Tumor- and Circulating-free DNA Methylation Identifies Clinically Relevant Small Cell Lung Cancer Subtypes

Overview

Journal Cancer Cell

Publisher Cell Press

Specialty Oncology

Date 2024 Jan 26

PMID 38278149

Authors

Simon Heeke

Carl M Gay

Marcos R Estecio

Hai Tran

Benjamin B Morris

Bingnan Zhang

Ximing Tang

Maria Gabriela Raso

Pedro Rocha

Siqi Lai

Edurne Arriola

Paul Hofman

Veronique Hofman

Prasad Kopparapu

Christine M Lovly

Kyle Concannon

Luana Guimaraes De Sousa

Whitney Elisabeth Lewis

Kimie Kondo

Xin Hu

Azusa Tanimoto

Natalie I Vokes

Monique B Nilsson

Allison Stewart

Maarten Jansen

Ildiko Horvath

Mina Gaga

Vasileios Panagoulias

Yael Raviv

Danny Frumkin

Adam Wasserstrom

Aharona Shuali

Catherine A Schnabel

Yuanxin Xi

Lixia Diao

Qi Wang

Jianjun Zhang

Peter Van Loo

Jing Wang

Ignacio I Wistuba

Lauren A Byers

John V Heymach

Affiliations

Soon will be listed here.

Abstract

Small cell lung cancer (SCLC) is an aggressive malignancy composed of distinct transcriptional subtypes, but implementing subtyping in the clinic has remained challenging, particularly due to limited tissue availability. Given the known epigenetic regulation of critical SCLC transcriptional programs, we hypothesized that subtype-specific patterns of DNA methylation could be detected in tumor or blood from SCLC patients. Using genomic-wide reduced-representation bisulfite sequencing (RRBS) in two cohorts totaling 179 SCLC patients and using machine learning approaches, we report a highly accurate DNA methylation-based classifier (SCLC-DMC) that can distinguish SCLC subtypes. We further adjust the classifier for circulating-free DNA (cfDNA) to subtype SCLC from plasma. Using the cfDNA classifier (cfDMC), we demonstrate that SCLC phenotypes can evolve during disease progression, highlighting the need for longitudinal tracking of SCLC during clinical treatment. These data establish that tumor and cfDNA methylation can be used to identify SCLC subtypes and might guide precision SCLC therapy.

Citing Articles

Utilizing ctDNA to discover mechanisms of resistance to targeted therapies in patients with metastatic NSCLC: towards more informative trials.

Ernst S, Aldea M, von der Thusen J, de Langen A, Smit E, Paats M Nat Rev Clin Oncol. 2025; .

PMID: 40087401 DOI: 10.1038/s41571-025-01011-3.

Genomic alterations and transcriptional phenotypes in circulating free DNA and matched metastatic tumor.

Takahashi N, Pongor L, Agrawal S, Shtumpf M, Gurjar A, Rajapakse V Genome Med. 2025; 17(1):15.

PMID: 40001151 PMC: 11863907. DOI: 10.1186/s13073-025-01438-4.

Genomic Profiling of Extensive Stage Small-Cell Lung Cancer Patients Identifies Molecular Factors Associated with Survival.

Canale M, Urbini M, Petracci E, Angeli D, Tedaldi G, Priano I Lung Cancer (Auckl). 2025; 16:11-23.

PMID: 39995768 PMC: 11849429. DOI: 10.2147/LCTT.S492825.

Epigenetic modifications in early stage lung cancer: pathogenesis, biomarkers, and early diagnosis.

Bi L, Wang X, Li J, Li W, Wang Z MedComm (2020). 2025; 6(3):e70080.

PMID: 39991629 PMC: 11843169. DOI: 10.1002/mco2.70080.

Epigenomic Echoes-Decoding Genomic and Epigenetic Instability to Distinguish Lung Cancer Types and Predict Relapse.

Baumann A, Buribayev Z, Wolkenhauer O, Salybekov A, Wolfien M Epigenomes. 2025; 9(1).

PMID: 39982247 PMC: 11843950. DOI: 10.3390/epigenomes9010005.

References

Howlader N, Forjaz G, Mooradian M, Meza R, Kong C, Cronin K . The Effect of Advances in Lung-Cancer Treatment on Population Mortality. N Engl J Med. 2020; 383(7):640-649. PMC: 8577315. DOI: 10.1056/NEJMoa1916623. View

Fuks F, Hurd P, Deplus R, Kouzarides T . The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase. Nucleic Acids Res. 2003; 31(9):2305-12. PMC: 154218. DOI: 10.1093/nar/gkg332. View

Church M, Carter L, Blackhall F . Liquid Biopsy in Small Cell Lung Cancer-A Route to Improved Clinical Care?. Cells. 2020; 9(12). PMC: 7761700. DOI: 10.3390/cells9122586. View

Wagner A, Devarakonda S, Skidmore Z, Krysiak K, Ramu A, Trani L . Recurrent WNT pathway alterations are frequent in relapsed small cell lung cancer. Nat Commun. 2018; 9(1):3787. PMC: 6141466. DOI: 10.1038/s41467-018-06162-9. View

Stewart C, Gay C, Xi Y, Sivajothi S, Sivakamasundari V, Fujimoto J . Single-cell analyses reveal increased intratumoral heterogeneity after the onset of therapy resistance in small-cell lung cancer. Nat Cancer. 2021; 1:423-436. PMC: 7842382. DOI: 10.1038/s43018-019-0020-z. View

Rudin C, Poirier J, Byers L, Dive C, Dowlati A, George J . Molecular subtypes of small cell lung cancer: a synthesis of human and mouse model data. Nat Rev Cancer. 2019; 19(5):289-297. PMC: 6538259. DOI: 10.1038/s41568-019-0133-9. View

Stickler S, Rath B, Hochmair M, Lang C, Weigl L, Hamilton G . Changes of protein expression during tumorosphere formation of small cell lung cancer circulating tumor cells. Oncol Res. 2023; 31(1):13-22. PMC: 10207976. DOI: 10.32604/or.2022.027281. View

Lo Y, Han D, Jiang P, Chiu R . Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies. Science. 2021; 372(6538). DOI: 10.1126/science.aaw3616. View

Paz-Ares L, Dvorkin M, Chen Y, Reinmuth N, Hotta K, Trukhin D . Durvalumab plus platinum-etoposide versus platinum-etoposide in first-line treatment of extensive-stage small-cell lung cancer (CASPIAN): a randomised, controlled, open-label, phase 3 trial. Lancet. 2019; 394(10212):1929-1939. DOI: 10.1016/S0140-6736(19)32222-6. View

10.

Krushkal J, Silvers T, Reinhold W, Sonkin D, Vural S, Connelly J . Epigenome-wide DNA methylation analysis of small cell lung cancer cell lines suggests potential chemotherapy targets. Clin Epigenetics. 2020; 12(1):93. PMC: 7318526. DOI: 10.1186/s13148-020-00876-8. View

11.

Poirier J, Gardner E, Connis N, Moreira A, de Stanchina E, Hann C . DNA methylation in small cell lung cancer defines distinct disease subtypes and correlates with high expression of EZH2. Oncogene. 2015; 34(48):5869-78. PMC: 4564363. DOI: 10.1038/onc.2015.38. View

12.

Shahrokh Esfahani M, Hamilton E, Mehrmohamadi M, Nabet B, Alig S, King D . Inferring gene expression from cell-free DNA fragmentation profiles. Nat Biotechnol. 2022; 40(4):585-597. PMC: 9337986. DOI: 10.1038/s41587-022-01222-4. View

13.

Chen H, Gesumaria L, Park Y, Oliver T, Singer D, Ge K . BET Inhibitors Target the SCLC-N Subtype of Small-Cell Lung Cancer by Blocking NEUROD1 Transactivation. Mol Cancer Res. 2022; 21(2):91-101. PMC: 9898120. DOI: 10.1158/1541-7786.MCR-22-0594. View

14.

Tlemsani C, Pongor L, Elloumi F, Girard L, Huffman K, Roper N . SCLC-CellMiner: A Resource for Small Cell Lung Cancer Cell Line Genomics and Pharmacology Based on Genomic Signatures. Cell Rep. 2020; 33(3):108296. PMC: 7643325. DOI: 10.1016/j.celrep.2020.108296. View

15.

Tang M, Abbas H, Negrao M, Ramineni M, Hu X, Hubert S . The histologic phenotype of lung cancers is associated with transcriptomic features rather than genomic characteristics. Nat Commun. 2021; 12(1):7081. PMC: 8648877. DOI: 10.1038/s41467-021-27341-1. View

16.

Van Paemel R, De Koker A, Caggiano C, Morlion A, Mestdagh P, De Wilde B . Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome. Epigenetics. 2020; 16(7):797-807. PMC: 8216177. DOI: 10.1080/15592294.2020.1827714. View

17.

Gay C, Stewart C, Park E, Diao L, Groves S, Heeke S . Patterns of transcription factor programs and immune pathway activation define four major subtypes of SCLC with distinct therapeutic vulnerabilities. Cancer Cell. 2021; 39(3):346-360.e7. PMC: 8143037. DOI: 10.1016/j.ccell.2020.12.014. View

18.

Pongor L, Tlemsani C, Elloumi F, Arakawa Y, Jo U, Gross J . Integrative epigenomic analyses of small cell lung cancer cells demonstrates the clinical translational relevance of gene body methylation. iScience. 2022; 25(11):105338. PMC: 9619308. DOI: 10.1016/j.isci.2022.105338. View

19.

Borromeo M, Savage T, Kollipara R, He M, Augustyn A, Osborne J . ASCL1 and NEUROD1 Reveal Heterogeneity in Pulmonary Neuroendocrine Tumors and Regulate Distinct Genetic Programs. Cell Rep. 2016; 16(5):1259-1272. PMC: 4972690. DOI: 10.1016/j.celrep.2016.06.081. View

20.

Tian Y, Li Q, Yang Z, Zhang S, Xu J, Wang Z . Single-cell transcriptomic profiling reveals the tumor heterogeneity of small-cell lung cancer. Signal Transduct Target Ther. 2022; 7(1):346. PMC: 9532437. DOI: 10.1038/s41392-022-01150-4. View