators

Affiliations

¹ Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA.
² Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; New York Genome Center, New York, NY, USA; Tri-institutional Ph.D. Program in Computational Biology and Medicine, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
³ Section of Medical Oncology, Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA.
⁴ Department of Genetics, Computational Medicine Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
⁵ Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
⁶ Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
⁷ University of Tennessee Health Science Center, UTHSC Center for Cancer Research, TN, USA.
⁸ National Cancer Institute, Bethesda, MD, USA.
⁹ Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
¹⁰ Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, PR, Brazil.
¹¹ Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA.
¹² Broad Institute of MIT and Harvard, Cambridge, MA, USA; Massachusetts General Hospital Cancer Center, Boston, MA, USA.
¹³ Caryl and Israel Englander Institute for Precision Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
¹⁴ University of California, San Francisco, San Francisco, CA, USA; Buck Institute for Research on Aging, Novato, CA, USA.
¹⁵ Van Andel Institute, Grand Rapids, MI, USA.
¹⁶ Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
¹⁷ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
¹⁸ Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
¹⁹ Harvard Medical School, Boston, MA, USA.
²⁰ Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA.
²¹ Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
²² University of California, San Francisco, San Francisco, CA, USA.
²³ New York Genome Center, New York, NY, USA.
²⁴ Tri-institutional Ph.D. Program in Computational Biology and Medicine, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
²⁵ Buck Institute for Research on Aging, Novato, CA, USA.
²⁶ Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
²⁷ Thoracic Pathology, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
²⁸ Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA.
²⁹ Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
³⁰ Department of Pathology, University Health Network, Princess Margaret Cancer Centre, Toronto, ON, Canada.
³¹ Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University, Jerusalem, Israel.
³² Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA. Electronic address: matthew_meyerson@dfci.harvard.edu.
³³ Section of Medical Oncology, Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA. Electronic address: rgovindan@wustl.edu.
³⁴ Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; New York Genome Center, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA. Electronic address: mai9037@med.cornell.edu.

PMID: 33535033
PMCID: PMC8009291
DOI: 10.1016/j.celrep.2021.108707

Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway

Jian Carrot-Zhang et al. Cell Rep. 2021.

. 2021 Feb 2;34(5):108707.

doi: 10.1016/j.celrep.2021.108707.

Authors

Collaborators

Affiliations

¹ Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA.
² Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; New York Genome Center, New York, NY, USA; Tri-institutional Ph.D. Program in Computational Biology and Medicine, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
³ Section of Medical Oncology, Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA.
⁴ Department of Genetics, Computational Medicine Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
⁵ Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
⁶ Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
⁷ University of Tennessee Health Science Center, UTHSC Center for Cancer Research, TN, USA.
⁸ National Cancer Institute, Bethesda, MD, USA.
⁹ Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
¹⁰ Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, PR, Brazil.
¹¹ Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA.
¹² Broad Institute of MIT and Harvard, Cambridge, MA, USA; Massachusetts General Hospital Cancer Center, Boston, MA, USA.
¹³ Caryl and Israel Englander Institute for Precision Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
¹⁴ University of California, San Francisco, San Francisco, CA, USA; Buck Institute for Research on Aging, Novato, CA, USA.
¹⁵ Van Andel Institute, Grand Rapids, MI, USA.
¹⁶ Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
¹⁷ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
¹⁸ Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
¹⁹ Harvard Medical School, Boston, MA, USA.
²⁰ Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO, USA.
²¹ Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
²² University of California, San Francisco, San Francisco, CA, USA.
²³ New York Genome Center, New York, NY, USA.
²⁴ Tri-institutional Ph.D. Program in Computational Biology and Medicine, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
²⁵ Buck Institute for Research on Aging, Novato, CA, USA.
²⁶ Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
²⁷ Thoracic Pathology, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
²⁸ Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA.
²⁹ Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
³⁰ Department of Pathology, University Health Network, Princess Margaret Cancer Centre, Toronto, ON, Canada.
³¹ Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University, Jerusalem, Israel.
³² Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA. Electronic address: matthew_meyerson@dfci.harvard.edu.
³³ Section of Medical Oncology, Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA. Electronic address: rgovindan@wustl.edu.
³⁴ Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; New York Genome Center, New York, NY, USA; Caryl and Israel Englander Institute for Precision Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA. Electronic address: mai9037@med.cornell.edu.

PMID: 33535033
PMCID: PMC8009291
DOI: 10.1016/j.celrep.2021.108707

Erratum in

Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway.
Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TC, Wong CK, Choi HY, Felau I, Robertson AG, Castro MAA, Bao L, Rheinbay E, Liu EM, Trieu T, Haan D, Yau C, Hinoue T, Liu Y, Shapira O, Kumar K, Mungall KL, Zhang H, June-Koo Lee J, Berger A, Gao GF, Zhitomirsky B, Liang WW, Zhou M, Moorthi S, Berger AH, Collisson EA, Zody MC, Ding L, Cherniack AD, Getz G, Elemento O, Benz CC, Stuart J, Zenklusen JC, Beroukhim R, Chang JC, Campbell JD, Hayes DN, Yang L, Laird PW, Weinstein JN, Kwiatkowski DJ, Tsao MS, Travis WD, Khurana E, Berman BP, Hoadley KA, Robine N; TCGA Research Network; Meyerson M, Govindan R, Imielinski M. Carrot-Zhang J, et al. Cell Rep. 2021 Feb 23;34(8):108784. doi: 10.1016/j.celrep.2021.108784. Cell Rep. 2021. PMID: 33626341 Free PMC article. No abstract available.

Abstract

RTK/RAS/RAF pathway alterations (RPAs) are a hallmark of lung adenocarcinoma (LUAD). In this study, we use whole-genome sequencing (WGS) of 85 cases found to be RPA(-) by previous studies from The Cancer Genome Atlas (TCGA) to characterize the minority of LUADs lacking apparent alterations in this pathway. We show that WGS analysis uncovers RPA(+) in 28 (33%) of the 85 samples. Among the remaining 57 cases, we observe focal deletions targeting the promoter or transcription start site of STK11 (n = 7) or KEAP1 (n = 3), and promoter mutations associated with the increased expression of ILF2 (n = 6). We also identify complex structural variations associated with high-level copy number amplifications. Moreover, an enrichment of focal deletions is found in TP53 mutant cases. Our results indicate that RPA(-) cases demonstrate tumor suppressor deletions and genome instability, but lack unique or recurrent genetic lesions compensating for the lack of RPAs. Larger WGS studies of RPA(-) cases are required to understand this important LUAD subset.

Keywords: TCGA; driver; genome analysis; lung adenocarcinoma; noncoding; oncogene; precision oncology; structural variation; tumor suppressor; whole genome sequencing.

PubMed Disclaimer

Conflict of interest statement

Declaration of interests M.M. is listed as the inventor on the patent for the EGFR mutation analysis for lung cancer diagnosis licensed to LabCorp; holds research support from Bayer, Janssen, and Ono; and serves as scientific advisory board chair for OrigiMed. P.W.L. serves on the scientific advisory boards of AnchorDx and Progenity. D.J.K. has research support from Revolution Medicines and Genentech and is a consultant to AADi.

Figures

**Figure 1.. Identification of RPA(–) LUADs**
(A) Identification of 118 RPA(–)_E LUAD cases from the 501 TCGA LUAD cohort, defined by WES or RNA-seq analysis. Eighty-five of the 118 samples were sent for WGS. The RTK/RAS/RAF pathway alterations used to define the RPA(+) or RPA(–) cases are listed in Table S1. (B) WGS uncovered genomic alterations in the RTK/RAS/RAF pathway in 28/85 samples; 57/85 samples remain as RPA(–) after WGS analysis. (C) Visualization of sequencing reads covering a *KRAS* p.G12C mutation in WGS (upper panel) and WES (lower panel) for sample (TCGA-55–7574). Both read depth and the number of reads supporting the mutation are higher in WGS than in WES. (D) An example of *EGFR* amplification coupled with *EGFR* overexpression in TCGA-50–5939. In the second panel, purity-adjusted copy number and SV junctions (red lines) support a BFBC event underlying the amplification. Lower panels indicate WGS read depth and gene location in the region. CN, copy number. (E) Example of a *RASA1* simple deletion spanning from exon 21 to the end of the gene (12 kbp) coupled with *RASA1* loss of expression in TCGA-55–8614. See also Figure S1.

**Figure 2.. Recurrent coding alterations in RPA(–)_G LUADs**
(A) Overview of genomic alterations in 57 RPA(–)_G LUADs. Genes significantly mutated (*) or significantly amplified/deleted in the RPA(–)_G samples are listed. (B and C) Example of *KEAP1* (3 kbp length) (B) and (C) *STK11* (8 kbp length) simple, homozygous deletion (CN = 0), resulting in loss of expression. The distribution of the *KEAP1* or *STK11* expression is plotted based on the full TCGA LUAD cohort. (D) Expression comparison of samples with loss-of-function alterations in *STK11* and (E) *KEAP1* to other RPA(–)_G LUAD samples. p values are calculated from Mann-Whitney U tests. Boxplots show median, interquartile range, and 1.5 times the interquartile range. See also Figure S1.

**Figure 3.. Identification of *ILF2* promoter mutations in RPA(–)_G LUADs**
(A) Three genes with non-coding mutations nominated through recurrence analysis across LUAD-related ATAC peaks (left). Red dots indicate loci with FDR < 0.25. (B) Same as (A), but restricted to ATAC-seq peaks in genes with RSEM ≥ 10 across TCGA LUAD and recurrently amplified in RPA(–)_G samples. Red dots indicate FDR < 0.1. (C) Among 57 RPA(–)_G samples, 6 SNVs are observed in the promoter region of *ILF2*; all are located within ATAC-seq peaks. (D) Expression comparison of RPA(–)_G samples with *ILF2* promoter mutations and amplifications. p values are calculated from linear regression analysis correlating expression, adjusting for the local copy number of *ILF2* and purity. Boxplot shows median, interquartile range, and 1.5 times the interquartile range. See also Figure S3.

**Figure 4.. Classification of SVs in RPA(–)_G LUADs**
(A) Identification of simple and complex SV events. Upper panel: SVs resulting in copy-number gain (double minute, BFBC, tyfonas, pyrgo, simple duplication). Lower panel: SVs resulting in copy-number loss (chromothripsis, rigma, chromoplexy, templated insertion chain, simple deletion). Key indicates the range of event count of SV types observed in each sample. (B) Expression quantile of genes located in SV types with copy-number gain. (C) Simple deletion count is more significantly enriched in the *TP53* mutant RPA(–)_G samples than in the *TP53*-wild-type RPA(–)_G samples. p value is obtained from Mann-Whitney U test. Violin plots reflect kernel density estimations. (D and E) Example of a double minute in TCGA-55–5899 spanning 3 genes (D), and (E) 2 of which (*UBL3* and *LIG4*) showed marked overexpression relative to RNA-seq data for the full TCGA LUAD cohort. See also Figure S4.

See this image and copyright information in PMC

References

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Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway

Collaborators

Affiliations

Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway

Authors

Collaborators

Affiliations

Erratum in

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources

Medical

Research Materials

Miscellaneous