Single-cell sequencing uncovers clonal dynamics profiles and therapeutic resistance biomarkers in relapsed and refractory peripheral T-cell lymphoma

Single-cell sequencing uncovers clonal dynamics profiles and therapeutic resistance biomarkers in relapsed and refractory peripheral T-cell lymphoma | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Single-cell sequencing uncovers clonal dynamics profiles and therapeutic resistance biomarkers in relapsed and refractory peripheral T-cell lymphoma Xianhuo Wang, Ning Zhang, Jingwei Yu, Hengqi Liu, Zechao Hu, Shen Meng, and 11 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8304942/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Peripheral T-cell lymphoma (PTCL) is a heterogeneous and highly aggressive subtype of non-Hodgkin lymphoma. Approximately 30% of patients develop relapsed or refractory (R/R) PTCL due to disease recurrence or failure to achieve complete remission after first-line therapy. The molecular and cellular mechanisms underlying treatment resistance in R/R PTCL patients remain unclear, despite therapeutic advances. Single-cell RNA sequencing was used to systematically characterize the transcriptional profiles of malignant T-cell clones and reactive T lymphocytes in seven tumor samples from six R/R PTCL patients to characterize the transcriptomic landscape of R/R PTCL and identify potential epigenetic biomarkers of drug response. We observed significant upregulation of genes associated with cell proliferation, oncogenic signaling, and immune modulation in R/R PTCL. Within the tumor microenvironment, we identified specific protumorigenic ligand–receptor interactions, including CXCL13–CXCR5, CCL5–CCR5, and CD74–MIF interactions, which may facilitate immune evasion by malignant T cells. Longitudinal data from a patient who progressed following dual epigenetic therapy revealed marked downregulation of immune response-related genes (HLA-DRA/DPA1/DRB5, CD74, C1QC, and LYZ) and functional reprogramming of tumor-associated macrophages. This study delineates the transcriptional heterogeneity of malignant T-cell clones in R/R PTCL and suggests its contribution to resistance to epigenetic therapies. These findings provide novel insights into the molecular mechanisms underlying treatment resistance and highlight potential avenues for therapeutic intervention in R/R PTCL. Biological sciences/Cancer/Haematological cancer/Lymphoma/Non-hodgkin lymphoma Biological sciences/Immunology/Tumour immunology/Immunosurveillance relapsed and refractory peripheral T-cell lymphoma single-cell sequencing clonal dynamics epigenetic regulation Full Text Additional Declarations There is NO conflict of interest to disclose. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8304942","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":557635752,"identity":"6d8d500f-0045-4cc8-963d-b86121d9b69f","order_by":0,"name":"Xianhuo Wang","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA+ElEQVRIie3QsWrCQBzH8d8pXJaLrieKvoIlkLV9lMtiFu0oGXW5LKVdHcS+Red/COiS9gVcUrrmATIUNIk4OHhZC70vgcBxn/zvAthsfzJiVL948wBj7sRkBAKEG+L1RKZaCHD9aEOCnXyaGskjO+SpqxG8Op/7HxGloZZQKKMP08FUTTwunkNPZOlCD9fEXrKjiVBNxhxzf+jq40KPSHWZNpFkVRPB+0VDQi7VtIWkuEyRlymqndAeyfaruoss/ME2Oz3o6icnprs4m8N3XiwRvL/NfVlEs8kkjpO8jO4TSELH5afbRbq/v6q/Ait/jVtsNpvtv3cGbO9VFl6lBwYAAAAASUVORK5CYII=","orcid":"https://orcid.org/0000-0002-7663-2923","institution":"Tianjin Medical University Cancer Institute and Hospital","correspondingAuthor":true,"prefix":"","firstName":"Xianhuo","middleName":"","lastName":"Wang","suffix":""},{"id":557635753,"identity":"d7254b4c-206d-4917-8c26-a6002dad7da0","order_by":1,"name":"Ning Zhang","email":"","orcid":"","institution":"Tianjin Medical University Cancer Institute and Hospital","correspondingAuthor":false,"prefix":"","firstName":"Ning","middleName":"","lastName":"Zhang","suffix":""},{"id":557635754,"identity":"11b465d5-23fc-4305-aad8-c87f5d9b3c27","order_by":2,"name":"Jingwei Yu","email":"","orcid":"","institution":"Tianjin Medical University Cancer Institute and Hospital","correspondingAuthor":false,"prefix":"","firstName":"Jingwei","middleName":"","lastName":"Yu","suffix":""},{"id":557635755,"identity":"164db52c-967d-450d-b655-fc6cf951a3b0","order_by":3,"name":"Hengqi Liu","email":"","orcid":"","institution":"Tianjin Medical University Cancer Institute and Hospital","correspondingAuthor":false,"prefix":"","firstName":"Hengqi","middleName":"","lastName":"Liu","suffix":""},{"id":557635756,"identity":"6f82a61d-8973-488d-895f-cabf50b4fa71","order_by":4,"name":"Zechao Hu","email":"","orcid":"","institution":"Tianjin Medical University Cancer Institute and Hospital","correspondingAuthor":false,"prefix":"","firstName":"Zechao","middleName":"","lastName":"Hu","suffix":""},{"id":557635757,"identity":"b3e26201-51ee-4b05-9cbe-ab5461f52d1a","order_by":5,"name":"Shen Meng","email":"","orcid":"","institution":"Tianjin Medical University Cancer Institute and Hospital","correspondingAuthor":false,"prefix":"","firstName":"Shen","middleName":"","lastName":"Meng","suffix":""},{"id":557635758,"identity":"45d43988-c21d-41cb-8693-cfb900533f88","order_by":6,"name":"Cong Sun","email":"","orcid":"","institution":"Tianjin Medical University Cancer Institute and Hospital","correspondingAuthor":false,"prefix":"","firstName":"Cong","middleName":"","lastName":"Sun","suffix":""},{"id":557635759,"identity":"d2038f77-679d-4b77-9928-4a841c597a28","order_by":7,"name":"Yaxiao Lu","email":"","orcid":"","institution":"Tianjin Medical University Cancer Institute and Hospital","correspondingAuthor":false,"prefix":"","firstName":"Yaxiao","middleName":"","lastName":"Lu","suffix":""},{"id":557635760,"identity":"a2081ae8-ebc0-4cef-8685-46659e8f7700","order_by":8,"name":"Xia Liu","email":"","orcid":"","institution":"Tianjin Medical University Cancer Institute and Hospital","correspondingAuthor":false,"prefix":"","firstName":"Xia","middleName":"","lastName":"Liu","suffix":""},{"id":557635761,"identity":"135d52d8-028c-4ba6-9bae-e6dfcf97fb13","order_by":9,"name":"Zheng Song","email":"","orcid":"","institution":"Tianjin Medical University Cancer Institute and Hospital","correspondingAuthor":false,"prefix":"","firstName":"Zheng","middleName":"","lastName":"Song","suffix":""},{"id":557635762,"identity":"c17ba541-5872-4cbf-934d-f534fb4efa16","order_by":10,"name":"Lanfang Li","email":"","orcid":"","institution":"Tianjin Medical University Cancer Institute and Hospital","correspondingAuthor":false,"prefix":"","firstName":"Lanfang","middleName":"","lastName":"Li","suffix":""},{"id":557635763,"identity":"2e66c568-7770-4986-908e-6dcddc95f754","order_by":11,"name":"Lihua Qiu","email":"","orcid":"","institution":"Tianjin Medical University Cancer Institute and Hospital","correspondingAuthor":false,"prefix":"","firstName":"Lihua","middleName":"","lastName":"Qiu","suffix":""},{"id":557635764,"identity":"1d1f3f8b-7779-4f0b-9106-cb35684d03d1","order_by":12,"name":"Zhengzi Qian","email":"","orcid":"","institution":"Tianjin Medical University Cancer Institute and Hospital","correspondingAuthor":false,"prefix":"","firstName":"Zhengzi","middleName":"","lastName":"Qian","suffix":""},{"id":557635765,"identity":"83448556-d44d-42b2-8b1b-55fa6aca32e4","order_by":13,"name":"Shiyong Shiyong Zhou","email":"","orcid":"","institution":"Tianjin Medical University Cancer Institute and Hospital","correspondingAuthor":false,"prefix":"","firstName":"Shiyong","middleName":"Shiyong","lastName":"Zhou","suffix":""},{"id":557635766,"identity":"0b75c604-a1a1-4b50-a679-6a612015a6c1","order_by":14,"name":"Bin Meng","email":"","orcid":"","institution":"Tianjin Medical University Cancer Institute and Hospital","correspondingAuthor":false,"prefix":"","firstName":"Bin","middleName":"","lastName":"Meng","suffix":""},{"id":557635767,"identity":"531e2b6c-91a5-4c8b-85cb-4547393c0149","order_by":15,"name":"Wenchen Gong","email":"","orcid":"","institution":"Tianjin Medical University Cancer Institute and Hospital","correspondingAuthor":false,"prefix":"","firstName":"Wenchen","middleName":"","lastName":"Gong","suffix":""},{"id":557635768,"identity":"81d85269-063d-4b59-b701-88a01e9e0785","order_by":16,"name":"Hui-Lai Zhang","email":"","orcid":"https://orcid.org/0000-0002-0091-0026","institution":"Departments of Lymphoma","correspondingAuthor":false,"prefix":"","firstName":"Hui-Lai","middleName":"","lastName":"Zhang","suffix":""}],"badges":[],"createdAt":"2025-12-08 07:51:22","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8304942/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8304942/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":98108672,"identity":"ce75b8b9-93c0-4435-8648-21b736e7fa49","added_by":"auto","created_at":"2025-12-13 01:30:55","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":4249804,"visible":true,"origin":"","legend":"","description":"","filename":"Figure1.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8304942/v1/ecf034951103c0119b4d806e.pdf"},{"id":98108668,"identity":"17b08c7e-35fc-4da6-bc19-30f89fb70200","added_by":"auto","created_at":"2025-12-13 01:30:55","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":357557,"visible":true,"origin":"","legend":"","description":"","filename":"Manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8304942/v1/a0768b4d2c8fe2f82d0f810d.pdf"},{"id":98108675,"identity":"a1441bae-43f2-4a9e-82d0-1625fa44d71c","added_by":"auto","created_at":"2025-12-13 01:30:55","extension":"pdf","order_by":2,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":13454446,"visible":true,"origin":"","legend":"","description":"","filename":"Figure2.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8304942/v1/828dda8c4bf4022724910c49.pdf"},{"id":98108669,"identity":"848e7751-edbd-42e2-a27f-cb698b89d2ae","added_by":"auto","created_at":"2025-12-13 01:30:55","extension":"pdf","order_by":3,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":857231,"visible":true,"origin":"","legend":"","description":"","filename":"Figure3.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8304942/v1/707cd3a1a5dcce4c0d77d7c1.pdf"},{"id":98430171,"identity":"0529eb7b-99a5-48c9-b8ad-1da279491872","added_by":"auto","created_at":"2025-12-17 16:44:55","extension":"pdf","order_by":4,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":4112880,"visible":true,"origin":"","legend":"","description":"","filename":"Figure4.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8304942/v1/6d4f16e882b1101775425dc9.pdf"},{"id":98431316,"identity":"a142b492-3717-422f-ad30-67d71c310b36","added_by":"auto","created_at":"2025-12-17 16:47:30","extension":"pdf","order_by":5,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":4829881,"visible":true,"origin":"","legend":"","description":"","filename":"Figure5.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8304942/v1/aab321ff2be532ef43d616f5.pdf"},{"id":98108673,"identity":"c684ad8c-d08c-4669-9685-c78ab1dce897","added_by":"auto","created_at":"2025-12-13 01:30:55","extension":"pdf","order_by":6,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":1390168,"visible":true,"origin":"","legend":"","description":"","filename":"Figure6.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8304942/v1/7ffe1739d08ba60aa0c60087.pdf"},{"id":98108670,"identity":"8762849a-1882-4404-9d78-969b24c57d6d","added_by":"auto","created_at":"2025-12-13 01:30:55","extension":"json","order_by":7,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":16714,"visible":true,"origin":"","legend":"","description":"","filename":"25LEU2027.json","url":"https://assets-eu.researchsquare.com/files/rs-8304942/v1/9447e89a387ac94484076073.json"},{"id":100364176,"identity":"58cfa301-692f-4363-834b-a3a323a555c0","added_by":"auto","created_at":"2026-01-16 07:52:50","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":9571151,"visible":true,"origin":"","legend":"","description":"","filename":"Manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8304942/v1_covered_7badc4bd-9d97-47d2-9f90-31e4a1ef9004.pdf"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e conflict of interest to disclose.","formattedTitle":"Single-cell sequencing uncovers clonal dynamics profiles and therapeutic resistance biomarkers in relapsed and refractory peripheral T-cell lymphoma","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"relapsed and refractory peripheral T-cell lymphoma, single-cell sequencing, clonal dynamics, epigenetic regulation","lastPublishedDoi":"10.21203/rs.3.rs-8304942/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8304942/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003ePeripheral T-cell lymphoma (PTCL) is a heterogeneous and highly aggressive subtype of non-Hodgkin lymphoma. Approximately 30% of patients develop relapsed or refractory (R/R) PTCL due to disease recurrence or failure to achieve complete remission after first-line therapy. The molecular and cellular mechanisms underlying treatment resistance in R/R PTCL patients remain unclear, despite therapeutic advances. Single-cell RNA sequencing was used to systematically characterize the transcriptional profiles of malignant T-cell clones and reactive T lymphocytes in seven tumor samples from six R/R PTCL patients to characterize the transcriptomic landscape of R/R PTCL and identify potential epigenetic biomarkers of drug response. We observed significant upregulation of genes associated with cell proliferation, oncogenic signaling, and immune modulation in R/R PTCL. Within the tumor microenvironment, we identified specific protumorigenic ligand–receptor interactions, including CXCL13–CXCR5, CCL5–CCR5, and CD74–MIF interactions, which may facilitate immune evasion by malignant T cells. Longitudinal data from a patient who progressed following dual epigenetic therapy revealed marked downregulation of immune response-related genes (HLA-DRA/DPA1/DRB5, CD74, C1QC, and LYZ) and functional reprogramming of tumor-associated macrophages. This study delineates the transcriptional heterogeneity of malignant T-cell clones in R/R PTCL and suggests its contribution to resistance to epigenetic therapies. These findings provide novel insights into the molecular mechanisms underlying treatment resistance and highlight potential avenues for therapeutic intervention in R/R PTCL.\u003c/p\u003e","manuscriptTitle":"Single-cell sequencing uncovers clonal dynamics profiles and therapeutic resistance biomarkers in relapsed and refractory peripheral T-cell lymphoma","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-12-13 01:30:51","doi":"10.21203/rs.3.rs-8304942/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"e24152c4-bf7d-4750-a0aa-243d097def64","owner":[],"postedDate":"December 13th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":59350841,"name":"Biological sciences/Cancer/Haematological cancer/Lymphoma/Non-hodgkin lymphoma"},{"id":59350842,"name":"Biological sciences/Immunology/Tumour immunology/Immunosurveillance"}],"tags":[],"updatedAt":"2026-01-12T13:49:23+00:00","versionOfRecord":[],"versionCreatedAt":"2025-12-13 01:30:51","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8304942","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8304942","identity":"rs-8304942","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}