PhD Scientific Days 2025

Poster Session I. - D: Pathological and Oncological Sciences

Molecular characterisation of CLL patients resistant to targeted therapy using cCLL, a comprehensive NGS-based approach

Name of the presenter

László Tamás

Institute/workplace of the presenter

HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University

Authors

Tamás László¹, Lili Kotmayer², Gabriella Szepesi³, Marcell Matúz³, Lajos Hegyi³, Stefánia Gróf³, Judit Demeter⁴, Ildikó Istenes⁴, Ilona Tárkányi⁵, Gergely Szombath⁵, Péter Farkas⁵, Zsolt Nagy⁵, Alexandra Balogh⁵, Réka Bicskó⁶, Lajos Gergely⁶, Róbert Szász⁶, Gábor Mikala⁷, Árpád Bátai⁷, András Masszi⁸, Péter A. Király⁸, Erika Szaleczky⁸, Beáta M. Deák⁸, Piroska Pettendi⁹, Natália Jóni¹⁰, Nóra Adamkovich¹¹, Timea Gurbity¹¹, Árpád Illés⁶, Tamás Masszi⁵, Donát Alpár³, Csaba Bödör³

1: HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University
2: HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University; MTA-SE Lendület Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University; Department of Hematology, St. Jude Children’s Research Hospital, Memphis, US
3: HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University; MTA-SE Lendület Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University
4: Department of Internal Medicine and Oncology, Semmelweis University
5: Department of Internal Medicine and Hematology, Semmelweis University
6: Division of Hematology, Department of Internal Medicine, University of Debrecen
7: Central Hospital of Southern Pest – National Institute of Hematology and Infectious Diseases, Budapest
8: National Institute of Oncology, Budapest
9: Hetényi Géza Hospital and Clinic of County Jász-Nagykun-Szolnok, Szolnok
10: Markhot Ferenc Teaching Hospital, Eger
11: 2nd Department of Internal Medicine and Cardiology Center, University of Szeged

Text of the abstract

Introduction: In recent years, introduction of targeted treatment modalities has revolutionized the management of chronic lymphocytic leukemia (CLL). Despite having substantial evidence on molecular biomarkers associated with chemo-immunotherapy, there is limited data regarding their prognostic/predictive value or role in resistance in the context of targeted therapies.

Aims: In our study, we aimed to scrutinize the molecular profile and subclonal dynamics of CLL patients treated with targeted agents using a novel comprehensive deep-sequencing approach.

Method: We have collected 48 serial samples from 20 CLL patients treated with ibrutinib and venetoclax. An integrative next generation sequencing (NGS) approach (cCLL-SOPHiA Genetics) was used for molecular characterisation of samples, enabling the assesment of the IGHV- and TP53 status, copy number profile as well as additional prognostically relevant mutations in one reaction.

Results: Our cohort showed high-risk molecular characteristics revealing a median of 3 CLL-related mutations in pre-treatment samples with 95% (19/20) of patients presenting with unmutated IGHV status. NGS demonstrated a robust correlation with Sanger sequencing (r=0.84 Spearman’s correlation) in assessing the IGHV mutation status and outperformed Sanger sequencing which failed to detect clonal rearrangements in 3 cases. Eighty-five percent (17/20) of patients experienced disease progression on ibrutinib, with a median progression-free survival of 32 months, while relapse on venetoclax occurred after a median of 25.5 months. BTK and PLCG2 mutations were identified in 75% (13/17) of cases with ibrutinib failure. One additional case harboured mutation without evidence of disease progression. BCL2 mutations were identified in 6/10 cases with venetoclax failure. No resistance mutations were identified in pre-treatment samples. Most common resistance mutations (BTK and PLG2 for ibrutinib and BCL2 for venetoclax) were validated by ddPCR, demonstrating a strong concordance with NGS (r=0,98, Spearman’s correlation).

Conclusion: We demonstrated the feasibility of cCLL, an integrative, all in one reaction deep sequencing approach in detailed molecular charaterization of CLL in the context of targeted therapies.

Funding: FK20_134253, K21_137948, H2020_739593, BO/00125/22, EKÖP-2024-114, SE250 scholarship