Cell-free epigenomes enhanced fragmentomics-based model for early detection of lung cancer
Yadong Wang
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorQiang Guo
Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China
Search for more papers by this authorZhicheng Huang
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorLiyang Song
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorFei Zhao
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorTiantian Gu
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorZhe Feng
Department of Cardiothoracic Surgery, the Sixth Hospital of Beijing, Beijing, China
Search for more papers by this authorHaibo Wang
Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China
Search for more papers by this authorBowen Li
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorDaoyun Wang
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorBin Zhou
Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China
Search for more papers by this authorChao Guo
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorYuan Xu
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorYang Song
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorZhibo Zheng
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorZhongxing Bing
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorHaochen Li
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorXiaoqing Yu
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorKa Luk Fung
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorHeqing Xu
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorJianhong Shi
Department of Scientific Research, Affiliated Hospital of Hebei University, Baoding, China
Search for more papers by this authorMeng Chen
Department of Scientific Research, Affiliated Hospital of Hebei University, Baoding, China
Search for more papers by this authorShuai Hong
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorHaoxuan Jin
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorShiyuan Tong
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorSibo Zhu
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorChen Zhu
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorJinlei Song
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorJing Liu
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorShanqing Li
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorCorresponding Author
Hefei Li
Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China
Correspondence
Hefei Li, Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China.
Email: [email protected]
Xueguang Sun, Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China.
Email: [email protected]
Naixin Liang, Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
Email: [email protected]
Search for more papers by this authorCorresponding Author
Xueguang Sun
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Correspondence
Hefei Li, Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China.
Email: [email protected]
Xueguang Sun, Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China.
Email: [email protected]
Naixin Liang, Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
Email: [email protected]
Search for more papers by this authorCorresponding Author
Naixin Liang
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Correspondence
Hefei Li, Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China.
Email: [email protected]
Xueguang Sun, Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China.
Email: [email protected]
Naixin Liang, Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
Email: [email protected]
Search for more papers by this authorYadong Wang
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorQiang Guo
Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China
Search for more papers by this authorZhicheng Huang
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorLiyang Song
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorFei Zhao
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorTiantian Gu
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorZhe Feng
Department of Cardiothoracic Surgery, the Sixth Hospital of Beijing, Beijing, China
Search for more papers by this authorHaibo Wang
Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China
Search for more papers by this authorBowen Li
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorDaoyun Wang
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorBin Zhou
Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China
Search for more papers by this authorChao Guo
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorYuan Xu
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorYang Song
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorZhibo Zheng
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorZhongxing Bing
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorHaochen Li
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorXiaoqing Yu
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorKa Luk Fung
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorHeqing Xu
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorJianhong Shi
Department of Scientific Research, Affiliated Hospital of Hebei University, Baoding, China
Search for more papers by this authorMeng Chen
Department of Scientific Research, Affiliated Hospital of Hebei University, Baoding, China
Search for more papers by this authorShuai Hong
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorHaoxuan Jin
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorShiyuan Tong
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorSibo Zhu
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorChen Zhu
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorJinlei Song
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorJing Liu
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Search for more papers by this authorShanqing Li
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Search for more papers by this authorCorresponding Author
Hefei Li
Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China
Correspondence
Hefei Li, Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China.
Email: [email protected]
Xueguang Sun, Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China.
Email: [email protected]
Naixin Liang, Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
Email: [email protected]
Search for more papers by this authorCorresponding Author
Xueguang Sun
Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China
Correspondence
Hefei Li, Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China.
Email: [email protected]
Xueguang Sun, Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China.
Email: [email protected]
Naixin Liang, Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
Email: [email protected]
Search for more papers by this authorCorresponding Author
Naixin Liang
Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
Correspondence
Hefei Li, Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China.
Email: [email protected]
Xueguang Sun, Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China.
Email: [email protected]
Naixin Liang, Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
Email: [email protected]
Search for more papers by this authorYadong Wang, Qiang Guo, Zhicheng Huang, Liyang Song and Fei Zhao contributed equally to this work.
Abstract
Background
Lung cancer is a leading cause of cancer mortality, highlighting the need for innovative non-invasive early detection methods. Although cell-free DNA (cfDNA) analysis shows promise, its sensitivity in early-stage lung cancer patients remains a challenge. This study aimed to integrate insights from epigenetic modifications and fragmentomic features of cfDNA using machine learning to develop a more accurate lung cancer detection model.
Methods
To address this issue, a multi-centre prospective cohort study was conducted, with participants harbouring suspicious malignant lung nodules and healthy volunteers recruited from two clinical centres. Plasma cfDNA was analysed for its epigenetic and fragmentomic profiles using chromatin immunoprecipitation sequencing, reduced representation bisulphite sequencing and low-pass whole-genome sequencing. Machine learning algorithms were then employed to integrate the multi-omics data, aiding in the development of a precise lung cancer detection model.
Results
Cancer-related changes in cfDNA fragmentomics were significantly enriched in specific genes marked by cell-free epigenomes. A total of 609 genes were identified, and the corresponding cfDNA fragmentomic features were utilised to construct the ensemble model. This model achieved a sensitivity of 90.4% and a specificity of 83.1%, with an AUC of 0.94 in the independent validation set. Notably, the model demonstrated exceptional sensitivity for stage I lung cancer cases, achieving 95.1%. It also showed remarkable performance in detecting minimally invasive adenocarcinoma, with a sensitivity of 96.2%, highlighting its potential for early detection in clinical settings.
Conclusions
With feature selection guided by multiple epigenetic sequencing approaches, the cfDNA fragmentomics-based machine learning model demonstrated outstanding performance in the independent validation cohort. These findings highlight its potential as an effective non-invasive strategy for the early detection of lung cancer.
Keypoints
- Our study elucidated the regulatory relationships between epigenetic modifications and their effects on fragmentomic features.
- Identifying epigenetically regulated genes provided a critical foundation for developing the cfDNA fragmentomics-based machine learning model.
- The model demonstrated exceptional clinical performance, highlighting its substantial potential for translational application in clinical practice.
CONFLICT OF INTEREST STATEMENT
L. S., F. Z., T. G., S. H., H. J., S. T., S. Z., C. Z., J. S., J. L. and X. S. are employees of Shanghai Weihe Medical Laboratory Co., Ltd, Shanghai, China. All other authors have declared no conflicts of interest.
Open Research
DATA AVAILABILITY STATEMENT
The data supporting the findings of this study have been deposited in Genome Sequence Archive (Genome Sequence Archive for Human in BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences) under accession number PRJCA033843. This study does not employ any new algorithms, and the code used for statistical analysis is available on request from the corresponding author Naixin Liang.
The study was conducted in accordance with the Declaration of Helsinki and approved by the ethics committee of Affiliated Hospital of Hebei University (Approval No. HDFYLL-IIT-023-005) and Peking Union Medical College Hospital (Approval No. I-23PJ1205). Written informed consent was obtained from all enrolled participants prior participation.
Supporting Information
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REFERENCES
- 1Bray F, Laversanne M, Sung H, et al. Global cancer statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2024; 74(3): 229-263.
- 2Goldstraw P, Chansky K, Crowley J, et al. The IASLC lung cancer staging project: proposals for revision of the TNM stage groupings in the forthcoming (eighth) edition of the TNM classification for lung cancer. J Thorac Oncol. 2016; 11(1): 39-51.
- 3Aberle DR, Adams AM, Berg CD, et al. Reduced lung-cancer mortality with low-dose computed tomographic screening. N Engl J Med. 2011; 365(5): 395-409.
- 4Chen K, He Y, Wang W, et al. Development of new techniques and clinical applications of liquid biopsy in lung cancer management. Sci Bull (Beijing). 2024; 69(10): 1556-1568.
- 5Stejskal P, Goodarzi H, Srovnal J, et al. Circulating tumor nucleic acids: biology, release mechanisms, and clinical relevance. Mol Cancer. 2023; 22(1): 15.
- 6Zhang K, Fu R, Liu R, et al. Circulating cell-free DNA-based multi-cancer early detection. Trends Cancer. 2024; 10(2): 161-174.
- 7Snyder MW, Kircher M, Hill AJ, et al. Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell. 2016; 164(1-2): 57-68.
- 8Sun K, Jiang P, Cheng SH, et al. Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin. Genome Res. 2019; 29(3): 418-427.
- 9Serpas L, Chan RWY, Jiang P, et al. Dnase1l3 deletion causes aberrations in length and end-motif frequencies in plasma DNA. Proc Natl Acad Sci USA. 2019; 116(2): 641-649.
- 10Jiang P, Sun K, Peng W, et al. Plasma DNA end-motif profiling as a fragmentomic marker in cancer, pregnancy, and transplantation. Cancer Discov. 2020; 10(5): 664-673.
- 11Zhu D, Wang H, Wu W, et al. Circulating cell-free DNA fragmentation is a stepwise and conserved process linked to apoptosis. BMC Biol. 2023; 21(1): 253.
- 12Mathios D, Johansen JS, Cristiano S, et al. Detection and characterization of lung cancer using cell-free DNA fragmentomes. Nat Commun. 2021; 12(1): 5060.
- 13Kim J, Hong SP, Lee S, et al. Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids. Hum Genomics. 2023; 17(1): 96.
- 14Yotsukura M, Asamura H, Motoi N, et al. Long-term prognosis of patients with resected adenocarcinoma in situ and minimally invasive adenocarcinoma of the lung. J Thorac Oncol. 2021; 16(8): 1312-1320.
- 15Esfahani MS, Hamilton EG, Mehrmohamadi M, et al. Inferring gene expression from cell-free DNA fragmentation profiles. Nat Biotechnol. 2022; 40(4): 585-597.
- 16Stanley KE, Jatsenko T, Tuveri S, et al. Cell type signatures in cell-free DNA fragmentation profiles reveal disease biology. Nat Commun. 2024; 15(1): 2220.
- 17Maansson CT, Thomsen LS, Meldgaard P, et al. Integration of cell-free DNA end motifs and fragment lengths can identify active genes in liquid biopsies. Int J Mol Sci. 2024; 25(2): 1243.
- 18Liang W, Zhao Y, Huang W, et al. Non-invasive diagnosis of early-stage lung cancer using high-throughput targeted DNA methylation sequencing of circulating tumor DNA (ctDNA). Theranostics. 2019; 9(7): 2056-2070.
- 19Liu MC, Oxnard GR, Klein EA, et al. Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA. Ann Oncol. 2020; 31(6): 745-759.
- 20Sadeh R, Sharkia I, Fialkoff G, et al. ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin. Nat Biotechnol. 2021; 39(5): 586-598.
- 21Baca SC, Seo JH, Davidsohn MP, et al. Liquid biopsy epigenomic profiling for cancer subtyping. Nat Med. 2023; 29(11): 2737-2741.
- 22Zhu G, Guo YA, Ho D, et al. Tissue-specific cell-free DNA degradation quantifies circulating tumor DNA burden. Nat Commun. 2021; 12(1): 2229.
- 23Parreno V, Loubiere V, Schuettengruber B, et al. Transient loss of polycomb components induces an epigenetic cancer fate. Nature. 2024; 629(8012): 688-696.
- 24Fialkoff G, Takahashi N, Sharkia I, et al. Subtyping of small cell lung cancer using plasma cell-free nucleosomes. bioRxiv. 2022. 2022.2006.2024.497386.
- 25Trier Maansson C, Meldgaard P, Stougaard M, et al. Cell-free chromatin immunoprecipitation can determine tumor gene expression in lung cancer patients. Mol Oncol. 2023; 17(5): 722-736.
- 26Brouwer I, Kerklingh E, van Leeuwen F, et al. Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting. Nat Struct Mol Biol. 2023; 30(5): 692-702.
- 27Tolstorukov MY, Sansam CG, Lu P, et al. Swi/Snf chromatin remodeling/tumor suppressor complex establishes nucleosome occupancy at target promoters. Proc Natl Acad Sci USA. 2013; 110(25): 10165-10170.
- 28Chen L, Abou-Alfa GK, Zheng B, et al. Genome-scale profiling of circulating cell-free DNA signatures for early detection of hepatocellular carcinoma in cirrhotic patients. Cell Res. 2021; 31(5): 589-592.
- 29Pham TMQ, Phan TH, Jasmine TX, et al. Multimodal analysis of genome-wide methylation, copy number aberrations, and end motif signatures enhances detection of early-stage breast cancer. Front Oncol. 2023; 13:1127086.
- 30Kakinuma R, Noguchi M, Ashizawa K, et al. Natural history of pulmonary subsolid nodules: a prospective multicenter study. J Thorac Oncol. 2016; 11(7): 1012-1028.
- 31Stackpole ML, Zeng W, Li S, et al. Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer. Nat Commun. 2022; 13(1): 5566.
- 32Zhou Z, Ma ML, Chan RWY, et al. Fragmentation landscape of cell-free DNA revealed by deconvolutional analysis of end motifs. Proc Natl Acad Sci USA. 2023; 120(17):e2220982120.
- 33Wu T, Hu E, Xu S, et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation (Camb). 2021; 2(3):100141.
- 34Guo S, Xu Z, Dong X, et al. GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets. Nucleic Acids Res. 2023; 51(D1): D964-d968.
- 35Hubbell E, Clarke CA, Aravanis AM, et al. Modeled reductions in late-stage cancer with a multi-cancer early detection test. Cancer Epidemiol Biomarkers Prev. 2021; 30(3): 460-468.
- 36Han B, Zheng R, Zeng H, et al. Cancer incidence and mortality in China, 2022. J Natl Cancer Cent. 2024; 4(1): 47-53.
- 37Zeng H, Ran X, An L, et al. Disparities in stage at diagnosis for five common cancers in China: a multicentre, hospital-based, observational study. Lancet Public Health. 2021; 6(12): e877-e887.
- 38He S, Li H, Cao M, et al. Survival of 7,311 lung cancer patients by pathological stage and histological classification: a multicenter hospital-based study in China. Transl Lung Cancer Res. 2022; 11(8): 1591-1605.
- 39Lo YMD, Han DSC, Jiang P, et al. Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies. Science. 2021; 372(6538).
- 40Maluchenko NV, Nilov DK, Pushkarev SV, et al. Mechanisms of nucleosome reorganization by PARP1. Int J Mol Sci. 2021; 22(22).
- 41Bradner JE, Hnisz D, Young RA. Transcriptional addiction in cancer. Cell. 2017; 168(4): 629-643.
- 42Carter B, Zhao K. The epigenetic basis of cellular heterogeneity. Nat Rev Genet. 2021; 22(4): 235-250.
- 43Han DSC, Ni M, Chan RWY, et al. The biology of cell-free DNA fragmentation and the roles of DNASE1, DNASE1L3, and DFFB. Am J Hum Genet. 2020; 106(2): 202-214.
- 44Tian XY, Li J, Liu TH, et al. The overexpression of AUF1 in colorectal cancer predicts a poor prognosis and promotes cancer progression by activating ERK and AKT pathways. Cancer Med. 2020; 9(22): 8612-8623.
- 45Clayton NS, Ridley AJ. Targeting Rho GTPase signaling networks in cancer. Front Cell Dev Biol. 2020; 8: 222.
- 46Wee P, Wang Z. Epidermal growth factor receptor cell proliferation signaling pathways. Cancers (Basel). 2017; 9(5): 52.
- 47Fiala C, Diamandis EP. Utility of circulating tumor DNA in cancer diagnostics with emphasis on early detection. BMC Med. 2018; 16(1): 166.
- 48Markus H, Chandrananda D, Moore E, et al. Refined characterization of circulating tumor DNA through biological feature integration. Sci Rep. 2022; 12(1): 1928.
- 49Sanchez C, Roch B, Mazard T, et al. Circulating nuclear DNA structural features, origins, and complete size profile revealed by fragmentomics. JCI Insight. 2021; 6(7):e144561.
- 50Cristiano S, Leal A, Phallen J, et al. Genome-wide cell-free DNA fragmentation in patients with cancer. Nature. 2019; 570(7761): 385-389.
- 51Oberhofer A, Bronkhorst AJ, Uhlig C, et al. Tracing the origin of cell-free DNA molecules through tissue-specific epigenetic signatures. Diagnostics (Basel). 2022; 12(8): 1834.
- 52Yang J, Xu J, Wang W, et al. Epigenetic regulation in the tumor microenvironment: molecular mechanisms and therapeutic targets. Signal Transduct Target Ther. 2023; 8(1): 210.
- 53Fu K, Bonora G, Pellegrini M. Interactions between core histone marks and DNA methyltransferases predict DNA methylation patterns observed in human cells and tissues. Epigenetics. 2020; 15(3): 272-282.
- 54Ginno PA, Gaidatzis D, Feldmann A, et al. A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity. Nat Commun. 2020; 11(1): 2680.
- 55Hu X, Estecio MR, Chen R, et al. Evolution of DNA methylome from precancerous lesions to invasive lung adenocarcinomas. Nat Commun. 2021; 12(1): 687.
- 56Zhang Y, Fu F, Zhang Q, et al. Evolutionary proteogenomic landscape from pre-invasive to invasive lung adenocarcinoma. Cell Rep Med. 2024; 5(1):101358.
- 57Dejima H, Hu X, Chen R, et al. Immune evolution from preneoplasia to invasive lung adenocarcinomas and underlying molecular features. Nat Commun. 2021; 12(1): 2722.
- 58LaFave LM, Kartha VK, Ma S, et al. Epigenomic state transitions characterize tumor progression in mouse lung adenocarcinoma. Cancer Cell. 2020; 38(2): 212-228.e213.
- 59Haga Y, Sakamoto Y, Kajiya K, et al. Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma. Nat Commun. 2023; 14(1): 8375.
- 60Tan T, Shi P, Abbas MN, et al. Epigenetic modification regulates tumor progression and metastasis through EMT (Review). Int J Oncol. 2022; 60(6): 70.
- 61Chabon JJ, Hamilton EG, Kurtz DM, et al. Integrating genomic features for non-invasive early lung cancer detection. Nature. 2020; 580(7802): 245-251.
- 62Liang N, Li B, Jia Z, et al. Ultrasensitive detection of circulating tumour DNA via deep methylation sequencing aided by machine learning. Nat Biomed Eng. 2021; 5(6): 586-599.
- 63Mazzone PJ, Bach PB, Carey J, et al. Clinical validation of a cell-free DNA fragmentome assay for augmentation of lung cancer early detection. Cancer Discov. 2024; 14(11): 2224-2242.
- 64Li Y, Jiang G, Wu W, et al. Multi-omics integrated circulating cell-free DNA genomic signatures enhanced the diagnostic performance of early-stage lung cancer and postoperative minimal residual disease. EBioMedicine. 2023; 91:104553.
- 65Chen K, Sun J, Zhao H, et al. Non-invasive lung cancer diagnosis and prognosis based on multi-analyte liquid biopsy. Mol Cancer. 2021; 20(1): 23.
- 66Saji H, Okada M, Tsuboi M, et al. Segmentectomy versus lobectomy in small-sized peripheral non-small-cell lung cancer (JCOG0802/WJOG4607L): a multicentre, open-label, phase 3, randomised, controlled, non-inferiority trial. Lancet. 2022; 399(10335): 1607-1617.
- 67Altorki N, Wang X, Kozono D, et al. Lobar or sublobar resection for peripheral stage IA non-small-cell lung cancer. N Engl J Med. 2023; 388(6): 489-498.
- 68Wang Q, Song X, Zhao F, et al. Noninvasive diagnosis of pulmonary nodules using a circulating tsRNA-based nomogram. Cancer Sci. 2023; 114(12): 4607-4621.
- 69He J, Wang B, Tao J, et al. Accurate classification of pulmonary nodules by a combined model of clinical, imaging, and cell-free DNA methylation biomarkers: a model development and external validation study. Lancet Digit Health. 2023; 5(10): e647-e656.
