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Cortés-López M, Chamely P, Hawkins AG, Stanley RF, Swett AD, Ganesan S, Mouhieddine TH, Dai X, Kluegel L, Chen C, Batta K, Furer N, Vedula RS, Beaulaurier J, Drong AW, Hickey S, Dusaj N, Mullokandov G, Stasiw AM, Su J, Chaligné R, Juul S, Harrington E, Knowles DA, Potenski CJ, Wiseman DH, Tanay A, Shlush L, Lindsley RC, Ghobrial IM, Taylor J, Abdel-Wahab O, Gaiti F, Landau DA. Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths. Cell Stem Cell 2023; 30:1262-1281.e8. [PMID: 37582363 PMCID: PMC10528176 DOI: 10.1016/j.stem.2023.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 05/28/2023] [Accepted: 07/18/2023] [Indexed: 08/17/2023]
Abstract
RNA splicing factors are recurrently mutated in clonal blood disorders, but the impact of dysregulated splicing in hematopoiesis remains unclear. To overcome technical limitations, we integrated genotyping of transcriptomes (GoT) with long-read single-cell transcriptomics and proteogenomics for single-cell profiling of transcriptomes, surface proteins, somatic mutations, and RNA splicing (GoT-Splice). We applied GoT-Splice to hematopoietic progenitors from myelodysplastic syndrome (MDS) patients with mutations in the core splicing factor SF3B1. SF3B1mut cells were enriched in the megakaryocytic-erythroid lineage, with expansion of SF3B1mut erythroid progenitor cells. We uncovered distinct cryptic 3' splice site usage in different progenitor populations and stage-specific aberrant splicing during erythroid differentiation. Profiling SF3B1-mutated clonal hematopoiesis samples revealed that erythroid bias and cell-type-specific cryptic 3' splice site usage in SF3B1mut cells precede overt MDS. Collectively, GoT-Splice defines the cell-type-specific impact of somatic mutations on RNA splicing, from early clonal outgrowths to overt neoplasia, directly in human samples.
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Affiliation(s)
- Mariela Cortés-López
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Paulina Chamely
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Allegra G Hawkins
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, PA, USA
| | - Robert F Stanley
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ariel D Swett
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Saravanan Ganesan
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Tarek H Mouhieddine
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xiaoguang Dai
- Oxford Nanopore Technologies Inc., New York, NY, USA
| | - Lloyd Kluegel
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Celine Chen
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kiran Batta
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
| | - Nili Furer
- Weizmann Institute of Science, Department of Molecular Cell Biology, Rehovot, Israel
| | - Rahul S Vedula
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Scott Hickey
- Oxford Nanopore Technologies Inc., San Francisco, CA, USA
| | - Neville Dusaj
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gavriel Mullokandov
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Adam M Stasiw
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Jiayu Su
- New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA
| | - Ronan Chaligné
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sissel Juul
- Oxford Nanopore Technologies Inc., New York, NY, USA
| | | | - David A Knowles
- New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA; Department of Computer Science, Columbia University, New York, NY, USA
| | - Catherine J Potenski
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Daniel H Wiseman
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
| | - Amos Tanay
- Weizmann Institute of Science, Department of Computer Science and Applied Mathematics, Rehovot, Israel
| | - Liran Shlush
- Weizmann Institute of Science, Department of Molecular Cell Biology, Rehovot, Israel
| | - Robert C Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Irene M Ghobrial
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Federico Gaiti
- University Health Network, Princess Margaret Cancer Centre, Toronto, ON, Canada; University of Toronto, Medical Biophysics, Toronto, ON, Canada.
| | - Dan A Landau
- New York Genome Center, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
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