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

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 SuRonan 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

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	1262-1281.e8
Journal	Cell Stem Cell
Volume	30
Issue number	9
DOIs	https://doi.org/10.1016/j.stem.2023.07.012
Publication status	Published - 7 Sept 2023

Keywords

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

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10.1016/j.stem.2023.07.012

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Cortés-López, M., Chamely, P., Hawkins, A. G., Stanley, R. F., Swett, A. D., Ganesan, S., Mouhieddine, T. H., Dai, X., Kluegel, L., Chen, C., Batta, K., Furer, N., Vedula, R. S., Beaulaurier, J., Drong, A. W., Hickey, S., Dusaj, N., Mullokandov, G., Stasiw, A. M., ... Landau, D. A. (2023). Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths. Cell Stem Cell, 30(9), 1262-1281.e8. https://doi.org/10.1016/j.stem.2023.07.012

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

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.",

keywords = "Humans, RNA Splice Sites, Multiomics, RNA Splicing/genetics, Myelodysplastic Syndromes/genetics, RNA Splicing Factors/genetics, Mutation/genetics, Phosphoproteins/genetics",

author = "Mariela Cort{\'e}s-L{\'o}pez and Paulina Chamely and Hawkins, {Allegra G} and Stanley, {Robert F} and Swett, {Ariel D} and Saravanan Ganesan and Mouhieddine, {Tarek H} and Xiaoguang Dai and Lloyd Kluegel and Celine Chen and Kiran Batta and Nili Furer and Vedula, {Rahul S} and John Beaulaurier and Drong, {Alexander W} and Scott Hickey and Neville Dusaj and Gavriel Mullokandov and Stasiw, {Adam M} and Jiayu Su and Ronan Chalign{\'e} and Sissel Juul and Eoghan Harrington and Knowles, {David A} and Potenski, {Catherine J} and Wiseman, {Daniel H} and Amos Tanay and Liran Shlush and Lindsley, {Robert C} and Ghobrial, {Irene M} and Justin Taylor and Omar Abdel-Wahab and Federico Gaiti and Landau, {Dan A}",

year = "2023",

month = sep,

day = "7",

doi = "10.1016/j.stem.2023.07.012",

language = "English",

volume = "30",

pages = "1262--1281.e8",

journal = "Cell Stem Cell",

issn = "1934-5909",

publisher = "Cell Press",

number = "9",

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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 2023, 'Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths', Cell Stem Cell, vol. 30, no. 9, pp. 1262-1281.e8. https://doi.org/10.1016/j.stem.2023.07.012

TY - JOUR

T1 - Single-cell multi-omics defines the cell-type-specific impact of splicing aberrations in human hematopoietic clonal outgrowths

AU - Cortés-López, Mariela

AU - Chamely, Paulina

AU - Hawkins, Allegra G

AU - Stanley, Robert F

AU - Swett, Ariel D

AU - Ganesan, Saravanan

AU - Mouhieddine, Tarek H

AU - Dai, Xiaoguang

AU - Kluegel, Lloyd

AU - Chen, Celine

AU - Batta, Kiran

AU - Furer, Nili

AU - Vedula, Rahul S

AU - Beaulaurier, John

AU - Drong, Alexander W

AU - Hickey, Scott

AU - Dusaj, Neville

AU - Mullokandov, Gavriel

AU - Stasiw, Adam M

AU - Su, Jiayu

AU - Chaligné, Ronan

AU - Juul, Sissel

AU - Harrington, Eoghan

AU - Knowles, David A

AU - Potenski, Catherine J

AU - Wiseman, Daniel H

AU - Tanay, Amos

AU - Shlush, Liran

AU - Lindsley, Robert C

AU - Ghobrial, Irene M

AU - Taylor, Justin

AU - Abdel-Wahab, Omar

AU - Gaiti, Federico

AU - Landau, Dan A

PY - 2023/9/7

Y1 - 2023/9/7

N2 - 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.

AB - 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.

KW - Humans

KW - RNA Splice Sites

KW - Multiomics

KW - RNA Splicing/genetics

KW - Myelodysplastic Syndromes/genetics

KW - RNA Splicing Factors/genetics

KW - Mutation/genetics

KW - Phosphoproteins/genetics

U2 - 10.1016/j.stem.2023.07.012

DO - 10.1016/j.stem.2023.07.012

M3 - Article

C2 - 37582363

SN - 1934-5909

VL - 30

SP - 1262-1281.e8

JO - Cell Stem Cell

JF - Cell Stem Cell

IS - 9

ER -

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

Abstract

Keywords

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