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Benbarche S, Pineda JMB, Galvis LB, Biswas J, Liu B, Wang E, Zhang Q, Hogg SJ, Lyttle K, Dahi A, Lewis AM, Sarchi M, Rahman J, Fox N, Ai Y, Mehta S, Garippa R, Ortiz-Pacheco J, Li Z, Monetti M, Stanley RF, Doulatov S, Bradley RK, Abdel-Wahab O. GPATCH8 modulates mutant SF3B1 mis-splicing and pathogenicity in hematologic malignancies. Mol Cell 2024; 84:1886-1903.e10. [PMID: 38688280 PMCID: PMC11102302 DOI: 10.1016/j.molcel.2024.04.006] [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: 09/26/2023] [Revised: 03/04/2024] [Accepted: 04/09/2024] [Indexed: 05/02/2024]
Abstract
Mutations in the RNA splicing factor gene SF3B1 are common across hematologic and solid cancers and result in widespread alterations in splicing, yet there is currently no therapeutic means to correct this mis-splicing. Here, we utilize synthetic introns uniquely responsive to mutant SF3B1 to identify trans factors required for aberrant mutant SF3B1 splicing activity. This revealed the G-patch domain-containing protein GPATCH8 as required for mutant SF3B1-induced splicing alterations and impaired hematopoiesis. GPATCH8 is involved in quality control of branchpoint selection, interacts with the RNA helicase DHX15, and functionally opposes SURP and G-patch domain containing 1 (SUGP1), a G-patch protein recently implicated in SF3B1-mutant diseases. Silencing of GPATCH8 corrected one-third of mutant SF3B1-dependent splicing defects and was sufficient to improve dysfunctional hematopoiesis in SF3B1-mutant mice and primary human progenitors. These data identify GPATCH8 as a novel splicing factor required for mis-splicing by mutant SF3B1 and highlight the therapeutic impact of correcting aberrant splicing in SF3B1-mutant cancers.
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Affiliation(s)
- Salima Benbarche
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jose Mario Bello Pineda
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Laura Baquero Galvis
- Division of Hematology/Oncology, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jeetayu Biswas
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bo Liu
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Wang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Qian Zhang
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simon J Hogg
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kadeen Lyttle
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ariana Dahi
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander M Lewis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martina Sarchi
- Division of Hematology/Oncology, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jahan Rahman
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nina Fox
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuxi Ai
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sanjoy Mehta
- Gene Editing and Screening Core Facility, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Ralph Garippa
- Gene Editing and Screening Core Facility, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Juliana Ortiz-Pacheco
- Proteomics Innovation Laboratory, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Zhuoning Li
- Proteomics Innovation Laboratory, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Mara Monetti
- Proteomics Innovation Laboratory, Memorial Sloan Kettering Institute and Cancer Center, New York, NY, USA
| | - Robert F Stanley
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sergei Doulatov
- Division of Hematology/Oncology, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Robert K Bradley
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Liu ZS, Sinha S, Bannister M, Song A, Arriaga-Gomez E, McKeeken AJ, Bonner EA, Hanson BK, Sarchi M, Takashima K, Zong D, Corral VM, Nguyen E, Yoo J, Chiraphapphaiboon W, Leibson C, McMahon MC, Rai S, Swisher EM, Sachs Z, Chatla S, Stirewalt DL, Deeg HJ, Skorski T, Papapetrou EP, Walter MJ, Graubert TA, Doulatov S, Lee SC, Nguyen HD. R-Loop Accumulation in Spliceosome Mutant Leukemias Confers Sensitivity to PARP1 Inhibition by Triggering Transcription-Replication Conflicts. Cancer Res 2024; 84:577-597. [PMID: 37967363 PMCID: PMC10922727 DOI: 10.1158/0008-5472.can-23-3239] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/17/2023]
Abstract
RNA splicing factor (SF) gene mutations are commonly observed in patients with myeloid malignancies. Here we showed that SRSF2- and U2AF1-mutant leukemias are preferentially sensitive to PARP inhibitors (PARPi), despite being proficient in homologous recombination repair. Instead, SF-mutant leukemias exhibited R-loop accumulation that elicited an R-loop-associated PARP1 response, rendering cells dependent on PARP1 activity for survival. Consequently, PARPi induced DNA damage and cell death in SF-mutant leukemias in an R-loop-dependent manner. PARPi further increased aberrant R-loop levels, causing higher transcription-replication collisions and triggering ATR activation in SF-mutant leukemias. Ultimately, PARPi-induced DNA damage and cell death in SF-mutant leukemias could be enhanced by ATR inhibition. Finally, the level of PARP1 activity at R-loops correlated with PARPi sensitivity, suggesting that R-loop-associated PARP1 activity could be predictive of PARPi sensitivity in patients harboring SF gene mutations. This study highlights the potential of targeting different R-loop response pathways caused by spliceosome gene mutations as a therapeutic strategy for treating cancer. SIGNIFICANCE Spliceosome-mutant leukemias accumulate R-loops and require PARP1 to resolve transcription-replication conflicts and genomic instability, providing rationale to repurpose FDA-approved PARP inhibitors for patients carrying spliceosome gene mutations.
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Affiliation(s)
- Zhiyan Silvia Liu
- Molecular Pharmacology and Therapeutics Graduate Program, Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- These authors contributed equally
| | - Sayantani Sinha
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- These authors contributed equally
| | - Maxwell Bannister
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Axia Song
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Erica Arriaga-Gomez
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Alexander J. McKeeken
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN, USA
| | - Elizabeth A. Bonner
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | - Benjamin K. Hanson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN, USA
| | - Martina Sarchi
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Molecular Medicine, University of Pavia, 27100 Pavia PV, Italy
| | - Kouhei Takashima
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Regenerative Medicine and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Advancement of Blood Cancer Therapies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dawei Zong
- Molecular Pharmacology and Therapeutics Graduate Program, Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Victor M. Corral
- Molecular Pharmacology and Therapeutics Graduate Program, Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Evan Nguyen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jennifer Yoo
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | | | - Cassandra Leibson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Matthew C. McMahon
- Molecular Pharmacology and Therapeutics Graduate Program, Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Sumit Rai
- Massachusetts General Hospital Cancer Center, Charlestown, MA
| | - Elizabeth M. Swisher
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, WA 98195
| | - Zohar Sachs
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Srinivas Chatla
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Derek L. Stirewalt
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - H. Joachim Deeg
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Tomasz Skorski
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Eirini P. Papapetrou
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Institute for Regenerative Medicine and Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Advancement of Blood Cancer Therapies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew J. Walter
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St Louis, MO, USA
| | | | - Sergei Doulatov
- Division of Hematology and Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Stanley C. Lee
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Hai Dang Nguyen
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
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3
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Blümke A, Ijeoma E, Simon J, Wellington R, Purwaningrum M, Doulatov S, Leber E, Scatena M, Giachelli CM. Comparison of osteoclast differentiation protocols from human induced pluripotent stem cells of different tissue origins. Stem Cell Res Ther 2023; 14:319. [PMID: 37936199 PMCID: PMC10631132 DOI: 10.1186/s13287-023-03547-6] [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: 06/20/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Ever since their discovery, induced pluripotent stem cells (iPSCs) have been extensively differentiated into a large variety of cell types. However, a limited amount of work has been dedicated to differentiating iPSCs into osteoclasts. While several differentiation protocols have been published, it remains unclear which protocols or differentiation methods are preferable regarding the differentiation of osteoclasts. METHODS In this study, we compared the osteoclastogenesis capacity of a peripheral blood mononuclear cell (PBMC)-derived iPSC line to a fibroblast-derived iPSC line in conjunction with either embryoid body-based or monolayer-based differentiation strategies. Both cell lines and differentiation protocols were investigated regarding their ability to generate osteoclasts and their inherent robustness and ease of use. The ability of both cell lines to remain undifferentiated while propagating using a feeder-free system was assessed using alkaline phosphatase staining. This was followed by evaluating mesodermal differentiation and the characterization of hematopoietic progenitor cells using flow cytometry. Finally, osteoclast yield and functionality based on resorptive activity, Cathepsin K and tartrate-resistant acid phosphatase (TRAP) expression were assessed. The results were validated using qRT-PCR throughout the differentiation stages. RESULTS Embryoid body-based differentiation yielded CD45+, CD14+, CD11b+ subpopulations which in turn differentiated into osteoclasts which demonstrated TRAP positivity, Cathepsin K expression and mineral resorptive capabilities. This was regardless of which iPSC line was used. Monolayer-based differentiation yielded lower quantities of hematopoietic cells that were mostly CD34+ and did not subsequently differentiate into osteoclasts. CONCLUSIONS The outcome of this study demonstrates the successful differentiation of osteoclasts from iPSCs in conjunction with the embryoid-based differentiation method, while the monolayer-based method did not yield osteoclasts. No differences were observed regarding osteoclast differentiation between the PBMC and fibroblast-derived iPSC lines.
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Affiliation(s)
- Alexander Blümke
- Department of Bioengineering, Department of Medicine, University of Washington, Foege Hall University of Washington, 3720 15th, Ave NE, Box 355061, Seattle, WA, 98195, USA
- Department of Orthopedics and Trauma Surgery, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Erica Ijeoma
- Department of Bioengineering, Department of Medicine, University of Washington, Foege Hall University of Washington, 3720 15th, Ave NE, Box 355061, Seattle, WA, 98195, USA
| | - Jessica Simon
- Department of Bioengineering, Department of Medicine, University of Washington, Foege Hall University of Washington, 3720 15th, Ave NE, Box 355061, Seattle, WA, 98195, USA
| | - Rachel Wellington
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, School of Medicine, University of Washington, Seattle, WA, USA
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Medania Purwaningrum
- Department of Bioengineering, Department of Medicine, University of Washington, Foege Hall University of Washington, 3720 15th, Ave NE, Box 355061, Seattle, WA, 98195, USA
- Department of Biochemistry, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sergei Doulatov
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Elizabeth Leber
- Department of Bioengineering, Department of Medicine, University of Washington, Foege Hall University of Washington, 3720 15th, Ave NE, Box 355061, Seattle, WA, 98195, USA
| | - Marta Scatena
- Department of Bioengineering, Department of Medicine, University of Washington, Foege Hall University of Washington, 3720 15th, Ave NE, Box 355061, Seattle, WA, 98195, USA
| | - Cecilia M Giachelli
- Department of Bioengineering, Department of Medicine, University of Washington, Foege Hall University of Washington, 3720 15th, Ave NE, Box 355061, Seattle, WA, 98195, USA.
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4
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Blümke A, Ijeoma E, Simon J, Wellington R, Purwaningrum M, Doulatov S, Leber E, Scatena M, Giachelli CM. Comparison of osteoclast differentiation protocols from human induced pluripotent stem cells of different tissue origins. RESEARCH SQUARE 2023:rs.3.rs-3089289. [PMID: 37461708 PMCID: PMC10350192 DOI: 10.21203/rs.3.rs-3089289/v1] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Background Ever since their discovery, induced pluripotent stem cells (iPSCs) have been extensively differentiated into a large variety of cell types. However, a limited amount of work has been dedicated to differentiating iPSCs into osteoclasts. While several differentiation protocols have been published, it remains unclear which protocols or differentiation methods are preferrable regarding the differentiation of osteoclasts. Methods In this study we compare the osteoclastogenesis capacity of a peripheral blood mononuclear cell (PBMC)-derived iPSC line to a fibroblast-derived iPSC line in conjunction with either embryoid body-based or monolayer-based differentiation strategies. Both cell lines and differentiation protocols were investigated regarding their ability to generate osteoclasts and their inherent robustness and ease of use. The ability of both cell lines to remain undifferentiated while propagating using a feeder-free system was assessed using alkaline phosphatase staining. This was followed by evaluating mesodermal differentiation and the characterization of hematopoietic progenitor cells using flow cytometry. Finally, osteoclast yield and functionality based on resorptive activity, Cathepsin K and tartrate-resistant acid phosphatase (TRAP) expression were assessed. Results were validated using qRT-PCR throughout the differentiation stages. Results Embryoid-body based differentiation yielded CD45+, CD14+, CD11b+ subpopulations which in turn differentiated into osteoclasts which demonstrated TRAP positivity, Cathepsin K expression and mineral resorptive capabilities. This was regardless of which iPSC line was used. Monolayer-based differentiation yielded lower quantities of hematopoietic cells that were mostly CD34+ and did not subsequently differentiate into osteoclasts. Conclusions The outcome of this study demonstrates the successful differentiation of osteoclasts from iPSCs in conjunction with the embryoid-based differentiation method, while the monolayer-based method did not yield osteoclasts. No differences were observed regarding osteoclast differentiation between the PBMC and fibroblast-derived iPSC lines.
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Affiliation(s)
| | - Erica Ijeoma
- University of Washington Department of Bioengineering
| | - Jessica Simon
- University of Washington Department of Bioengineering
| | | | | | | | | | - Marta Scatena
- University of Washington Department of Bioengineering
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5
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Doulatov S. iPSC Models of Leukemia Come of Age. Blood Cancer Discov 2023; 4:252-253. [PMID: 37067903 PMCID: PMC10320630 DOI: 10.1158/2643-3230.bcd-23-0041] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/18/2023] Open
Abstract
SUMMARY In this issue of Blood Cancer Discovery, Kotini and colleagues present a strategy for large-scale reprogramming of primary human acute myeloid leukemias (AML) to induced pluripotent stem cell (iPSC). They show that the hematopoietic differentiation of AML iPSCs gives rise to transplantable leukemias with remarkable molecular similarity to the original patients' AML, providing new models and insights into the disease. See related article by Kotini et al., p. 318 (7) .
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Affiliation(s)
- Sergei Doulatov
- Division of Hematology, Department of Medicine, University of Washington, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle, Washington
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
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Nguyen DH, Sinha S, Liu ZS, Bannister MH, Arriaga-Gomez E, Song A, Zong D, Sarchi M, Corral V, Chiraphapphaiboon W, Yoo J, McMahon M, Leibson C, Stirewalt DL, Deeg HJ, Rai S, Walter M, Graubert TA, Doulatov S, Lee SC. Abstract 6183: PARP inhibitors preferentially sensitize splicing factor mutant myeloid neoplasms. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-6183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Somatic heterozygous mutations in genes encoding for RNA splicing factors (SF) SRSF2, U2AF1, and SF3B1 are frequently mutated in patients with hematologic malignancies, representing a unique genetic vulnerability for targeted therapy. In the current study, we performed a focused drug screen with inhibitors targeting different DNA damage response and DNA metabolic pathways to identify novel therapeutic vulnerabilities generated by SF mutations. We generated a murine leukemia model by overexpressing the MLL-AF9 fusion oncogene on an Srsf2P95H/+ background, a mutational combination that is found in ~10% of MLL-rearranged leukemias. We surprisingly found that MLL-AF9 Srsf2P95H/+ mutant leukemias are sensitive to inhibitors targeting ADP-ribosyltransferases (PARP). PARP inhibitor sensitivity was also observed in isogenic murine MLL-AF9 U2af1s34/+ cells compared to MLL-AF9 U2af1+/+ cells. Second, murine Srsf2P95H leukemias showed improved prolonged survival when treated with olaparib (PARPi) compared to vehicle treatment in vivo. Third, human primary AML patient samples that harbor SF mutations are sensitive to PARPi compared to non-SF mutant samples. These data highlight that both SRSF2P95H and U2AF1S34F mutations create a common vulnerability that is dependent on PARP activity for survival. To evaluate PARP activity, we used isogenic K562 leukemia cells expressing SRSF2P95H and U2AF1S34F mutations from their endogenous loci and monitored ADP-ribosylation (ADPr) levels, a marker of PARP activity. Both SRSF2P95H and U2AF1S34F cells exhibited elevated levels of ADPr compared to wildtype cells in a PARP1- dependent manner. PARPi preferentially induced DNA damage and cell death in SF mutant cells. Surprisingly, we found that SRSF2P95H and U2AF1S34F cells are not defective in homologous recombination repair. Instead, the increased PARP1-mediated ADPr in SF-mutant cells is caused by accumulated R loops, a group of transcription intermediates containing RNA:DNA hybrids and displaced single-stranded DNA. To determine whether PARPi sensitivity is due to R-loop accumulation, we overexpressed RNase H1, an enzyme that specifically cleaves the RNA moiety within RNA:DNA hybrids in U2AF1S34F cells. Overexpression of RNase H1 significantly reduced ADPr levels and suppressed the PARPi-induced U2AF1S34F cell growth inhibition. Collectively, these results suggest that spliceosome mutants induce R-loop accumulation and elicit an R-loop-associated PARP1 response to promote cell survival. In summary, our data establish a previously unknown link between R-loop-induced PARP1 response and RNA splicing perturbation and provide a mechanistic rationale to evaluate the clinical efficacy of PARP inhibitors in spliceosome-mutant malignancies. Furthermore, our study highlights a new therapeutic potential of targeting the R-loop tolerance pathways caused by different spliceosome gene mutations.
Citation Format: Dang Hai Nguyen, Sayantani Sinha, Zhiyan Silvia Liu, Maxwell Henry Bannister, Erica Arriaga-Gomez, Axia Song, Dawei Zong, Martina Sarchi, Victor Corral, Wannasiri Chiraphapphaiboon, Jennifer Yoo, Matthew McMahon, Cassandra Leibson, Derek L. Stirewalt, H Joachim Deeg, Sumit Rai, Matthew Walter, Timothy A. Graubert, Sergei Doulatov, Stanley C. Lee. PARP inhibitors preferentially sensitize splicing factor mutant myeloid neoplasms. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6183.
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Affiliation(s)
| | | | | | | | | | - Axia Song
- 2Fred Hutchinson Cancer Center, Seattle, WA
| | - Dawei Zong
- 1University of Minnesota, Minneapolis, MN
| | | | | | | | | | | | | | | | | | - Sumit Rai
- 4Massachusetts General Hospital Cancer Center, Charlestown, MA
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Stolla MC, Reilly A, Bergantinos R, Stewart S, Thom N, Clough CA, Wellington R, Stolitenko R, Abkowitz JL, Doulatov S. ATG4A regulates human erythroid maturation and mitochondrial clearance. Blood Adv 2022; 6:3579-3589. [PMID: 35443024 PMCID: PMC9631553 DOI: 10.1182/bloodadvances.2021005910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 03/15/2022] [Indexed: 01/09/2023] Open
Abstract
Autophagy is a self-degradation pathway that is essential for erythropoiesis. During erythroid differentiation, autophagy facilitates the degradation of macromolecules and the programmed clearance of mitochondria. Impaired mitochondrial clearance results in anemia and alters the lifespan of red blood cells in vivo. While several essential autophagy genes contribute to autophagy in erythropoiesis, little is known about erythroid-specific mediators of this pathway. Genetic analysis of primary human erythroid and nonerythroid cells revealed the selective upregulation of the core autophagy gene ATG4A in maturing human erythroid cells. Because the function of ATG4A in erythropoiesis is unknown, we evaluated its role using an ex vivo model of human erythropoiesis. Depletion of ATG4A in primary human hematopoietic stem and progenitor cells selectively impaired erythroid but not myeloid lineage differentiation, resulting in reduced red cell production, delayed terminal differentiation, and impaired enucleation. Loss of ATG4A impaired autophagy and mitochondrial clearance, giving rise to reticulocytes with retained mitochondria and autophagic vesicles. In summary, our study identifies ATG4A as a cell type-specific regulator of autophagy in erythroid development.
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Affiliation(s)
| | | | | | | | - Neele Thom
- Division of Hematology, Department of Medicine
| | - Courtnee A. Clough
- Division of Hematology, Department of Medicine
- Molecular and Cellular Biology Program
| | - Rachel C. Wellington
- Division of Hematology, Department of Medicine
- Molecular and Cellular Biology Program
| | | | - Janis L. Abkowitz
- Division of Hematology, Department of Medicine
- Institute for Stem Cell and Regenerative Medicine, and
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Sergei Doulatov
- Division of Hematology, Department of Medicine
- Molecular and Cellular Biology Program
- Institute for Stem Cell and Regenerative Medicine, and
- Department of Genome Sciences, University of Washington, Seattle, WA
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8
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Reilly A, Philip Creamer J, Stewart S, Stolla MC, Wang Y, Du J, Wellington R, Busch S, Estey EH, Becker PS, Fang M, Keel SB, Abkowitz JL, Soma LA, Ma J, Duan Z, Doulatov S. Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function. Cell Stem Cell 2022; 29:577-592.e8. [PMID: 35278369 PMCID: PMC9018112 DOI: 10.1016/j.stem.2022.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 05/18/2021] [Revised: 01/05/2022] [Accepted: 02/15/2022] [Indexed: 11/19/2022]
Abstract
Abnormal nuclear morphology is a hallmark of malignant cells widely used in cancer diagnosis. Pelger-Huët anomaly (PHA) is a common abnormality of neutrophil nuclear morphology of unknown molecular etiology in myeloid neoplasms (MNs). We show that loss of nuclear lamin B1 (LMNB1) encoded on chromosome 5q, which is frequently deleted in MNs, induces defects in nuclear morphology and human hematopoietic stem cell (HSC) function associated with malignancy. LMNB1 deficiency alters genome organization inducing in vitro and in vivo expansion of HSCs, myeloid-biased differentiation with impaired lymphoid commitment, and genome instability due to defective DNA damage repair. Nuclear dysmorphology of neutrophils in patients with MNs is associated with 5q deletions spanning the LMNB1 locus, and lamin B1 loss is both necessary and sufficient to cause PHA in normal and 5q-deleted neutrophils. LMNB1 loss thus causes acquired PHA and links abnormal nuclear morphology with HSCs and progenitor cell fate determination via genome organization.
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Affiliation(s)
- Andreea Reilly
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - J Philip Creamer
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sintra Stewart
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Massiel C Stolla
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Yuchuan Wang
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jing Du
- Division of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Rachel Wellington
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Stephanie Busch
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Elihu H Estey
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Pamela S Becker
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Division of Hematology/Oncology, Chao Family Comprehensive Cancer Center, University of California Irvine, Irvine, CA 92617, USA; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Min Fang
- Department of Clinical Transplant Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Siobán B Keel
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Janis L Abkowitz
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Lorinda A Soma
- Division of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jian Ma
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Zhijun Duan
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sergei Doulatov
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, USA.
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9
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Clough CA, Pangallo J, Sarchi M, Ilagan JO, North K, Bergantinos R, Stolla MC, Naru J, Nugent P, Kim E, Stirewalt DL, Subramaniam AR, Abdel-Wahab O, Abkowitz JL, Bradley RK, Doulatov S. Coordinated missplicing of TMEM14C and ABCB7 causes ring sideroblast formation in SF3B1-mutant myelodysplastic syndrome. Blood 2022; 139:2038-2049. [PMID: 34861039 PMCID: PMC8972092 DOI: 10.1182/blood.2021012652] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 11/22/2021] [Indexed: 11/20/2022] Open
Abstract
SF3B1 splicing factor mutations are near-universally found in myelodysplastic syndromes (MDS) with ring sideroblasts (RS), a clonal hematopoietic disorder characterized by abnormal erythroid cells with iron-loaded mitochondria. Despite this remarkably strong genotype-to-phenotype correlation, the mechanism by which mutant SF3B1 dysregulates iron metabolism to cause RS remains unclear due to an absence of physiological models of RS formation. Here, we report an induced pluripotent stem cell model of SF3B1-mutant MDS that for the first time recapitulates robust RS formation during in vitro erythroid differentiation. Mutant SF3B1 induces missplicing of ∼100 genes throughout erythroid differentiation, including proposed RS driver genes TMEM14C, PPOX, and ABCB7. All 3 missplicing events reduce protein expression, notably occurring via 5' UTR alteration, and reduced translation efficiency for TMEM14C. Functional rescue of TMEM14C and ABCB7, but not the non-rate-limiting enzyme PPOX, markedly decreased RS, and their combined rescue nearly abolished RS formation. Our study demonstrates that coordinated missplicing of mitochondrial transporters TMEM14C and ABCB7 by mutant SF3B1 sequesters iron in mitochondria, causing RS formation.
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Affiliation(s)
- Courtnee A Clough
- Molecular and Cellular Biology Program and
- Department of Medicine, Division of Hematology, University of Washington, Seattle, WA
| | - Joseph Pangallo
- Molecular and Cellular Biology Program and
- Computational Biology Program, Public Health Sciences Division and
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Martina Sarchi
- Department of Medicine, Division of Hematology, University of Washington, Seattle, WA
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Janine O Ilagan
- Computational Biology Program, Public Health Sciences Division and
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Khrystyna North
- Computational Biology Program, Public Health Sciences Division and
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Rochelle Bergantinos
- Department of Medicine, Division of Hematology, University of Washington, Seattle, WA
| | - Massiel C Stolla
- Department of Medicine, Division of Hematology, University of Washington, Seattle, WA
| | - Jasmine Naru
- Seattle Cancer Care Alliance, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Patrick Nugent
- Molecular and Cellular Biology Program and
- Computational Biology Program, Public Health Sciences Division and
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Eunhee Kim
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
- Department of Biological Sciences, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology, South Korea
| | - Derek L Stirewalt
- Seattle Cancer Care Alliance, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Arvind R Subramaniam
- Computational Biology Program, Public Health Sciences Division and
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York; and
| | - Janis L Abkowitz
- Department of Medicine, Division of Hematology, University of Washington, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle WA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division and
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Sergei Doulatov
- Department of Medicine, Division of Hematology, University of Washington, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle WA
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10
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Clough C, Pangallo J, Sarchi M, Ilagan J, North K, Bergantinos R, Naru J, Nugent P, Kim E, Stirewalt D, Subramaniam A, Abdel-Wahab O, Abkowitz J, Bradley R, Doulatov S. 3009 – MIS-SPLICING OF TMEM14C ALTERS PORPHYRIN AVAILABILITY PROMOTING RING SIDEROBLAST FORMATION IN SF3B1-MUTANT MYELODYSPLASTIC SYNDROMES. Exp Hematol 2021. [DOI: 10.1016/j.exphem.2021.12.231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Taylor AM, Macari ER, Chan IT, Blair MC, Doulatov S, Vo LT, Raiser DM, Siva K, Basak A, Pirouz M, Shah AN, McGrath K, Humphries JM, Stillman E, Alter BP, Calo E, Gregory RI, Sankaran VG, Flygare J, Ebert BL, Zhou Y, Daley GQ, Zon LI. Calmodulin inhibitors improve erythropoiesis in Diamond-Blackfan anemia. Sci Transl Med 2021; 12:12/566/eabb5831. [PMID: 33087503 DOI: 10.1126/scitranslmed.abb5831] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022]
Abstract
Diamond-Blackfan anemia (DBA) is a rare hematopoietic disease characterized by a block in red cell differentiation. Most DBA cases are caused by mutations in ribosomal proteins and characterized by higher than normal activity of the tumor suppressor p53. Higher p53 activity is thought to contribute to DBA phenotypes by inducing apoptosis during red blood cell differentiation. Currently, there are few therapies available for patients with DBA. We performed a chemical screen using zebrafish ribosomal small subunit protein 29 (rps29) mutant embryos that have a p53-dependent anemia and identified calmodulin inhibitors that rescued the phenotype. Our studies demonstrated that calmodulin inhibitors attenuated p53 protein amount and activity. Treatment with calmodulin inhibitors led to decreased p53 translation and accumulation but does not affect p53 stability. A U.S. Food and Drug Administration-approved calmodulin inhibitor, trifluoperazine, rescued hematopoietic phenotypes of DBA models in vivo in zebrafish and mouse models. In addition, trifluoperazine rescued these phenotypes in human CD34+ hematopoietic stem and progenitor cells. Erythroid differentiation was also improved in CD34+ cells isolated from a patient with DBA. This work uncovers a potential avenue of therapeutic development for patients with DBA.
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Affiliation(s)
- Alison M Taylor
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Elizabeth R Macari
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Iris T Chan
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Megan C Blair
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Sergei Doulatov
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Linda T Vo
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - David M Raiser
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Division of Hematology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kavitha Siva
- Stem Cell Center, Lund University, Lund 22184, Sweden
| | - Anindita Basak
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Mehdi Pirouz
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Arish N Shah
- MIT Department of Biology and David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Katherine McGrath
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Jessica M Humphries
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Emma Stillman
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Rockville, MD 20850, USA
| | - Eliezer Calo
- MIT Department of Biology and David H. Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Richard I Gregory
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Johan Flygare
- Stem Cell Center, Lund University, Lund 22184, Sweden
| | - Benjamin L Ebert
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Yi Zhou
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA
| | - George Q Daley
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Leonard I Zon
- Stem Cell Program, Boston Children's Hospital and Harvard Stem Cell Institute, Boston, MA 02115, USA. .,Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA.,Stem Cell and Regenerative Biology Department, Harvard University, Boston, MA 02115, USA
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12
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Reilly A, Doulatov S. Induced pluripotent stem cell models of myeloid malignancies and clonal evolution. Stem Cell Res 2021; 52:102195. [PMID: 33592565 PMCID: PMC10115516 DOI: 10.1016/j.scr.2021.102195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022] Open
Abstract
Reprogramming of cells from patients with genetic disorders to pluripotency is a promising avenue to understanding disease biology. A number of induced pluripotent stem cell (iPSC) models of inherited monogenic blood disorders have been reported over the past decade. However, the application of iPSCs for modeling of hematological malignancies has only recently been explored. Blood malignancies comprise a spectrum of genetically heterogeneous disorders marked by the acquisition of somatic mutations and chromosomal aberrations. This genetic heterogeneity presents unique challenges for iPSC modeling, but also opportunities to capture genetically distinct states and generate models of stepwise progression from normal to malignant hematopoiesis. Here we briefly review the current state of this field, highlighting current models of acquired pre-malignant and malignant blood disorders and clonal evolution, and challenges including barriers to reprogramming and differentiation of iPSCs into bona fide hematopoietic stem cells.
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Affiliation(s)
- Andreea Reilly
- Division of Hematology, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, United States
| | - Sergei Doulatov
- Division of Hematology, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, United States.
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13
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Abstract
PURPOSE OF REVIEW Myeloid malignancies comprise a spectrum of genetically heterogeneous disorders marked by the stepwise acquisition of somatic mutations and clonal evolution. The blood and bone marrow of patients typically consists of a mix of different clones and subclones along the path of clonal evolution that cannot be deconvoluted with most current approaches. Here, we review the application of induced pluripotent stem cell (iPSC) technology to the study of the clonal architecture and clonal evolution of these diseases, focusing on myelodysplastic syndromes and acute myeloid leukemia. RECENT FINDINGS Reprogramming to pluripotency allows capture of the genomes of single somatic cells into stable iPSC lines. In addition, precise genome editing can introduce specific driver mutations, isolated, and in combinations, into normal iPSCs. Studies utilizing these approaches have elucidated the clonal composition and mutational order in patients with myeloid neoplasms. Importantly, they have also enabled functional interrogation of the cellular and molecular consequences of individual mutations and their combinations and allowed testing of the effects of drugs on distinct disease clones. SUMMARY Human iPSCs are important tools to elucidate the mechanisms of progression from normal to malignant haematopoiesis and empower drug testing and drug discovery.
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Affiliation(s)
- Sergei Doulatov
- Division of Hematology, Department of Medicine, University of Washington, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle, Washington
- Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Eirini P. Papapetrou
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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14
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Cesana M, Guo MH, Cacchiarelli D, Wahlster L, Barragan J, Doulatov S, Vo LT, Salvatori B, Trapnell C, Clement K, Cahan P, Tsanov KM, Sousa PM, Tazon-Vega B, Bolondi A, Giorgi FM, Califano A, Rinn JL, Meissner A, Hirschhorn JN, Daley GQ. A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development. Cell Stem Cell 2019; 22:575-588.e7. [PMID: 29625070 DOI: 10.1016/j.stem.2018.03.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 10/10/2017] [Accepted: 03/14/2018] [Indexed: 12/21/2022]
Abstract
While gene expression dynamics have been extensively cataloged during hematopoietic differentiation in the adult, less is known about transcriptome diversity of human hematopoietic stem cells (HSCs) during development. To characterize transcriptional and post-transcriptional changes in HSCs during development, we leveraged high-throughput genomic approaches to profile miRNAs, lincRNAs, and mRNAs. Our findings indicate that HSCs manifest distinct alternative splicing patterns in key hematopoietic regulators. Detailed analysis of the splicing dynamics and function of one such regulator, HMGA2, identified an alternative isoform that escapes miRNA-mediated targeting. We further identified the splicing kinase CLK3 that, by regulating HMGA2 splicing, preserves HMGA2 function in the setting of an increase in let-7 miRNA levels, delineating how CLK3 and HMGA2 form a functional axis that influences HSC properties during development. Collectively, our study highlights molecular mechanisms by which alternative splicing and miRNA-mediated post-transcriptional regulation impact the molecular identity and stage-specific developmental features of human HSCs.
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Affiliation(s)
- Marcella Cesana
- Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Michael H Guo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA; Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Davide Cacchiarelli
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli 80078, Italy; Department of Translational Medicine, University of Naples "Federico II", Naples 80131, Italy
| | - Lara Wahlster
- Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Jessica Barragan
- Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Sergei Doulatov
- Division of Hematology, University of Washington, Seattle, WA 98195, USA
| | - Linda T Vo
- Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Beatrice Salvatori
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98115, USA
| | - Kendell Clement
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Patrick Cahan
- Department of Biomedical Engineering, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kaloyan M Tsanov
- Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Patricia M Sousa
- Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Barbara Tazon-Vega
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Adriano Bolondi
- Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Federico M Giorgi
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Departments of Biomedical Informatics, Biochemistry and Molecular Biophysics, JP Sulzberger Columbia Genome Center, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - John L Rinn
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; University of Colorado Boulder Biofrontiers, Boulder, CO 80301, USA
| | - Alexander Meissner
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Joel N Hirschhorn
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA; Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - George Q Daley
- Stem Cell Program, Division of Hematology/Oncology, Manton Center for Orphan Disease Research, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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15
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Hsu J, Reilly A, Hayes BJ, Clough CA, Konnick EQ, Torok-Storb B, Gulsuner S, Wu D, Becker PS, Keel SB, Abkowitz JL, Doulatov S. Reprogramming identifies functionally distinct stages of clonal evolution in myelodysplastic syndromes. Blood 2019; 134:186-198. [PMID: 31010849 PMCID: PMC6624967 DOI: 10.1182/blood.2018884338] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 04/01/2019] [Indexed: 12/16/2022] Open
Abstract
Myeloid neoplasms, including myelodysplastic syndromes (MDS), are genetically heterogeneous disorders driven by clonal acquisition of somatic mutations in hematopoietic stem and progenitor cells (HPCs). The order of premalignant mutations and their impact on HPC self-renewal and differentiation remain poorly understood. We show that episomal reprogramming of MDS patient samples generates induced pluripotent stem cells from single premalignant cells with a partial complement of mutations, directly informing the temporal order of mutations in the individual patient. Reprogramming preferentially captured early subclones with fewer mutations, which were rare among single patient cells. To evaluate the functional impact of clonal evolution in individual patients, we differentiated isogenic MDS induced pluripotent stem cells harboring up to 4 successive clonal abnormalities recapitulating a progressive decrease in hematopoietic differentiation potential. SF3B1, in concert with epigenetic mutations, perturbed mitochondrial function leading to accumulation of damaged mitochondria during disease progression, resulting in apoptosis and ineffective erythropoiesis. Reprogramming also informed the order of premalignant mutations in patients with complex karyotype and identified 5q deletion as an early cytogenetic anomaly. The loss of chromosome 5q cooperated with TP53 mutations to perturb genome stability, promoting acquisition of structural and karyotypic abnormalities. Reprogramming thus enables molecular and functional interrogation of preleukemic clonal evolution, identifying mitochondrial function and chromosome stability as key pathways affected by acquisition of somatic mutations in MDS.
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Affiliation(s)
- Jasper Hsu
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
| | - Andreea Reilly
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
| | - Brian J Hayes
- Fred Hutchinson Cancer Research Center, Seattle, WA; and
| | - Courtnee A Clough
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
| | | | | | | | - David Wu
- Department of Laboratory Medicine
| | - Pamela S Becker
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
- Fred Hutchinson Cancer Research Center, Seattle, WA; and
- Institute for Stem Cell and Regenerative Medicine, and
| | - Siobán B Keel
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
| | - Janis L Abkowitz
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, and
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Sergei Doulatov
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA
- Institute for Stem Cell and Regenerative Medicine, and
- Department of Genome Sciences, University of Washington, Seattle, WA
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16
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Seo A, Gulsuner S, Pierce S, Ben-Harosh M, Shalev H, Walsh T, Krasnov T, Dgany O, Doulatov S, Tamary H, Shimamura A, King MC. Inherited thrombocytopenia associated with mutation of UDP-galactose-4-epimerase (GALE). Hum Mol Genet 2019; 28:133-142. [PMID: 30247636 DOI: 10.1093/hmg/ddy334] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/07/2018] [Indexed: 12/11/2022] Open
Abstract
Severe thrombocytopenia, characterized by dysplastic megakaryocytes and intracranial bleeding, was diagnosed in six individuals from a consanguineous kindred. Three of the individuals were successfully treated by bone marrow transplant. Whole-exome sequencing and homozygosity mapping of multiple family members, coupled with whole-genome sequencing to reveal shared non-coding variants, revealed one potentially functional variant segregating with thrombocytopenia under a recessive model: GALE p.R51W (c.C151T, NM_001127621). The mutation is extremely rare (allele frequency = 2.5 × 10-05), and the likelihood of the observed co-segregation occurring by chance is 1.2 × 10-06. GALE encodes UDP-galactose-4-epimerase, an enzyme of galactose metabolism and glycosylation responsible for two reversible reactions: interconversion of UDP-galactose with UDP-glucose and interconversion of UDP-N-acetylgalactosamine with UDP-N-acetylglucosamine. The mutation alters an amino acid residue that is conserved from yeast to humans. The variant protein has both significantly lower enzymatic activity for both interconversion reactions and highly significant thermal instability. Proper glycosylation is critical to normal hematopoiesis, in particular to megakaryocyte and platelet development, as reflected in the presence of thrombocytopenia in the context of congenital disorders of glycosylation. Mutations in GALE have not previously been associated with thrombocytopenia. Our results suggest that GALE p.R51W is inadequate for normal glycosylation and thereby may impair megakaryocyte and platelet development. If other mutations in GALE are shown to have similar consequences, this gene may be proven to play a critical role in hematopoiesis.
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Affiliation(s)
- Aaron Seo
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Suleyman Gulsuner
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Sarah Pierce
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Miri Ben-Harosh
- Department of Pediatric Hematology/Oncology, Soroka Medical Center, Faculty of Medicine, Ben-Gurion University, Beer Sheva, Israel
| | - Hanna Shalev
- Department of Pediatric Hematology/Oncology, Soroka Medical Center, Faculty of Medicine, Ben-Gurion University, Beer Sheva, Israel
| | - Tom Walsh
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Tanya Krasnov
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Orly Dgany
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel
| | - Sergei Doulatov
- Department of Medicine, Division of Hematology, University of Washington, Seattle, WA, USA
| | - Hannah Tamary
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva, Israel.,Hematology Unit, Schneider Children's Medical Center, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Akiko Shimamura
- Department of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Mary-Claire King
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
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17
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Doulatov S, Vo LT, Macari ER, Wahlster L, Kinney MA, Taylor AM, Barragan J, Gupta M, McGrath K, Lee HY, Humphries JM, DeVine A, Narla A, Alter BP, Beggs AH, Agarwal S, Ebert BL, Gazda HT, Lodish HF, Sieff CA, Schlaeger TM, Zon LI, Daley GQ. Drug discovery for Diamond-Blackfan anemia using reprogrammed hematopoietic progenitors. Sci Transl Med 2017; 9:9/376/eaah5645. [PMID: 28179501 DOI: 10.1126/scitranslmed.aah5645] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/10/2016] [Accepted: 10/27/2016] [Indexed: 12/13/2022]
Abstract
Diamond-Blackfan anemia (DBA) is a congenital disorder characterized by the failure of erythroid progenitor differentiation, severely curtailing red blood cell production. Because many DBA patients fail to respond to corticosteroid therapy, there is considerable need for therapeutics for this disorder. Identifying therapeutics for DBA requires circumventing the paucity of primary patient blood stem and progenitor cells. To this end, we adopted a reprogramming strategy to generate expandable hematopoietic progenitor cells from induced pluripotent stem cells (iPSCs) from DBA patients. Reprogrammed DBA progenitors recapitulate defects in erythroid differentiation, which were rescued by gene complementation. Unbiased chemical screens identified SMER28, a small-molecule inducer of autophagy, which enhanced erythropoiesis in a range of in vitro and in vivo models of DBA. SMER28 acted through autophagy factor ATG5 to stimulate erythropoiesis and up-regulate expression of globin genes. These findings present an unbiased drug screen for hematological disease using iPSCs and identify autophagy as a therapeutic pathway in DBA.
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Affiliation(s)
- Sergei Doulatov
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Linda T Vo
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Elizabeth R Macari
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Melissa A Kinney
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alison M Taylor
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Jessica Barragan
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Manav Gupta
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Katherine McGrath
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Hsiang-Ying Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jessica M Humphries
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Alex DeVine
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Anupama Narla
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA.,Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alan H Beggs
- Harvard Medical School, Boston, MA 02115, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA.,Manton Center for Orphan Disease Research, Boston, MA 02115, USA
| | - Suneet Agarwal
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Manton Center for Orphan Disease Research, Boston, MA 02115, USA
| | - Benjamin L Ebert
- Harvard Medical School, Boston, MA 02115, USA.,Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Hanna T Gazda
- Harvard Medical School, Boston, MA 02115, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA.,Manton Center for Orphan Disease Research, Boston, MA 02115, USA
| | - Harvey F Lodish
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Departments of Biology and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Colin A Sieff
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Thorsten M Schlaeger
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA.,Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Leonard I Zon
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA. .,Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - George Q Daley
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA. .,Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA.,Harvard Medical School, Boston, MA 02115, USA.,Manton Center for Orphan Disease Research, Boston, MA 02115, USA
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18
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Abstract
Autophagy, a central pathway for cellular homeostasis, plays diverse roles in development, cancer, aging, and neurodegeneration. In a new report in Nature, Ho et al. (2017) show that autophagy is essential for maintaining the replicative quiescence of hematopoietic stem cells throughout life by limiting the number of active mitochondria.
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Affiliation(s)
- Sergei Doulatov
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA.
| | - George Q Daley
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA; Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
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19
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Sugimura R, Jha DK, Han A, Soria-Valles C, da Rocha EL, Lu YF, Goettel JA, Serrao E, Rowe RG, Malleshaiah M, Wong I, Sousa P, Zhu TN, Ditadi A, Keller G, Engelman AN, Snapper SB, Doulatov S, Daley GQ. Haematopoietic stem and progenitor cells from human pluripotent stem cells. Nature 2017; 545:432-438. [PMID: 28514439 PMCID: PMC5872146 DOI: 10.1038/nature22370] [Citation(s) in RCA: 328] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 04/13/2017] [Indexed: 12/20/2022]
Abstract
A variety of tissue lineages can be differentiated from pluripotent stem cells by mimicking embryonic development through stepwise exposure to morphogens, or by conversion of one differentiated cell type into another by enforced expression of master transcription factors. Here, to yield functional human haematopoietic stem cells, we perform morphogen-directed differentiation of human pluripotent stem cells into haemogenic endothelium followed by screening of 26 candidate haematopoietic stem-cell-specifying transcription factors for their capacity to promote multi-lineage haematopoietic engraftment in mouse hosts. We recover seven transcription factors (ERG, HOXA5, HOXA9, HOXA10, LCOR, RUNX1 and SPI1) that are sufficient to convert haemogenic endothelium into haematopoietic stem and progenitor cells that engraft myeloid, B and T cells in primary and secondary mouse recipients. Our combined approach of morphogen-driven differentiation and transcription-factor-mediated cell fate conversion produces haematopoietic stem and progenitor cells from pluripotent stem cells and holds promise for modelling haematopoietic disease in humanized mice and for therapeutic strategies in genetic blood disorders.
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Affiliation(s)
- Ryohichi Sugimura
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Manton Center for Orphan Disease Research, Boston, Massachusetts 02115, USA
| | - Deepak Kumar Jha
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Manton Center for Orphan Disease Research, Boston, Massachusetts 02115, USA
| | - Areum Han
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Clara Soria-Valles
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Manton Center for Orphan Disease Research, Boston, Massachusetts 02115, USA
| | - Edroaldo Lummertz da Rocha
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Manton Center for Orphan Disease Research, Boston, Massachusetts 02115, USA
| | - Yi-Fen Lu
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Manton Center for Orphan Disease Research, Boston, Massachusetts 02115, USA
| | - Jeremy A Goettel
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Erik Serrao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts, 02215, USA
| | - R Grant Rowe
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Mohan Malleshaiah
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Irene Wong
- Department of Biology, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Patricia Sousa
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Manton Center for Orphan Disease Research, Boston, Massachusetts 02115, USA
| | - Ted N Zhu
- Program in Computer Science, Harvard University, Cambridge, Massachusetts, USA
| | - Andrea Ditadi
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Gordon Keller
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts, 02215, USA
| | - Scott B Snapper
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Division of Gastroenterology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Sergei Doulatov
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Manton Center for Orphan Disease Research, Boston, Massachusetts 02115, USA
| | - George Q Daley
- Stem Cell Transplantation Program, Division of Pediatric Hematology and Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Manton Center for Orphan Disease Research, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
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20
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Doulatov S, Vo L, Macari E, Wahlster L, Taylor A, Gupta M, McGrath K, Narla A, Alter B, Gazda H, Sieff C, Agrawal S, Beggs A, Ebert B, Schlaeger T, Zon L, Daley G. Drug discovery using induced pluripotent stem cells identifies autophagy as a therapeutic pathway for anemia. Exp Hematol 2016. [DOI: 10.1016/j.exphem.2016.06.063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Wang LD, Rao TN, Rowe RG, Nguyen PT, Sullivan JL, Pearson DS, Doulatov S, Wu L, Lindsley RC, Zhu H, DeAngelo DJ, Daley GQ, Wagers AJ. The role of Lin28b in myeloid and mast cell differentiation and mast cell malignancy. Leukemia 2015; 29:1320-30. [PMID: 25655194 PMCID: PMC4456252 DOI: 10.1038/leu.2015.19] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 12/23/2014] [Accepted: 12/31/2014] [Indexed: 02/06/2023]
Abstract
Mast cells (MCs) are critical components of the innate immune system and important for host defense, allergy, autoimmunity, tissue regeneration and tumor progression. Dysregulated MC development leads to systemic mastocytosis (SM), a clinically variable but often devastating family of hematologic disorders. Here we report that induced expression of Lin28, a heterochronic gene and pluripotency factor implicated in driving a fetal hematopoietic program, caused MC accumulation in adult mice in target organs such as the skin and peritoneal cavity. In vitro assays revealed a skewing of myeloid commitment in LIN28B-expressing hematopoietic progenitors, with increased levels of LIN28B in common myeloid and basophil-MC progenitors altering gene expression patterns to favor cell fate choices that enhanced MC specification. In addition, LIN28B-induced MCs appeared phenotypically and functionally immature, and in vitro assays suggested a slowing of MC terminal differentiation in the context of LIN28B upregulation. Finally, interrogation of human MC leukemia samples revealed upregulation of LIN28B in abnormal MCs from patients with SM. This work identifies Lin28 as a novel regulator of innate immune function and a new protein of interest in MC disease.
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MESH Headings
- Aged
- Aged, 80 and over
- Animals
- Blotting, Western
- Bone Marrow Transplantation
- Cell Differentiation
- Cells, Cultured
- DNA-Binding Proteins/physiology
- Female
- Flow Cytometry
- Hematopoiesis/physiology
- Humans
- Leukemia, Mast-Cell/metabolism
- Leukemia, Mast-Cell/pathology
- Leukemia, Mast-Cell/therapy
- Male
- Mast Cells/cytology
- Mast Cells/metabolism
- Mastocytosis, Systemic/metabolism
- Mastocytosis, Systemic/pathology
- Mastocytosis, Systemic/therapy
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Middle Aged
- Myeloid Cells/cytology
- Myeloid Cells/metabolism
- RNA, Messenger/genetics
- RNA-Binding Proteins/metabolism
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
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Affiliation(s)
- Leo D. Wang
- Joslin Diabetes Center, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Dana-Farber/Boston Children’s Center for Cancer and Blood Disorders, Boston, MA, USA
- Department of Medicine, Boston Children’s Hospital, Boston, MA, USA
| | - Tata Nageswara Rao
- Joslin Diabetes Center, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - R. Grant Rowe
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Dana-Farber/Boston Children’s Center for Cancer and Blood Disorders, Boston, MA, USA
- Department of Medicine, Boston Children’s Hospital, Boston, MA, USA
- Manton Center for Orphan Disease Research, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Phi T. Nguyen
- Joslin Diabetes Center, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Jessica L. Sullivan
- Joslin Diabetes Center, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Daniel S. Pearson
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Dana-Farber/Boston Children’s Center for Cancer and Blood Disorders, Boston, MA, USA
- Department of Medicine, Boston Children’s Hospital, Boston, MA, USA
- Manton Center for Orphan Disease Research, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
- Medical Scientist Training Program, Harvard Medical School, Boston, MA, USA
| | - Sergei Doulatov
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Dana-Farber/Boston Children’s Center for Cancer and Blood Disorders, Boston, MA, USA
- Department of Medicine, Boston Children’s Hospital, Boston, MA, USA
- Manton Center for Orphan Disease Research, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Linwei Wu
- Children’s Research Institute, Department of Pediatrics and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Organ Transplant Center, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - R. Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Hematology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Hao Zhu
- Children’s Research Institute, Department of Pediatrics and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Daniel J. DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - George Q. Daley
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Dana-Farber/Boston Children’s Center for Cancer and Blood Disorders, Boston, MA, USA
- Department of Medicine, Boston Children’s Hospital, Boston, MA, USA
- Manton Center for Orphan Disease Research, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Division of Hematology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Amy J. Wagers
- Joslin Diabetes Center, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
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22
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Laurenti E, Frelin C, Xie S, Ferrari R, Dunant CF, Zandi S, Neumann A, Plumb I, Doulatov S, Chen J, April C, Fan JB, Iscove N, Dick JE. CDK6 levels regulate quiescence exit in human hematopoietic stem cells. Cell Stem Cell 2015; 16:302-13. [PMID: 25704240 PMCID: PMC4359055 DOI: 10.1016/j.stem.2015.01.017] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/10/2015] [Accepted: 01/28/2015] [Indexed: 02/06/2023]
Abstract
Regulated blood production is achieved through the hierarchical organization of dormant hematopoietic stem cell (HSC) subsets that differ in self-renewal potential and division frequency, with long-term (LT)-HSCs dividing the least. The molecular mechanisms underlying this variability in HSC division kinetics are unknown. We report here that quiescence exit kinetics are differentially regulated within human HSC subsets through the expression level of CDK6. LT-HSCs lack CDK6 protein. Short-term (ST)-HSCs are also quiescent but contain high CDK6 protein levels that permit rapid cell cycle entry upon mitogenic stimulation. Enforced CDK6 expression in LT-HSCs shortens quiescence exit and confers competitive advantage without impacting function. Computational modeling suggests that this independent control of quiescence exit kinetics inherently limits LT-HSC divisions and preserves the HSC pool to ensure lifelong hematopoiesis. Thus, differential expression of CDK6 underlies heterogeneity in stem cell quiescence states that functionally regulates this highly regenerative system.
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Affiliation(s)
- Elisa Laurenti
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada.
| | - Catherine Frelin
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Stephanie Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Robin Ferrari
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Ecole Normale Supérieure de Cachan, Département de Biologie, Cachan, 94235, France
| | - Cyrille F Dunant
- Ecole Polytechnique Fédérale de Lausanne, LMC, Station 12, Lausanne, CH-1015, Switzerland
| | - Sasan Zandi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Andrea Neumann
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Ian Plumb
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Sergei Doulatov
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, Harvard Stem Cell Institute, Boston, MA 02115, USA
| | | | | | | | - Norman Iscove
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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23
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Doulatov S, Vo LT, Chou SS, Kim PG, Arora N, Li H, Hadland BK, Bernstein ID, Collins JJ, Zon LI, Daley GQ. Induction of multipotential hematopoietic progenitors from human pluripotent stem cells via respecification of lineage-restricted precursors. Cell Stem Cell 2014; 13:459-70. [PMID: 24094326 DOI: 10.1016/j.stem.2013.09.002] [Citation(s) in RCA: 204] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/20/2013] [Accepted: 09/06/2013] [Indexed: 01/19/2023]
Abstract
Human pluripotent stem cells (hPSCs) represent a promising source of patient-specific cells for disease modeling, drug screens, and cellular therapies. However, the inability to derive engraftable human hematopoietic stem and progenitor cells (HSPCs) has limited their characterization to in vitro assays. We report a strategy to respecify lineage-restricted CD34(+)CD45(+) myeloid precursors derived from hPSCs into multilineage progenitors that can be expanded in vitro and engrafted in vivo. HOXA9, ERG, and RORA conferred self-renewal and multilineage potential in vitro and maintained primitive CD34(+)CD38(-) cells. Screening cells via transplantation revealed that two additional factors, SOX4 and MYB, conferred engraftment. Progenitors specified with all five factors gave rise to reproducible short-term engraftment with myeloid and erythroid lineages. Erythroid precursors underwent hemoglobin switching in vivo, silencing embryonic and activating adult globin expression. Our combinatorial screening approach establishes a strategy for obtaining transcription-factor-mediated engraftment of blood progenitors from human pluripotent cells.
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Affiliation(s)
- Sergei Doulatov
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children's Hospital Boston and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
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24
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Vo L, Doulatov S, Macari ER, Chou SS, Gupta M, Godfrey M, McGrath K, Schlaeger T, Zon LI, Daley G. Engineering hematopoietic stem and progenitor cells from human pluripotent stem cells for modeling congenital anemias. Exp Hematol 2014. [DOI: 10.1016/j.exphem.2014.07.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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25
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Affiliation(s)
- Sergei Doulatov
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children's Hospital Boston and Dana Farber Cancer Institute; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Broad Institute; Harvard Stem Cell Institute; Boston, MA 02115, USA
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26
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Abstract
Despite its complexity, blood is probably the best understood developmental system, largely due to seminal experimentation in the mouse. Clinically, hematopoietic stem cell (HSC) transplantation represents the most widely deployed regenerative therapy, but human HSCs have only been characterized relatively recently. The discovery that immune-deficient mice could be engrafted with human cells provided a powerful approach for studying HSCs. We highlight 2 decades of studies focusing on isolation and molecular regulation of human HSCs, therapeutic applications, and early lineage commitment steps, and compare mouse and humanized models to identify both conserved and species-specific mechanisms that will aid future preclinical research.
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Affiliation(s)
- Sergei Doulatov
- Division of Stem Cell and Developmental Biology, Campbell Family Institute for Cancer Research/Ontario Cancer Institute, Toronto, ON M5G 1L7, Canada
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27
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Notta F, Doulatov S, Laurenti E, Poeppl A, Jurisica I, Dick JE. Isolation of single human hematopoietic stem cells capable of long-term multilineage engraftment. Science 2011; 333:218-21. [PMID: 21737740 DOI: 10.1126/science.1201219] [Citation(s) in RCA: 581] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Lifelong blood cell production is dependent on rare hematopoietic stem cells (HSCs) to perpetually replenish mature cells via a series of lineage-restricted intermediates. Investigating the molecular state of HSCs is contingent on the ability to purify HSCs away from transiently engrafting cells. We demonstrated that human HSCs remain infrequent, using current purification strategies based on Thy1 (CD90) expression. By tracking the expression of several adhesion molecules in HSC-enriched subsets, we revealed CD49f as a specific HSC marker. Single CD49f(+) cells were highly efficient in generating long-term multilineage grafts, and the loss of CD49f expression identified transiently engrafting multipotent progenitors (MPPs). The demarcation of human HSCs and MPPs will enable the investigation of the molecular determinants of HSCs, with a goal of developing stem cell-based therapeutics.
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Affiliation(s)
- Faiyaz Notta
- Division of Stem Cell and Developmental Biology, Campbell Family Institute for Cancer Research/Ontario Cancer Institute, Toronto, Ontario, Canada
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28
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Notta F, Mullighan CG, Y.Wang JC, Poeppl A, Doulatov S, Phillips LA, Ma J, Minden MD, Downing JR, Dick JE. Erratum: Evolution of human BCR–ABL1 lymphoblastic leukaemia-initiating cells. Nature 2011. [DOI: 10.1038/nature09877] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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29
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Bigley V, Haniffa M, Doulatov S, Wang XN, Dickinson R, McGovern N, Jardine L, Pagan S, Dimmick I, Chua I, Wallis J, Lordan J, Morgan C, Kumararatne DS, Doffinger R, van der Burg M, van Dongen J, Cant A, Dick JE, Hambleton S, Collin M. The human syndrome of dendritic cell, monocyte, B and NK lymphoid deficiency. ACTA ACUST UNITED AC 2011; 208:227-34. [PMID: 21242295 PMCID: PMC3039861 DOI: 10.1084/jem.20101459] [Citation(s) in RCA: 230] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Congenital or acquired cellular deficiencies in humans have the potential to reveal much about normal hematopoiesis and immune function. We show that a recently described syndrome of monocytopenia, B and NK lymphoid deficiency additionally includes the near absence of dendritic cells. Four subjects showed severe depletion of the peripheral blood HLA-DR(+) lineage(-) compartment, with virtually no CD123(+) or CD11c(+) dendritic cells (DCs) and very few CD14(+) or CD16(+) monocytes. The only remaining HLA-DR(+) lineage(-) cells were circulating CD34(+) progenitor cells. Dermal CD14(+) and CD1a(+) DC were also absent, consistent with their dependence on blood-derived precursors. In contrast, epidermal Langerhans cells and tissue macrophages were largely preserved. Combined loss of peripheral DCs, monocytes, and B and NK lymphocytes was mirrored in the bone marrow by complete absence of multilymphoid progenitors and depletion of granulocyte-macrophage progenitors. Depletion of the HLA-DR(+) peripheral blood compartment was associated with elevated serum fms-like tyrosine kinase ligand and reduced circulating CD4(+)CD25(hi)FoxP3(+) T cells, supporting a role for DC in T reg cell homeostasis.
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Affiliation(s)
- Venetia Bigley
- Institute of Cellular Medicine, Newcastle University, Framlington Place, Newcastle upon Tyne, England, UK
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31
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Doulatov S, Notta F, Rice KL, Howell L, Zelent A, Licht JD, Dick JE. PLZF is a regulator of homeostatic and cytokine-induced myeloid development. Genes Dev 2009; 23:2076-87. [PMID: 19723763 DOI: 10.1101/gad.1788109] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A major question in hematopoiesis is how the system maintains long-term homeostasis whereby the generation of large numbers of differentiated cells is balanced with the requirement for maintenance of progenitor pools, while remaining sufficiently flexible to respond to periods of perturbed cellular output during infection or stress. We focused on the development of the myeloid lineage and present evidence that promyelocytic leukemia zinc finger (PLZF) provides a novel function that is critical for both normal and stress-induced myelopoiesis. During homeostasis, PLZF restricts proliferation and differentiation of human cord blood-derived myeloid progenitors to maintain a balance between the progenitor and mature cell compartments. Analysis of PLZF promoter-binding sites revealed that it represses transcription factors involved in normal myeloid differentiation, including GFI-1, C/EBPalpha, and LEF-1, and induces negative regulators DUSP6 and ID2. Loss of ID2 relieves PLZF-mediated repression of differentiation identifying it as a functional target of PLZF in myelopoiesis. Furthermore, induction of ERK1/2 by myeloid cytokines, reflective of a stress response, leads to nuclear export and inactivation of PLZF, which augments mature cell production. Thus, negative regulators of differentiation can serve to maintain developmental systems in a primed state, so that their inactivation by extrinsic signals can induce proliferation and differentiation to rapidly satisfy increased demand for mature cells.
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Affiliation(s)
- Sergei Doulatov
- Division of Cell and Molecular Biology, University Health Network, Toronto, Ontario M5G 1L7, Canada
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32
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Guo H, Tse LV, Barbalat R, Sivaamnuaiphorn S, Xu M, Doulatov S, Miller JF. Diversity-generating retroelement homing regenerates target sequences for repeated rounds of codon rewriting and protein diversification. Mol Cell 2008; 31:813-23. [PMID: 18922465 DOI: 10.1016/j.molcel.2008.07.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Revised: 06/19/2008] [Accepted: 07/01/2008] [Indexed: 10/21/2022]
Abstract
Diversity-generating retroelements (DGRs) introduce vast amounts of sequence diversity into target genes. During mutagenic homing, adenine residues are converted to random nucleotides in a unidirectional, reverse transcriptase-dependent transposition process from a donor template repeat (TR) to a recipient variable repeat (VR). Using a Bordetella bacteriophage DGR as a model, we demonstrate that homing occurs through a TR-containing RNA intermediate and is RecA independent. Marker transfer studies show that cDNA integration at the 3' end of VR occurs within a (G/C)(14) element, and deletion analysis demonstrates that the reaction is independent of 5' end cDNA integration. cDNA integration at the 5' end of VR requires only short stretches of sequence homology. We propose that homing occurs through a unique target DNA-primed reverse transcription mechanism that precisely regenerates target sequences. This nonproliferative "copy and replace" mechanism enables repeated rounds of protein diversification and optimization of ligand-receptor interactions.
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Affiliation(s)
- Huatao Guo
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
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33
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McMahon SA, Miller JL, Lawton JA, Kerkow DE, Hodes A, Marti-Renom MA, Doulatov S, Narayanan E, Sali A, Miller JF, Ghosh P. The C-type lectin fold as an evolutionary solution for massive sequence variation. Nat Struct Mol Biol 2005; 12:886-92. [PMID: 16170324 DOI: 10.1038/nsmb992] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2005] [Accepted: 08/02/2005] [Indexed: 11/09/2022]
Abstract
Only few instances are known of protein folds that tolerate massive sequence variation for the sake of binding diversity. The most extensively characterized is the immunoglobulin fold. We now add to this the C-type lectin (CLec) fold, as found in the major tropism determinant (Mtd), a retroelement-encoded receptor-binding protein of Bordetella bacteriophage. Variation in Mtd, with its approximately 10(13) possible sequences, enables phage adaptation to Bordetella spp. Mtd is an intertwined, pyramid-shaped trimer, with variable residues organized by its CLec fold into discrete receptor-binding sites. The CLec fold provides a highly static scaffold for combinatorial display of variable residues, probably reflecting a different evolutionary solution for balancing diversity against stability from that in the immunoglobulin fold. Mtd variants are biased toward the receptor pertactin, and there is evidence that the CLec fold is used broadly for sequence variation by related retroelements.
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Affiliation(s)
- Stephen A McMahon
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California 92093, USA
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34
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Warner JK, Wang JCY, Takenaka K, Doulatov S, McKenzie JL, Harrington L, Dick JE. Direct evidence for cooperating genetic events in the leukemic transformation of normal human hematopoietic cells. Leukemia 2005; 19:1794-805. [PMID: 16094415 DOI: 10.1038/sj.leu.2403917] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Although genetic abnormalities associated with hematological malignancies are readily identified, the natural history of human leukemia cannot be observed because initiating and subsequent transforming events occur before clinical presentation. Furthermore, it has not been possible to study leukemogenesis in vitro as normal human cells do not spontaneously transform. Thus, the nature and sequence of genetic changes required to convert human hematopoietic cells into leukemia cells have never been directly examined. We have developed a system where the first step in the leukemogenic process is an engineered disruption of differentiation and self-renewal due to expression of the TLS-ERG oncogene, followed in some cases by overexpression of hTERT. In two of 13 experiments, transduced cells underwent step-wise transformation and immortalization through spontaneous acquisition of additional changes. The acquired karyotypic abnormalities and alterations including upregulation of Bmi-1 and telomerase all occur in acute myeloid leukemia (AML), establishing the relevance of this system. One resultant cell line studied in depth exhibits cellular properties characteristic of AML, notably a hierarchical organization initiated by leukemic stem cells that differentiate abnormally. These findings provide direct evidence for multiple cooperating events in human leukemogenesis, and provide a foundation for studying the genetic changes that occur during leukemic initiation and progression.
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Affiliation(s)
- J K Warner
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
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35
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Doulatov S, Hodes A, Dai L, Mandhana N, Liu M, Deora R, Simons RW, Zimmerly S, Miller JF. Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements. Nature 2004; 431:476-81. [PMID: 15386016 DOI: 10.1038/nature02833] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2004] [Accepted: 07/12/2004] [Indexed: 11/09/2022]
Abstract
Bordetella bacteriophages generate diversity in a gene that specifies host tropism. This microevolutionary adaptation is produced by a genetic element that combines the basic retroelement life cycle of transcription, reverse transcription and integration with site-directed, adenine-specific mutagenesis. Central to this process is a reverse transcriptase-mediated exchange between two repeats; one serving as a donor template (TR) and the other as a recipient of variable sequence information (VR). Here we describe the genetic basis for diversity generation. The directionality of information transfer is determined by a 21-base-pair sequence present at the 3' end of VR. On the basis of patterns of marker transfer in response to variant selective pressures, we propose that a TR reverse transcript is mutagenized, integrated into VR as a single non-coding strand, and then partially converted to the parental VR sequence. This allows the diversity-generating system to minimize variability to the subset of bases under selection. Using the Bordetella phage cassette as a signature, we have identified numerous related elements in diverse bacteria. These elements constitute a new family of retroelements with the potential to confer selective advantages to their host genomes.
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Affiliation(s)
- Sergei Doulatov
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
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