Cancer Chemotherapy Accelerates the Loss of Clonal Diversity in Hematopoietic Stem Cells and Promotes the Convergent Evolution of Therapy-Related Clonal Hematopoiesis

Approximately 20,000 to 200,000 hematopoietic stem cells (HSCs) contribute to adult human hematopoiesis (Lee-Six et al. Nature 2018). HSCs lose clonal diversity with age, which is partly driven by the expansion of HSCs acquiring driver mutations (i.e., clonal hematopoiesis [CH]) (Mitchell et al. Nature 2022). HSCs are also subject to various types of external stressors such as chemotherapy. How the external stressors shape HSC clonality and dynamics remains unknown.

To understand the influence of cancer chemotherapy on clonality and dynamics of hematopoietic stem and progenitor cells (HSPCs), we performed whole genome sequencing of 1,120 single-HSPC derived colonies from 10 patients with multiple myeloma (ages 46-65). We generated methocult colonies from GCSF mobilized peripheral blood stem cells (PBSCs) collected at the time of autologous stem cell transplant (ASCT, median 86 colonies per PBSCs). Previous chemotherapy exposure included a melphalan-based (MEL) regimen in 2 patients, a cyclophosphamide-based (CY) regimen in 2 patients, and lenalidomide (LEN) and/or bortezomib (BTZ)-based regimens in 6 patients.

Despite the history of chemotherapy treatment, the number of somatic mutations in treated-HSPCs was comparable to that of age-matched HSPCs from normal individuals (Mitchell et al. Nature 2022), except in two patients with MEL treatment exhibiting significantly increased numbers of somatic mutations (median 2,339 vs. 1,146 somatic mutations per cell, P < 0.001). The excess mutations observed in MEL-treated HSPCs were consistent with the MEL-related mutation signature, SBS-MM1. None of the other patients' HPSCs showed treatment-related signatures. Importantly, HSPCs treated with CY, a similar alkylating agent, did not show an increased number of mutations or treatment-related signatures. This is likely because HSCs metabolize CY to an inactive form through aldehyde dehydrogenase (ALDH), which allows HSCs to escape from CY-induced DNA damage.

Using shared and unique somatic mutations, we reconstructed phylogenetic trees of the HSPCs. Overall, we observed decreased clonal diversity of HSPCs in the current cohort compared to age-matched normal individuals (Mitchell et al. Nature 2022). The clonality of treated-HSPCs resembled that of individuals with advanced age (age>75 years) in normal individuals. Low clonal diversity was particularly evident in MEL and CY-treated patients, whereas HSPCs treated with LEN and BTZ showed relatively preserved clonal diversity.

TP53 and PPM1D mutations were the most frequent driver mutations representing the clades of phylogenies. We observed multiple clades in the same patients having different mutations in the same genes (TP53 and PPM1D), which is consistent with the convergent evolution, the findings suggestive of strong selective pressure from chemotherapy.

We also developed mathematical models simulating the population dynamics of HSCs with or without chemotherapy. These models showed that the loss of clonal diversity is accelerated by the administration of cytotoxic chemotherapy.

Our results suggest that cytotoxic chemotherapy accelerates the loss of clonal diversity in HSPCs and promotes convergent evolution of clonal hematopoiesis driven by the mutations in DNA damaging pathway genes (TP53 and PPM1D), which likely forms the basis of therapy-related toxicities in hematopoiesis. However, the impact of cancer chemotherapy differs between drugs, and more studies are needed to systematically evaluate the differential effect of chemotherapies.

Kantarjian:NOVA Research: Honoraria; Jazz Pharmaceuticals: Research Funding; Pfizer: Honoraria, Research Funding; AbbVie: Honoraria, Research Funding; KAHR Medical Ltd: Honoraria, Membership on an entity's Board of Directors or advisory committees; Ipsen Pharmaceuticals: Honoraria, Membership on an entity's Board of Directors or advisory committees; Ascentage: Membership on an entity's Board of Directors or advisory committees, Research Funding; ImmunoGen: Research Funding; Amgen: Honoraria, Research Funding; Novartis: Honoraria, Research Funding; Astellas Health: Honoraria, Membership on an entity's Board of Directors or advisory committees; Daiichi-Sankyo: Consultancy, Research Funding; Takeda: Honoraria. DiNardo:Servier: Consultancy, Honoraria, Research Funding; Astellas: Honoraria; GlaxoSmithKline: Membership on an entity's Board of Directors or advisory committees; Bristol Myers Squibb: Honoraria, Research Funding; AbbVie: Consultancy, Research Funding; Notable Labs: Current holder of stock options in a privately-held company, Membership on an entity's Board of Directors or advisory committees; Bluebird Bio: Honoraria; Foghorn: Honoraria, Research Funding; ImmuneOnc: Honoraria, Research Funding; LOXO: Research Funding; Gilead: Honoraria; Forma: Research Funding; GenMab: Membership on an entity's Board of Directors or advisory committees; Kura: Honoraria, Membership on an entity's Board of Directors or advisory committees; Jazz: Honoraria; Astex: Research Funding; Novartis: Honoraria; Takeda: Honoraria; Cleave: Research Funding. Daver:Agios, Celgene, SOBI and STAR Therapeutics: Consultancy, Membership on an entity's Board of Directors or advisory committees; Kartos and Jazz Pharmaceuticals: Other: Data monitoring committee member; Karyopham Therapeutics and Newave Pharmaceutical: Research Funding; Astellas, AbbVie, Genentech, Daiichi-Sankyo, Novartis, Jazz, Amgen, Servier, Karyopharm, Trovagene, Trillium, Syndax, Gilead, Pfizer, Bristol Myers Squibb, Kite, Actinium, Arog, Immunogen, Arcellx, and Shattuck: Consultancy, Other: Advisory Role; Astellas, AbbVie, Genentech, Daiichi-Sankyo, Gilead, Immunogen, Pfizer, Bristol Myers Squibb, Trovagene, Servier, Novimmune, Incyte, Hanmi, Fate, Amgen, Kite, Novartis, Astex, KAHR, Shattuck, Sobi, Glycomimetics, Trillium: Research Funding. Colla:Amgen: Research Funding. Orlowski:Abbvie, BioTheryX, Inc., Bristol-Myers Squibb, Janssen Biotech, Karyopharm Therapeutics, Inc., Meridian Therapeutics, Monte Rosa Therapeutics, Neoleukin Corporation, Oncopeptides AB, Regeneron Pharmaceuticals, Inc., Sanofi-Aventis, and Takeda Pharmaceutic: Honoraria, Membership on an entity's Board of Directors or advisory committees; CARsgen Therapeutics, Celgene/Bristol Myers Squibb, Exelixis, Janssen Biotech, Sanofi-Aventis, Takeda Pharmaceuticals North America, Inc.: Research Funding; Asylia Therapeutics, Inc., BioTheryX, Inc., Heidelberg Pharma, Inc.: Research Funding; Asylia Therapeutics, Inc.: Current equity holder in private company. Champlin:Omeros: Consultancy; Actinium: Consultancy; Kadmon: Consultancy; Johnson &Johnson: Consultancy; Bluebird: Other: Data Safety Monitoring Board; General Oncology: Other: Data Safety Monitoring Board; Cell Source Inc.: Research Funding. Shpall:Bayer: Honoraria; NY blood center: Consultancy; axio: Consultancy; adaptimmune: Consultancy; Affimed: Other: License agreement; Fibroblasts and FibroBiologics: Consultancy; Takeda: Patents & Royalties; Navan: Consultancy. Garcia-Manero:Acceleron Pharma: Consultancy; Genentech: Honoraria, Research Funding; Curis: Honoraria, Research Funding; Aprea: Honoraria; Astex: Consultancy, Honoraria, Research Funding; AbbVie: Honoraria, Research Funding; BMS: Consultancy, Honoraria, Research Funding; Novartis: Honoraria, Research Funding; Gilead Sciences: Research Funding. Takahashi:Illumina: Honoraria; Mission Bio: Honoraria; Ostuka Pharmaceuticals: Honoraria; Agios: Consultancy; GSK: Consultancy; Celgene/BMS: Consultancy; Novartis: Consultancy; Symbio Pharmaceuticals: Consultancy.