1
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Zhang X, Song B, Carlino MJ, Li G, Ferchen K, Chen M, Thompson EN, Kain BN, Schnell D, Thakkar K, Kouril M, Jin K, Hay SB, Sen S, Bernardicius D, Ma S, Bennett SN, Croteau J, Salvatori O, Lye MH, Gillen AE, Jordan CT, Singh H, Krause DS, Salomonis N, Grimes HL. An immunophenotype-coupled transcriptomic atlas of human hematopoietic progenitors. Nat Immunol 2024; 25:703-715. [PMID: 38514887 PMCID: PMC11003869 DOI: 10.1038/s41590-024-01782-4] [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: 11/08/2023] [Accepted: 02/07/2024] [Indexed: 03/23/2024]
Abstract
Analysis of the human hematopoietic progenitor compartment is being transformed by single-cell multimodal approaches. Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) enables coupled surface protein and transcriptome profiling, thereby revealing genomic programs underlying progenitor states. To perform CITE-seq systematically on primary human bone marrow cells, we used titrations with 266 CITE-seq antibodies (antibody-derived tags) and machine learning to optimize a panel of 132 antibodies. Multimodal analysis resolved >80 stem, progenitor, immune, stromal and transitional cells defined by distinctive surface markers and transcriptomes. This dataset enables flow cytometry solutions for in silico-predicted cell states and identifies dozens of cell surface markers consistently detected across donors spanning race and sex. Finally, aligning annotations from this atlas, we nominate normal marrow equivalents for acute myeloid leukemia stem cell populations that differ in clinical response. This atlas serves as an advanced digital resource for hematopoietic progenitor analyses in human health and disease.
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Affiliation(s)
- Xuan Zhang
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Baobao Song
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Immunology Graduate Program, University of Cincinnati, Cincinnati, OH, USA
| | - Maximillian J Carlino
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University, New Haven, CT, USA
| | - Guangyuan Li
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kyle Ferchen
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mi Chen
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University, New Haven, CT, USA
| | - Evrett N Thompson
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Bailee N Kain
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Dan Schnell
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kairavee Thakkar
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michal Kouril
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kang Jin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Stuart B Hay
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sidharth Sen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - David Bernardicius
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Siyuan Ma
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sierra N Bennett
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | | | | | - Austin E Gillen
- Division of Hematology, University of Colorado School of Medicine, Aurora, CO, USA
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
| | - Craig T Jordan
- Division of Hematology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Harinder Singh
- Departments of Immunology and Computational and Systems Biology, Center for Systems Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Diane S Krause
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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2
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Wu Q, Zhang J, Kumar S, Shen S, Kincaid M, Johnson CB, Zhang YS, Turcotte R, Alt C, Ito K, Homan S, Sherman BE, Shao TY, Slaughter A, Weinhaus B, Song B, Filippi MD, Grimes HL, Lin CP, Ito K, Way SS, Kofron JM, Lucas D. Resilient anatomy and local plasticity of naive and stress haematopoiesis. Nature 2024; 627:839-846. [PMID: 38509363 PMCID: PMC10972750 DOI: 10.1038/s41586-024-07186-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/26/2022] [Accepted: 02/09/2024] [Indexed: 03/22/2024]
Abstract
The bone marrow adjusts blood cell production to meet physiological demands in response to insults. The spatial organization of normal and stress responses are unknown owing to the lack of methods to visualize most steps of blood production. Here we develop strategies to image multipotent haematopoiesis, erythropoiesis and lymphopoiesis in mice. We combine these with imaging of myelopoiesis1 to define the anatomy of normal and stress haematopoiesis. In the steady state, across the skeleton, single stem cells and multipotent progenitors distribute through the marrow enriched near megakaryocytes. Lineage-committed progenitors are recruited to blood vessels, where they contribute to lineage-specific microanatomical structures composed of progenitors and immature cells, which function as the production sites for each major blood lineage. This overall anatomy is resilient to insults, as it was maintained after haemorrhage, systemic bacterial infection and granulocyte colony-stimulating factor (G-CSF) treatment, and during ageing. Production sites enable haematopoietic plasticity as they differentially and selectively modulate their numbers and output in response to insults. We found that stress responses are variable across the skeleton: the tibia and the sternum respond in opposite ways to G-CSF, and the skull does not increase erythropoiesis after haemorrhage. Our studies enable in situ analyses of haematopoiesis, define the anatomy of normal and stress responses, identify discrete microanatomical production sites that confer plasticity to haematopoiesis, and uncover unprecedented heterogeneity of stress responses across the skeleton.
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Affiliation(s)
- Qingqing Wu
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Jizhou Zhang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Sumit Kumar
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Siyu Shen
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Morgan Kincaid
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Courtney B Johnson
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yanan Sophia Zhang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Raphaël Turcotte
- Center for Systems Biology and Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Ruth L. and David S. Gottesman Institute for Stem Cell, Regenerative Medicine Research, Department of Cell Biology and Stem Cell Institute, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Clemens Alt
- Center for Systems Biology and Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Kyoko Ito
- Ruth L. and David S. Gottesman Institute for Stem Cell, Regenerative Medicine Research, Department of Cell Biology and Stem Cell Institute, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Shelli Homan
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Bryan E Sherman
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Tzu-Yu Shao
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Anastasiya Slaughter
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Benjamin Weinhaus
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Baobao Song
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Marie Dominique Filippi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - H Leighton Grimes
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Charles P Lin
- Advanced Microscopy Program, Center for Systems Biology and Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Keisuke Ito
- Ruth L. and David S. Gottesman Institute for Stem Cell, Regenerative Medicine Research, Department of Cell Biology and Stem Cell Institute, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sing Sing Way
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - J Matthew Kofron
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Daniel Lucas
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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3
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Venkatasubramanian M, Schwartz L, Ramachandra N, Bennett J, Subramanian KR, Chen X, Gordon-Mitchell S, Fromowitz A, Pradhan K, Shechter D, Sahu S, Heiser D, Scherle P, Chetal K, Kulkarni A, Myers KC, Weirauch MT, Grimes HL, Starczynowski DT, Verma A, Salomonis N. Broad de-regulated U2AF1 splicing is prognostic and augments leukemic transformation via protein arginine methyltransferase activation. bioRxiv 2024:2024.02.04.578798. [PMID: 38370617 PMCID: PMC10871255 DOI: 10.1101/2024.02.04.578798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The role of splicing dysregulation in cancer is underscored by splicing factor mutations; however, its impact in the absence of such rare mutations is poorly understood. To reveal complex patient subtypes and putative regulators of pathogenic splicing in Acute Myeloid Leukemia (AML), we developed a new approach called OncoSplice. Among diverse new subtypes, OncoSplice identified a biphasic poor prognosis signature that partially phenocopies U2AF1-mutant splicing, impacting thousands of genes in over 40% of adult and pediatric AML cases. U2AF1-like splicing co-opted a healthy circadian splicing program, was stable over time and induced a leukemia stem cell (LSC) program. Pharmacological inhibition of the implicated U2AF1-like splicing regulator, PRMT5, rescued leukemia mis-splicing and inhibited leukemic cell growth. Genetic deletion of IRAK4, a common target of U2AF1-like and PRMT5 treated cells, blocked leukemia development in xenograft models and induced differentiation. These analyses reveal a new prognostic alternative-splicing mechanism in malignancy, independent of splicing-factor mutations.
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Affiliation(s)
- Meenakshi Venkatasubramanian
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH
| | - Leya Schwartz
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Nandini Ramachandra
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Joshua Bennett
- Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Krithika R. Subramanian
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Xiaoting Chen
- Divisions of Human Genetics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Shanisha Gordon-Mitchell
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Ariel Fromowitz
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Kith Pradhan
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - David Shechter
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Srabani Sahu
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Diane Heiser
- Prelude Therapeutics Incorporated, Wilmington, DE
| | | | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Aishwarya Kulkarni
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH
| | - Kasiani C. Myers
- Division of Bone Marrow Transplantation and Immune Deficiency, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Matthew T. Weirauch
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Divisions of Human Genetics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - H. Leighton Grimes
- Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Daniel T. Starczynowski
- Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Division of Bone Marrow Transplantation and Immune Deficiency, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Amit Verma
- Blood Cancer Institute, Albert Einstein College of Medicine, Montefiore Medical Center, The Bronx, NY
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
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4
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Li G, Mahajan S, Ma S, Jeffery ED, Zhang X, Bhattacharjee A, Venkatasubramanian M, Weirauch MT, Miraldi ER, Grimes HL, Sheynkman GM, Tilburgs T, Salomonis N. Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. Sci Transl Med 2024; 16:eade2886. [PMID: 38232136 DOI: 10.1126/scitranslmed.ade2886] [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] [Received: 08/05/2022] [Accepted: 12/13/2023] [Indexed: 01/19/2024]
Abstract
Immunotherapy has emerged as a crucial strategy to combat cancer by "reprogramming" a patient's own immune system. Although immunotherapy is typically reserved for patients with a high mutational burden, neoantigens produced from posttranscriptional regulation may provide an untapped reservoir of common immunogenic targets for new targeted therapies. To comprehensively define tumor-specific and likely immunogenic neoantigens from patient RNA-Seq, we developed Splicing Neo Antigen Finder (SNAF), an easy-to-use and open-source computational workflow to predict splicing-derived immunogenic MHC-bound peptides (T cell antigen) and unannotated transmembrane proteins with altered extracellular epitopes (B cell antigen). This workflow uses a highly accurate deep learning strategy for immunogenicity prediction (DeepImmuno) in conjunction with new algorithms to rank the tumor specificity of neoantigens (BayesTS) and to predict regulators of mis-splicing (RNA-SPRINT). T cell antigens from SNAF were frequently evidenced as HLA-presented peptides from mass spectrometry (MS) and predict response to immunotherapy in melanoma. Splicing neoantigen burden was attributed to coordinated splicing factor dysregulation. Shared splicing neoantigens were found in up to 90% of patients with melanoma, correlated to overall survival in multiple cancer cohorts, induced T cell reactivity, and were characterized by distinct cells of origin and amino acid preferences. In addition to T cell neoantigens, our B cell focused pipeline (SNAF-B) identified a new class of tumor-specific extracellular neoepitopes, which we termed ExNeoEpitopes. ExNeoEpitope full-length mRNA predictions were tumor specific and were validated using long-read isoform sequencing and in vitro transmembrane localization assays. Therefore, our systematic identification of splicing neoantigens revealed potential shared targets for therapy in heterogeneous cancers.
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Affiliation(s)
- Guangyuan Li
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Shweta Mahajan
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Siyuan Ma
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Erin D Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Xuan Zhang
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Anukana Bhattacharjee
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Meenakshi Venkatasubramanian
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Computer Science, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Matthew T Weirauch
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
- Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Emily R Miraldi
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Tamara Tilburgs
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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5
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Govindarajah V, Sakabe M, Good S, Solomon M, Arasu A, Chen N, Zhang X, Grimes HL, Kendler A, Xin M, Reynaud D. Gestational diabetes in mice induces hematopoietic memory that affects the long-term health of the offspring. J Clin Invest 2024; 134:e169730. [PMID: 37988162 PMCID: PMC10786695 DOI: 10.1172/jci169730] [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: 03/03/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023] Open
Abstract
Gestational diabetes is a common medical complication of pregnancy that is associated with adverse perinatal outcomes and an increased risk of metabolic diseases and atherosclerosis in adult offspring. The mechanisms responsible for this delayed pathological transmission remain unknown. In mouse models, we found that the development of atherosclerosis in adult offspring born to diabetic pregnancy can be in part linked to hematopoietic alterations. Although they do not show any gross metabolic disruptions, the adult offspring maintain hematopoietic features associated with diabetes, indicating the acquisition of a lasting diabetic hematopoietic memory. We show that the induction of this hematopoietic memory during gestation relies on the activity of the advanced glycation end product receptor (AGER) and the nucleotide binding and oligomerization domain-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome, which lead to increased placental inflammation. In adult offspring, we find that this memory is associated with DNA methyltransferase 1 (DNMT1) upregulation and epigenetic changes in hematopoietic progenitors. Together, our results demonstrate that the hematopoietic system can acquire a lasting memory of gestational diabetes and that this memory constitutes a pathway connecting gestational health to adult pathologies.
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Affiliation(s)
| | | | - Samantha Good
- Division of Experimental Hematology and Cancer Biology and
| | | | - Ashok Arasu
- Division of Experimental Hematology and Cancer Biology and
| | - Nong Chen
- Division of Experimental Hematology and Cancer Biology and
| | - Xuan Zhang
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, Ohio, USA
| | - H. Leighton Grimes
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center (CCHMC), Cincinnati, Ohio, USA
- Department of Pediatrics and
| | - Ady Kendler
- Department of Pathology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Mei Xin
- Division of Experimental Hematology and Cancer Biology and
- Department of Pediatrics and
| | - Damien Reynaud
- Division of Experimental Hematology and Cancer Biology and
- Department of Pediatrics and
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6
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Solomon M, Song B, Govindarajah V, Good S, Arasu A, Hinton EB, Thakkar K, Bartram J, Filippi MD, Cancelas JA, Salomonis N, Grimes HL, Reynaud D. Slow cycling and durable Flt3+ progenitors contribute to hematopoiesis under native conditions. J Exp Med 2024; 221:e20231035. [PMID: 37910046 PMCID: PMC10620607 DOI: 10.1084/jem.20231035] [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: 06/16/2023] [Revised: 09/18/2023] [Accepted: 10/13/2023] [Indexed: 11/03/2023] Open
Abstract
The dynamics of the hematopoietic flux responsible for blood cell production in native conditions remains a matter of debate. Using CITE-seq analyses, we uncovered a distinct progenitor population that displays a cell cycle gene signature similar to the one found in quiescent hematopoietic stem cells. We further determined that the CD62L marker can be used to phenotypically enrich this population in the Flt3+ multipotent progenitor (MPP4) compartment. Functional in vitro and in vivo analyses validated the heterogeneity of the MPP4 compartment and established the quiescent/slow-cycling properties of the CD62L- MPP4 cells. Furthermore, studies under native conditions revealed a novel hierarchical organization of the MPP compartments in which quiescent/slow-cycling MPP4 cells sustain a prolonged hematopoietic activity at steady-state while giving rise to other lineage-biased MPP populations. Altogether, our data characterize a durable and productive quiescent/slow-cycling hematopoietic intermediary within the MPP4 compartment and highlight early paths of progenitor differentiation during unperturbed hematopoiesis.
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Affiliation(s)
- Michael Solomon
- Division of Experimental Hematology and Cancer Biology, Stem Cell Program, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Baobao Song
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Immunology Graduate Program, University of Cincinnati, Cincinnati, OH, USA
| | - Vinothini Govindarajah
- Division of Experimental Hematology and Cancer Biology, Stem Cell Program, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Samantha Good
- Division of Experimental Hematology and Cancer Biology, Stem Cell Program, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Ashok Arasu
- Division of Experimental Hematology and Cancer Biology, Stem Cell Program, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - E. Broderick Hinton
- Division of Experimental Hematology and Cancer Biology, Stem Cell Program, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Kairavee Thakkar
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - James Bartram
- Division of Experimental Hematology and Cancer Biology, Stem Cell Program, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Marie-Dominique Filippi
- Division of Experimental Hematology and Cancer Biology, Stem Cell Program, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jose A. Cancelas
- Division of Experimental Hematology and Cancer Biology, Stem Cell Program, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Hoxworth Blood Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - H. Leighton Grimes
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Damien Reynaud
- Division of Experimental Hematology and Cancer Biology, Stem Cell Program, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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7
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Ozga M, Nicolet D, Mrózek K, Yilmaz AS, Kohlschmidt J, Larkin KT, Blachly JS, Oakes CC, Buss J, Walker CJ, Orwick S, Jurinovic V, Rothenberg-Thurley M, Dufour A, Schneider S, Sauerland MC, Görlich D, Krug U, Berdel WE, Woermann BJ, Hiddemann W, Braess J, Subklewe M, Spiekermann K, Carroll AJ, Blum WG, Powell BL, Kolitz JE, Moore JO, Mayer RJ, Larson RA, Uy GL, Stock W, Metzeler KH, Grimes HL, Byrd JC, Salomonis N, Herold T, Mims AS, Eisfeld AK. Sex-associated differences in frequencies and prognostic impact of recurrent genetic alterations in adult acute myeloid leukemia (Alliance, AMLCG). Leukemia 2024; 38:45-57. [PMID: 38017103 PMCID: PMC10776397 DOI: 10.1038/s41375-023-02068-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 06/24/2023] [Revised: 09/25/2023] [Accepted: 10/09/2023] [Indexed: 11/30/2023]
Abstract
Clinical outcome of patients with acute myeloid leukemia (AML) is associated with demographic and genetic features. Although the associations of acquired genetic alterations with patients' sex have been recently analyzed, their impact on outcome of female and male patients has not yet been comprehensively assessed. We performed mutational profiling, cytogenetic and outcome analyses in 1726 adults with AML (749 female and 977 male) treated on frontline Alliance for Clinical Trials in Oncology protocols. A validation cohort comprised 465 women and 489 men treated on frontline protocols of the German AML Cooperative Group. Compared with men, women more often had normal karyotype, FLT3-ITD, DNMT3A, NPM1 and WT1 mutations and less often complex karyotype, ASXL1, SRSF2, U2AF1, RUNX1, or KIT mutations. More women were in the 2022 European LeukemiaNet intermediate-risk group and more men in adverse-risk group. We found sex differences in co-occurring mutation patterns and prognostic impact of select genetic alterations. The mutation-associated splicing events and gene-expression profiles also differed between sexes. In patients aged <60 years, SF3B1 mutations were male-specific adverse outcome prognosticators. We conclude that sex differences in AML-associated genetic alterations and mutation-specific differential splicing events highlight the importance of patients' sex in analyses of AML biology and prognostication.
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Affiliation(s)
- Michael Ozga
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Deedra Nicolet
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
- Alliance Statistics and Data Management Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Krzysztof Mrózek
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA.
| | - Ayse S Yilmaz
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
| | - Jessica Kohlschmidt
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
- Alliance Statistics and Data Management Center, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Karilyn T Larkin
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
| | - James S Blachly
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
| | - Christopher C Oakes
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
| | - Jill Buss
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
| | - Christopher J Walker
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
| | - Shelley Orwick
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Vindi Jurinovic
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Maja Rothenberg-Thurley
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Annika Dufour
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - Stephanie Schneider
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- Institute of Human Genetics, University Hospital, LMU Munich, Munich, Germany
| | | | - Dennis Görlich
- Institute of Biostatistics and Clinical Research, University of Münster, Münster, Germany
| | - Utz Krug
- Department of Medicine 3, Klinikum Leverkusen, Leverkusen, Germany
| | - Wolfgang E Berdel
- Department of Medicine, Hematology and Oncology, University of Münster, Münster, Germany
| | | | - Wolfgang Hiddemann
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan Braess
- Department of Oncology and Hematology, Hospital Barmherzige Brüder, Regensburg, Germany
| | - Marion Subklewe
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Karsten Spiekermann
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Bayard L Powell
- Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Jonathan E Kolitz
- Monter Cancer Center, Hofstra Northwell School of Medicine, Lake Success, NY, USA
| | - Joseph O Moore
- Duke Cancer Institute, Duke University Health System, Durham, NC, USA
| | - Robert J Mayer
- Department of Medical Oncology, Dana-Farber/Partners CancerCare, Boston, MA, USA
| | | | - Geoffrey L Uy
- Division of Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Wendy Stock
- University of Chicago Medical Center, Chicago, IL, USA
| | - Klaus H Metzeler
- Department of Hematology, Cellular Therapy, and Hemostaseology, Leipzig University Hospital, Leipzig, Germany
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital, University of Cincinnati, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - John C Byrd
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital, University of Cincinnati, Cincinnati, OH, USA
| | - Tobias Herold
- Laboratory for Leukemia Diagnostics, Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Alice S Mims
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA
| | - Ann-Kathrin Eisfeld
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center, Clara D. Bloomfield Center for Leukemia Outcomes Research, Columbus, OH, USA.
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Zhang X, Grimes HL. Improved detection of measurable residual disease in acute myeloid leukemia. Sci Adv 2023; 9:eadk2533. [PMID: 37729410 PMCID: PMC10511198 DOI: 10.1126/sciadv.adk2533] [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] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
A novel multiplex single-cell genomic and immunophenotypic strategy leverages the sensitivity of MRD detection and distinguishes leukemic and preleukemic subpopulations.
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Affiliation(s)
- Xuan Zhang
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - H. Leighton Grimes
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
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9
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Kesarwani M, Kincaid Z, Azhar M, Menke J, Schwieterman J, Ansari S, Reaves A, Deininger ME, Levine R, Grimes HL, Azam M. MAPK-negative feedback regulation confers dependence to JAK2 V617F signaling. Leukemia 2023; 37:1686-1697. [PMID: 37430058 PMCID: PMC10976185 DOI: 10.1038/s41375-023-01959-0] [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: 02/05/2023] [Revised: 06/11/2023] [Accepted: 06/27/2023] [Indexed: 07/12/2023]
Abstract
Despite significant advances in developing selective JAK2 inhibitors, JAK2 kinase inhibitor (TKI) therapy is ineffective in suppressing the disease. Reactivation of compensatory MEK-ERK and PI3K survival pathways sustained by inflammatory cytokine signaling causes treatment failure. Concomitant inhibition of MAPK pathway and JAK2 signaling showed improved in vivo efficacy compared to JAK2 inhibition alone but lacked clonal selectivity. We hypothesized that cytokine signaling in JAK2V617F induced MPNs increases the apoptotic threshold that causes TKI persistence or refractoriness. Here, we show that JAK2V617F and cytokine signaling converge to induce MAPK negative regulator, DUSP1. Enhanced DUSP1 expression blocks p38 mediated p53 stabilization. Deletion of Dusp1 increases p53 levels in the context of JAK2V617F signaling that causes synthetic lethality to Jak2V617F expressing cells. However, inhibition of Dusp1 by a small molecule inhibitor (BCI) failed to impart Jak2V617F clonal selectivity due to pErk1/2 rebound caused by off-target inhibition of Dusp6. Ectopic expression of Dusp6 and BCI treatment restored clonal selectively and eradicated the Jak2V617F cells. Our study shows that inflammatory cytokines and JAK2V617F signaling converge to induce DUSP1, which downregulates p53 and establishes a higher apoptotic threshold. These data suggest that selectively targeting DUSP1 may provide a curative response in JAK2V617F-driven MPN.
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Affiliation(s)
- Meenu Kesarwani
- Division of Pathology, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Zachary Kincaid
- Division of Pathology, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Mohammad Azhar
- Division of Pathology, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Jacob Menke
- Division of Pathology, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | | | - Sekhu Ansari
- Division of Pathology, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Angela Reaves
- Division of Pathology, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Michael E Deininger
- Versiti Blood Research Institute and Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ross Levine
- Center for Hematologic Malignancies, and Molecular Cancer Medicine Service, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Mohammad Azam
- Division of Pathology, Cincinnati Children's Hospital, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, OH, USA.
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10
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Thompson EN, Carlino MJ, Scanlon VM, Grimes HL, Krause DS. Assay optimization for the objective quantification of human multilineage colony-forming units. Exp Hematol 2023; 124:36-44.e3. [PMID: 37271449 PMCID: PMC10527702 DOI: 10.1016/j.exphem.2023.05.007] [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: 02/24/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/06/2023]
Abstract
Colony-forming unit (CFU) assays are a powerful tool in hematopoietic research because they allow researchers to functionally test the lineage potential of individual stem and progenitor cells. Assaying for lineage potential is important for determining and validating the identity of progenitor populations isolated by methods such as fluorescence-activated cell sorting (FACS). However, current methods for CFU assays are limited in their ability to robustly assay multipotent progenitors with the ability to differentiate down the myeloid, erythroid, and megakaryocytic lineages because of the lack of specific growth factors necessary for certain lineage outputs. In addition, manual counting of colony types is subjective resulting in user to user variability in assessments of cell types based on colony and cell morphologies. We demonstrate that the addition of granulocyte colony-stimulating factor (G-CSF), macrophage (M)-CSF, and granulocyte-macrophage (GM)-CSF into a collagen-based MegaCult medium containing IL-3, IL-6, SCF, EPO, and TPO allows for the differentiation of common myeloid progenitors into expected proportions of colonies containing granulocytic (G), monocytic (M), erythroid (E), and megakaryocytic (Mk) cells. Additionally, we demonstrate an objective method using in situ immunofluorescence (IF) with anti-CD66b, anti-CD14, anti-CD235a, and anti-CD41 to detect G, M, E, and Mk cells, respectively. IF stained colonies can be analyzed individually at a microscope or using high-throughput microscopy. Thus, our improvements to the culture conditions and method for assay readout increase the accuracy, reproducibility, and throughput of the myeloid CFU assay.
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Affiliation(s)
- Evrett N Thompson
- Department of Cell Biology, Yale School of Medicine, New Haven, CT; Yale Stem Cell Center, New Haven, CT
| | - Maximillian J Carlino
- Yale Stem Cell Center, New Haven, CT; Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Vanessa M Scanlon
- Yale Stem Cell Center, New Haven, CT; Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT; Center for Regenerative Medicine and Skeletal Development, University of Connecticut Health, Farmington, CT
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Diane S Krause
- Department of Cell Biology, Yale School of Medicine, New Haven, CT; Yale Stem Cell Center, New Haven, CT; Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT; Department of Pathology, Yale School of Medicine, New Haven, CT.
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11
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Basu J, Olsson A, Ferchen K, Titerina EK, Chetal K, Nicolas E, Czyzewicz P, Levchenko D, Ge L, Hua X, Grimes HL, Salomonis N, Kappes DJ. ThPOK is a critical multifaceted regulator of myeloid lineage development. Nat Immunol 2023; 24:1295-1307. [PMID: 37474652 PMCID: PMC10792516 DOI: 10.1038/s41590-023-01549-3] [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: 01/06/2021] [Accepted: 06/06/2023] [Indexed: 07/22/2023]
Abstract
The transcription factor ThPOK (encoded by Zbtb7b) is well known for its role as a master regulator of CD4 lineage commitment in the thymus. Here, we report an unexpected and critical role of ThPOK as a multifaceted regulator of myeloid lineage commitment, differentiation and maturation. Using reporter and knockout mouse models combined with single-cell RNA-sequencing, progenitor transfer and colony assays, we show that ThPOK controls monocyte-dendritic cell versus granulocyte lineage production during homeostatic differentiation, and serves as a brake for neutrophil maturation in granulocyte lineage-specified cells through transcriptional regulation of lineage-specific transcription factors and RNA via altered messenger RNA splicing to reprogram intron retention.
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Affiliation(s)
- Jayati Basu
- Fox Chase Cancer Center, Philadelphia, PA, USA.
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Andre Olsson
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Kyle Ferchen
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Elizaveta K Titerina
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kashish Chetal
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | | | | | | | - Lu Ge
- Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Xiang Hua
- Fox Chase Cancer Center, Philadelphia, PA, USA
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Nathan Salomonis
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.
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12
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Ferchen K, Salomonis N, Grimes HL. pyInfinityFlow: Optimized imputation and analysis of high-dimensional Flow Cytometry data for millions of cells. Bioinformatics 2023; 39:7142555. [PMID: 37097893 PMCID: PMC10166583 DOI: 10.1093/bioinformatics/btad287] [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] [Received: 11/23/2022] [Revised: 03/09/2023] [Accepted: 04/24/2023] [Indexed: 04/26/2023] Open
Abstract
MOTIVATION While conventional flow cytometry is limited to dozens of markers, new experimental and computational strategies, such as Infinity Flow, allow for the generation and imputation of hundreds of cell surface protein markers in millions of cells. Here, we describe an end-to-end analysis workflow for Infinity Flow data in Python. RESULTS pyInfinityFlow enables the efficient analysis of millions of cells, without down-sampling, through direct integration with well-established Python packages for single-cell genomics analysis. pyInfinityFlow accurately identifies both common and extremely rare cell populations which are challenging to define from single-cell genomics studies alone. We demonstrate that this workflow can nominate novel markers to design new flow cytometry gating strategies for predicted cell populations. pyInfinityFlow can be extended to diverse cell discovery analyses with flexibility to adapt to diverse Infinity Flow experimental designs. AVAILABILITY pyInfinityFlow is freely available in GitHub (https://github.com/KyleFerchen/pyInfinityFlow) and on PyPI (https://pypi.org/project/pyInfinityFlow/). Package documentation with tutorials on a test dataset is available by Read the Docs (pyinfinityflow.readthedocs.io). The scripts and data for reproducing the results are available at (https://github.com/KyleFerchen/pyInfinityFlow/tree/main/analysis_scripts), along with the raw flow cytometry input data. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kyle Ferchen
- University of Cincinnati, Cancer and Cellular Biology, Cincinnati, OH
- Cincinnati Children's Hospital Medical Center, Immunobiology, Cincinnati, OH
| | - Nathan Salomonis
- Cincinnati Children's Hospital Medical Center, Biomedical Informatics, Cincinnati, OH
- University of Cincinnati, Department of Pediatrics
| | - H Leighton Grimes
- Cincinnati Children's Hospital Medical Center, Immunobiology, Cincinnati, OH
- University of Cincinnati, Department of Pediatrics
- Cincinnati Children's Hospital Medical Center, Experimental Hematology and Cancer Biology, Cincinnati, OH
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13
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Li G, Song B, Singh H, Surya Prasath VB, Leighton Grimes H, Salomonis N. Decision level integration of unimodal and multimodal single cell data with scTriangulate. Nat Commun 2023; 14:406. [PMID: 36697445 PMCID: PMC9876931 DOI: 10.1038/s41467-023-36016-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
Decisively delineating cell identities from uni- and multimodal single-cell datasets is complicated by diverse modalities, clustering methods, and reference atlases. We describe scTriangulate, a computational framework to mix-and-match multiple clustering results, modalities, associated algorithms, and resolutions to achieve an optimal solution. Rather than ensemble approaches which select the "consensus", scTriangulate picks the most stable solution through coalitional iteration. When evaluated on diverse multimodal technologies, scTriangulate outperforms alternative approaches to identify high-confidence cell-populations and modality-specific subtypes. Unlike existing integration strategies that rely on modality-specific joint embedding or geometric graphs, scTriangulate makes no assumption about the distributions of raw underlying values. As a result, this approach can solve unprecedented integration challenges, including the ability to automate reference cell-atlas construction, resolve clonal architecture within molecularly defined cell-populations and subdivide clusters to discover splicing-defined disease subtypes. scTriangulate is a flexible strategy for unified integration of single-cell or multimodal clustering solutions, from nearly unlimited sources.
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Affiliation(s)
- Guangyuan Li
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Baobao Song
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Immunology Graduate Program, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Harinder Singh
- Center for Systems Immunology and the Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - V B Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA.,Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA.,Department of Computer Science, University of Cincinnati, Cincinnati, OH 45221, USA
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Immunology Graduate Program, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA. .,Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA.
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA. .,Immunology Graduate Program, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA. .,Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA. .,Department of Computer Science, University of Cincinnati, Cincinnati, OH 45221, USA.
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14
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Romano L, Seu KG, Papoin J, Muench DE, Konstantinidis D, Olsson A, Schlum K, Chetal K, Chasis JA, Mohandas N, Barnes BJ, Zheng Y, Grimes HL, Salomonis N, Blanc L, Kalfa TA. Erythroblastic islands foster granulopoiesis in parallel to terminal erythropoiesis. Blood 2022; 140:1621-1634. [PMID: 35862735 PMCID: PMC9707396 DOI: 10.1182/blood.2022015724] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 01/28/2022] [Accepted: 06/26/2022] [Indexed: 12/14/2022] Open
Abstract
The erythroblastic island (EBI), composed of a central macrophage surrounded by maturing erythroblasts, is the erythroid precursor niche. Despite numerous studies, its precise composition is still unclear. Using multispectral imaging flow cytometry, in vitro island reconstitution, and single-cell RNA sequencing of adult mouse bone marrow (BM) EBI-component cells enriched by gradient sedimentation, we present evidence that the CD11b+ cells present in the EBIs are neutrophil precursors specifically associated with BM EBI macrophages, indicating that erythro-(myelo)-blastic islands are a site for terminal granulopoiesis and erythropoiesis. We further demonstrate that the balance between these dominant and terminal differentiation programs is dynamically regulated within this BM niche by pathophysiological states that favor granulopoiesis during anemia of inflammation and favor erythropoiesis after erythropoietin stimulation. Finally, by molecular profiling, we reveal the heterogeneity of EBI macrophages by cellular indexing of transcriptome and epitope sequencing of mouse BM EBIs at baseline and after erythropoietin stimulation in vivo and provide a searchable online viewer of these data characterizing the macrophage subsets serving as hematopoietic niches. Taken together, our findings demonstrate that EBIs serve a dual role as niches for terminal erythropoiesis and granulopoiesis and the central macrophages adapt to optimize production of red blood cells or neutrophils.
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Affiliation(s)
- Laurel Romano
- Division of Hematology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Katie G. Seu
- Division of Hematology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Julien Papoin
- Laboratory of Developmental Erythropoiesis, Les Nelkin Memorial Laboratory of Pediatric Oncology, Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY
| | - David E. Muench
- Immunology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, San Diego, CA
| | | | | | - Katrina Schlum
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Kashish Chetal
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA
| | - Joel Anne Chasis
- Life Sciences Division, University of California, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Narla Mohandas
- Red Cell Physiology Laboratory, New York Blood Center, New York, NY
| | - Betsy J. Barnes
- Department of Molecular Medicine and Pediatrics, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY
- Center for Autoimmune Musculoskeletal and Hematopoietic Diseases, Feinstein Institutes for Medical Research, Manhasset, NY
| | - Yi Zheng
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - H. Leighton Grimes
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Lionel Blanc
- Laboratory of Developmental Erythropoiesis, Les Nelkin Memorial Laboratory of Pediatric Oncology, Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY
- Department of Molecular Medicine and Pediatrics, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY
| | - Theodosia A. Kalfa
- Division of Hematology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
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15
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Leighton Grimes H, Ferchen K, Salomonis N, Song B, Zhang X. 2007 – IDENTIFICATION AND ISOLATION OF HEMATOPOIETIC STEM CELLS AND PROGENITORS WITH DISCRETE DEVELOPMENTAL GENE EXPRESSION PROGRAMS. Exp Hematol 2022. [DOI: 10.1016/j.exphem.2022.07.039] [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: 11/26/2022]
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16
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Bono C, Guerrero P, Jordán-Pla A, Erades A, Salomonis N, Grimes HL, Gil ML, Yáñez A. GM-CSF Programs Hematopoietic Stem and Progenitor Cells During Candida albicans Vaccination for Protection Against Reinfection. Front Immunol 2021; 12:790309. [PMID: 34975887 PMCID: PMC8715000 DOI: 10.3389/fimmu.2021.790309] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/25/2021] [Indexed: 11/19/2022] Open
Abstract
More mechanistic studies are needed to reveal the hidden details of in vivo-induced trained immunity. Here, using a Candida albicans live vaccine mouse model we show that vaccination protects mice against a secondary infection and increases the number of bone marrow, and especially, splenic trained monocytes. Moreover, vaccination expands and reprograms hematopoietic stem and progenitor cells (HSPCs) early during infection and mobilize them transiently to the spleen to produce trained macrophages. Trained HSPCs are not only primed for myeloid cell production but also reprogramed to produce a greater amount of proinflammatory cytokines in response to a second challenge. Additionally, their adoptive transfer is sufficient to protect mice against reinfection. Mechanistically, autocrine GM-CSF activation of HSPCs is responsible for the trained phenotype and essential for the vaccine-induced protection. Our findings reveal a fundamental role for HSPCs in the trained immune protective response, opening new avenues for disease prevention and treatment.
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Affiliation(s)
- Cristina Bono
- Departamento de Microbiología y Ecología, Facultad de Ciencias Biológicas, Instituto de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
| | - Paula Guerrero
- Departamento de Microbiología y Ecología, Facultad de Ciencias Biológicas, Instituto de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
| | - Antonio Jordán-Pla
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Facultad de Ciencias Biológicas, Instituto de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
| | - Ana Erades
- Departamento de Microbiología y Ecología, Facultad de Ciencias Biológicas, Instituto de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - H. Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology and Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - M. Luisa Gil
- Departamento de Microbiología y Ecología, Facultad de Ciencias Biológicas, Instituto de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
| | - Alberto Yáñez
- Departamento de Microbiología y Ecología, Facultad de Ciencias Biológicas, Instituto de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
- *Correspondence: Alberto Yáñez,
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17
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Zhang X, Grimes HL. Why Single-Cell Sequencing Has Promise in MDS. Front Oncol 2021; 11:769753. [PMID: 34926276 PMCID: PMC8675176 DOI: 10.3389/fonc.2021.769753] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/16/2021] [Indexed: 11/22/2022] Open
Abstract
Myelodysplastic syndromes (MDS) are a heterogeneous group of diseases characterized by ineffective hematopoiesis. The risk of MDS is associated with aging and the accumulation of somatic mutations in hematopoietic stem cells and progenitors (HSPC). While advances in DNA sequencing in the past decade unveiled clonal selection driven by mutations in MDS, it is unclear at which stage the HSPCs are trapped or what prevents mature cells output. Single-cell-sequencing techniques in recent years have revolutionized our understanding of normal hematopoiesis by identifying the transitional cell states between classical hematopoietic hierarchy stages, and most importantly the biological activities behind cell differentiation and lineage commitment. Emerging studies have adapted these powerful tools to investigate normal hematopoiesis as well as the clonal heterogeneity in myeloid malignancies and provide a progressive description of disease pathogenesis. This review summarizes the potential of growing single-cell-sequencing techniques, the evolving efforts to elucidate hematopoiesis in physiological conditions and MDS at single-cell resolution, and discuss how they may fill the gaps in our current understanding of MDS biology.
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Affiliation(s)
- Xuan Zhang
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - H. Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, United States
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18
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Steele H, Song B, Willicut A, Grimes HL, Herro R. Isolation of primary immune cells from fibrotic skin, esophageal, and gut tissue. J Immunol Methods 2021; 497:113107. [PMID: 34352237 DOI: 10.1016/j.jim.2021.113107] [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: 03/09/2021] [Revised: 07/12/2021] [Accepted: 07/24/2021] [Indexed: 11/15/2022]
Abstract
Understanding the interplay between immune and structural cells is important for studying fibrosis and inflammation; however, primary immune cell isolation from organs that are typically enriched in stromal cells, like the lung, esophagus, or gut, proves to be an ongoing challenge. In fibrotic conditions, this challenge becomes even greater as infiltrating cells become trapped in the robust extracellular matrix (ECM). This protocol details a method to isolate cells at high yield from stroma-rich organs that can be used for further analyses via flow cytometry, stimulation, or culturing. Validation of this method is confirmed by flow cytometry data assessing immune cell populations of interest. This protocol can be completed in approximately 5-6 h.
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Affiliation(s)
- Hope Steele
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Immunology Graduate Program, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Baobao Song
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Immunology Graduate Program, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ashley Willicut
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Rana Herro
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.
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19
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Song B(A, Grimes HL, Salomonis N, Ferchen K, Zhang X. 3127 – COMPREHENSIVE ATLAS OF MIXED-LINEAGE STATES. Exp Hematol 2021. [DOI: 10.1016/j.exphem.2021.12.344] [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: 11/28/2022]
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20
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Basu J, Reis BS, Peri S, Zha J, Hua X, Ge L, Ferchen K, Nicolas E, Czyzewicz P, Cai KQ, Tan Y, Fuxman Bass JI, Walhout AJM, Grimes HL, Grivennikov SI, Mucida D, Kappes DJ. Essential role of a ThPOK autoregulatory loop in the maintenance of mature CD4 + T cell identity and function. Nat Immunol 2021; 22:969-982. [PMID: 34312548 DOI: 10.1038/s41590-021-00980-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/21/2021] [Indexed: 12/13/2022]
Abstract
The transcription factor ThPOK (encoded by the Zbtb7b gene) controls homeostasis and differentiation of mature helper T cells, while opposing their differentiation to CD4+ intraepithelial lymphocytes (IELs) in the intestinal mucosa. Thus CD4 IEL differentiation requires ThPOK transcriptional repression via reactivation of the ThPOK transcriptional silencer element (SilThPOK). In the present study, we describe a new autoregulatory loop whereby ThPOK binds to the SilThPOK to maintain its own long-term expression in CD4 T cells. Disruption of this loop in vivo prevents persistent ThPOK expression, leads to genome-wide changes in chromatin accessibility and derepresses the colonic regulatory T (Treg) cell gene expression signature. This promotes selective differentiation of naive CD4 T cells into GITRloPD-1loCD25lo (Triplelo) Treg cells and conversion to CD4+ IELs in the gut, thereby providing dominant protection from colitis. Hence, the ThPOK autoregulatory loop represents a key mechanism to physiologically control ThPOK expression and T cell differentiation in the gut, with potential therapeutic relevance.
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Affiliation(s)
- Jayati Basu
- Blood Cell Development and Cancer, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Bernardo S Reis
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Suraj Peri
- Biostatistics and Bioinformatics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Jikun Zha
- Blood Cell Development and Cancer, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Xiang Hua
- Blood Cell Development and Cancer, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Lu Ge
- Blood Cell Development and Cancer, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Kyle Ferchen
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital 10 Medical Center, Cincinnati, OH, USA
| | - Emmanuelle Nicolas
- Blood Cell Development and Cancer, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Philip Czyzewicz
- Blood Cell Development and Cancer, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Kathy Q Cai
- Cancer Signaling and Epigenetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Yinfei Tan
- Cancer Biology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Juan I Fuxman Bass
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Albertha J M Walhout
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - H Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital 10 Medical Center, Cincinnati, OH, USA
| | - Sergei I Grivennikov
- Cancer Prevention and Control, Fox Chase Cancer Center, Philadelphia, PA, USA.,Cedars-Sinai Medical Center, Departments of Medicine and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA
| | - Daniel Mucida
- Laboratory of Mucosal Immunology, The Rockefeller University, New York, NY, USA
| | - Dietmar J Kappes
- Blood Cell Development and Cancer, Fox Chase Cancer Center, Philadelphia, PA, USA.
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21
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Agresta L, O'Brien MM, O'Brien EJ, Norris RE, Breese EH, Burns KC, Mizukawa B, Ryan TD, Desai PB, Vinks A, Grimes HL, Absalon M, Perentesis JP. V2 Trial: A phase I study of venetoclax and CPX-351 for young patients with relapsed/refractory acute leukemia. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.tps7052] [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: 11/20/2022] Open
Abstract
TPS7052 Background: Despite significant advances in therapy for acute myeloid leukemia (AML), 30-40% of young patients will relapse, after which prognosis is poor. In young patients, curative-intent salvage therapy involves intensive re-induction followed by hematopoietic stem cell transplant. Recently, the COG Phase II study of CPX-351 (liposomal cytarabine:daunorubicin, Vyxeos™) in pediatric patients with AML in first relapse (NCT02642965) demonstrated a CR/CRi rate of 81.3%. Separately, our first-in-pediatrics CPX-351 Phase I (NCT01943682) showed 48% in a heavily pre-treated pediatric cohort with multiply relapsed and refractory (R/R) AML. Our integrated pilot study of single cell RNA sequencing (scRNA-seq) done before, during, and after CPX-351 showed p53 targets over time with enrichment for genes regulating apoptosis (ex.: FAS, BAX), suggesting blasts may be primed for apoptosis following CPX-351. Venetoclax is a small molecule inhibitor of the anti-apoptotic protein BCL-2, a regulator of apoptotic balance in some leukemias. Based on our preclinical data, we developed a Phase I study to investigate venetoclax with CPX-351 for the treatment of young patients with R/R acute leukemias. Methods: The V2 Trial (NCT03826992) is a single-institution Phase I study to evaluate the safety and tolerability of venetoclax with CPX-351 in patients ages 1-39 years with R/R acute leukemias. Inclusion diagnoses include AML, mixed phenotype acute leukemia (MPAL), KMT2A-rearranged acute lymphoblastic leukemia (ALL), and T-ALL. Exclusion criteria include CNS status 3, bone marrow failure syndromes, and prior cardiotoxic exposures above acceptable risk thresholds. Subjects receive a single course of CPX-351 at the FDA approved adult dose on Days 1, 3, 5 with concurrent daily venetoclax. In the dose exploration phase, venetoclax dosing is 400 mg daily (or allometrically-scaled equivalent) for 21 (Dose Level 0) or 14 days (Dose Level -1) using a rolling 6 design. Primary endpoints are determination of the recommended phase 2 dose of venetoclax in combination with CPX-351 and description of toxicities. Secondary endpoints include estimations of CR/CRp/CRi +/- MRD negativity in the context of a phase I study and evaluation of therapy-related cardiac dysfunction. Correlative studies include analysis of venetoclax pharmacokinetics with concomitant CPX-351. At the initial dose level, DLT were encountered and the study is now continuing enrollment at Dose Level -1. Clinical trial information: NCT03826992.
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Affiliation(s)
- Laura Agresta
- Michigan State University College of Human Medicine, East Lansing, MI
| | | | | | | | | | | | | | - Thomas D Ryan
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Pankaj B Desai
- University of Cincinnati, College of Pharmacy, Cincinnati, OH
| | - A.a. Vinks
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | - Michael Absalon
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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22
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Serrano-Lopez J, Hegde S, Kumar S, Serrano J, Fang J, Wellendorf AM, Roche PA, Rangel Y, Carrington LJ, Geiger H, Grimes HL, Luther S, Maillard I, Sanchez-Garcia J, Starczynowski DT, Cancelas JA. Inflammation rapidly recruits mammalian GMP and MDP from bone marrow into regional lymphatics. eLife 2021; 10:e66190. [PMID: 33830019 PMCID: PMC8137144 DOI: 10.7554/elife.66190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 04/07/2021] [Indexed: 12/22/2022] Open
Abstract
Innate immune cellular effectors are actively consumed during systemic inflammation, but the systemic traffic and the mechanisms that support their replenishment remain unknown. Here, we demonstrate that acute systemic inflammation induces the emergent activation of a previously unrecognized system of rapid migration of granulocyte-macrophage progenitors and committed macrophage-dendritic progenitors, but not other progenitors or stem cells, from bone marrow (BM) to regional lymphatic capillaries. The progenitor traffic to the systemic lymphatic circulation is mediated by Ccl19/Ccr7 and is NF-κB independent, Traf6/IκB-kinase/SNAP23 activation dependent, and is responsible for the secretion of pre-stored Ccl19 by a subpopulation of CD205+/CD172a+ conventional dendritic cells type 2 and upregulation of BM myeloid progenitor Ccr7 signaling. Mature myeloid Traf6 signaling is anti-inflammatory and necessary for lymph node myeloid cell development. This report unveils the existence and the mechanistic basis of a very early direct traffic of myeloid progenitors from BM to lymphatics during inflammation.
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Affiliation(s)
- Juana Serrano-Lopez
- Divisions of Experimental Hematology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Shailaja Hegde
- Divisions of Experimental Hematology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of MedicineCincinnatiUnited States
- Hoxworth Blood Center, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Sachin Kumar
- Divisions of Experimental Hematology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Josefina Serrano
- Hematology Department, Reina Sofía University Hospital/Maimonides Biomedical Research Institute of Córdoba (IMIBIC)/University of CórdobaCórdobaSpain
| | - Jing Fang
- Divisions of Experimental Hematology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Ashley M Wellendorf
- Divisions of Experimental Hematology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Paul A Roche
- Center for Cancer Research, National Cancer InstituteBethesdaUnited States
- Experimental Immunology Branch, National Cancer Institute, National Institutes of HealthBethesdaUnited States
| | - Yamileth Rangel
- Hematology Department, Reina Sofía University Hospital/Maimonides Biomedical Research Institute of Córdoba (IMIBIC)/University of CórdobaCórdobaSpain
| | | | - Hartmut Geiger
- Divisions of Experimental Hematology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of MedicineCincinnatiUnited States
- Institute of Molecular Medicine, Ulm UniversityUlmGermany
| | - H Leighton Grimes
- Immunobiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of MedicineCincinnatiUnited States
| | - Sanjiv Luther
- Center for Immunity and Infection, Department of Biochemistry, University of LausanneEpalingesSwitzerland
| | - Ivan Maillard
- University of Pennsylvania Perelman School of MedicinePhiladelphiaUnited States
| | - Joaquin Sanchez-Garcia
- Hematology Department, Reina Sofía University Hospital/Maimonides Biomedical Research Institute of Córdoba (IMIBIC)/University of CórdobaCórdobaSpain
| | - Daniel T Starczynowski
- Divisions of Experimental Hematology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of MedicineCincinnatiUnited States
- Department of Cancer Biology, University of CincinnatiCincinnatiUnited States
| | - Jose A Cancelas
- Divisions of Experimental Hematology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of MedicineCincinnatiUnited States
- Hoxworth Blood Center, University of Cincinnati College of MedicineCincinnatiUnited States
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23
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Zhang J, Wu Q, Johnson CB, Pham G, Kinder JM, Olsson A, Slaughter A, May M, Weinhaus B, D'Alessandro A, Engel JD, Jiang JX, Kofron JM, Huang LF, Prasath VBS, Way SS, Salomonis N, Grimes HL, Lucas D. In situ mapping identifies distinct vascular niches for myelopoiesis. Nature 2021; 590:457-462. [PMID: 33568812 PMCID: PMC8020897 DOI: 10.1038/s41586-021-03201-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [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: 04/03/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023]
Abstract
In contrast to nearly all other tissues, the anatomy of cell differentiation in the bone marrow remains unknown. This is owing to a lack of strategies for examining myelopoiesis-the differentiation of myeloid progenitors into a large variety of innate immune cells-in situ in the bone marrow. Such strategies are required to understand differentiation and lineage-commitment decisions, and to define how spatial organizing cues inform tissue function. Here we develop approaches for imaging myelopoiesis in mice, and generate atlases showing the differentiation of granulocytes, monocytes and dendritic cells. The generation of granulocytes and dendritic cells-monocytes localizes to different blood-vessel structures known as sinusoids, and displays lineage-specific spatial and clonal architectures. Acute systemic infection with Listeria monocytogenes induces lineage-specific progenitor clusters to undergo increased self-renewal of progenitors, but the different lineages remain spatially separated. Monocyte-dendritic cell progenitors (MDPs) map with nonclassical monocytes and conventional dendritic cells; these localize to a subset of blood vessels expressing a major regulator of myelopoiesis, colony-stimulating factor 1 (CSF1, also known as M-CSF)1. Specific deletion of Csf1 in endothelium disrupts the architecture around MDPs and their localization to sinusoids. Subsequently, there are fewer MDPs and their ability to differentiate is reduced, leading to a loss of nonclassical monocytes and dendritic cells during both homeostasis and infection. These data indicate that local cues produced by distinct blood vessels are responsible for the spatial organization of definitive blood cell differentiation.
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Affiliation(s)
- Jizhou Zhang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
| | - Qingqing Wu
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
| | - Courtney B Johnson
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
| | - Giang Pham
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jeremy M Kinder
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Andre Olsson
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anastasiya Slaughter
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Margot May
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
| | - Benjamin Weinhaus
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO, USA
| | - James Douglas Engel
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jean X Jiang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - J Matthew Kofron
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - L Frank Huang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
| | - V B Surya Prasath
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sing Sing Way
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - H Leighton Grimes
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Daniel Lucas
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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24
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Ferchen K, Song B, Grimes HL. A primer on single-cell genomics in myeloid biology. Curr Opin Hematol 2021; 28:11-17. [PMID: 33186153 PMCID: PMC9205579 DOI: 10.1097/moh.0000000000000623] [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] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Understanding the fast-moving field of single-cell technologies, as applied to myeloid biology, requires an appreciation of basic molecular, informatics, and biological concepts. Here, we highlight both key and recent articles to illustrate basic concepts for those new to molecular single-cell analyses in myeloid hematology. RECENT FINDINGS Recent studies apply single-cell omics to discover novel cell populations, construct relationships between cell populations, reconfigure the organization of hematopoiesis, and study hematopoietic lineage tree and fate choices. Accompanying development of technologies, new informatic tools have emerged, providing exciting new insights. SUMMARY Hematopoietic stem and progenitor cells are regulated by complex intrinsic and extrinsic factors to produce blood cell types. In this review, we discuss recent advances in single-cell omics to profile these cells, methods to infer cell type identify, and trajectories from molecular omics data to ultimately derive new insights into hematopoietic stem and progenitor cell biology. We further discuss future applications of these technologies to understand hematopoietic cell interactions, function, and development. The goal is to offer a comprehensive overview of current single-cell technologies and their impact on our understanding of myeloid cell development for those new to single-cell analyses.
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Affiliation(s)
- Kyle Ferchen
- Division of Immunobiology, Cincinnati Children’s Hospital, Cincinnati, OH, USA
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Baobao Song
- Division of Immunobiology, Cincinnati Children’s Hospital, Cincinnati, OH, USA
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - H. Leighton Grimes
- Division of Immunobiology, Cincinnati Children’s Hospital, Cincinnati, OH, USA
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25
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Ye H, Minhajuddin M, Krug A, Pei S, Chou CH, Culp-Hill R, Ponder J, De Bloois E, Schniedewind B, Amaya ML, Inguva A, Stevens BM, Pollyea DA, Christians U, Grimes HL, D'Alessandro A, Jordan CT. The Hepatic Microenvironment Uniquely Protects Leukemia Cells through Induction of Growth and Survival Pathways Mediated by LIPG. Cancer Discov 2020; 11:500-519. [PMID: 33028621 DOI: 10.1158/2159-8290.cd-20-0318] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/11/2020] [Accepted: 10/02/2020] [Indexed: 12/19/2022]
Abstract
Due to the disseminated nature of leukemia, malignant cells are exposed to many different tissue microenvironments, including a variety of extramedullary sites. In the present study, we demonstrate that leukemic cells residing in the liver display unique biological properties and also contribute to systemic changes that influence physiologic responses to chemotherapy. Specifically, the liver microenvironment induces metabolic adaptations via upregulating expression of endothelial lipase in leukemia cells, which not only stimulates tumor cell proliferation through polyunsaturated fatty acid-mediated pathways, but also promotes survival by stabilizing antiapoptotic proteins. Additionally, hepatic infiltration and tissue damage caused by malignant cells induces release of liver-derived enzymes capable of degrading chemotherapy drugs, an event that further protects leukemia cells from conventional therapies. Together, these studies demonstrate a unique role for liver in modulating the pathogenesis of leukemic disease and suggest that the hepatic microenvironment may protect leukemia cells from chemotherapeutic challenge. SIGNIFICANCE: The studies presented herein demonstrate that the liver provides a microenvironment in which leukemia cells acquire unique metabolic properties. The adaptations that occur in the liver confer increased resistance to chemotherapy. Therefore, we propose that therapies designed to overcome liver-specific metabolic changes will yield improved outcomes for patients with leukemia.This article is highlighted in the In This Issue feature, p. 211.
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Affiliation(s)
- Haobin Ye
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
| | - Mohammad Minhajuddin
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Anna Krug
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Shanshan Pei
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Chih-Hsing Chou
- Division of Immunobiology, Cincinnati Children's Hospital, Cincinnati, Ohio
| | - Rachel Culp-Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jessica Ponder
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Erik De Bloois
- Department of Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Björn Schniedewind
- Department of Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Maria L Amaya
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Anagha Inguva
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Brett M Stevens
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Daniel A Pollyea
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Uwe Christians
- Department of Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital, Cincinnati, Ohio
| | - Angelo D'Alessandro
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado.,Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Craig T Jordan
- Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
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Dwivedi P, Chutipongtanate S, Muench DE, Azam M, Grimes HL, Greis KD. SWATH-Proteomics of Ibrutinib's Action in Myeloid Leukemia Initiating Mutated G-CSFR Signaling. Proteomics Clin Appl 2020; 14:e1900144. [PMID: 32319217 PMCID: PMC7492401 DOI: 10.1002/prca.201900144] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 12/20/2019] [Revised: 03/28/2020] [Indexed: 11/06/2022]
Abstract
PURPOSE To evaluate cellular protein changes in response to treatment with an approved drug, ibrutinib, in cells expressing normal or mutated granulocyte-colony stimulating factor receptor (G-CSFR). G-CSFR mutations are associated with some hematological malignancies. Previous studies show the efficacy of ibrutinib (a Bruton's tyrosine kinase inhibitor) in mutated G-CSFR leukemia models but do not address broader signaling mechanisms. EXPERIMENTAL DESIGN A label-free quantitative proteomics workflow to evaluate the cellular effects of ibrutinib treatment is established. This includes three biological replicates of normal and mutated G-CSFR expressed in a mouse progenitor cell (32D cell line) with and without ibrutinib treatment. RESULTS The proteomics dataset shows about 1000 unique proteins quantified with nearly 400 significant changes (p value < 0.05), suggesting a highly dynamic network of cellular signaling in response to ibrutinib. Importantly, the dataset is very robust with coefficients of variation for quantitation at 13.0-20.4% resulting in dramatic patterns of protein differences among the groups. CONCLUSIONS AND CLINICAL RELEVANCE This robust dataset is available for further mining, hypothesis generation, and testing. A detailed understanding of the restructuring of the proteomics signaling cascades by ibrutinib in leukemia biology will provide new avenues to explore its use for other related malignancies.
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Affiliation(s)
- Pankaj Dwivedi
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio 45267 USA
| | - Somchai Chutipongtanate
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio 45267 USA
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400 Thailand
| | - David E. Muench
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45267 USA
| | - Mohammad Azam
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45267 USA
| | - H. Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45267 USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45267 USA
| | - Kenneth D. Greis
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio 45267 USA
- Correspondence: , (513) 558 7102
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27
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Zhang J, Wu Q, Johnson C, Olsson A, Salomonis N, Slaughter A, May M, Weinhaus B, D'Alessandro A, Engel J, Jiang J, Koffron JM, Huang LF, Grimes HL, Lucas D. 3045 – MAPPING MYELOID DIFFERENTIATION IDENTIFIES A CSF1+ VASCULAR NICHE FOR MYELOPOIESIS. Exp Hematol 2020. [DOI: 10.1016/j.exphem.2020.09.065] [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: 10/22/2022]
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28
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Kwok I, Becht E, Xia Y, Ng M, Teh YC, Tan L, Evrard M, Li JLY, Tran HTN, Tan Y, Liu D, Mishra A, Liong KH, Leong K, Zhang Y, Olsson A, Mantri CK, Shyamsunder P, Liu Z, Piot C, Dutertre CA, Cheng H, Bari S, Ang N, Biswas SK, Koeffler HP, Tey HL, Larbi A, Su IH, Lee B, St John A, Chan JKY, Hwang WYK, Chen J, Salomonis N, Chong SZ, Grimes HL, Liu B, Hidalgo A, Newell EW, Cheng T, Ginhoux F, Ng LG. Combinatorial Single-Cell Analyses of Granulocyte-Monocyte Progenitor Heterogeneity Reveals an Early Uni-potent Neutrophil Progenitor. Immunity 2020; 53:303-318.e5. [PMID: 32579887 DOI: 10.1016/j.immuni.2020.06.005] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [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: 01/23/2020] [Revised: 04/14/2020] [Accepted: 06/02/2020] [Indexed: 02/07/2023]
Abstract
Granulocyte-monocyte progenitors (GMPs) have been previously defined for their potential to generate various myeloid progenies such as neutrophils and monocytes. Although studies have proposed lineage heterogeneity within GMPs, it is unclear if committed progenitors already exist among these progenitors and how they may behave differently during inflammation. By combining single-cell transcriptomic and proteomic analyses, we identified the early committed progenitor within the GMPs responsible for the strict production of neutrophils, which we designate as proNeu1. Our dissection of the GMP hierarchy led us to further identify a previously unknown intermediate proNeu2 population. Similar populations could be detected in human samples. proNeu1s, but not proNeu2s, selectively expanded during the early phase of sepsis at the expense of monocytes. Collectively, our findings help shape the neutrophil maturation trajectory roadmap and challenge the current definition of GMPs.
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Affiliation(s)
- Immanuel Kwok
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Etienne Becht
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Yu Xia
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore; Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Melissa Ng
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Ye Chean Teh
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore; Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117558, Singapore
| | - Leonard Tan
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Maximilien Evrard
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Jackson L Y Li
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Hoa T N Tran
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Yingrou Tan
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore; National Skin Centre, 1 Mandalay Road, Singapore 308205, Singapore
| | - Dehua Liu
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Archita Mishra
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Ka Hang Liong
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Keith Leong
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Yuning Zhang
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Andre Olsson
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Chinmay Kumar Mantri
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Pavithra Shyamsunder
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Zhaoyuan Liu
- Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China
| | - Cecile Piot
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Charles-Antoine Dutertre
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin 300020, China; Department of Stem Cell and Regenerative Medicine, Peking Union Medical College, Tianjin 300020, China
| | - Sudipto Bari
- Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Nicholas Ang
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Subhra K Biswas
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - H Philip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Cedars-Sinai Medical Center, Division of Hematology/Oncology, UCLA School of Medicine, Los Angeles, CA 90048, USA; Department of Hematology-Oncology, National University Cancer Institute of Singapore, National University Hospital, Singapore 119074, Singapore
| | - Hong Liang Tey
- National Skin Centre, 1 Mandalay Road, Singapore 308205, Singapore
| | - Anis Larbi
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - I-Hsin Su
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Bernett Lee
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Ashley St John
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore; Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA; SingHealth Duke-National University of Singapore Global Health Institute, Singapore 168753, Singapore
| | - Jerry K Y Chan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore; Experimental Fetal Medicine Group, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - William Y K Hwang
- Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; National Cancer Centre Singapore, Singapore 169610, Singapore; Department of Hematology, Singapore General Hospital, Singapore 169608, Singapore
| | - Jinmiao Chen
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Shu Zhen Chong
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - H Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Bing Liu
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China; State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China
| | - Andrés Hidalgo
- Area of Cell & Developmental Biology, Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid 28029, Spain
| | - Evan W Newell
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China; Center for Stem Cell Medicine, Chinese Academy of Medical Sciences, Tianjin 300020, China; Department of Stem Cell and Regenerative Medicine, Peking Union Medical College, Tianjin 300020, China
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore; Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai 200025, China; Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 169856, Singapore
| | - Lai Guan Ng
- Singapore Immunology Network (SIgN), A∗STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138648, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; State Key Laboratory of Experimental Hematology, Institute of Hematology, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; National Cancer Centre Singapore, Singapore 169610, Singapore.
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29
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Hinge A, He J, Bartram J, Javier J, Xu J, Fjellman E, Sesaki H, Li T, Yu J, Wunderlich M, Mulloy J, Kofron M, Salomonis N, Grimes HL, Filippi MD. Asymmetrically Segregated Mitochondria Provide Cellular Memory of Hematopoietic Stem Cell Replicative History and Drive HSC Attrition. Cell Stem Cell 2020; 26:420-430.e6. [PMID: 32059807 DOI: 10.1016/j.stem.2020.01.016] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/29/2019] [Accepted: 01/23/2020] [Indexed: 01/08/2023]
Abstract
The metabolic requirements of hematopoietic stem cells (HSCs) change with their cell cycle activity. However, the underlying role of mitochondria remains ill-defined. Here we found that, after mitochondrial activation with replication, HSCs irreversibly remodel the mitochondrial network and that this network is not repaired after HSC re-entry into quiescence, contrary to hematopoietic progenitors. HSCs keep and accumulate dysfunctional mitochondria through asymmetric segregation during active division. Mechanistically, mitochondria aggregate and depolarize after stress because of loss of activity of the mitochondrial fission regulator Drp1 onto mitochondria. Genetic and pharmacological studies indicate that inactivation of Drp1 causes loss of HSC regenerative potential while maintaining HSC quiescence. Molecularly, HSCs carrying dysfunctional mitochondria can re-enter quiescence but fail to synchronize the transcriptional control of core cell cycle and metabolic components in subsequent division. Thus, loss of fidelity of mitochondrial morphology and segregation is one type of HSC divisional memory and drives HSC attrition.
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Affiliation(s)
- Ashwini Hinge
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Research Foundation, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jingyi He
- Pediatric Research Institute, Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, P.R China
| | - James Bartram
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Research Foundation, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jose Javier
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Research Foundation, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Juying Xu
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Research Foundation, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ellen Fjellman
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Research Foundation, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Hiromi Sesaki
- Department of Cell Biology, John Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tingyu Li
- Child Nutrition Research Center in the Children's Hospital of Chongqing Medical University, Chongqing Key Laboratory of Child Nutrition and Health, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, P.R China
| | - Jie Yu
- Department of Hematology and Oncology, Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, P.R China
| | - Mark Wunderlich
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Research Foundation, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - James Mulloy
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Research Foundation, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Matthew Kofron
- Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH, USA
| | - H Leighton Grimes
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Research Foundation, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH, USA
| | - Marie-Dominique Filippi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Research Foundation, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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30
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Lu YC, Sanada C, Xavier-Ferrucio J, Wang L, Zhang PX, Grimes HL, Venkatasubramanian M, Chetal K, Aronow B, Salomonis N, Krause DS. The Molecular Signature of Megakaryocyte-Erythroid Progenitors Reveals a Role for the Cell Cycle in Fate Specification. Cell Rep 2019; 25:2083-2093.e4. [PMID: 30463007 PMCID: PMC6336197 DOI: 10.1016/j.celrep.2018.10.084] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [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] [Received: 04/19/2018] [Revised: 08/14/2018] [Accepted: 10/24/2018] [Indexed: 12/25/2022] Open
Abstract
Megakaryocytic-erythroid progenitors (MEPs) give rise to the cells that produce red blood cells and platelets. Although the mechanisms underlying megakaryocytic (MK) and erythroid (E) maturation have been described, those controlling their specification from MEPs are unknown. Single-cell RNA sequencing of primary human MEPs, common myeloid progenitors (CMPs), megakaryocyte progenitors, and E progenitors revealed a distinct transitional MEP signature. Inferred regulatory transcription factors (TFs) were associated with differential expression of cell cycle regulators. Genetic manipulation of selected TFs validated their role in lineage specification and demonstrated coincident modulation of the cell cycle. Genetic and pharmacologic modulation demonstrated that cell cycle activation is sufficient to promote E versus MK specification. These findings, obtained from healthy human cells, lay a foundation to study the mechanisms underlying benign and malignant disease states of the megakaryocytic and E lineages. Bipotent megakaryocytic-erythroid progenitors (MEPs) produce megakaryocytic and erythroid cells. Using single-cell RNA sequencing of primary human MEPs and their upstream and downstream progenitors, Lu et al. show that MEPs are a unique transitional population. Functional and molecular studies show that MEP lineage fate is toggled by cell cycle speed.
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Affiliation(s)
- Yi-Chien Lu
- Department of Laboratory Medicine and Yale Stem Cell Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA.
| | - Chad Sanada
- Department of Laboratory Medicine and Yale Stem Cell Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Juliana Xavier-Ferrucio
- Department of Laboratory Medicine and Yale Stem Cell Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Lin Wang
- Department of Laboratory Medicine and Yale Stem Cell Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Ping-Xia Zhang
- Department of Laboratory Medicine and Yale Stem Cell Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - Meenakshi Venkatasubramanian
- Division of Biomedical Informatics, Cincinnati Children's Hospital, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children's Hospital, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Bruce Aronow
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Diane S Krause
- Department of Laboratory Medicine and Yale Stem Cell Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
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31
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DePasquale EAK, Schnell DJ, Van Camp PJ, Valiente-Alandí Í, Blaxall BC, Grimes HL, Singh H, Salomonis N. DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data. Cell Rep 2019; 29:1718-1727.e8. [PMID: 31693907 PMCID: PMC6983270 DOI: 10.1016/j.celrep.2019.09.082] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 07/25/2019] [Accepted: 09/25/2019] [Indexed: 01/06/2023] Open
Abstract
Methods for single-cell RNA sequencing (scRNA-seq) have greatly advanced in recent years. While droplet- and well-based methods have increased the capture frequency of cells for scRNA-seq, these technologies readily produce technical artifacts, such as doublet cell captures. Doublets occurring between distinct cell types can appear as hybrid scRNA-seq profiles, but do not have distinct transcriptomes from individual cell states. We introduce DoubletDecon, an approach that detects doublets with a combination of deconvolution analyses and the identification of unique cell-state gene expression. We demonstrate the ability of DoubletDecon to identify synthetic, mixed-species, genetic, and cell-hashing cell doublets from scRNA-seq datasets of varying cellular complexity with a high sensitivity relative to alternative approaches. Importantly, this algorithm prevents the prediction of valid mixed-lineage and transitional cell states as doublets by considering their unique gene expression. DoubletDecon has an easy-to-use graphical user interface and is compatible with diverse species and unsupervised population detection algorithms.
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Affiliation(s)
- Erica A K DePasquale
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Daniel J Schnell
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Heart Institute and Center for Translational Fibrosis Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Pieter-Jan Van Camp
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Íñigo Valiente-Alandí
- Heart Institute and Center for Translational Fibrosis Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Burns C Blaxall
- Heart Institute and Center for Translational Fibrosis Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45221, USA
| | - H Leighton Grimes
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45221, USA; Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Harinder Singh
- Center for Systems Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15620, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45221, USA; Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45221, USA.
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32
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Adelman ER, Huang HT, Roisman A, Olsson A, Colaprico A, Qin T, Lindsley RC, Bejar R, Salomonis N, Grimes HL, Figueroa ME. Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia. Cancer Discov 2019; 9:1080-1101. [PMID: 31085557 PMCID: PMC7080409 DOI: 10.1158/2159-8290.cd-18-1474] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/31/2022]
Abstract
Aging is associated with functional decline of hematopoietic stem cells (HSC) as well as an increased risk of myeloid malignancies. We performed an integrative characterization of epigenomic and transcriptomic changes, including single-cell RNA sequencing, during normal human aging. Lineage-CD34+CD38- cells [HSC-enriched (HSCe)] undergo age-associated epigenetic reprogramming consisting of redistribution of DNA methylation and reductions in H3K27ac, H3K4me1, and H3K4me3. This reprogramming of aged HSCe globally targets developmental and cancer pathways that are comparably altered in acute myeloid leukemia (AML) of all ages, encompassing loss of 4,646 active enhancers, 3,091 bivalent promoters, and deregulation of several epigenetic modifiers and key hematopoietic transcription factors, such as KLF6, BCL6, and RUNX3. Notably, in vitro downregulation of KLF6 results in impaired differentiation, increased colony-forming potential, and changes in expression that recapitulate aging and leukemia signatures. Thus, age-associated epigenetic reprogramming may form a predisposing condition for the development of age-related AML. SIGNIFICANCE: AML, which is more frequent in the elderly, is characterized by epigenetic deregulation. We demonstrate that epigenetic reprogramming of human HSCs occurs with age, affecting cancer and developmental pathways. Downregulation of genes epigenetically altered with age leads to impairment in differentiation and partially recapitulates aging phenotypes.This article is highlighted in the In This Issue feature, p. 983.
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Affiliation(s)
- Emmalee R Adelman
- Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida.,Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Hsuan-Ting Huang
- Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Alejandro Roisman
- Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - André Olsson
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Antonio Colaprico
- Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - R Coleman Lindsley
- Department of Medical Oncology, Division of Hematological Malignancies, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Rafael Bejar
- Division of Hematology and Oncology, Moores Cancer Center, University of California, San Diego, La Jolla, California
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - H Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Maria E Figueroa
- Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida. .,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
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33
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Duy C, Teater M, Garrett-Bakelman FE, Lee TC, Meydan C, Glass JL, Li M, Hellmuth JC, Mohammad HP, Smitheman KN, Shih AH, Abdel-Wahab O, Tallman MS, Guzman ML, Muench D, Grimes HL, Roboz GJ, Kruger RG, Creasy CL, Paietta EM, Levine RL, Carroll M, Melnick AM. Rational Targeting of Cooperating Layers of the Epigenome Yields Enhanced Therapeutic Efficacy against AML. Cancer Discov 2019; 9:872-889. [PMID: 31076479 DOI: 10.1158/2159-8290.cd-19-0106] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/17/2019] [Accepted: 05/07/2019] [Indexed: 02/06/2023]
Abstract
Disruption of epigenetic regulation is a hallmark of acute myeloid leukemia (AML), but epigenetic therapy is complicated by the complexity of the epigenome. Herein, we developed a long-term primary AML ex vivo platform to determine whether targeting different epigenetic layers with 5-azacytidine and LSD1 inhibitors would yield improved efficacy. This combination was most effective in TET2 mut AML, where it extinguished leukemia stem cells and particularly induced genes with both LSD1-bound enhancers and cytosine-methylated promoters. Functional studies indicated that derepression of genes such as GATA2 contributes to drug efficacy. Mechanistically, combination therapy increased enhancer-promoter looping and chromatin-activating marks at the GATA2 locus. CRISPRi of the LSD1-bound enhancer in patient-derived TET2 mut AML was associated with dampening of therapeutic GATA2 induction. TET2 knockdown in human hematopoietic stem/progenitor cells induced loss of enhancer 5-hydroxymethylation and facilitated LSD1-mediated enhancer inactivation. Our data provide a basis for rational targeting of cooperating aberrant promoter and enhancer epigenetic marks driven by mutant epigenetic modifiers. SIGNIFICANCE: Somatic mutations of genes encoding epigenetic modifiers are a hallmark of AML and potentially disrupt many components of the epigenome. Our study targets two different epigenetic layers at promoters and enhancers that cooperate to aberrant gene silencing, downstream of the actions of a mutant epigenetic regulator.This article is highlighted in the In This Issue feature, p. 813.
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Affiliation(s)
- Cihangir Duy
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York.
| | - Matt Teater
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Francine E Garrett-Bakelman
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York.,Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia.,Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Tak C Lee
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Cem Meydan
- Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York
| | - Jacob L Glass
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meng Li
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Johannes C Hellmuth
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | | | | | - Alan H Shih
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | - Monica L Guzman
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | - David Muench
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Gail J Roboz
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York
| | | | | | | | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Martin Carroll
- Division of Hematology and Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Ari M Melnick
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York. .,Department of Pharmacology, Weill Cornell Medicine, New York, New York
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34
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Dwivedi P, Muench DE, Wagner M, Azam M, Grimes HL, Greis KD. Phospho serine and threonine analysis of normal and mutated granulocyte colony stimulating factor receptors. Sci Data 2019; 6:21. [PMID: 30967555 PMCID: PMC6480977 DOI: 10.1038/s41597-019-0015-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 02/11/2019] [Indexed: 11/18/2022] Open
Abstract
Granulocyte colony stimulating factor receptor (G-CSFR) plays an important role in the production of neutrophil granulocytes. Mutated G-CSFRs have been directly associated with two distinct malignant phenotypes in patients, e.g. acute myeloid leukemia (AML) and chronic neutrophilic leukemia (CNL). However, the signaling mechanism of the mutated G-CSFRs is not well understood. Here, we present a comprehensive SILAC-based quantitative phosphoserine and phosphothreonine dataset of the normal and mutated G-CSFRs signaling using the BaF3 cell-line-based in vitro model system. High pH reversed phase concatenation and Titanium Dioxide Spin Tip column were utilized to increase the dynamic range and detection of the phosphoproteome of G-CSFRs. The dataset was further analyzed using several computational tools to validate the quality of the dataset. Overall, this dataset is the first global phosphoproteomics analysis of both normal and disease-associated-mutant G-CSFRs. We anticipate that this dataset will have a strong potential to decipher the phospho-signaling differences between the normal and malignant G-CSFR biology with therapeutic implications. The phosphoproteomic dataset is available via the PRIDE partner repository.
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Affiliation(s)
- Pankaj Dwivedi
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio, 45267, USA
| | - David E Muench
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Michael Wagner
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Mohammad Azam
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - H Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Kenneth D Greis
- Department of Cancer Biology, University of Cincinnati, Cincinnati, Ohio, 45267, USA.
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35
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Dwivedi P, Muench DE, Wagner M, Azam M, Grimes HL, Greis KD. Time resolved quantitative phospho-tyrosine analysis reveals Bruton's Tyrosine kinase mediated signaling downstream of the mutated granulocyte-colony stimulating factor receptors. Leukemia 2019; 33:75-87. [PMID: 29977015 PMCID: PMC6320735 DOI: 10.1038/s41375-018-0188-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/31/2018] [Accepted: 06/06/2018] [Indexed: 12/26/2022]
Abstract
Granulocyte-colony stimulating factor receptor (G-CSFR) controls myeloid progenitor proliferation and differentiation to neutrophils. Mutations in CSF3R (encoding G-CSFR) have been reported in patients with chronic neutrophilic leukemia (CNL) and acute myeloid leukemia (AML); however, despite years of research, the malignant downstream signaling of the mutated G-CSFRs is not well understood. Here, we used a quantitative phospho-tyrosine analysis to generate a comprehensive signaling map of G-CSF induced tyrosine phosphorylation in the normal versus mutated (proximal: T618I and truncated: Q741x) G-CSFRs. Unbiased clustering and kinase enrichment analysis identified rapid induction of phospho-proteins associated with endocytosis by the wild type G-CSFR only; while G-CSFR mutants showed abnormal kinetics of canonical Stat3, Stat5, and Mapk phosphorylation, and aberrant activation of Bruton's Tyrosine Kinase (Btk). Mutant-G-CSFR-expressing cells displayed enhanced sensitivity (3-5-fold lower IC50) for ibrutinib-based chemical inhibition of Btk. Primary murine progenitor cells from G-CSFR-Q741x knock-in mice validated activation of Btk by the mutant receptor and retrovirally transduced human CD34+ umbilical cord blood cells expressing mutant receptors displayed enhanced sensitivity to Ibrutinib. A significantly lower clonogenic potential was displayed by both murine and human primary cells expressing mutated receptors upon ibrutinib treatment. Finally, a dramatic synergy was observed between ibrutinib and ruxolinitib at lower dose of the individual drug. Altogether, these data demonstrate the strength of unsupervised proteomics analyses in dissecting oncogenic pathways, and suggest repositioning Ibrutinib for therapy of myeloid leukemia bearing CSF3R mutations. Phospho-tyrosine data are available via ProteomeXchange with identifier PXD009662.
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MESH Headings
- Adenine/analogs & derivatives
- Agammaglobulinaemia Tyrosine Kinase/antagonists & inhibitors
- Agammaglobulinaemia Tyrosine Kinase/genetics
- Agammaglobulinaemia Tyrosine Kinase/metabolism
- Animals
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Cells, Cultured
- Humans
- Leukemia, Myeloid, Acute
- Leukemia, Neutrophilic, Chronic
- Mice
- Mutation
- Phosphoproteins/metabolism
- Phosphorylation
- Piperidines
- Precursor Cells, B-Lymphoid/metabolism
- Precursor Cells, B-Lymphoid/pathology
- Protein-Tyrosine Kinases/analysis
- Protein-Tyrosine Kinases/metabolism
- Proteome/analysis
- Pyrazoles/pharmacology
- Pyrimidines/pharmacology
- Receptors, Granulocyte Colony-Stimulating Factor/genetics
- Receptors, Granulocyte Colony-Stimulating Factor/metabolism
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Affiliation(s)
- Pankaj Dwivedi
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - David E Muench
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Michael Wagner
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mohammad Azam
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - H Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
| | - Kenneth D Greis
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA.
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36
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Hay SB, Ferchen K, Chetal K, Grimes HL, Salomonis N. The Human Cell Atlas bone marrow single-cell interactive web portal. Exp Hematol 2018; 68:51-61. [PMID: 30243574 PMCID: PMC6296228 DOI: 10.1016/j.exphem.2018.09.004] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [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] [Received: 07/27/2018] [Revised: 09/11/2018] [Accepted: 09/14/2018] [Indexed: 01/17/2023]
Abstract
The Human Cell Atlas (HCA) is expected to facilitate the creation of reference cell profiles, marker genes, and gene regulatory networks that will provide a deeper understanding of healthy and disease cell types from clinical biospecimens. The hematopoietic system includes dozens of distinct, transcriptionally coherent cell types, including intermediate transitional populations that have not been previously described at a molecular level. Using the first data release from the HCA bone marrow tissue project, we resolved common, rare, and potentially transitional cell populations from over 100,000 hematopoietic cells spanning 35 transcriptionally coherent groups across eight healthy donors using emerging new computational approaches. These data highlight novel mixed-lineage progenitor populations and putative trajectories governing granulocytic, monocytic, lymphoid, erythroid, megakaryocytic, and eosinophil specification. Our analyses suggest significant variation in cell-type composition and gene expression among donors, including biological processes affected by donor age. To enable broad exploration of these findings, we provide an interactive website to probe intra-cell and extra-cell population differences within and between donors and reference markers for cellular classification and cellular trajectories through associated progenitor states.
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Affiliation(s)
- Stuart B Hay
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kyle Ferchen
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - H Leighton Grimes
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA; Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA; Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA.
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37
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Hayashi Y, Zhang Y, Yokota A, Yan X, Liu J, Choi K, Li B, Sashida G, Peng Y, Xu Z, Huang R, Zhang L, Freudiger GM, Wang J, Dong Y, Zhou Y, Wang J, Wu L, Bu J, Chen A, Zhao X, Sun X, Chetal K, Olsson A, Watanabe M, Romick-Rosendale LE, Harada H, Shih LY, Tse W, Bridges JP, Caligiuri MA, Huang T, Zheng Y, Witte DP, Wang QF, Qu CK, Salomonis N, Grimes HL, Nimer SD, Xiao Z, Huang G. Pathobiological Pseudohypoxia as a Putative Mechanism Underlying Myelodysplastic Syndromes. Cancer Discov 2018; 8:1438-1457. [PMID: 30139811 DOI: 10.1158/2159-8290.cd-17-1203] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 06/26/2018] [Accepted: 08/20/2018] [Indexed: 11/16/2022]
Abstract
Myelodysplastic syndromes (MDS) are heterogeneous hematopoietic disorders that are incurable with conventional therapy. Their incidence is increasing with global population aging. Although many genetic, epigenetic, splicing, and metabolic aberrations have been identified in patients with MDS, their clinical features are quite similar. Here, we show that hypoxia-independent activation of hypoxia-inducible factor 1α (HIF1A) signaling is both necessary and sufficient to induce dysplastic and cytopenic MDS phenotypes. The HIF1A transcriptional signature is generally activated in MDS patient bone marrow stem/progenitors. Major MDS-associated mutations (Dnmt3a, Tet2, Asxl1, Runx1, and Mll1) activate the HIF1A signature. Although inducible activation of HIF1A signaling in hematopoietic cells is sufficient to induce MDS phenotypes, both genetic and chemical inhibition of HIF1A signaling rescues MDS phenotypes in a mouse model of MDS. These findings reveal HIF1A as a central pathobiologic mediator of MDS and as an effective therapeutic target for a broad spectrum of patients with MDS.Significance: We showed that dysregulation of HIF1A signaling could generate the clinically relevant diversity of MDS phenotypes by functioning as a signaling funnel for MDS driver mutations. This could resolve the disconnection between genotypes and phenotypes and provide a new clue as to how a variety of driver mutations cause common MDS phenotypes. Cancer Discov; 8(11); 1438-57. ©2018 AACR. See related commentary by Chen and Steidl, p. 1355 This article is highlighted in the In This Issue feature, p. 1333.
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Affiliation(s)
- Yoshihiro Hayashi
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Yue Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Asumi Yokota
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Xiaomei Yan
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Jinqin Liu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Kwangmin Choi
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Bing Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Goro Sashida
- International Research Center for Medical Sciences, Kumamoto University, Chuo-ku, Kumamoto, Japan
| | - Yanyan Peng
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Zefeng Xu
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Rui Huang
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Lulu Zhang
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - George M Freudiger
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Jingya Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Yunzhu Dong
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Yile Zhou
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Jieyu Wang
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Lingyun Wu
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Hematology, Sixth Hospital Affiliated to Shanghai Jiaotong University, Shanghai, China
| | - Jiachen Bu
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Aili Chen
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xinghui Zhao
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Xiujuan Sun
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Andre Olsson
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Miki Watanabe
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Lindsey E Romick-Rosendale
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Hironori Harada
- Laboratory of Oncology, School of Life Science, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Lee-Yung Shih
- Department of Hematology and Oncology, Chang Gung Memorial Hospital-Linkou and Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - William Tse
- James Graham Brown Cancer Center, University of Louisville Hospital, Louisville, Kentucky
| | - James P Bridges
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | | | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Yi Zheng
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - David P Witte
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Qian-Fei Wang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Cheng-Kui Qu
- Division of Hematology/Oncology, Aflac Cancer and Blood Disorders Center, Emory University School of Medicine, Atlanta, Georgia
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - H Leighton Grimes
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Stephen D Nimer
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Zhijian Xiao
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.
| | - Gang Huang
- Divisions of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio. .,State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
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38
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Meyer SE, Muench DE, Rogers AM, Newkold TJ, Orr E, O'Brien E, Perentesis JP, Doench JG, Lal A, Morris PJ, Thomas CJ, Lieberman J, McGlinn E, Aronow BJ, Salomonis N, Grimes HL. miR-196b target screen reveals mechanisms maintaining leukemia stemness with therapeutic potential. J Exp Med 2018; 215:2115-2136. [PMID: 29997117 PMCID: PMC6080909 DOI: 10.1084/jem.20171312] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 07/25/2017] [Revised: 04/30/2018] [Accepted: 06/26/2018] [Indexed: 01/02/2023] Open
Abstract
We have shown that antagomiR inhibition of miRNA miR-21 and miR-196b activity is sufficient to ablate MLL-AF9 leukemia stem cells (LSC) in vivo. Here, we used an shRNA screening approach to mimic miRNA activity on experimentally verified miR-196b targets to identify functionally important and therapeutically relevant pathways downstream of oncogenic miRNA in MLL-r AML. We found Cdkn1b (p27Kip1) is a direct miR-196b target whose repression enhanced an embryonic stem cell-like signature associated with decreased leukemia latency and increased numbers of leukemia stem cells in vivo. Conversely, elevation of p27Kip1 significantly reduced MLL-r leukemia self-renewal, promoted monocytic differentiation of leukemic blasts, and induced cell death. Antagonism of miR-196b activity or pharmacologic inhibition of the Cks1-Skp2-containing SCF E3-ubiquitin ligase complex increased p27Kip1 and inhibited human AML growth. This work illustrates that understanding oncogenic miRNA target pathways can identify actionable targets in leukemia.
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MESH Headings
- Animals
- Carcinogenesis/genetics
- Carcinogenesis/pathology
- Cell Differentiation/genetics
- Cell Line, Tumor
- Cell Proliferation/genetics
- Cell Survival/genetics
- Chromosomes, Human, Pair 11/genetics
- Cyclin-Dependent Kinase Inhibitor p27/metabolism
- Cyclin-Dependent Kinases/metabolism
- Cyclins/metabolism
- Embryonic Stem Cells/metabolism
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/therapy
- Mice, Inbred C57BL
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Oncogenes
- RNA, Small Interfering/metabolism
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Affiliation(s)
- Sara E Meyer
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - David E Muench
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Andrew M Rogers
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Tess J Newkold
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Emily Orr
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Eric O'Brien
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - John P Perentesis
- Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Patrick J Morris
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Edwina McGlinn
- EMBL Australia, Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - H Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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39
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Yáñez A, Coetzee S, Olsson A, Muench D, Berman B, Hazelett D, Salomonis N, Grimes HL, Goodridge H. Granulocyte-Monocyte Progenitors and Monocyte-Dendritic Cell Progenitors Independently Produce Functionally Distinct Monocytes. Exp Hematol 2018. [DOI: 10.1016/j.exphem.2018.06.178] [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: 11/25/2022]
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40
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Muench D, Ferchen K, Olsson A, Dwivedi P, Greis K, Verma A, Salomonis N, Grimes HL. Understanding Early Stage Myelodysplastic Syndrome Pathobiology. Exp Hematol 2018. [DOI: 10.1016/j.exphem.2018.06.104] [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: 10/28/2022]
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41
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Zhang C, D'Alessandro A, Wellendorf AM, Mohmoud F, Serrano-Lopez J, Perentesis JP, Komurov K, Alexe G, Stegmaier K, Whitsett JA, Grimes HL, Cancelas JA. KLF5 controls glutathione metabolism to suppress p190-BCR-ABL+ B-cell lymphoblastic leukemia. Oncotarget 2018; 9:29665-29679. [PMID: 30038712 PMCID: PMC6049869 DOI: 10.18632/oncotarget.25667] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 06/06/2018] [Indexed: 12/31/2022] Open
Abstract
High-risk B-cell acute lymphoblastic leukemia (B-ALL) remains a therapeutic challenge despite advances in the use of tyrosine kinase inhibitors and chimeric-antigen-receptor engineered T cells. Lymphoblastic-leukemia precursors are highly sensitive to oxidative stress. KLF5 is a member of the Krüppel-like family of transcription factors. KLF5 expression is repressed in B-ALL, including BCR-ABL1+ B-ALL. Here, we demonstrate that forced expression of KLF5 in B-ALL cells bypasses the imatinib resistance which is not associated with mutations of BCR-ABL. Expression of Klf5 impaired leukemogenic activity of BCR-ABL1+ B-cell precursors in vitro and in vivo. The complete genetic loss of Klf5 reduced oxidative stress, increased regeneration of reduced glutathione and decreased apoptosis of leukemic precursors. Klf5 regulation of glutathione levels was mediated by its regulation of glutathione-S-transferase Mu 1 (Gstm1), an important regulator of glutathione-mediated detoxification and protein glutathionylation. Expression of Klf5 or the direct Klf5 target gene Gstm1 inhibited clonogenic activity of Klf5∆/∆ leukemic B-cell precursors and unveiled a Klf5-dependent regulatory loop in glutamine-dependent glutathione metabolism. In summary, we describe a novel mechanism of Klf5 B-ALL suppressor activity through its direct role on the metabolism of antioxidant glutathione levels, a crucial positive regulator of leukemic precursor survival.
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Affiliation(s)
- Cuiping Zhang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz, Aurora, CO, USA
| | - Ashley M Wellendorf
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Fatima Mohmoud
- Hoxworth Blood Center, University of Cincinnati, Cincinnati, OH, USA
| | - Juana Serrano-Lopez
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - John P Perentesis
- Department of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kakajan Komurov
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Gabriela Alexe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, Boston, MA, USA.,Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, Boston, MA, USA.,Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeffrey A Whitsett
- Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - H Leighton Grimes
- Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jose A Cancelas
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Hoxworth Blood Center, University of Cincinnati, Cincinnati, OH, USA
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42
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Kleeman B, Olsson A, Newkold T, Kofron M, DeLay M, Hildeman D, Grimes HL. A guide to choosing fluorescent protein combinations for flow cytometric analysis based on spectral overlap. Cytometry A 2018; 93:556-562. [PMID: 29533508 PMCID: PMC8008483 DOI: 10.1002/cyto.a.23360] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 07/10/2017] [Revised: 02/06/2018] [Accepted: 02/20/2018] [Indexed: 11/11/2022]
Abstract
The advent of facile genome engineering technologies has made the generation of knock-in gene-expression or fusion-protein reporters more tractable. Fluorescent protein labeling of specific genes combined with surface marker profiling can more specifically identify a cell population. However, the question of which fluorescent proteins to utilize to generate reporter constructs is made difficult by the number of candidate proteins and the lack of updated experimental data on newer fluorescent proteins. Compounding this problem, most fluorescent proteins are designed and tested for use in microscopy. To address this, we cloned and characterized the detection sensitivity, spectral overlap, and spillover spreading of 13 monomeric fluorescent proteins to determine utility in multicolor panels. We identified a group of five fluorescent proteins with high signal to noise ratio, minimal spectral overlap, and low spillover spreading making them compatible for multicolor experiments. Specifically, generating reporters with combinations of three of these proteins would allow efficient measurements even at low-level expression. Because the proteins are monomeric, they could function either as gene-expression or as fusion-protein reporters. Additionally, this approach can be generalized as new fluorescent proteins are developed to determine their usefulness in multicolor panels. © 2018 International Society for Advancement of Cytometry.
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Affiliation(s)
- Benjamin Kleeman
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Andre Olsson
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Tess Newkold
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Matt Kofron
- Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229
| | - Monica DeLay
- Division of Rheumatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - David Hildeman
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - H. Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, USA
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43
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Zhou Y, Yan X, Feng X, Bu J, Dong Y, Lin P, Hayashi Y, Huang R, Olsson A, Andreassen PR, Grimes HL, Wang QF, Cheng T, Xiao Z, Jin J, Huang G. Setd2 regulates quiescence and differentiation of adult hematopoietic stem cells by restricting RNA polymerase II elongation. Haematologica 2018; 103:1110-1123. [PMID: 29650642 PMCID: PMC6029524 DOI: 10.3324/haematol.2018.187708] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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] [Received: 01/03/2018] [Accepted: 04/06/2018] [Indexed: 12/27/2022] Open
Abstract
SET domain containing 2 (Setd2), encoding a histone methyltransferase, is associated with many hematopoietic diseases when mutated. By generating a novel exon 6 conditional knockout mouse model, we describe an essential role of Setd2 in maintaining the adult hematopoietic stem cells. Loss of Setd2 results in leukopenia, anemia, and increased platelets accompanied by hypocellularity, erythroid dysplasia, and mild fibrosis in bone marrow. Setd2 knockout mice show significantly decreased hematopoietic stem and progenitor cells except for erythroid progenitors. Setd2 knockout hematopoietic stem cells fail to establish long-term bone marrow reconstitution after transplantation because of the loss of quiescence, increased apoptosis, and reduced multiple-lineage terminal differentiation potential. Bioinformatic analysis revealed that the hematopoietic stem cells exit from quiescence and commit to differentiation, which lead to hematopoietic stem cell exhaustion. Mechanistically, we attribute an important Setd2 function in murine adult hematopoietic stem cells to the inhibition of the Nsd1/2/3 transcriptional complex, which recruits super elongation complex and controls RNA polymerase II elongation on a subset of target genes, including Myc. Our results reveal a critical role of Setd2 in regulating quiescence and differentiation of hematopoietic stem cells through restricting the NSDs/SEC mediated RNA polymerase II elongation.
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Affiliation(s)
- Yile Zhou
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Division of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Xiaomei Yan
- Division of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Xiaomin Feng
- Division of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Jiachen Bu
- Division of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, OH, USA.,Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
| | - Yunzhu Dong
- Division of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Peipei Lin
- Division of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Yoshihiro Hayashi
- Division of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Rui Huang
- Division of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Andre Olsson
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Paul R Andreassen
- Division of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, OH, USA
| | - H Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, OH, USA
| | - Qian-Fei Wang
- Laboratory of Genome Variations and Precision Bio-Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital and Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Zhijian Xiao
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital and Center for Stem Cell Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jie Jin
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Gang Huang
- Division of Pathology and Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, OH, USA
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44
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Lee JM, Govindarajah V, Goddard B, Hinge A, Muench DE, Filippi MD, Aronow B, Cancelas JA, Salomonis N, Grimes HL, Reynaud D. Obesity alters the long-term fitness of the hematopoietic stem cell compartment through modulation of Gfi1 expression. J Exp Med 2017; 215:627-644. [PMID: 29282250 PMCID: PMC5789409 DOI: 10.1084/jem.20170690] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [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] [Received: 04/13/2017] [Revised: 08/31/2017] [Accepted: 11/16/2017] [Indexed: 12/13/2022] Open
Abstract
Lee et al. show that established obesity alters the composition and long-term fitness of the hematopoietic stem cell (HSC) compartment, in part through a Gfi1-dependent HSC regulatory program that is activated by the chronic oxidative stress associated with this condition. Obesity is a chronic organismal stress that disrupts multiple systemic and tissue-specific functions. In this study, we describe the impact of obesity on the activity of the hematopoietic stem cell (HSC) compartment. We show that obesity alters the composition of the HSC compartment and its activity in response to hematopoietic stress. The impact of obesity on HSC function is progressively acquired but persists after weight loss or transplantation into a normal environment. Mechanistically, we establish that the oxidative stress induced by obesity dysregulates the expression of the transcription factor Gfi1 and that increased Gfi1 expression is required for the abnormal HSC function induced by obesity. These results demonstrate that obesity produces durable changes in HSC function and phenotype and that elevation of Gfi1 expression in response to the oxidative environment is a key driver of the altered HSC properties observed in obesity. Altogether, these data provide phenotypic and mechanistic insight into durable hematopoietic dysregulations resulting from obesity.
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Affiliation(s)
- Jung-Mi Lee
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Vinothini Govindarajah
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Bryan Goddard
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Ashwini Hinge
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - David E Muench
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Marie-Dominique Filippi
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Bruce Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Jose A Cancelas
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Hoxworth Blood Center, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Damien Reynaud
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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45
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Muench DE, Kappes DJ, Salomonis N, Myers KC, Grimes HL. Severe congenital neutropenia-associated mutations induce aberrant stage-specific genetic programs that underlie broad myeloid defects. Exp Hematol 2017. [DOI: 10.1016/j.exphem.2017.06.076] [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: 11/26/2022]
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46
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Yanez A, Coetzee S, Olsson A, Berman B, Hazelett D, Salomonis N, Grimes HL, Goodridge H. Independent production of distinct monocyte subsets by granulocyte-monocyte progenitors (GMPS) and monocyte-dendritic cell progenitors (MDPS). Exp Hematol 2017. [DOI: 10.1016/j.exphem.2017.06.052] [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: 10/19/2022]
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47
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Yáñez A, Goodridge HS, Grimes HL. Counting the cost of lineage decisions. Nat Immunol 2017; 18:872-873. [PMID: 28722717 DOI: 10.1038/ni.3794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alberto Yáñez
- Board of Governors Regenerative Medicine Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Helen S Goodridge
- Board of Governors Regenerative Medicine Institute and the Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - H Leighton Grimes
- Division of Immunobiology and Center for Systems Immunology and the Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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48
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Kurkewich JL, Hansen J, Klopfenstein N, Zhang H, Wood C, Boucher A, Hickman J, Muench DE, Grimes HL, Dahl R. The miR-23a~27a~24-2 microRNA cluster buffers transcription and signaling pathways during hematopoiesis. PLoS Genet 2017; 13:e1006887. [PMID: 28704388 PMCID: PMC5531666 DOI: 10.1371/journal.pgen.1006887] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [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: 08/18/2016] [Revised: 07/27/2017] [Accepted: 06/21/2017] [Indexed: 02/07/2023] Open
Abstract
MicroRNA cluster mirn23a has previously been shown to promote myeloid development at the expense of lymphoid development in overexpression and knockout mouse models. This polarization is observed early in hematopoietic development, with an increase in common lymphoid progenitors (CLPs) and a decrease in all myeloid progenitor subsets in adult bone marrow. The pool size of multipotential progenitors (MPPs) is unchanged; however, in this report we observe by flow cytometry that polarized subsets of MPPs are changed in the absence of mirn23a. Additionally, in vitro culture of MPPs and sorted MPP transplants showed that these cells have decreased myeloid and increased lymphoid potential in vitro and in vivo. We investigated the mechanism by which mirn23a regulates hematopoietic differentiation and observed that mirn23a promotes myeloid development of hematopoietic progenitors through regulation of hematopoietic transcription factors and signaling pathways. Early transcription factors that direct the commitment of MPPs to CLPs (Ikzf1, Runx1, Satb1, Bach1 and Bach2) are increased in the absence of mirn23a miRNAs as well as factors that commit the CLP to the B cell lineage (FoxO1, Ebf1, and Pax5). Mirn23a appears to buffer transcription factor levels so that they do not stochastically reach a threshold level to direct differentiation. Intriguingly, mirn23a also inversely regulates the PI3 kinase (PI3K)/Akt and BMP/Smad signaling pathways. Pharmacological inhibitor studies, coupled with dominant active/dominant negative biochemical experiments, show that both signaling pathways are critical to mirn23a’s regulation of hematopoietic differentiation. Lastly, consistent with mirn23a being a physiological inhibitor of B cell development, we observed that the essential B cell transcription factor EBF1 represses expression of mirn23a. In summary, our data demonstrates that mirn23a regulates a complex array of transcription and signaling pathways to modulate adult hematopoiesis. MicroRNAs (miRNAs) are small ~22 nucleotide long RNA molecules that are involved in regulating multiple cellular processes through inhibiting the expression of target proteins. We previously identified a gene (mirn23a) that codes for 3 miRNAs that control the development of immune cells in the bone marrow. The miRNAs promote the development of innate immune cells, macrophages and granulocytes, while repressing the development of B cells. Here we show that mirn23a miRNAs negatively affect the expression of multiple proteins that are involved in directing blood progenitor cells to become B cells. Additionally, we observed that modulation of FoxO1 and Smad proteins, downstream effectors of two signaling pathways (PI3 kinase/ Akt and BMP/ Smad), is critical to direct immune cell development. This is the first observation that these pathways are potentially coregulated during the commitment of blood progenitors to mature cells of the immune system. Consistent with mirn23a being a critical gene for committing progenitors to innate immune cells at the expense of B cells, we observed that a critical B cell protein represses the expression of mirn23a. In conclusion, we demonstrate the mirn23a regulation of blood development is due to a complex regulation of both transcription factors and signaling pathways.
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Affiliation(s)
- Jeffrey L. Kurkewich
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Harper Cancer Research Institute, South Bend, IN, United States of America
| | - Justin Hansen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Harper Cancer Research Institute, South Bend, IN, United States of America
| | - Nathan Klopfenstein
- Harper Cancer Research Institute, South Bend, IN, United States of America
- Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, IN, United States of America
| | - Helen Zhang
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Harper Cancer Research Institute, South Bend, IN, United States of America
| | - Christian Wood
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Harper Cancer Research Institute, South Bend, IN, United States of America
| | - Austin Boucher
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Harper Cancer Research Institute, South Bend, IN, United States of America
| | - Joseph Hickman
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Harper Cancer Research Institute, South Bend, IN, United States of America
| | - David E. Muench
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States of America
| | - H. Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States of America
| | - Richard Dahl
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Harper Cancer Research Institute, South Bend, IN, United States of America
- Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, IN, United States of America
- * E-mail:
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Kesarwani M, Kincaid Z, Gomaa A, Huber E, Rohrabaugh S, Siddiqui Z, Bouso MF, Latif T, Xu M, Komurov K, Mulloy JC, Cancelas JA, Grimes HL, Azam M. Targeting c-FOS and DUSP1 abrogates intrinsic resistance to tyrosine-kinase inhibitor therapy in BCR-ABL-induced leukemia. Nat Med 2017; 23:472-482. [PMID: 28319094 PMCID: PMC5424814 DOI: 10.1038/nm.4310] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [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] [Received: 08/11/2016] [Accepted: 02/21/2017] [Indexed: 12/26/2022]
Abstract
Tyrosine kinase inhibitor (TKI) therapy for human cancers is not curative, with relapse due to the continuing presence of tumor cells, referred to as minimal residual disease (MRD) cells. MRD stem or progenitor cells survival in the absence of oncogenic kinase signaling, a phenomenon referred to as intrinsic resistance, depends on diverse growth factors. Here, we report that oncogenic kinase and growth factor signaling converge to induce the expression of the signaling proteins c-Fos and Dusp1. Genetic deletion of c-Fos and Dusp1 suppressed tumor growth in a BCR-ABL-induced mouse model of chronic myeloid leukemia (CML). Pharmacological inhibition of c-Fos, Dusp1 and BCR-ABL eradicated MRD in multiple in vivo models, as well as in primary CML patient xenotransplanted mice. Growth factor signaling also conferred TKI resistance and induced c-FOS and DUSP1 expression in tumor cells modeling other types of kinase-driven leukemias. Our data demonstrate that c-Fos and Dusp1 expression levels determine the threshold of TKI efficacy, such that growth factor-induced expression of c-Fos and Dusp1 confers intrinsic resistance to TKI therapy in a wide-ranging set of leukemias, and may represent a unifying Achilles heel of kinase-driven cancers.
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Affiliation(s)
- Meenu Kesarwani
- Division of Experimental Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Zachary Kincaid
- Division of Experimental Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Ahmed Gomaa
- Division of Experimental Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Erika Huber
- Division of Experimental Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Sara Rohrabaugh
- Division of Experimental Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Zain Siddiqui
- Division of Experimental Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Muhammad F Bouso
- Division of Experimental Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Tahir Latif
- Department of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Ming Xu
- Department of Anesthesia and Critical Care, University of Chicago, Chicago, Illinois, USA
| | - Kakajan Komurov
- Division of Experimental Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - James C Mulloy
- Division of Experimental Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jose A Cancelas
- Division of Experimental Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - H Leighton Grimes
- Division of Experimental Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Mohammad Azam
- Division of Experimental Hematology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Division of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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50
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Li KP, Fähnrich A, Roy E, Cuda CM, Grimes HL, Perlman HR, Kalies K, Hildeman DA. Temporal Expression of Bim Limits the Development of Agonist-Selected Thymocytes and Skews Their TCRβ Repertoire. J Immunol 2016; 198:257-269. [PMID: 27852740 DOI: 10.4049/jimmunol.1601200] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/25/2016] [Indexed: 12/11/2022]
Abstract
CD8αα TCRαβ+ intestinal intraepithelial lymphocytes play a critical role in promoting intestinal homeostasis, although mechanisms controlling their development and peripheral homeostasis remain unclear. In this study, we examined the spatiotemporal role of Bim in the thymic selection of CD8αα precursors and the fate of these cells in the periphery. We found that T cell-specific expression of Bim during early/cortical, but not late/medullary, thymic development controls the agonist selection of CD8αα precursors and limits their private TCRβ repertoire. During this process, agonist-selected double-positive cells lose CD4/8 coreceptor expression and masquerade as double-negative (DN) TCRαβhi thymocytes. Although these DN thymocytes fail to re-express coreceptors after OP9-DL1 culture, they eventually mature and accumulate in the spleen where TCR and IL-15/STAT5 signaling promotes their conversion to CD8αα cells and their expression of gut-homing receptors. Adoptive transfer of splenic DN cells gives rise to CD8αα cells in the gut, establishing their precursor relationship in vivo. Interestingly, Bim does not restrict the IL-15-driven maturation of CD8αα cells that is critical for intestinal homeostasis. Thus, we found a temporal and tissue-specific role for Bim in limiting thymic agonist selection of CD8αα precursors and their TCRβ repertoire, but not in the maintenance of CD8αα intraepithelial lymphocytes in the intestine.
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Affiliation(s)
- Kun-Po Li
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45257
| | - Anke Fähnrich
- Institute for Anatomy, University of Lübeck, 23538 Lübeck, Germany; and
| | - Eron Roy
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45257
| | - Carla M Cuda
- Rheumatology Division, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45257
| | - Harris R Perlman
- Rheumatology Division, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Kathrin Kalies
- Institute for Anatomy, University of Lübeck, 23538 Lübeck, Germany; and
| | - David A Hildeman
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229; .,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45257
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