Integrating multi-omics features enables non-invasive early diagnosis and treatment response prediction of diffuse large B-cell lymphoma

Abstract

	•A comprehensive multi-omics solution to specifically obtain an extensive fragmentomics landscape, presented by breakpoint characteristics of nucleosomes, CpG islands, DNase clusters and enhancers, besides typical methylation, copy number alteration of cfDNA.
	•Integrated model of cfDNA multi-omics could be used for non-invasive early diagnosis of DLBCL.
	•Integrated model of cfDNA multi-omics could effectively evaluate the efficacy of R-CHOP before DLBCL treatment.

Keywords

cfDNA / DLBCL / early diagnosis / integrated model / multi-omics / treatment prediction

References

[1] Sehn LH, Salles G. Diffuse large B-cell lymphoma. N Engl J Med. 2021;384:842-858.

[2] Susanibar-Adaniya S, Barta SK. 2021 Update on diffuse large B cell lymphoma: a review of current data and potential applications on risk stratification and management. Am J Hematol. 2021;96:617-629.

[3] Persky DO, Unger JM, Spier CM, et al. Phase II study of rituximab plus three cycles of CHOP and involved-field radiotherapy for patients with limited-stage aggressive B-cell lymphoma: Southwest Oncology Group Study 0014. J Clin Oncol. 2008;26:2258-2263.

[4] NIH. Cancer Stat Facts: NHL -Diffuse Large B-Cell Lymphoma (DLBCL). Accessed March 17, 2021. https://seer.cancer.gov/statfacts/html/dlbcl.html

[5] Coiffier B, Lepage E, Briere J, et al. CHOP chemotherapy plus rituximab compared with CHOP alone in elderly patients with diffuse large-B-cell lymphoma. N Engl J Med. 2002;346:235-242.

[6] Habermann TM, Weller EA, Morrison VA, et al. Rituximab-CHOP versus CHOP alone or with maintenance rituximab in older patients with diffuse large B-cell lymphoma. J Clin Oncol. 2006;24:3121-3127.

[7] Candelaria M, Dueñas-Gonzalez A. Rituximab in combination with cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) in diffuse large B-cell lymphoma. Ther Adv Hematol. 2021;12:1-14.

[8] Crump M, Neelapu SS, Farooq U, et al. Outcomes in refractory diffuse large B-cell lymphoma: results from the international SCHOLAR-1 study. Blood. 2017;130:1800-1808.

[9] Liu Y, Barta SK. Diffuse large B-cell lymphoma:2019 update on diagnosis, risk stratification, and treatment. Am J Hematol. 2019;94:604-616.

[10] Mamot C, Klingbiel D, Hitz F, et al. Final results of a prospective evaluation of the predictive value of interim positron emission tomography in patients with diffuse large B-cell lymphoma treated with R-CHOP-14 (SAKK 38/07). J Clin Oncol. 2015;33:2523-2529.

[11] Mikhaeel NG, Heymans MW, Eertink JJ, et al. Proposed new dynamic prognostic index for diffuse large B-cell lymphoma: international metabolic prognostic index. J Clin Oncol. 2022;40:2352-2360.

[12] Ruppert AS, Dixon JG, Salles G, et al. International prognostic indices in diffuse large B-cell lymphoma: a comparison of IPI, R-IPI, and NCCN-IPI. Blood. 2020;135:2041-2048.

[13] Tang H, Zhou H, Wei J, Liu H, Qian W, Chen X. Clinicopathologic significance and therapeutic implication of de novo CD5+ diffuse large B-cell lymphoma. Hematology. 2019;24:446-454.

[14] Ting CY, Chang KM, Kuan JW, et al. Clinical significance of BCL2, C-MYC, and BCL6 genetic abnormalities, Epstein-Barr virus infection, CD5 protein expression, germinal center B cell/non-germinal center B-cell subtypes, co-expression of MYC/BCL2 proteins and co-expression of MYC/BCL2/BCL6 proteins in diffuse large B-cell lymphoma: a clinical and pathological correlation study of 120 patients. Int J Med Sci. 2019;16:556-566.

[15] Hu S, Xu-Monette ZY, Balasubramanyam A, et al. CD30 expression defines a novel subgroup of diffuse large B-cell lymphoma with favorable prognosis and distinct gene expression signature: a report from the International DLBCL Rituximab-CHOP Consortium Program Study. Blood. 2013;121:2715-2724.

[16] Wang XJ, Seegmiller AC, Reddy NM, Li S. CD30 expression and its correlation with MYC rearrangement in de novo diffuse large B-cell lymphoma. Eur J Haematol. 2016;97:39-47.

[17] Yoon DH, Choi DR, Ahn HJ, et al. Ki-67 expression as a prognostic factor in diffuse large B-cell lymphoma patients treated with rituximab plus CHOP. Eur J Haematol. 2010;85:149-157.

[18] Broyde A, Boycov O, Strenov Y, Okon E, Shpilberg O, Bairey O. Role and prognostic significance of the Ki-67 index in non-Hodgkin’s lymphoma. Am J Hematol. 2009;84:338-343.

[19] Wan JCM, Massie C, Garcia-Corbacho J, et al. Liquid biopsies come of age: towards implementation of circulating tumour DNA. Nat Rev Cancer. 2017;17:223-238.

[20] Diaz LA Jr, Bardelli A. Liquid biopsies: genotyping circulating tumor DNA. J Clin Oncol. 2014;32:579-586.

[21] Thierry AR, Mouliere F, El Messaoudi S, et al. Clinical validation of the detection of KRAS and BRAF mutations from circulating tumor DNA. Nat Med. 2014;20:430-435.

[22] Alix-Panabières C, Pantel K. Clinical applications of circulating tumor cells and circulating tumor DNA as liquid biopsy. Cancer Discov. 2016;6:479-491.

[23] Lebofsky R, Decraene C, Bernard V, et al. Circulating tumor DNA as a non-invasive substitute to metastasis biopsy for tumor genotyping and personalized medicine in a prospective trial across all tumor types. Mol Oncol. 2015;9:783-790.

[24] van der Pol Y, Mouliere F. Toward the early detection of cancer by decoding the epigenetic and environmental fingerprints of cell-free DNA. Cancer Cell. 2019;36:350-368.

[25] Foda ZH, Annapragada AV, Boyapati K, et al. Detecting liver cancer using cell-free DNA fragmentomes. Cancer Discov. 2023;13:616-631.

[26] Mathios D, Johansen JS, Cristiano S, et al. Detection and characterization of lung cancer using cell-free DNA fragmentomes. Nat Commun. 2021;12:5060.

[27] Jiang P, Sun K, Tong YK, et al. Preferred end coordinates and somatic variants as signatures of circulating tumor DNA associated with hepatocellular carcinoma. Proc Natl Acad Sci U S A. 2018;115:E10925-E10933.

[28] Chabon JJ, Hamilton EG, Kurtz DM, et al. Integrating genomic features for non-invasive early lung cancer detection. Nature. 2020;580:245-251.

[29] Chen 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;31:589-592.

[30] Lennon AM, Buchanan AH, Kinde I, et al. Feasibility of blood testing combined with PET-CT to screen for cancer and guide intervention. Science. 2020;369(6499):eabb9601.

[31] Cohen JD, Li L, Wang Y, et al. Detection and localization of surgically resectable cancers with a multi-analyte blood test. Science. 2018;359:926-930.

[32] Hu X, Luo K, Shi H, et al. Integrated 5-hydroxymethylcytosine and fragmentation signatures as enhanced biomarkers in lung cancer. Clin Epigenetics. 2022;14:15.

[33] Bie F, Wang Z, Li Y, et al. Multimodal analysis of cell-free DNA whole-methylome sequencing for cancer detection and localization. Nat Commun. 2023;14:6042.

[34] Nguyen VTC, Nguyen TH, Doan NNT, et al. Multimodal analysis of methylomics and fragmentomics in plasma cell-free DNA for multi-cancer early detection and localization. eLife. 2023;12:RP89083.

[35] Boyle AP, Davis S, Shulha HP, et al. High-resolution mapping and characterization of open chromatin across the genome. Cell. 2008;132:311-322.

[36] John S, Sabo PJ, Thurman RE, et al. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nat Genet. 2011;43:264-268.

[37] Song L, Zhang Z, Grasfeder LL, et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res. 2011;21:1757-1767.

[38] Bal E, Kumar R, Hadigol M, et al. Super-enhancer hypermutation alters oncogene expression in B cell lymphoma. Nature. 2022;607:808-815.

[39] Snyder MW, Kircher M, Hill AJ, Daza RM, Shendure J. Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell. 2016;164:57-68.

[40] Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Res. 2017;27:491-499.

[41] Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011;27:1571-1572.

[42] Jühling F, Kretzmer H, Bernhart SH, Otto C, Stadler PF, Hoffmann S. metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. Genome Res. 2016;26:256-262.

[43] Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841-842.

[44] Scheinin I, Sie D, Bengtsson H, et al. DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res. 2014;24:2022-2032.

[45] Pedregosa F, Varoquaux G, Gramfort A, et al. Scikit-learn: machine learning in Python. J Mach Learn Res. 2011;12:2825-2830.

[46] Yu G, Wang LG, He QY. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics. 2015;31:2382-2383.

[47] Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. Omics. 2012;16:284-287.

[48] Vaisvila R, Ponnaluri VKC, Sun Z, et al. Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA. Genome Res. 2021;31:1280-1289.

[49] Van Heertum RL, Scarimbolo R, Wolodzko JG, et al. Lugano 2014 criteria for assessing FDG-PET/CT in lymphoma: an operational approach for clinical trials. Drug Des Devel Ther. 2017;11:1719-1728.

[50] deVos T, Tetzner R, Model F, et al. Circulating methylated SEPT9 DNA in plasma is a biomarker for colorectal cancer. Clin Chem. 2009;55:1337-1346.

[51] Church TR, Wandell M, Lofton-Day C, et al. Prospective evaluation of methylated SEPT9 in plasma for detection of asymptomatic colorectal cancer. Gut. 2014;63:317-325.

[52] Liu J, Dai L, Wang Q, et al. Multimodal analysis of cfDNA methylomes for early detecting esophageal squamous cell carcinoma and precancerous lesions. Nat Commun. 2024;15:3700.

[53] Wang S, Mouliere F, Pegtel DM, Chamuleau MED. Turning the tide in aggressive lymphoma: liquid biopsy for risk-adapted treatment strategies. Trends Mol Med. 2024;30(7):660-672.

[54] Qin W, Gao S. Application of PET/CT and clinical factors in the therapeutic and prognostic evaluation of diffuse large B cell lymphoma. Int J Radiat Med Nucl Med. 2017;41(6):437-442.

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2025 The Author(s). Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.