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Campillo-Marcos I, Casado-Pelaez M, Davalos V, Ferrer G, Mata C, Mereu E, Roué G, Valcárcel D, Molero A, Zamora L, Xicoy B, Palomo L, Acha P, Manzanares A, Tobiasson M, Hellström-Lindberg E, Solé F, Esteller M. Single-cell Multiomics Analysis of Myelodysplastic Syndromes and Clinical Response to Hypomethylating Therapy. Cancer Res Commun 2024; 4:365-377. [PMID: 38300528 PMCID: PMC10860538 DOI: 10.1158/2767-9764.crc-23-0389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/18/2023] [Accepted: 01/26/2024] [Indexed: 02/02/2024]
Abstract
Alterations in epigenetic marks, such as DNA methylation, represent a hallmark of cancer that has been successfully exploited for therapy in myeloid malignancies. Hypomethylating agents (HMA), such as azacitidine, have become standard-of-care therapy to treat myelodysplastic syndromes (MDS), myeloid neoplasms that can evolve into acute myeloid leukemia. However, our capacity to identify who will respond to HMAs, and the duration of response, remains limited. To shed light on this question, we have leveraged the unprecedented analytic power of single-cell technologies to simultaneously map the genome and immunoproteome of MDS samples throughout clinical evolution. We were able to chart the architecture and evolution of molecular clones in precious paired bone marrow MDS samples at diagnosis and posttreatment to show that a combined imbalance of specific cell lineages with diverse mutational profiles is associated with the clinical response of patients with MDS to hypomethylating therapy. SIGNIFICANCE MDS are myeloid clonal hemopathies with a low 5-year survival rate, and approximately half of the cases do not respond to standard HMA therapy. Our innovative single-cell multiomics approach offers valuable biological insights and potential biomarkers associated with the demethylating agent efficacy. It also identifies vulnerabilities that can be targeted using personalized combinations of small drugs and antibodies.
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Affiliation(s)
- Ignacio Campillo-Marcos
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Marta Casado-Pelaez
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Veronica Davalos
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Gerardo Ferrer
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Caterina Mata
- Single Cell Unit, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Elisabetta Mereu
- Cellular Systems Genomics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Gael Roué
- Lymphoma Translational Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - David Valcárcel
- Department of Hematology, Experimental Hematology Group, Vall d'Hebron Institute of Oncology (VHIO), University Hospital Vall d'Hebron, Barcelona, Catalonia, Spain
| | - Antonieta Molero
- Department of Hematology, Experimental Hematology Group, Vall d'Hebron Institute of Oncology (VHIO), University Hospital Vall d'Hebron, Barcelona, Catalonia, Spain
| | - Lurdes Zamora
- Department of Hematology, ICO-IJC-Hospital Germans Trias i Pujol, UAB, Badalona, Spain
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Blanca Xicoy
- Department of Hematology, ICO-IJC-Hospital Germans Trias i Pujol, UAB, Badalona, Spain
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Laura Palomo
- Department of Hematology, Experimental Hematology Group, Vall d'Hebron Institute of Oncology (VHIO), University Hospital Vall d'Hebron, Barcelona, Catalonia, Spain
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Pamela Acha
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Ana Manzanares
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Magnus Tobiasson
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden; Medical Unit Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Eva Hellström-Lindberg
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden; Medical Unit Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Francesc Solé
- Myelodysplastic Syndromes Research Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
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Bauer KC, Huus KE, Brown EM, Bozorgmehr T, Petersen C, Cirstea MS, Woodward SE, McCoy J, Hun J, Pamplona R, Ayala V, Finlay BB. Dietary Intervention Reverses Fatty Liver and Altered Gut Microbiota during Early-Life Undernutrition. mSystems 2020; 5:e00499-20. [PMID: 32900869 PMCID: PMC7483509 DOI: 10.1128/msystems.00499-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/01/2020] [Indexed: 01/04/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD), largely studied as a condition of overnutrition, also presents in undernourished populations. Like NAFLD, undernutrition disrupts systemic metabolism and has been linked to gut microbiota dysbiosis. Indeed, chronic exposures to fecal microbes contribute to undernutrition pathology in regions with poor sanitation. Despite a growing prevalence of fatty liver disease, the influence of undernutrition and the gut microbiota remain largely unexplored. Here, we utilize an established murine model (C57BL/6J mice placed on a malnourished diet that received iterative Escherichia coli/Bacteroidales gavage [MBG mice]) that combines a protein/fat-deficient diet and iterative exposure to specific, fecal microbes. Fecal-oral contamination exacerbates triglyceride accumulation in undernourished mice. MBG livers exhibit diffuse lipidosis accompanied by striking shifts in fatty acid, glycerophospholipid, and retinol metabolism. Multiomic analyses revealed metabolomic pathways linked to the undernourished gut microbiome and hepatic steatosis, including phenylacetate metabolism. Intriguingly, fatty liver features were observed only in the early-life, but not adult, MBG model despite similar liver metabolomic profiles. Importantly, we demonstrate that dietary intervention largely mitigates aberrant metabolomic and microbiome features in MBG mice. These findings indicate a crucial window in early-life development that, when disrupted by nutritional deficiency, may significantly influence liver function. Our work provides a multifaceted study of how diet and gut microbes inform fatty liver progression and reversal during undernutrition.IMPORTANCE Nonalcoholic fatty liver disease (NAFLD) remains a global epidemic, but it is often studied in the context of obesity and aging. Nutritional deficits, however, also trigger hepatic steatosis, influencing health trajectories in undernourished pediatric populations. Here, we report that exposure to specific gut microbes impacts fatty liver pathology in mice fed a protein/fat-deficient diet. We utilize a multiomics approach to (i) characterize NAFLD in the context of early undernutrition and (ii) examine the impact of diet and gut microbes in the pathology and reversal of hepatic steatosis. We provide compelling evidence that an early-life, critical development window facilitates undernutrition-induced fatty liver pathology. Moreover, we demonstrate that sustained dietary intervention largely reverses fatty liver features and microbiome shifts observed during early-life malnutrition.
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Affiliation(s)
- K C Bauer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Microbiology and Immunology Department, University of British Columbia, Vancouver, British Columbia, Canada
| | - K E Huus
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Microbiology and Immunology Department, University of British Columbia, Vancouver, British Columbia, Canada
| | - E M Brown
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Microbiology and Immunology Department, University of British Columbia, Vancouver, British Columbia, Canada
| | - T Bozorgmehr
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - C Petersen
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - M S Cirstea
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Microbiology and Immunology Department, University of British Columbia, Vancouver, British Columbia, Canada
| | - S E Woodward
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Microbiology and Immunology Department, University of British Columbia, Vancouver, British Columbia, Canada
| | - J McCoy
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - J Hun
- The Metabolomics Innovation Centre, University of Victoria, British Columbia, Canada
| | - R Pamplona
- Institut de Recerca Biomèdica de Lleida (IRB-Lleida), Lleida, Spain
- Department of Metabolomic Physiology, Universitat de Lleida, Lleida, Spain
| | - V Ayala
- Institut de Recerca Biomèdica de Lleida (IRB-Lleida), Lleida, Spain
- Department of Metabolomic Physiology, Universitat de Lleida, Lleida, Spain
| | - B B Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Microbiology and Immunology Department, University of British Columbia, Vancouver, British Columbia, Canada
- Biochemistry and Molecular Biology Department, University of British Columbia, Vancouver, Canada
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