Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths

Mariela Cortés-López; Paulina Chamely; Allegra G Hawkins; Robert F Stanley; Ariel D Swett; Saravanan Ganesan; Tarek H Mouhieddine; Xiaoguang Dai; Lloyd Kluegel; Celine Chen; Kiran Batta; Nili Furer; Rahul S Vedula; John Beaulaurier; Alexander W Drong; Scott Hickey; Neville Dusaj; Gavriel Mullokandov; Adam M Stasiw; Jiayu Su; Ronan Chaligné; Sissel Juul; Eoghan Harrington; David A Knowles; Catherine J Potenski; Daniel H Wiseman; Amos Tanay; Liran Shlush; Robert C Lindsley; Irene M Ghobrial; Justin Taylor; Omar Abdel-Wahab; Federico Gaiti; Dan A Landau

doi:10.1016/j.stem.2023.07.012

Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths

Cell Stem Cell. 2023 Sep 7;30(9):1262-1281.e8. doi: 10.1016/j.stem.2023.07.012. Epub 2023 Aug 14.

Authors

Mariela Cortés-López¹, Paulina Chamely¹, Allegra G Hawkins², Robert F Stanley³, Ariel D Swett¹, Saravanan Ganesan¹, Tarek H Mouhieddine⁴, Xiaoguang Dai⁵, Lloyd Kluegel¹, Celine Chen⁶, Kiran Batta⁷, Nili Furer⁸, Rahul S Vedula⁴, John Beaulaurier⁹, Alexander W Drong⁵, Scott Hickey⁹, Neville Dusaj⁶, Gavriel Mullokandov¹, Adam M Stasiw¹, Jiayu Su¹⁰, Ronan Chaligné¹¹, Sissel Juul⁵, Eoghan Harrington⁵, David A Knowles¹², Catherine J Potenski¹, Daniel H Wiseman⁷, Amos Tanay¹³, Liran Shlush⁸, Robert C Lindsley⁴, Irene M Ghobrial⁴, Justin Taylor¹⁴, Omar Abdel-Wahab³, Federico Gaiti¹⁵, Dan A Landau¹⁶

Affiliations

¹ 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.
² Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, PA, USA.
³ Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
⁴ Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
⁵ Oxford Nanopore Technologies Inc., New York, NY, USA.
⁶ 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.
⁷ Division of Cancer Sciences, The University of Manchester, Manchester, UK.
⁸ Weizmann Institute of Science, Department of Molecular Cell Biology, Rehovot, Israel.
⁹ Oxford Nanopore Technologies Inc., San Francisco, CA, USA.
¹⁰ New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA.
¹¹ Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
¹² 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.
¹³ Weizmann Institute of Science, Department of Computer Science and Applied Mathematics, Rehovot, Israel.
¹⁴ Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA.
¹⁵ University Health Network, Princess Margaret Cancer Centre, Toronto, ON, Canada; University of Toronto, Medical Biophysics, Toronto, ON, Canada. Electronic address: [email protected].
¹⁶ 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. Electronic address: [email protected].

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. SF3B1^mut cells were enriched in the megakaryocytic-erythroid lineage, with expansion of SF3B1^mut 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 SF3B1^mut 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.

Keywords: BAX; RNA-seq; SF3B1; clonal hematopoiesis; genotyping; long-read sequencing; multi-omics; myelodysplastic syndrome; single cell; splicing.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Humans
Multiomics
Mutation / genetics
Myelodysplastic Syndromes* / genetics
Myelodysplastic Syndromes* / metabolism
Phosphoproteins / genetics
Phosphoproteins / metabolism
RNA Splice Sites*
RNA Splicing / genetics
RNA Splicing Factors / genetics
RNA Splicing Factors / metabolism

Substances

RNA Splice Sites
RNA Splicing Factors
Phosphoproteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding