Identification of genetic subtypes in follicular lymphoma.


Journal

Blood cancer journal
ISSN: 2044-5385
Titre abrégé: Blood Cancer J
Pays: United States
ID NLM: 101568469

Informations de publication

Date de publication:
07 Aug 2024
Historique:
received: 28 02 2024
accepted: 24 07 2024
revised: 17 07 2024
medline: 8 8 2024
pubmed: 8 8 2024
entrez: 7 8 2024
Statut: epublish

Résumé

Follicular lymphoma (FL) exhibits considerable variability in biological features and clinical trajectories across patients. To dissect the diversity of FL, we utilized a Bernoulli mixture model to identify genetic subtypes in 713 pre-treatment tumor tissue samples. Our analysis revealed the existence of five subtypes with unique genetic profiles that correlated with clinicopathological characteristics. The clusters were enriched in specific mutations as follows: CS (CREBBP and STAT6), TT (TNFAIP3 and TP53), GM (GNA13 and MEF2B), Q (quiescent, for low mutation burden), and AR (mutations of mTOR pathway-related genes). The subtype Q was enriched for patients with stage I disease and associated with a lower proliferative history than the other subtypes. The AR subtype was unique in its enrichment for IgM-expressing FL cases and was associated with advanced-stage and more than 4 nodal sites. The existence of subtypes was validated in an independent cohort of 418 samples from the GALLIUM trial. Notably, patients assigned to the TT subtype consistently experienced inferior progression-free survival when treated with immunochemotherapy. Our findings offer insight into core pathways distinctly linked with each FL cluster and are expected to be informative in the era of targeted therapies.

Identifiants

pubmed: 39112453
doi: 10.1038/s41408-024-01111-w
pii: 10.1038/s41408-024-01111-w
doi:

Substances chimiques

Biomarkers, Tumor 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

128

Subventions

Organisme : Terry Fox Research Institute (Institut de Recherche Terry Fox)
ID : 1079
Organisme : Leukemia and Lymphoma Society (Leukemia & Lymphoma Society)
ID : 6599-20
Organisme : Leukemia and Lymphoma Society of Canada (Leukemia & Lymphoma Society of Canada)
ID : 513421
Organisme : Else Kröner-Fresenius-Stiftung (Else Kroner-Fresenius Foundation)
ID : 2021_EKES.13
Organisme : Deutsche Forschungsgemeinschaft (German Research Foundation)
ID : WE 4679/2

Informations de copyright

© 2024. The Author(s).

Références

Anderson JR, Armitage JO, Weisenburger DD. Epidemiology of the non-Hodgkin’s lymphomas: distributions of the major subtypes differ by geographic locations. Non-Hodgkin’s Lymphoma Classification Project. Ann Oncol. 1998;9:717–20.
pubmed: 9739436 doi: 10.1023/A:1008265532487
Casulo C, Byrtek M, Dawson KL, Zhou X, Farber CM, Flowers CR, et al. Early relapse of follicular lymphoma after rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone defines patients at high risk for death: an analysis from the National LymphoCare Study. J Clin Oncol. 2015;33:2516–22.
pubmed: 26124482 pmcid: 4879714 doi: 10.1200/JCO.2014.59.7534
Mozessohn L, Cheung MC, Crump M, Buckstein R, Berinstein N, Imrie K, et al. Chemoimmunotherapy resistant follicular lymphoma: predictors of resistance, association with transformation and prognosis. Leuk Lymphoma. 2014;55:2502–7.
pubmed: 24450580 doi: 10.3109/10428194.2014.885513
Freeman CL, Kridel R, Moccia AA, Savage KJ, Villa DR, Scott DW, et al. Early progression after bendamustine-rituximab is associated with high risk of transformation in advanced stage follicular lymphoma. Blood. 2019;134:761–4.
pubmed: 31300404 doi: 10.1182/blood.2019000258
Casulo C, Dixon JG, Le-Rademacher J, Hoster E, Hochster HS, Hiddemann W, et al. Validation of POD24 as a robust early clinical end point of poor survival in FL from 5225 patients on 13 clinical trials. Blood. 2022;139:1684–93.
pubmed: 34614146 doi: 10.1182/blood.2020010263
Pastore A, Jurinovic V, Kridel R, Hoster E, Staiger AM, Szczepanowski M, et al. Integration of gene mutations in risk prognostication for patients receiving first-line immunochemotherapy for follicular lymphoma: a retrospective analysis of a prospective clinical trial and validation in a population-based registry. Lancet Oncol. 2015;16:1111–22.
pubmed: 26256760 doi: 10.1016/S1470-2045(15)00169-2
Jurinovic V, Kridel R, Staiger AM, Szczepanowski M, Horn H, Dreyling MH, et al. Clinicogenetic risk models predict early progression of follicular lymphoma after first-line immunochemotherapy. Blood. 2016;128:1112–20.
pubmed: 27418643 pmcid: 5457130 doi: 10.1182/blood-2016-05-717355
Huet S, Tesson B, Jais JP, Feldman AL, Magnano L, Thomas E, et al. A gene-expression profiling score for prediction of outcome in patients with follicular lymphoma: a retrospective training and validation analysis in three international cohorts. Lancet Oncol. 2018;19:549–61.
pubmed: 29475724 pmcid: 5882539 doi: 10.1016/S1470-2045(18)30102-5
Silva A, Bassim S, Sarkozy C, Mottok A, Lackraj T, Jurinovic V, et al. Convergence of risk prediction models in follicular lymphoma. Haematologica. 2019;104:e252–5.
pubmed: 30606786 pmcid: 6545859 doi: 10.3324/haematol.2018.209031
Bolen CR, Mattiello F, Herold M, Hiddemann W, Huet S, Klapper W, et al. Treatment dependence of prognostic gene expression signatures in de novo follicular lymphoma. Blood. 2021;137:2704–7.
pubmed: 33512481 pmcid: 8120142 doi: 10.1182/blood.2020008119
Dave SS, Wright G, Tan B, Rosenwald A, Gascoyne RD, Chan WC, et al. Prediction of survival in follicular lymphoma based on molecular features of tumor-infiltrating immune cells. N Engl J Med. 2004;351:2159–69.
pubmed: 15548776 doi: 10.1056/NEJMoa041869
Tobin JWD, Keane C, Gunawardana J, Mollee P, Birch S, Hoang T, et al. Progression of disease within 24 months in follicular lymphoma is associated with reduced intratumoral immune infiltration. J Clin Oncol. 2019;37:3300–9.
pubmed: 31461379 pmcid: 6881104 doi: 10.1200/JCO.18.02365
Mondello P, Fama A, Larson MC, Feldman AL, Villasboas JC, Yang ZZ, et al. Lack of intrafollicular memory CD4 + T cells is predictive of early clinical failure in newly diagnosed follicular lymphoma. Blood Cancer J. 2021;11:130.
pubmed: 34267181 pmcid: 8282842 doi: 10.1038/s41408-021-00521-4
Han G, Deng Q, Marques-Piubelli ML, Dai E, Dang M, Ma MCJ, et al. Follicular lymphoma microenvironment characteristics associated with tumor cell mutations and MHC class II expression. Blood Cancer Discov. 2022;3:428–43.
pubmed: 35687817 pmcid: 9894575 doi: 10.1158/2643-3230.BCD-21-0075
Liu Q, Silva A, Kridel R. Predicting early progression in follicular lymphoma. Ann Lymphoma. 2021;5:11.
doi: 10.21037/aol-20-46
Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, et al. Cell-of-origin patterns dominate the molecular classification of 10,000 tumors from 33 types of cancer. Cell. 2018;173:291–304.e6.
pubmed: 29625048 pmcid: 5957518 doi: 10.1016/j.cell.2018.03.022
Arora A, Olshen AB, Seshan VE, Shen R. Pan-cancer identification of clinically relevant genomic subtypes using outcome-weighted integrative clustering. Genome Med. 2020;12:110.
pubmed: 33272320 pmcid: 7716509 doi: 10.1186/s13073-020-00804-8
Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, et al. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018;24:679–90.
pubmed: 29713087 pmcid: 6613387 doi: 10.1038/s41591-018-0016-8
Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, et al. Genetics and pathogenesis of diffuse large b-cell lymphoma. N Engl J Med. 2018;378:1396–407.
pubmed: 29641966 pmcid: 6010183 doi: 10.1056/NEJMoa1801445
Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, et al. A probabilistic classification tool for genetic subtypes of diffuse large B cell lymphoma with therapeutic implications. Cancer Cell. 2020;37:551–68.e14.
pubmed: 32289277 pmcid: 8459709 doi: 10.1016/j.ccell.2020.03.015
Lacy SE, Barrans SL, Beer PA, Painter D, Smith AG, Roman E, et al. Targeted sequencing in DLBCL, molecular subtypes, and outcomes: a Haematological Malignancy Research Network report. Blood. 2020;135:1759–71.
pubmed: 32187361 pmcid: 7259825 doi: 10.1182/blood.2019003535
Glas AM, Knoops L, Delahaye L, Kersten MJ, Kibbelaar RE, Wessels LA, et al. Gene-expression and immunohistochemical study of specific T-cell subsets and accessory cell types in the transformation and prognosis of follicular lymphoma. J Clin Oncol. 2007;25:390–8.
pubmed: 17200149 doi: 10.1200/JCO.2006.06.1648
Lackraj T, Goswami R, Kridel R. Pathogenesis of follicular lymphoma. Best Pract Res Clin Haematol. 2018;31:2–14.
pubmed: 29452662 doi: 10.1016/j.beha.2017.10.006
Kridel R, Chan FC, Mottok A, Boyle M, Farinha P, Tan K, et al. Histological transformation and progression in follicular lymphoma: a clonal evolution study. PLoS Med. 2016;13:e1002197.
pubmed: 27959929 pmcid: 5154502 doi: 10.1371/journal.pmed.1002197
Evens AM, Hong F, Habermann TM, Advani RH, Gascoyne RD, Witzig TE, et al. A three-arm randomized phase II study of bendamustine/rituximab with bortezomib induction or lenalidomide continuation in untreated follicular lymphoma: ECOG-ACRIN E2408. Clin Cancer Res. 2020;26:4468–77.
pubmed: 32532790 pmcid: 7722783 doi: 10.1158/1078-0432.CCR-20-1345
Kahl BS, Hong F, Williams ME, Gascoyne RD, Wagner LI, Krauss JC, et al. Rituximab extended schedule or re-treatment trial for low-tumor burden follicular lymphoma: eastern cooperative oncology group protocol e4402. J Clin Oncol. 2014;32:3096–102.
pubmed: 25154829 pmcid: 4171355 doi: 10.1200/JCO.2014.56.5853
Marcus R, Davies A, Ando K, Klapper W, Opat S, Owen C, et al. Obinutuzumab for the first-line treatment of follicular lymphoma. N Engl J Med. 2017;377:1331–44.
pubmed: 28976863 doi: 10.1056/NEJMoa1614598
Van der Auwera GA, O’Connor BD. Genomics in the cloud: using Docker, GATK, and WDL in Terra. “O’Reilly Media, Inc.”; 2020. p. 496.
Benjamin D, Sato T, Cibulskis K, Getz G, Stewart C, Lichtenstein L. Calling Somatic SNVs and Indels with Mutect2 [Internet]. Available from: https://doi.org/10.1101/861054 .
Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020;581:434–43.
pubmed: 32461654 pmcid: 7334197 doi: 10.1038/s41586-020-2308-7
Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.
pubmed: 20601685 pmcid: 2938201 doi: 10.1093/nar/gkq603
Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res. 2018;28:1747–56.
pubmed: 30341162 pmcid: 6211645 doi: 10.1101/gr.239244.118
Skvortsova K, Stirzaker C, Taberlay P. The DNA methylation landscape in cancer. Essays Biochem. 2019;63:797–811.
pubmed: 31845735 pmcid: 6923322 doi: 10.1042/EBC20190037
Kretzmer H, Bernhart SH, Wang W, Haake A, Weniger MA, Bergmann AK, et al. DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control. Nat Genet. 2015;47:1316–25.
pubmed: 26437030 pmcid: 5444523 doi: 10.1038/ng.3413
Duran-Ferrer M, Clot G, Nadeu F, Beekman R, Baumann T, Nordlund J, et al. The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome. Nat Cancer. 2020;1:1066–81.
pubmed: 34079956 pmcid: 8168619 doi: 10.1038/s43018-020-00131-2
Wang X, Nissen M, Gracias D, Kusakabe M, Simkin G, Jiang A, et al. Single-cell profiling reveals a memory B cell-like subtype of follicular lymphoma with increased transformation risk [Internet]. Nat Commun. 2022;13:6772. https://doi.org/10.1038/s41467-022-34408-0 .
doi: 10.1038/s41467-022-34408-0 pubmed: 36351924 pmcid: 9646774
Scherer F, Navarrete MA, Bertinetti-Lapatki C, Boehm J, Schmitt-Graeff A, Veelken H. Isotype-switched follicular lymphoma displays dissociation between activation-induced cytidine deaminase expression and somatic hypermutation. Leuk Lymphoma. 2016;57:151–60.
pubmed: 25860234 doi: 10.3109/10428194.2015.1037758
Amin R, Mourcin F, Uhel F, Pangault C, Ruminy P, Dupré L, et al. DC-SIGN-expressing macrophages trigger activation of mannosylated IgM B-cell receptor in follicular lymphoma. Blood. 2015;126:1911–20.
pubmed: 26272216 pmcid: 4626662 doi: 10.1182/blood-2015-04-640912
Song L, Cohen D, Ouyang Z, Cao Y, Hu X, Liu XS. TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data. Nat Methods. 2021;18:627–30.
pubmed: 33986545 pmcid: 9328942 doi: 10.1038/s41592-021-01142-2
O’Shea D, O’Riain C, Taylor C, Waters R, Carlotti E, Macdougall F, et al. The presence of TP53 mutation at diagnosis of follicular lymphoma identifies a high-risk group of patients with shortened time to disease progression and poorer overall survival. Blood. 2008;112:3126–9.
pubmed: 18628487 pmcid: 2954748 doi: 10.1182/blood-2008-05-154013
Burack WR, Li H, Adlowitz D, Spence JM, Rimsza LM, Shadman M, et al. Subclonal TP53 mutations are frequent and predict resistance to radioimmunotherapy in follicular lymphoma. Blood Adv. 2023;7:5082–90.
pubmed: 37379264 pmcid: 10471938 doi: 10.1182/bloodadvances.2022009467
Koues OI, Kowalewski RA, Chang LW, Pyfrom SC, Schmidt JA, Luo H, et al. Enhancer sequence variants and transcription-factor deregulation synergize to construct pathogenic regulatory circuits in B-cell lymphoma. Immunity. 2015;42:186–98.
pubmed: 25607463 doi: 10.1016/j.immuni.2014.12.021
Crouch S, Painter D, Barrans SL, Roman E, Beer PA, Cooke SL, et al. Molecular subclusters of follicular lymphoma: a report from the United Kingdom’s Haematological Malignancy Research Network. Blood Adv. 2022;6:5716–31.
pubmed: 35363872 pmcid: 9619185 doi: 10.1182/bloodadvances.2021005284
Dreval K, Hilton LK, Cruz M, Shaalan H, Ben-Neriah S, Boyle M, et al. Genetic subdivisions of follicular lymphoma defined by distinct coding and noncoding mutation patterns. Blood. 2023;142:561–73.
pubmed: 37084389 pmcid: 10644066 doi: 10.1182/blood.2022018719
Okosun J, Wolfson RL, Wang J, Araf S, Wilkins L, Castellano BM, et al. Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma. Nat Genet. 2016;48:183–8.
pubmed: 26691987 doi: 10.1038/ng.3473

Auteurs

Victoria Shelton (V)

Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada.

Rajesh Detroja (R)

Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada.

Ting Liu (T)

Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada.

Keren Isaev (K)

Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada.

Anjali Silva (A)

Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada.
Vector Institute, Toronto, ON, Canada.

Verena Passerini (V)

Department of Internal Medicine III, Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany.

Mehran Bakhtiari (M)

Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada.

Lourdes Calvente (L)

Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada.

Michael Hong (M)

Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada.

Michael Y He (MY)

Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada.

Saloni Modi (S)

Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada.

Samantha A Hershenfeld (SA)

Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada.

Maja Ludvigsen (M)

Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
Department of Hematology, Aarhus University Hospital, Aarhus, Denmark.

Charlotte Madsen (C)

Department of Hematology, Aarhus University Hospital, Aarhus, Denmark.

Stephen Hamilton-Dutoit (S)

Department of Pathology, Aarhus University Hospital, Aarhus, Denmark.

Francesco Annibale d'Amore (FA)

Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
Department of Hematology, Aarhus University Hospital, Aarhus, Denmark.

Marianne Brodtkorb (M)

Department of Oncology, Oslo University Hospital, Oslo, Norway.

Nathalie A Johnson (NA)

Jewish General Hospital, Montreal, QC, Canada.

Tara Baetz (T)

Department of Oncology, Queen's University, Kingston, ON, Canada.

David LeBrun (D)

Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada.

Josh W D Tobin (JWD)

Mater Research University of Queensland, Brisbane, QLD, Australia.
Department of Haematology, Princess Alexandra Hospital, Brisbane, QLD, Australia.

Maher K Gandhi (MK)

Mater Research University of Queensland, Brisbane, QLD, Australia.
Department of Haematology, Princess Alexandra Hospital, Brisbane, QLD, Australia.

Andrew J Mungall (AJ)

Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada.

Wei Xu (W)

Department of Biostatistics, Princess Margaret Cancer Centre, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.

Susana Ben-Neriah (S)

BC Cancer, Vancouver, BC, Canada.

Christian Steidl (C)

BC Cancer, Vancouver, BC, Canada.

Jan Delabie (J)

Laboratory and Medicine Program, University Health Network, Toronto, ON, Canada.

Rosemarie Tremblay-LeMay (R)

Laboratory and Medicine Program, University Health Network, Toronto, ON, Canada.

Opeyemi Jegede (O)

Dana Farber Cancer Institute, Boston, MA, USA.

Oliver Weigert (O)

Department of Internal Medicine III, Ludwig-Maximilians-University (LMU) Hospital, Munich, Germany.
German Cancer Consortium (DKTK), Munich, Germany.
German Cancer Research Center (DKFZ), Heidelberg, Germany.

Brad Kahl (B)

Washington University, St. Louis, MO, USA.

Andrew M Evens (AM)

Rutgers Cancer Institute, New Brunswick, NJ, USA.

Robert Kridel (R)

Princess Margaret Cancer Centre-University Health Network, Toronto, ON, Canada. robert.kridel@uhn.ca.

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female
Humans United States Aged Cross-Sectional Studies Medicare Part C
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH