1
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Stonehouse OJ, Biben C, Weber TS, Garnham A, Fennell KA, Farley A, Terreaux AF, Alexander WS, Dawson MA, Naik SH, Taoudi S. Clonal analysis of fetal hematopoietic stem/progenitor cells reveals how post-transplantation capabilities are distributed. Stem Cell Reports 2024; 19:1189-1204. [PMID: 39094562 PMCID: PMC11368694 DOI: 10.1016/j.stemcr.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 07/02/2024] [Accepted: 07/02/2024] [Indexed: 08/04/2024] Open
Abstract
It has been proposed that adult hematopoiesis is sustained by multipotent progenitors (MPPs) specified during embryogenesis. Adult-like hematopoietic stem cell (HSC) and MPP immunophenotypes are present in the fetus, but knowledge of their functional capacity is incomplete. We found that fetal MPP populations were functionally similar to adult cells, albeit with some differences in lymphoid output. Clonal assessment revealed that lineage biases arose from differences in patterns of single-/bi-lineage differentiation. Long-term (LT)- and short-term (ST)-HSC populations were distinguished from MPPs according to capacity for clonal multilineage differentiation. We discovered that a large cohort of long-term repopulating units (LT-RUs) resides within the ST-HSC population; a significant portion of these were labeled using Flt3-cre. This finding has two implications: (1) use of the CD150+ LT-HSC immunophenotype alone will significantly underestimate the size and diversity of the LT-RU pool and (2) LT-RUs in the ST-HSC population have the attributes required to persist into adulthood.
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Affiliation(s)
- Olivia J Stonehouse
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; The University of Melbourne, Melbourne, Victoria, Australia; Lowy Cancer Research Centre, UNSW, Sydney, New South Wales, Australia
| | - Christine Biben
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; The University of Melbourne, Melbourne, Victoria, Australia
| | - Tom S Weber
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; The University of Melbourne, Melbourne, Victoria, Australia
| | - Alexandra Garnham
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; The University of Melbourne, Melbourne, Victoria, Australia
| | - Katie A Fennell
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alison Farley
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; The University of Melbourne, Melbourne, Victoria, Australia
| | - Antoine F Terreaux
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; The University of Melbourne, Melbourne, Victoria, Australia
| | - Warren S Alexander
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; The University of Melbourne, Melbourne, Victoria, Australia
| | - Mark A Dawson
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia; The University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Shalin H Naik
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; The University of Melbourne, Melbourne, Victoria, Australia
| | - Samir Taoudi
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia; The University of Melbourne, Melbourne, Victoria, Australia; School of Cellular and Molecular Medicine, University of Bristol, Bristol, England, UK.
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2
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Elias HK, Mitra S, da Silva MB, Rajagopalan A, Gipson B, Lee N, Kousa AI, Ali MAE, Grassman S, Zhang X, DeWolf S, Smith M, Andrlova H, Argyropoulos KV, Sharma R, Fei T, Sun JC, Dunbar CE, Park CY, Leslie CS, Bhandoola A, van den Brink MRM. An epigenetically distinct HSC subset supports thymic reconstitution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597775. [PMID: 38895335 PMCID: PMC11185715 DOI: 10.1101/2024.06.06.597775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Hematopoietic stem cells (HSCs) with multilineage potential are critical for effective T cell reconstitution and restoration of the adaptive immune system after allogeneic Hematopoietic Cell Transplantation (allo-HCT). The Kit lo subset of HSCs is enriched for multipotential precursors, 1, 2 but their T-cell lineage potential has not been well-characterized. We therefore studied the thymic reconstituting and T-cell potential of Kit lo HSCs. Using a preclinical allo-HCT model, we demonstrate that Kit lo HSCs support better thymic recovery, and T-cell reconstitution resulting in improved T cell responses to infection post-HCT. Furthermore, Kit lo HSCs with augmented BM lymphopoiesis mitigate age-associated thymic alterations, thus enhancing T-cell recovery in middle-aged hosts. We find the frequency of the Kit lo subset declines with age, providing one explanation for the reduced frequency of T-competent HSCs and reduced T-lymphopoietic potential in BM precursors of aged mice. 3, 4, 5 Chromatin profiling revealed that Kit lo HSCs exhibit higher activity of lymphoid-specifying transcription factors (TFs), including Zbtb1 . Deletion of Zbtb1 in Kit lo HSCs diminished their T-cell potential, while reinstating Zbtb1 in megakaryocytic-biased Kit hi HSCs rescued T-cell potential, in vitro and in vivo . Finally, we discover an analogous Kit lo HSC subset with enhanced lymphoid potential in human bone marrow. Our results demonstrate that Kit lo HSCs with enhanced lymphoid potential have a distinct underlying epigenetic program.
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3
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Liu W, Kurkewich JL, Stoddart A, Khan S, Anandan D, Gaubil AN, Wolfgeher DJ, Jueng L, Kron SJ, McNerney ME. CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex. Cell Rep 2024; 43:114227. [PMID: 38735044 PMCID: PMC11163479 DOI: 10.1016/j.celrep.2024.114227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 03/16/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
CUX1 is a homeodomain-containing transcription factor that is essential for the development and differentiation of multiple tissues. CUX1 is recurrently mutated or deleted in cancer, particularly in myeloid malignancies. However, the mechanism by which CUX1 regulates gene expression and differentiation remains poorly understood, creating a barrier to understanding the tumor-suppressive functions of CUX1. Here, we demonstrate that CUX1 directs the BAF chromatin remodeling complex to DNA to increase chromatin accessibility in hematopoietic cells. CUX1 preferentially regulates lineage-specific enhancers, and CUX1 target genes are predictive of cell fate in vivo. These data indicate that CUX1 regulates hematopoietic lineage commitment and homeostasis via pioneer factor activity, and CUX1 deficiency disrupts these processes in stem and progenitor cells, facilitating transformation.
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Affiliation(s)
- Weihan Liu
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA; Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA
| | | | - Angela Stoddart
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Saira Khan
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Dhivyaa Anandan
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Alexandre N Gaubil
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Donald J Wolfgeher
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Lia Jueng
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA
| | - Stephen J Kron
- The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA; Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Megan E McNerney
- Department of Pathology, The University of Chicago, Chicago, IL 60637, USA; The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, IL 60637, USA; Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, IL 60637, USA.
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4
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Fowler JL, Zheng SL, Nguyen A, Chen A, Xiong X, Chai T, Chen JY, Karigane D, Banuelos AM, Niizuma K, Kayamori K, Nishimura T, Cromer MK, Gonzalez-Perez D, Mason C, Liu DD, Yilmaz L, Miquerol L, Porteus MH, Luca VC, Majeti R, Nakauchi H, Red-Horse K, Weissman IL, Ang LT, Loh KM. Lineage-tracing hematopoietic stem cell origins in vivo to efficiently make human HLF+ HOXA+ hematopoietic progenitors from pluripotent stem cells. Dev Cell 2024; 59:1110-1131.e22. [PMID: 38569552 PMCID: PMC11072092 DOI: 10.1016/j.devcel.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/05/2023] [Accepted: 03/01/2024] [Indexed: 04/05/2024]
Abstract
The developmental origin of blood-forming hematopoietic stem cells (HSCs) is a longstanding question. Here, our non-invasive genetic lineage tracing in mouse embryos pinpoints that artery endothelial cells generate HSCs. Arteries are transiently competent to generate HSCs for 2.5 days (∼E8.5-E11) but subsequently cease, delimiting a narrow time frame for HSC formation in vivo. Guided by the arterial origins of blood, we efficiently and rapidly differentiate human pluripotent stem cells (hPSCs) into posterior primitive streak, lateral mesoderm, artery endothelium, hemogenic endothelium, and >90% pure hematopoietic progenitors within 10 days. hPSC-derived hematopoietic progenitors generate T, B, NK, erythroid, and myeloid cells in vitro and, critically, express hallmark HSC transcription factors HLF and HOXA5-HOXA10, which were previously challenging to upregulate. We differentiated hPSCs into highly enriched HLF+ HOXA+ hematopoietic progenitors with near-stoichiometric efficiency by blocking formation of unwanted lineages at each differentiation step. hPSC-derived HLF+ HOXA+ hematopoietic progenitors could avail both basic research and cellular therapies.
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Affiliation(s)
- Jonas L Fowler
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Sherry Li Zheng
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Alana Nguyen
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Angela Chen
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Xiaochen Xiong
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Timothy Chai
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Julie Y Chen
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Daiki Karigane
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Allison M Banuelos
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kouta Niizuma
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kensuke Kayamori
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Toshinobu Nishimura
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - M Kyle Cromer
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Charlotte Mason
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Daniel Dan Liu
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Leyla Yilmaz
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Lucile Miquerol
- Aix-Marseille Université, CNRS UMR 7288, IBDM, Marseille 13288, France
| | - Matthew H Porteus
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Vincent C Luca
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Ravindra Majeti
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kristy Red-Horse
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Lay Teng Ang
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Kyle M Loh
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
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5
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Ha SY, Kim JY, Choi JH. Transcriptional regulation of genetic variants in the SLC40A1 promoter. THE KOREAN JOURNAL OF PHYSIOLOGY & PHARMACOLOGY : OFFICIAL JOURNAL OF THE KOREAN PHYSIOLOGICAL SOCIETY AND THE KOREAN SOCIETY OF PHARMACOLOGY 2024; 28:113-120. [PMID: 38414394 PMCID: PMC10902591 DOI: 10.4196/kjpp.2024.28.2.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/27/2023] [Accepted: 12/02/2023] [Indexed: 02/29/2024]
Abstract
Solute carrier 40A1 (SLC40A1) encodes ferroportin, which is the only known transmembrane protein that exports elemental iron from mammalian cells and is essential for iron homeostasis. Mutations in SLC40A1 are associated with iron-overload disorders. In addition to ferroportin diseases, SLC40A1 expression is downregulated in various cancer types. Despite the clinical significance of the SLC40A1 transporter, only a few studies have investigated genetic variants in SLC40A1. The present study was performed to identify genetic variations in the SLC40A1 promoter and functionally characterize each variant using in vitro assays. We investigated four haplotypes and five variants in the SLC40A1 promoter. We observed that haplotype 3 (H3) had significantly lower promoter activity than H1, whereas the activity of H4 was significantly higher than that of H1. Luciferase activity of H2 was comparable to that of H1. In addition, four variants of SLC40A1, c.-1355G>C, c.-662C>T, c.-98G>C, and c.-8C>G, showed significantly increased luciferase activity compared to the wild type (WT), whereas c.-750G>A showed significantly decreased luciferase activity compared to the WT. Three transcription factors, cAMP response element-binding protein-1 (CREB-1), chicken ovalbumin upstream promoter transcription factor 1, and hepatic leukemia factor (HLF), were predicted to bind to the promoter regions of SLC40A1 near c.-662C>T, c.-98G>C, and c.-8C>G, respectively. Among these, CREB-1 and HLF bound more strongly to the variant sequences than to the WT and functioned as activators of SLC40A1 transcription. Collectively, our findings indicate that the two SLC40A1 promoter haplotypes affect SLC40A1 transcription, which is regulated by CREB-1 and HLF.
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Affiliation(s)
- Seung Yeon Ha
- Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Jin-Young Kim
- Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Ji Ha Choi
- Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul 07804, Korea
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6
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McClatchy J, Strogantsev R, Wolfe E, Lin HY, Mohammadhosseini M, Davis BA, Eden C, Goldman D, Fleming WH, Conley P, Wu G, Cimmino L, Mohammed H, Agarwal A. Clonal hematopoiesis related TET2 loss-of-function impedes IL1β-mediated epigenetic reprogramming in hematopoietic stem and progenitor cells. Nat Commun 2023; 14:8102. [PMID: 38062031 PMCID: PMC10703894 DOI: 10.1038/s41467-023-43697-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
Clonal hematopoiesis (CH) is defined as a single hematopoietic stem/progenitor cell (HSPC) gaining selective advantage over a broader range of HSPCs. When linked to somatic mutations in myeloid malignancy-associated genes, such as TET2-mediated clonal hematopoiesis of indeterminate potential or CHIP, it represents increased risk for hematological malignancies and cardiovascular disease. IL1β is elevated in patients with CHIP, however, its effect is not well understood. Here we show that IL1β promotes expansion of pro-inflammatory monocytes/macrophages, coinciding with a failure in the demethylation of lymphoid and erythroid lineage associated enhancers and transcription factor binding sites, in a mouse model of CHIP with hematopoietic-cell-specific deletion of Tet2. DNA-methylation is significantly lost in wild type HSPCs upon IL1β administration, which is resisted by Tet2-deficient HSPCs, and thus IL1β enhances the self-renewing ability of Tet2-deficient HSPCs by upregulating genes associated with self-renewal and by resisting demethylation of transcription factor binding sites related to terminal differentiation. Using aged mouse models and human progenitors, we demonstrate that targeting IL1 signaling could represent an early intervention strategy in preleukemic disorders. In summary, our results show that Tet2 is an important mediator of an IL1β-promoted epigenetic program to maintain the fine balance between self-renewal and lineage differentiation during hematopoiesis.
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Affiliation(s)
- J McClatchy
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - R Strogantsev
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - E Wolfe
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - H Y Lin
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - M Mohammadhosseini
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - B A Davis
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - C Eden
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - D Goldman
- Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, OR, USA
- Division of Pediatric Hematology and Oncology, Oregon Health & Science University, Portland, OR, USA
| | - W H Fleming
- Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, OR, USA
- Division of Pediatric Hematology and Oncology, Oregon Health & Science University, Portland, OR, USA
| | - P Conley
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - G Wu
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR, USA
| | - L Cimmino
- University of Miami, Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, Miami, USA
| | - H Mohammed
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - A Agarwal
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA.
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA.
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
- Division of Hematology & Medical Oncology, Oregon Health & Science University, Portland, OR, USA.
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA.
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7
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Hurwitz SN, Jung SK, Kobulsky DR, Fazelinia H, Spruce LA, Pérez EB, Groen N, Mesaros C, Kurre P. Neutral sphingomyelinase blockade enhances hematopoietic stem cell fitness through an integrated stress response. Blood 2023; 142:1708-1723. [PMID: 37699202 PMCID: PMC10667352 DOI: 10.1182/blood.2023022147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/14/2023] Open
Abstract
Hematopoietic stem and progenitor cell (HSPC) transplantation serves as a curative therapy for many benign and malignant hematopoietic disorders and as a platform for gene therapy. However, growing needs for ex vivo manipulation of HSPC-graft products are limited by barriers in maintaining critical self-renewal and quiescence properties. The role of sphingolipid metabolism in safeguarding these essential cellular properties has been recently recognized, but not yet widely explored. Here, we demonstrate that pharmacologic and genetic inhibition of neutral sphingomyelinase 2 (nSMase-2) leads to sustained improvements in long-term competitive transplantation efficiency after ex vivo culture. Mechanistically, nSMase-2 blockade activates a canonical integrated stress response (ISR) and promotes metabolic quiescence in human and murine HSPCs. These adaptations result in part from disruption in sphingolipid metabolism that impairs the release of nSMase-2-dependent extracellular vesicles (EVs). The aggregate findings link EV trafficking and the ISR as a regulatory dyad guarding HSPC homeostasis and long-term fitness. Translationally, transient nSMase-2 inhibition enables ex vivo graft manipulation with enhanced HSPC potency.
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Affiliation(s)
- Stephanie N. Hurwitz
- Comprehensive Bone Marrow Failure Center, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Seul K. Jung
- Comprehensive Bone Marrow Failure Center, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Danielle R. Kobulsky
- Comprehensive Bone Marrow Failure Center, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hossein Fazelinia
- Proteomics Core Facility, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Lynn A. Spruce
- Proteomics Core Facility, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Clementina Mesaros
- Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA
| | - Peter Kurre
- Comprehensive Bone Marrow Failure Center, Children's Hospital of Philadelphia, Philadelphia, PA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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8
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Han T, Chen T, Chen L, Li K, Xiang D, Dou L, Li H, Gu Y. HLF promotes ovarian cancer progression and chemoresistance via regulating Hippo signaling pathway. Cell Death Dis 2023; 14:606. [PMID: 37709768 PMCID: PMC10502110 DOI: 10.1038/s41419-023-06076-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/05/2023] [Accepted: 08/15/2023] [Indexed: 09/16/2023]
Abstract
Hepatic leukemia factor (HLF) is aberrantly expressed in human malignancies. However, the role of HLF in the regulation of ovarian cancer (OC) remains unknown. Herein, we reported that HLF expression was upregulated in OC tissues and ovarian cancer stem cells (CSCs). Functional studies have revealed that HLF regulates OC cell stemness, proliferation, and metastasis. Mechanistically, HLF transcriptionally activated Yes-associated protein 1 (YAP1) expression and subsequently modulated the Hippo signaling pathway. Moreover, we found that miR-520e directly targeted HLF 3'-UTR in OC cells. miR-520e expression was negatively correlated with HLF and YAP1 expression in OC tissues. The combined immunohistochemical (IHC) panels exhibited a better prognostic value for OC patients than any of these components alone. Importantly, the HLF/YAP1 axis determines the response of OC cells to carboplatin treatment and HLF depletion or the YAP1 inhibitor verteporfin abrogated carboplatin resistance. Analysis of patient-derived xenografts (PDXs) further suggested that HLF might predict carboplatin benefits in OC patients. In conclusion, these findings suggest a crucial role of the miR-520e/HLF/YAP1 axis in OC progression and chemoresistance, suggesting potential therapeutic targets for OC.
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Affiliation(s)
- Tao Han
- Department of Oncology, The First Affiliated Hospital of China Medical University, Shenyang, 110001, Liaoning, China
| | - Tingsong Chen
- Department of Cancer Intervention, Seventh People's Hospital of Shanghai University of TCM, Shanghai, 200001, China
| | - Lujun Chen
- Department of Oncology, The First Affiliated Hospital of China Medical University, Shenyang, 110001, Liaoning, China
- Postgraduate College, China Medical University, Shenyang, 110001, China
| | - Kerui Li
- Department of Oncology, The First Affiliated Hospital of China Medical University, Shenyang, 110001, Liaoning, China
| | - Daimin Xiang
- Clinical Cancer Institute, Center for Translational Medicine, Naval Military Medical University, Shanghai, 200433, China
- Department of hepatobiliary surgery, East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
| | - Lei Dou
- Department of Gynecology, The First Affiliated Hospital of China Medical University, Shenyang, 110001, Liaoning, China.
| | - Hengyu Li
- Department of Breast and Thyroid Surgery, Changhai Hospital, Naval Military Medical University, Shanghai, 200433, China.
| | - Yubei Gu
- Department of Gastroenterology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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9
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Lara-Astiaso D, Goñi-Salaverri A, Mendieta-Esteban J, Narayan N, Del Valle C, Gross T, Giotopoulos G, Beinortas T, Navarro-Alonso M, Aguado-Alvaro LP, Zazpe J, Marchese F, Torrea N, Calvo IA, Lopez CK, Alignani D, Lopez A, Saez B, Taylor-King JP, Prosper F, Fortelny N, Huntly BJP. In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis. Nat Genet 2023; 55:1542-1554. [PMID: 37580596 PMCID: PMC10484791 DOI: 10.1038/s41588-023-01471-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 07/11/2023] [Indexed: 08/16/2023]
Abstract
Cellular differentiation requires extensive alterations in chromatin structure and function, which is elicited by the coordinated action of chromatin and transcription factors. By contrast with transcription factors, the roles of chromatin factors in differentiation have not been systematically characterized. Here, we combine bulk ex vivo and single-cell in vivo CRISPR screens to characterize the role of chromatin factor families in hematopoiesis. We uncover marked lineage specificities for 142 chromatin factors, revealing functional diversity among related chromatin factors (i.e. barrier-to-autointegration factor subcomplexes) as well as shared roles for unrelated repressive complexes that restrain excessive myeloid differentiation. Using epigenetic profiling, we identify functional interactions between lineage-determining transcription factors and several chromatin factors that explain their lineage dependencies. Studying chromatin factor functions in leukemia, we show that leukemia cells engage homeostatic chromatin factor functions to block differentiation, generating specific chromatin factor-transcription factor interactions that might be therapeutically targeted. Together, our work elucidates the lineage-determining properties of chromatin factors across normal and malignant hematopoiesis.
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Affiliation(s)
- David Lara-Astiaso
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
| | | | | | - Nisha Narayan
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Cynthia Del Valle
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | - George Giotopoulos
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Tumas Beinortas
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Mar Navarro-Alonso
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | - Jon Zazpe
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Francesco Marchese
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Natalia Torrea
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Isabel A Calvo
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Cecile K Lopez
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Diego Alignani
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Aitziber Lopez
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Borja Saez
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | - Felipe Prosper
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Nikolaus Fortelny
- Department of Biosciences & Medical Biology, University of Salzburg, Salzburg, Austria.
| | - Brian J P Huntly
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
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10
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Bocova L, Hubens W, Engel C, Koschmieder S, Jost E, Wagner W. Quantification of hematopoietic stem and progenitor cells by targeted DNA methylation analysis. Clin Epigenetics 2023; 15:105. [PMID: 37370186 DOI: 10.1186/s13148-023-01521-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are quantified in daily clinical practice by flow cytometry. In this study, we provide proof of concept that HSPCs can also be estimated by targeted DNA methylation (DNAm) analysis. The DNAm levels at three individual CG dinucleotides (CpG sites) in the genes MYO1D, STK17A, and SP140 correlated with CD34+ cell numbers in mobilized peripheral blood and with blast counts in leukemia. In the future, such epigenetic biomarkers can support the evaluation of stem cell mobilization, HSPC harvesting, or blast count in leukemia.
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Affiliation(s)
- Ledio Bocova
- Institute for Stem Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Wouter Hubens
- Institute for Stem Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Cordula Engel
- Department of Gynecology and Obstetrics, University Hospital of RWTH Aachen, Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, University Hospital of RWTH Aachen, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Edgar Jost
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, University Hospital of RWTH Aachen, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Wolfgang Wagner
- Institute for Stem Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany.
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany.
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany.
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11
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Konturek-Ciesla A, Dhapola P, Zhang Q, Säwén P, Wan H, Karlsson G, Bryder D. Temporal multimodal single-cell profiling of native hematopoiesis illuminates altered differentiation trajectories with age. Cell Rep 2023; 42:112304. [PMID: 36961818 DOI: 10.1016/j.celrep.2023.112304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/16/2023] [Accepted: 03/08/2023] [Indexed: 03/25/2023] Open
Abstract
Aging negatively affects hematopoiesis, with consequences for immunity and acquired blood cell disorders. Although impairments in hematopoietic stem cell (HSC) function contribute to this, the in vivo dynamics of such changes remain obscure. Here, we integrate extensive longitudinal functional assessments of HSC-specific lineage tracing with single-cell transcriptome and epitope profiling. In contrast to recent suggestions from single-cell RNA sequencing alone, our data favor a defined structure of HSC/progenitor differentiation that deviates substantially from HSC-derived hematopoiesis following transplantation. Native age-dependent attrition in HSC differentiation manifests as drastically reduced lymphoid output through an early lymphoid-primed progenitor (MPP Ly-I). While in vitro activation fails to rescue lymphoid differentiation from most aged HSCs, robust lymphopoiesis can be achieved by culturing elevated numbers of candidate HSCs. Therefore, our data position rare chronologically aged HSC clones, fully competent at producing lymphoid offspring, as a prime target for approaches aimed to improve lymphopoiesis in the elderly.
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Affiliation(s)
- Anna Konturek-Ciesla
- Division of Molecular Hematology, Department of Laboratory Medicine, Medical Faculty, Lund University, Lund, Sweden
| | - Parashar Dhapola
- Division of Molecular Hematology, Department of Laboratory Medicine, Medical Faculty, Lund University, Lund, Sweden
| | - Qinyu Zhang
- Division of Molecular Hematology, Department of Laboratory Medicine, Medical Faculty, Lund University, Lund, Sweden
| | - Petter Säwén
- Division of Molecular Hematology, Department of Laboratory Medicine, Medical Faculty, Lund University, Lund, Sweden
| | - Haixia Wan
- Division of Molecular Hematology, Department of Laboratory Medicine, Medical Faculty, Lund University, Lund, Sweden
| | - Göran Karlsson
- Division of Molecular Hematology, Department of Laboratory Medicine, Medical Faculty, Lund University, Lund, Sweden
| | - David Bryder
- Division of Molecular Hematology, Department of Laboratory Medicine, Medical Faculty, Lund University, Lund, Sweden.
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12
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Xiang D, Gu M, Liu J, Dong W, Yang Z, Wang K, Fu J, Wang H. m6A RNA methylation-mediated upregulation of HLF promotes intrahepatic cholangiocarcinoma progression by regulating the FZD4/β-catenin signaling pathway. Cancer Lett 2023; 560:216144. [PMID: 36958694 DOI: 10.1016/j.canlet.2023.216144] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 02/25/2023] [Accepted: 03/21/2023] [Indexed: 03/25/2023]
Abstract
Hepatic leukemia factor (HLF) is aberrantly expressed in human malignancies. However, its role in regulating intrahepatic cholangiocarcinoma (ICC) remains unclear. This study aimed to define the role of HLF in ICC progression. Here, we showed that HLF expression is upregulated in ICC and predicts the poor prognosis in patients. Mechanistically, HLF activation in ICC is mediated by METTL3-dependent m6A methylation of the HLF mRNA. As per the results from the loss- or gain-of-function experiments, HLF promoted the self-renewal, tumorigenicity, proliferation and metastasis of ICC cells. RNA-seq and CUT&Tag analyses showed that frizzled-4 (FZD4) and forkhead box Q1 (FOXQ1) are target genes of HLF. Moreover, FOXQ1 transcriptionally activates METTL3 expression, forming a positive feedback loop, which subsequently activates WNT/β-catenin signaling and downstream tumor stemness. Furthermore, HLF expression was positively correlated with METTL3, IGF2BP3, FZD4 and FOXQ1 expression in ICC tissues in a large ICC cohort. The combined IHC panels exhibited a better prognostic value for patients with ICC than any of these components alone. In conclusions, these findings demonstrated that the METTL3/HLF/FOXQ1 regulatory circuit drove FZD4-mediated WNT/β-catenin activation in ICC progression, suggesting that targeting this axis could be novel therapeutic strategy for ICC.
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Affiliation(s)
- Daimin Xiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute(2), Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China; International Cooperation Laboratory on Signal Transduction, Ministry of Education Key Laboratory on Signaling Regulation and Targeting Therapy of Liver Cancer, Shanghai Key Laboratory of Hepato-biliary Tumor Biology, Third Affiliated Hospital of Naval Military Medical University, Shanghai, 200438, China; National Center for Liver Cancer, Shanghai, China
| | - Mingye Gu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute(2), Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China; International Cooperation Laboratory on Signal Transduction, Ministry of Education Key Laboratory on Signaling Regulation and Targeting Therapy of Liver Cancer, Shanghai Key Laboratory of Hepato-biliary Tumor Biology, Third Affiliated Hospital of Naval Military Medical University, Shanghai, 200438, China
| | - Junyu Liu
- International Cooperation Laboratory on Signal Transduction, Ministry of Education Key Laboratory on Signaling Regulation and Targeting Therapy of Liver Cancer, Shanghai Key Laboratory of Hepato-biliary Tumor Biology, Third Affiliated Hospital of Naval Military Medical University, Shanghai, 200438, China
| | - Wei Dong
- Department of Pathology, Third Affiliated Hospital of Naval Military Medical University, Shanghai, 200438, China
| | - Zhishi Yang
- Department of Hepatic Surgery, Third Affiliated Hospital of Naval Military Medical University, Shanghai, 200438, China
| | - Kui Wang
- Department of Hepatic Surgery, Third Affiliated Hospital of Naval Military Medical University, Shanghai, 200438, China.
| | - Jing Fu
- International Cooperation Laboratory on Signal Transduction, Ministry of Education Key Laboratory on Signaling Regulation and Targeting Therapy of Liver Cancer, Shanghai Key Laboratory of Hepato-biliary Tumor Biology, Third Affiliated Hospital of Naval Military Medical University, Shanghai, 200438, China; National Center for Liver Cancer, Shanghai, China.
| | - Hongyang Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute(2), Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China; International Cooperation Laboratory on Signal Transduction, Ministry of Education Key Laboratory on Signaling Regulation and Targeting Therapy of Liver Cancer, Shanghai Key Laboratory of Hepato-biliary Tumor Biology, Third Affiliated Hospital of Naval Military Medical University, Shanghai, 200438, China; National Center for Liver Cancer, Shanghai, China.
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13
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Hoch M, Rauthe J, Cesnulevicius K, Schultz M, Lescheid D, Wolkenhauer O, Chiurchiù V, Gupta S. Cell-Type-Specific Gene Regulatory Networks of Pro-Inflammatory and Pro-Resolving Lipid Mediator Biosynthesis in the Immune System. Int J Mol Sci 2023; 24:ijms24054342. [PMID: 36901771 PMCID: PMC10001763 DOI: 10.3390/ijms24054342] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Lipid mediators are important regulators in inflammatory responses, and their biosynthetic pathways are targeted by commonly used anti-inflammatory drugs. Switching from pro-inflammatory lipid mediators (PIMs) to specialized pro-resolving (SPMs) is a critical step toward acute inflammation resolution and preventing chronic inflammation. Although the biosynthetic pathways and enzymes for PIMs and SPMs have now been largely identified, the actual transcriptional profiles underlying the immune cell type-specific transcriptional profiles of these mediators are still unknown. Using the Atlas of Inflammation Resolution, we created a large network of gene regulatory interactions linked to the biosynthesis of SPMs and PIMs. By mapping single-cell sequencing data, we identified cell type-specific gene regulatory networks of the lipid mediator biosynthesis. Using machine learning approaches combined with network features, we identified cell clusters of similar transcriptional regulation and demonstrated how specific immune cell activation affects PIM and SPM profiles. We found substantial differences in regulatory networks in related cells, accounting for network-based preprocessing in functional single-cell analyses. Our results not only provide further insight into the gene regulation of lipid mediators in the immune response but also shed light on the contribution of selected cell types in their biosynthesis.
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Affiliation(s)
- Matti Hoch
- Department of Systems Biology and Bioinformatics, University of Rostock, 18055 Rostock, Germany
| | - Jannik Rauthe
- Department of Systems Biology and Bioinformatics, University of Rostock, 18055 Rostock, Germany
| | | | | | | | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, 18055 Rostock, Germany
- Leibniz-Institute for Food Systems Biology, Technical University of Munich, 85354 Freising, Germany
- Stellenbosch Institute of Advanced Study, Wallenberg Research Centre, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Valerio Chiurchiù
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
- Laboratory of Resolution of Neuroinflammation, IRCCS Santa Lucia Foundation, 00179 Rome, Italy
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, 18055 Rostock, Germany
- Correspondence:
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14
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Valakh V, Wise D, Zhu XA, Sha M, Fok J, Van Hooser SD, Schectman R, Cepeda I, Kirk R, O'Toole SM, Nelson SB. A transcriptional constraint mechanism limits the homeostatic response to activity deprivation in mammalian neocortex. eLife 2023; 12:e74899. [PMID: 36749029 PMCID: PMC10010687 DOI: 10.7554/elife.74899] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/03/2023] [Indexed: 02/08/2023] Open
Abstract
Healthy neuronal networks rely on homeostatic plasticity to maintain stable firing rates despite changing synaptic drive. These mechanisms, however, can themselves be destabilizing if activated inappropriately or excessively. For example, prolonged activity deprivation can lead to rebound hyperactivity and seizures. While many forms of homeostasis have been described, whether and how the magnitude of homeostatic plasticity is constrained remains unknown. Here, we uncover negative regulation of cortical network homeostasis by the PARbZIP family of transcription factors. In cortical slice cultures made from knockout mice lacking all three of these factors, the network response to prolonged activity withdrawal measured with calcium imaging is much stronger, while baseline activity is unchanged. Whole-cell recordings reveal an exaggerated increase in the frequency of miniature excitatory synaptic currents reflecting enhanced upregulation of recurrent excitatory synaptic transmission. Genetic analyses reveal that two of the factors, Hlf and Tef, are critical for constraining plasticity and for preventing life-threatening seizures. These data indicate that transcriptional activation is not only required for many forms of homeostatic plasticity but is also involved in restraint of the response to activity deprivation.
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Affiliation(s)
- Vera Valakh
- Department of Biology and Program in Neuroscience, Brandeis UniversityWalthamUnited States
| | - Derek Wise
- Department of Biology and Program in Neuroscience, Brandeis UniversityWalthamUnited States
| | - Xiaoyue Aelita Zhu
- Department of Biology and Program in Neuroscience, Brandeis UniversityWalthamUnited States
| | - Mingqi Sha
- Department of Biology and Program in Neuroscience, Brandeis UniversityWalthamUnited States
| | - Jaidyn Fok
- Department of Biology and Program in Neuroscience, Brandeis UniversityWalthamUnited States
| | - Stephen D Van Hooser
- Department of Biology and Program in Neuroscience, Brandeis UniversityWalthamUnited States
| | - Robin Schectman
- Department of Biology and Program in Neuroscience, Brandeis UniversityWalthamUnited States
| | - Isabel Cepeda
- Department of Biology and Program in Neuroscience, Brandeis UniversityWalthamUnited States
| | - Ryan Kirk
- Department of Biology and Program in Neuroscience, Brandeis UniversityWalthamUnited States
| | - Sean M O'Toole
- Department of Biology and Program in Neuroscience, Brandeis UniversityWalthamUnited States
| | - Sacha B Nelson
- Department of Biology and Program in Neuroscience, Brandeis UniversityWalthamUnited States
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15
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Rastogi N, Gonzalez JBM, Srivastava VK, Alanazi B, Alanazi RN, Hughes OM, O'Neill NS, Gilkes AF, Ashley N, Deshpande S, Andrews R, Mead A, Rodrigues NP, Knapper S, Darley RL, Tonks A. Nuclear factor I-C overexpression promotes monocytic development and cell survival in acute myeloid leukemia. Leukemia 2023; 37:276-287. [PMID: 36572750 PMCID: PMC9898032 DOI: 10.1038/s41375-022-01801-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022]
Abstract
Nuclear factor I-C (NFIC) belongs to a family of NFI transcription factors that binds to DNA through CAATT-boxes and are involved in cellular differentiation and stem cell maintenance. Here we show NFIC protein is significantly overexpressed in 69% of acute myeloid leukemia patients. Examination of the functional consequences of NFIC overexpression in HSPCs showed that this protein promoted monocytic differentiation. Single-cell RNA sequencing analysis further demonstrated that NFIC overexpressing monocytes had increased expression of growth and survival genes. In contrast, depletion of NFIC through shRNA decreased cell growth, increased cell cycle arrest and apoptosis in AML cell lines and AML patient blasts. Further, in AML cell lines (THP-1), bulk RNA sequencing of NFIC knockdown led to downregulation of genes involved in cell survival and oncogenic signaling pathways including mixed lineage leukemia-1 (MLL-1). Lastly, we show that NFIC knockdown in an ex vivo mouse MLL::AF9 pre-leukemic stem cell model, decreased their growth and colony formation and increased expression of myeloid differentiation markers Gr1 and Mac1. Collectively, our results suggest that NFIC is an important transcription factor in myeloid differentiation as well as AML cell survival and is a potential therapeutic target in AML.
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Affiliation(s)
- Namrata Rastogi
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK.
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, CF24 4HQ, Wales, UK.
| | - Juan Bautista Menendez Gonzalez
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, CF24 4HQ, Wales, UK
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Vikas Kumar Srivastava
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Bader Alanazi
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Prince Mohammed Medical City, AlJouf, Saudi Arabia
- Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Rehab N Alanazi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Northern Border University, Arar, 91431, Saudi Arabia
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Owen M Hughes
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Niamh S O'Neill
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Amanda F Gilkes
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Cardiff Experimental and Cancer Medicine Centre (ECMC), School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Neil Ashley
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Sumukh Deshpande
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Robert Andrews
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Adam Mead
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Neil P Rodrigues
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, CF24 4HQ, Wales, UK
| | - Steve Knapper
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Cardiff Experimental and Cancer Medicine Centre (ECMC), School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Richard L Darley
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Alex Tonks
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK.
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16
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Testa U, Castelli G, Pelosi E. Clonal Hematopoiesis: Role in Hematologic and Non-Hematologic Malignancies. Mediterr J Hematol Infect Dis 2022; 14:e2022069. [PMID: 36119457 PMCID: PMC9448266 DOI: 10.4084/mjhid.2022.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/18/2022] [Indexed: 02/08/2023] Open
Abstract
Hematopoietic stem cells (HSCs) ensure the coordinated and balanced production of all hematopoietic cell types throughout life. Aging is associated with a gradual decline of the self-renewal and regenerative potential of HSCs and with the development of clonal hematopoiesis. Clonal hematopoiesis of indeterminate potential (CHIP) defines the clonal expansion of genetically variant hematopoietic cells bearing one or more gene mutations and/or structural variants (such as copy number alterations). CHIP increases exponentially with age and is associated with cancers, including hematologic neoplasia, cardiovascular and other diseases. The presence of CHIP consistently increases the risk of hematologic malignancy, particularly in individuals who have CHIP in association with peripheral blood cytopenia.
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Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
| | - Germana Castelli
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
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17
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Koui Y, Ideue T, Boylan M, Anderson MJ, Osato M, Suda T, Yokomizo T, Mukouyama YS. Hepatic leukemia factor-expressing paraxial mesoderm cells contribute to the developing brain vasculature. Biol Open 2022; 11:276428. [PMID: 36017733 PMCID: PMC9493726 DOI: 10.1242/bio.059510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/22/2022] [Indexed: 11/20/2022] Open
Abstract
Recent genetic lineage tracing studies reveal heterogeneous origins of vascular endothelial cells and pericytes in the developing brain vasculature, despite classical experimental evidence for a mesodermal origin. Here we provide evidence through a genetic lineage tracing experiment that cephalic paraxial mesodermal cells give rise to endothelial cells and pericytes in the developing mouse brain. We show that Hepatic leukemia factor (Hlf) is transiently expressed by cephalic paraxial mesenchyme at embryonic day (E) 8.0-9.0 and the genetically-marked E8.0 Hlf-expressing cells mainly contribute to the developing brain vasculature. Interestingly, the genetically-marked E10.5 Hlf-expressing cells, which have been previously reported to contain embryonic hematopoietic stem cells, fail to contribute to the vascular cells. Combined, our genetic lineage tracing data demonstrate that a transient expression of Hlf marks a cephalic paraxial mesenchyme contributing to the developing brain vasculature.
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Affiliation(s)
- Yuta Koui
- Laboratory of Stem Cell and Neuro-Vascular Biology, Cell and Development Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Takako Ideue
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan
| | - Michael Boylan
- Cancer and Developmental Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Matthew J Anderson
- Cancer and Developmental Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Motomi Osato
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan.,Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Toshio Suda
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan.,Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Tomomasa Yokomizo
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan.,Microscopic and Developmental Anatomy, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Yoh-Suke Mukouyama
- Laboratory of Stem Cell and Neuro-Vascular Biology, Cell and Development Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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18
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Motta FC, Moseley RC, Cummins B, Deckard A, Haase SB. Conservation of dynamic characteristics of transcriptional regulatory elements in periodic biological processes. BMC Bioinformatics 2022; 23:94. [PMID: 35300586 PMCID: PMC8932128 DOI: 10.1186/s12859-022-04627-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 03/01/2022] [Indexed: 11/12/2022] Open
Abstract
Background Cell and circadian cycles control a large fraction of cell and organismal physiology by regulating large periodic transcriptional programs that encompass anywhere from 15 to 80% of the genome despite performing distinct functions. In each case, these large periodic transcriptional programs are controlled by gene regulatory networks (GRNs), and it has been shown through genetics and chromosome mapping approaches in model systems that at the core of these GRNs are small sets of genes that drive the transcript dynamics of the GRNs. However, it is unlikely that we have identified all of these core genes, even in model organisms. Moreover, large periodic transcriptional programs controlling a variety of processes certainly exist in important non-model organisms where genetic approaches to identifying networks are expensive, time-consuming, or intractable. Ideally, the core network components could be identified using data-driven approaches on the transcriptome dynamics data already available. Results This study shows that a unified set of quantified dynamic features of high-throughput time series gene expression data are more prominent in the core transcriptional regulators of cell and circadian cycles than in their outputs, in multiple organism, even in the presence of external periodic stimuli. Additionally, we observe that the power to discriminate between core and non-core genes is largely insensitive to the particular choice of quantification of these features. Conclusions There are practical applications of the approach presented in this study for network inference, since the result is a ranking of genes that is enriched for core regulatory elements driving a periodic phenotype. In this way, the method provides a prioritization of follow-up genetic experiments. Furthermore, these findings reveal something unexpected—that there are shared dynamic features of the transcript abundance of core components of unrelated GRNs that control disparate periodic phenotypes.
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Affiliation(s)
- Francis C Motta
- Department of Mathematical Sciences, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL, 33431, USA.
| | - Robert C Moseley
- Department of Biology, Duke University, 130 Science Drive, Durham, NC, 27708, USA
| | - Bree Cummins
- Department of Mathematical Sciences, Montana State University, P.O. Box 172400, Bozeman, MT, 59717, USA
| | | | - Steven B Haase
- Department of Biology, Duke University, 130 Science Drive, Durham, NC, 27708, USA
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19
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Hidalgo I, Wahlestedt M, Yuan O, Zhang Q, Bryder D, Pronk CJ. Bmi1 induction protects hematopoietic stem cells against pronounced long-term hematopoietic stress. Exp Hematol 2022; 109:35-44. [DOI: 10.1016/j.exphem.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/10/2022] [Accepted: 02/12/2022] [Indexed: 11/04/2022]
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20
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Wu Y, Yang L, Zhang L, Zheng X, Xu H, Wang K, Weng X. Identification of a Four-Gene Signature Associated with the Prognosis Prediction of Lung Adenocarcinoma Based on Integrated Bioinformatics Analysis. Genes (Basel) 2022; 13:genes13020238. [PMID: 35205284 PMCID: PMC8872064 DOI: 10.3390/genes13020238] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/03/2021] [Accepted: 11/17/2021] [Indexed: 12/19/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is often diagnosed at an advanced stage, so it is necessary to identify potential biomarkers for the early diagnosis and prognosis of LUAD. In our study, a gene co-expression network was constructed using weighted gene co-expression network analysis (WGCNA) in order to obtain the key modules and genes correlated with LUAD prognosis. Four hub genes (HLF, CHRDL1, SELENBP1, and TMEM163) were screened out using least absolute shrinkage and selection operator (LASSO)–Cox regression analysis; then, a prognostic model was established for predicting overall survival (OS) based on these four hub genes..Furthermore, the prognostic values of this four-gene signature were verified in four validation sets (GSE26939, GSE31210, GSE72094, and TCGA-LUAD) as well as in the GEPIA database. To assess the prognostic values of hub genes, receiver operating characteristic (ROC) curves were constructed and a nomogram was created. We found that a higher expression of four hub genes was associated with a lower risk of patient death. In a training set, it was demonstrated that this four-gene signature was a better prognostic factor than clinical factors such as age and stage of disease. Moreover, our results revealed that these four genes were suppressor factors of LUAD and that their high expression was associated with a lower risk of death. In summary, we demonstrated that this four-gene signature could be a potential prognostic factor for LUAD patients. These findings provide a theoretical basis for exploring potential biomarkers for LUAD prognosis prediction in the future.
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Affiliation(s)
- Yuan Wu
- Department of Respiratory Medicine, The Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Yiwu 322000, China; (Y.W.); (L.Y.); (L.Z.); (X.Z.); (H.X.)
| | - Lingge Yang
- Department of Respiratory Medicine, The Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Yiwu 322000, China; (Y.W.); (L.Y.); (L.Z.); (X.Z.); (H.X.)
| | - Long Zhang
- Department of Respiratory Medicine, The Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Yiwu 322000, China; (Y.W.); (L.Y.); (L.Z.); (X.Z.); (H.X.)
| | - Xinjie Zheng
- Department of Respiratory Medicine, The Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Yiwu 322000, China; (Y.W.); (L.Y.); (L.Z.); (X.Z.); (H.X.)
| | - Huan Xu
- Department of Respiratory Medicine, The Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Yiwu 322000, China; (Y.W.); (L.Y.); (L.Z.); (X.Z.); (H.X.)
| | - Kai Wang
- Department of Respiratory Medicine, The Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Yiwu 322000, China; (Y.W.); (L.Y.); (L.Z.); (X.Z.); (H.X.)
- Correspondence: (K.W.); (X.W.)
| | - Xianwu Weng
- Department of Cardiothoracic Surgery, The Fourth Affiliated Hospital, College of Medicine, Zhejiang University, Yiwu 322000, China
- Correspondence: (K.W.); (X.W.)
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21
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Lehnertz B, Chagraoui J, MacRae T, Tomellini E, Corneau S, Mayotte N, Boivin I, Durand A, Gracias D, Sauvageau G. HLF expression defines the human hematopoietic stem cell state. Blood 2021; 138:2642-2654. [PMID: 34499717 DOI: 10.1182/blood.2021010745] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 08/11/2021] [Indexed: 12/30/2022] Open
Abstract
Hematopoietic stem cells (HSCs) sustain blood cell homeostasis throughout life and can regenerate all blood lineages after transplantation. Despite this clear functional definition, highly enriched isolation of human HSCs can currently only be achieved through combinatorial assessment of multiple surface antigens. Although several transgenic HSC reporter mouse strains have been described, no analogous approach to prospectively isolate human HSCs has been reported. To identify genes with the most selective expression in human HSCs, we profiled population and single-cell transcriptomes of unexpanded and ex vivo cultured cord blood-derived hematopoietic stem and progenitor cells as well as peripheral blood, adult bone marrow, and fetal liver. On the basis of these analyses, we propose the master transcription factor HLF (hepatic leukemia factor) as one of the most specific HSC marker genes. To directly track its expression in human hematopoietic cells, we developed a genomic HLF reporter strategy, capable of selectively labeling the most immature blood cells on the basis of a single engineered parameter. Most importantly, HLF-expressing cells comprise all stem cell activity in culture and in vivo during serial transplantation. Taken together, these results experimentally establish HLF as a defining gene of the human HSC state and outline a new approach to continuously mark these cells with high fidelity.
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Affiliation(s)
- Bernhard Lehnertz
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Jalila Chagraoui
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Tara MacRae
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Elisa Tomellini
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Sophie Corneau
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Nadine Mayotte
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Isabel Boivin
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Aurélie Durand
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Deanne Gracias
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
| | - Guy Sauvageau
- Molecular Genetics of Stem Cells Laboratory, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montreal, QC, Canada; and
- Department of Medicine, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
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22
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FLT3-ITD allelic ratio and HLF expression predict FLT3 inhibitor efficacy in adult AML. Sci Rep 2021; 11:23565. [PMID: 34876631 PMCID: PMC8651734 DOI: 10.1038/s41598-021-03010-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/01/2021] [Indexed: 11/21/2022] Open
Abstract
FLT3 internal tandem duplication (FLT3-ITD) is a frequent mutation in acute myeloid leukemia (AML) and remains a strong prognostic factor due to high rate of disease recurrence. Several FLT3-targeted agents have been developed, but determinants of variable responses to these agents remain understudied. Here, we investigated the role FLT3-ITD allelic ratio (ITD-AR), ITD length, and associated gene expression signatures on FLT3 inhibitor response in adult AML. We performed fragment analysis, ex vivo drug testing, and next generation sequencing (RNA, exome) to 119 samples from 87 AML patients and 13 healthy bone marrow controls. We found that ex vivo response to FLT3 inhibitors is significantly associated with ITD-AR, but not with ITD length. Interestingly, we found that the HLF gene is overexpressed in FLT3-ITD+ AML and associated with ITD-AR. The retrospective analysis of AML patients treated with FLT3 inhibitor sorafenib showed that patients with high HLF expression and ITD-AR had better clinical response to therapy compared to those with low ITD-AR and HLF expression. Thus, our findings suggest that FLT3 ITD-AR together with increased HLF expression play a role in variable FLT3 inhibitor responses observed in FLT3-ITD+ AML patients.
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23
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Characterization of a genomic region 8 kb downstream of GFI1B associated with myeloproliferative neoplasms. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166259. [PMID: 34450246 DOI: 10.1016/j.bbadis.2021.166259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 08/07/2021] [Accepted: 08/23/2021] [Indexed: 11/23/2022]
Abstract
A genomic locus 8 kb downstream of the transcription factor GFI1B (Growth Factor Independence 1B) predisposes to clonal hematopoiesis and myeloproliferative neoplasms. One of the most significantly associated polymorphisms in this region is rs621940-G. GFI1B auto-represses GFI1B, and altered GFI1B expression contributes to myeloid neoplasms. We studied whether rs621940-G affects GFI1B expression and growth of immature cells. GFI1B ChIP-seq showed clear binding to the rs621940 locus. Preferential binding of various hematopoietic transcription factors to either the rs621940-C or -G allele was observed, but GFI1B showed no preference. In gene reporter assays the rs621940 region inhibited GFI1B promoter activity with the G-allele having less suppressive effects compared to the C-allele. However, CRISPR-Cas9 mediated deletion of the locus in K562 cells did not alter GFI1B expression nor auto-repression. In healthy peripheral blood mononuclear cells GFI1B expression did not differ consistently between the rs621940 alleles. Long range and targeted deep sequencing did not detect consistent effects of rs621940-G on allelic GFI1B expression either. Finally, we observed that myeloid colony formation was not significantly affected by either rs621940 allele in 193 healthy donors. Together, these findings show no evidence that rs621940 or its locus affect GFI1B expression, auto-repression or growth of immature myeloid cells.
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24
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Georgolopoulos G, Psatha N, Iwata M, Nishida A, Som T, Yiangou M, Stamatoyannopoulos JA, Vierstra J. Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation. Nat Commun 2021; 12:6790. [PMID: 34815405 PMCID: PMC8611072 DOI: 10.1038/s41467-021-27159-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 10/20/2021] [Indexed: 11/08/2022] Open
Abstract
Lineage commitment and differentiation is driven by the concerted action of master transcriptional regulators at their target chromatin sites. Multiple efforts have characterized the key transcription factors (TFs) that determine the various hematopoietic lineages. However, the temporal interactions between individual TFs and their chromatin targets during differentiation and how these interactions dictate lineage commitment remains poorly understood. Here we perform dense, daily, temporal profiling of chromatin accessibility (DNase I-seq) and gene expression changes (total RNA-seq) along ex vivo human erythropoiesis to comprehensively define developmentally regulated DNase I hypersensitive sites (DHSs) and transcripts. We link both distal DHSs to their target gene promoters and individual TFs to their target DHSs, revealing that the regulatory landscape is organized in distinct sequential regulatory modules that regulate lineage restriction and maturation. Finally, direct comparison of transcriptional dynamics (bulk and single-cell) and lineage potential between erythropoiesis and megakaryopoiesis uncovers differential fate commitment dynamics between the two lineages as they exit the stem and progenitor stage. Collectively, these data provide insights into the temporally regulated synergy of the cis- and the trans-regulatory components underlying hematopoietic lineage commitment and differentiation.
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Affiliation(s)
- Grigorios Georgolopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA, USA.
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | | | - Mineo Iwata
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Andrew Nishida
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Tannishtha Som
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Minas Yiangou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - John A Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Division of Oncology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jeff Vierstra
- Altius Institute for Biomedical Sciences, Seattle, WA, USA.
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25
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Tang W, He J, Huang T, Bai Z, Wang C, Wang H, Yang R, Ni Y, Hou J, Wang J, Zhou J, Yao Y, Gong Y, Hou S, Liu B, Lan Y. Hlf Expression Marks Early Emergence of Hematopoietic Stem Cell Precursors With Adult Repopulating Potential and Fate. Front Cell Dev Biol 2021; 9:728057. [PMID: 34589491 PMCID: PMC8473784 DOI: 10.3389/fcell.2021.728057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022] Open
Abstract
In the aorta-gonad-mesonephros (AGM) region of mouse embryos, pre-hematopoietic stem cells (pre-HSCs) are generated from rare and specialized hemogenic endothelial cells (HECs) via endothelial-to-hematopoietic transition, followed by maturation into bona fide hematopoietic stem cells (HSCs). As HECs also generate a lot of hematopoietic progenitors not fated to HSCs, powerful tools that are pre-HSC/HSC-specific become urgently critical. Here, using the gene knockin strategy, we firstly developed an Hlf-tdTomato reporter mouse model and detected Hlf-tdTomato expression exclusively in the hematopoietic cells including part of the immunophenotypic CD45– and CD45+ pre-HSCs in the embryonic day (E) 10.5 AGM region. By in vitro co-culture together with long-term transplantation assay stringent for HSC precursor identification, we further revealed that unlike the CD45– counterpart in which both Hlf-tdTomato-positive and negative sub-populations harbored HSC competence, the CD45+ E10.5 pre-HSCs existed exclusively in Hlf-tdTomato-positive cells. The result indicates that the cells should gain the expression of Hlf prior to or together with CD45 to give rise to functional HSCs. Furthermore, we constructed a novel Hlf-CreER mouse model and performed time-restricted genetic lineage tracing by a single dose induction at E9.5. We observed the labeling in E11.5 AGM precursors and their contribution to the immunophenotypic HSCs in fetal liver (FL). Importantly, these Hlf-labeled early cells contributed to and retained the size of the HSC pool in the bone marrow (BM), which continuously differentiated to maintain a balanced and long-term multi-lineage hematopoiesis in the adult. Therefore, we provided another valuable mouse model to specifically trace the fate of emerging HSCs during development.
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Affiliation(s)
- Wanbo Tang
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Jian He
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Tao Huang
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Zhijie Bai
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China
| | - Chaojie Wang
- Key Laboratory for Regenerative Medicine of Ministry of Education, School of Medicine, Institute of Hematology, Jinan University, Guangzhou, China
| | - Haizhen Wang
- Key Laboratory for Regenerative Medicine of Ministry of Education, School of Medicine, Institute of Hematology, Jinan University, Guangzhou, China
| | - Ruichuang Yang
- National Clinical Research Center for Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yanli Ni
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jun Hou
- National Clinical Research Center for Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Junliang Wang
- Department of Radiotherapy, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jie Zhou
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yingpeng Yao
- Key Laboratory for Regenerative Medicine of Ministry of Education, School of Medicine, Institute of Hematology, Jinan University, Guangzhou, China
| | - Yandong Gong
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Siyuan Hou
- Key Laboratory for Regenerative Medicine of Ministry of Education, School of Medicine, Institute of Hematology, Jinan University, Guangzhou, China
| | - Bing Liu
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China.,Key Laboratory for Regenerative Medicine of Ministry of Education, School of Medicine, Institute of Hematology, Jinan University, Guangzhou, China.,State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, School of Medicine, Institute of Hematology, Jinan University, Guangzhou, China
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26
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Single-cell ATAC-seq reveals GATA2-dependent priming defect in myeloid and a maturation bottleneck in lymphoid lineages. Blood Adv 2021; 5:2673-2686. [PMID: 34170284 DOI: 10.1182/bloodadvances.2020002992] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/22/2021] [Indexed: 12/22/2022] Open
Abstract
Germline heterozygous mutations in GATA2 are associated with a syndrome characterized by cytopenias, atypical infections, and increased risk of hematologic malignancies. Here, we generated a zebrafish mutant of gata2b that recapitulated the myelomonocytopenia and B-cell lymphopenia of GATA2 deficiency syndrome. Using single-cell assay for transposase accessible chromatin with sequencing of marrow cells, we showed that loss of gata2b led to contrasting alterations in chromosome accessibility in early myeloid and lymphoid progenitors, associated with defects in gene expression. Within the myeloid lineage in gata2b mutant zebrafish, we identified an attenuated myeloid differentiation with reduced transcriptional priming and skewing away from the monocytic program. In contrast, in early lymphoid progenitors, gata2b loss led to accumulation of B-lymphoid transcription factor accessibility coupled with increased expression of the B-cell lineage-specification program. However, gata2b mutant zebrafish had incomplete B-cell lymphopoiesis with loss of lineage-specific transcription factor accessibility in differentiating B cells, in the context of aberrantly reduced oxidative metabolic pathways. Our results establish that transcriptional events in early progenitors driven by Gata2 are required to complete normal differentiation.
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27
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Martin-Rufino JD, Sankaran VG. Deciphering transcriptional and functional heterogeneity in hematopoiesis with single-cell genomics. Curr Opin Hematol 2021; 28:269-276. [PMID: 33901135 PMCID: PMC8169609 DOI: 10.1097/moh.0000000000000657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Single-cell genomic approaches have uncovered cell fate biases and heterogeneity within hematopoietic subpopulations. However, standard single-cell transcriptomics suffers from high sampling noise, which particularly skews the distribution of lowly expressed genes, such as transcription factors (TFs). This might preclude the identification of rare transcripts that define cell identity and demarcate cell fate biases. Moreover, these studies need to go hand in hand with relevant functional assays to ensure that observed gene expression changes represent biologically meaningful alterations. RECENT FINDINGS Single-cell lineage tracing and functional validation studies have uncovered cell fate bias within transcriptionally distinct hematopoietic stem and progenitor subpopulations. Novel markers identified using these strategies have been proposed to prospectively isolate functionally distinct subpopulations, including long-term hematopoietic stem cells for ex vivo applications. Furthermore, the continuous nature of hematopoiesis has prompted the study of the relationship between stochastic transcriptional noise in hematopoietic TFs and cell fate determination. SUMMARY An understanding of the limitations of single-cell genomic approaches and follow-up functional assays is critical to discern the technical and biological contribution of noise in hematopoietic heterogeneity, to identify rare gene expression states, and to uncover functionally distinct subpopulations within hematopoiesis. SUPPLEMENTARY VIDEO http://links.lww.com/COH/A23.
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Affiliation(s)
- Jorge D. Martin-Rufino
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
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28
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Lee IS, Sahu D, Hur H, Yook JH, Kim BS, Goel A. Discovery and validation of an expression signature for recurrence prediction in high-risk diffuse-type gastric cancer. Gastric Cancer 2021; 24:655-665. [PMID: 33523340 DOI: 10.1007/s10120-021-01155-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Diffuse type gastric cancer (DGC), represented by low sensitivity to chemotherapy and poor prognosis, is a heterogenous malignancy in which patient subsets exhibit diverse oncological risk-profiles. This study aimed to develop molecular biomarkers for robust prognostic risk-stratification and improve survival outcomes in patients with diffuse type gastric cancer (DGC). METHODS We undertook a systematic and comprehensive discovery and validation effort to identify recurrence prediction biomarkers by analyzing genome-wide transcriptomic profiling data from 157 patients with DGC, followed by their validation in 254 patients from 2 clinical cohorts. RESULTS Genome-wide transcriptomic profiling identified a 7-gene panel for robust prediction of recurrence in DGC patients (AUC = 0.91), which was successfully validated in an independent dataset (AUC = 0.86). Examination of 180 specimens from a training cohort allowed us to establish a gene-based risk prediction model (AUC = 0.78; 95% CI 0.71-0.84), which was subsequently validated in an independent cohort of 74 GC patients (AUC = 0.83; 95% CI 0.72-0.90). The Kaplan-Meier analyses exhibited a consistently superior performance of our risk-prediction model in the identification of high- and low-risk patient subgroups, which was significantly improved when we combined our gene signature with the tumor stage in both clinical cohorts (AUC of 0.83 in the training cohort and 0.89 in the validation cohort). Finally, for an easier clinical translation, we established a nomogram that robustly predicted prognosis in patients with DGC. CONCLUSIONS Our novel transcriptomic signature for risk-stratification and identification of high-risk patients with recurrence could serve as an important clinical decision-making tool in patients with DGC.
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Affiliation(s)
- In-Seob Lee
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Biomedical Research Center, 1218 S. Fifth Avenue, Monrovia, CA, 91016, USA.,Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Divya Sahu
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Biomedical Research Center, 1218 S. Fifth Avenue, Monrovia, CA, 91016, USA
| | - Hoon Hur
- Department of Surgery, Ajou University of School of Medicine, Suwon, South Korea.,Cancer Biology Graduate Program, Ajou University Graduate School of Medicine, Suwon, South Korea
| | - Jeong-Hwan Yook
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Byung-Sik Kim
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Biomedical Research Center, 1218 S. Fifth Avenue, Monrovia, CA, 91016, USA.
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29
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Liu Q, Ge H, Liu P, Li Y. High Hepatic leukemia factor expression indicates a favorable survival in glioma patients. Medicine (Baltimore) 2021; 100:e23980. [PMID: 33578515 PMCID: PMC7886392 DOI: 10.1097/md.0000000000023980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/30/2020] [Indexed: 01/05/2023] Open
Abstract
Hepatic leukemia factor (HLF) is an oncogenic transcript factor, but its role in gliomas is unclear.With the open-access data from the Cancer Genome Atlatls (TCGA), HLF expression was compared between normal and glioma tissues and its correlation to patient survival, age, gender, race, and tumor grade was analyzed. Multivariate Cox regression was adopted to explore the independent risk factors for patient survival. Survivals between high and low HLF expression, and high and low model predicted risk subgroups were compared. 1, 2, 3, and 5-year patient survival were predicted with the Cox regression model. Gene set enrichment analysis (GSEA) was performed to predict the potential function of HLF.Expression and clinical data of 5 normal brain samples and 655 glioma samples were obtained from TCGA. HLF expression was downregulated in gliomas than normal brain tissue (P = .007), and negatively related to patient age and advancing tumor grade (P < .001). HLF was a protective factor for patient survival (OR = 0.81, 95%CI 0.67-0.99, P = .035). Patients' survivals were poorer in low HLF expression subgroups and the Cox regression model predicted high-risk subgroups (P < .001). The accuracy of the model in predicting 1, 2, 3, and 5-year patient survival was 0.864, 0.895, 0.907, and 0.893, respectively. GSEA revealed HLF mainly took part in regulating tumor cell metabolism and cell cycle.HLF was downregulated in gliomas than normal tissue, negatively related to patient age and tumor grade, and was an independent protective factor for glioma patients.
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Transcriptome Response of Atlantic Salmon ( Salmo salar) to a New Piscine Orthomyxovirus. Pathogens 2020; 9:pathogens9100807. [PMID: 33007914 PMCID: PMC7600774 DOI: 10.3390/pathogens9100807] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 01/12/2023] Open
Abstract
Pilchard orthomyxovirus (POMV) is an emerging pathogen of concern to the salmon industry in Australia. To explore the molecular events that underpin POMV infection, we challenged Atlantic salmon (Salmo salar) post-smolts in seawater via cohabitation. Tissue samples of the head kidney and liver were collected from moribund and surviving individuals and analyzed using transcriptome sequencing. Viral loads were higher in the head kidney compared to the liver, yet the liver presented more upregulated genes. Fish infected with POMV showed a strong innate immune response that included the upregulation of pathogen recognition receptors such as RIG-I and Toll-like receptors as well as the induction of interferon-stimulated genes (MX, ISG15). Moribund fish also presented a dramatic induction of pro-inflammatory cytokines, contributing to severe tissue damage and morbidity. An induction of major histocompatibility complex (MHC) class I genes (B2M) and markers of T cell-mediated immunity (CD8-alpha, CD8-beta, Perforin-1, Granzyme-A) was observed in both moribund fish and survivors. In addition, differential connectivity analysis showed that three key regulators (RELA/p65, PRDM1, and HLF) related to cell-mediated immunity had significant differences in connectivity in "clinically healthy" versus "clinically affected" or moribund fish. Collectively, our results show that T cell-mediated immunity plays a central role in the response of Atlantic salmon to the infection with POMV.
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Astori A, Tingvall-Gustafsson J, Kuruvilla J, Coyaud E, Laurent EMN, Sunnerhagen M, Åhsberg J, Ungerbäck J, Strid T, Sigvardsson M, Raught B, Somasundaram R. ARID1a Associates with Lymphoid-Restricted Transcription Factors and Has an Essential Role in T Cell Development. THE JOURNAL OF IMMUNOLOGY 2020; 205:1419-1432. [PMID: 32747500 DOI: 10.4049/jimmunol.1900959] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 06/29/2020] [Indexed: 11/19/2022]
Abstract
Maturation of lymphoid cells is controlled by the action of stage and lineage-restricted transcription factors working in concert with the general transcription and chromatin remodeling machinery to regulate gene expression. To better understand this functional interplay, we used Biotin Identification in human embryonic kidney cells to identify proximity interaction partners for GATA3, TCF7 (TCF1), SPI1, HLF, IKZF1, PAX5, ID1, and ID2. The proximity interaction partners shared among the lineage-restricted transcription factors included ARID1a, a BRG1-associated factor complex component. CUT&RUN analysis revealed that ARID1a shared binding with TCF7 and GATA3 at a substantial number of putative regulatory elements in mouse T cell progenitors. In support of an important function for ARID1a in lymphocyte development, deletion of Arid1a in early lymphoid progenitors in mice resulted in a pronounced developmental arrest in early T cell development with a reduction of CD4+CD8+ cells and a 20-fold reduction in thymic cellularity. Exploring gene expression patterns in DN3 cells from Wt and Arid1a-deficient mice suggested that the developmental block resided in the DN3a to DN3b transition, indicating a deficiency in β-selection. Our work highlights the critical importance of functional interactions between stage and lineage-restricted factors and the basic transcription machinery during lymphocyte differentiation.
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Affiliation(s)
- Audrey Astori
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | | | - Jacob Kuruvilla
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Etienne Coyaud
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Estelle M N Laurent
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden; and
| | - Josefine Åhsberg
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Jonas Ungerbäck
- Division of Molecular Hematology, Lund University, 22184 Lund, Sweden
| | - Tobias Strid
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Mikael Sigvardsson
- Division of Molecular Hematology, Lund University, 22184 Lund, Sweden; .,Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 3K1, Canada
| | - Rajesh Somasundaram
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85 Linköping, Sweden
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Huang Y, Bourquin JP. Targeting the oncogenic activity of TCF3-HLF in leukemia. Mol Cell Oncol 2020; 7:1709391. [PMID: 32391417 DOI: 10.1080/23723556.2019.1709391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 12/21/2019] [Accepted: 12/23/2019] [Indexed: 10/24/2022]
Abstract
The oncogenic fusion transcription factor TCF3-HLF identifies an aggressive subtype of acute lymphoblastic leukemia. TCF3-HLF imposes a malignant program by activation of lineage-specific oncogenic enhancers. Among critical cofactors of the TCF3-HLF complex we identified EP300, which functional inhibition results in potent anti-leukemic activity by interference with the specific gene expression.
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Affiliation(s)
- Yun Huang
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Jean-Pierre Bourquin
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
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Chen J, Liu A, Lin Z, Wang B, Chai X, Chen S, Lu W, Zheng M, Cao T, Zhong M, Li R, Wu M, Lu Z, Pang W, Huang W, Xiao L, Lin D, Wang Z, Lei F, Chen X, Long W, Zheng Y, Chen Q, Zeng J, Ren D, Li J, Zhang X, Huang Y. Downregulation of the circadian rhythm regulator HLF promotes multiple-organ distant metastases in non-small cell lung cancer through PPAR/NF-κb signaling. Cancer Lett 2020; 482:56-71. [PMID: 32289442 DOI: 10.1016/j.canlet.2020.04.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/01/2020] [Accepted: 04/07/2020] [Indexed: 12/24/2022]
Abstract
Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related death due to its early recurrence and widespread metastatic potential. Accumulating studies have reported that dysregulation of circadian rhythms-associated regulators is implicated in the recurrence and metastasis of NSCLC. Therefore, identification of metastasis-associated circadian rhythm genes is clinically necessary. Here we report that the circadian gene hepatic leukemia factor (HLF), which was dramatically reduced in early-relapsed NSCLC tissues, was significantly correlated with early progression and distant metastasis in NSCLC patients. Upregulating HLF inhibited, while silencing HLF promoted lung colonization, as well as metastasis of NSCLC cells to bone, liver and brain in vivo. Importantly, downexpression of HLF promoted anaerobic metabolism to support anchorage-independent growth of NSCLC cells under low nutritional condition by activating NF-κB/p65 signaling through disrupting translocation of PPARα and PPARγ. Further investigations revealed that both genetic deletion and methylation contribute to downexpression of HLF in NSCLC tissues. In conclusion, our results shed light on a plausible mechanism by which HLF inhibits distant metastasis in NSCLC, suggesting that HLF may serve as a novel target for clinical intervention in NSCLC.
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Affiliation(s)
- Jiarong Chen
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China; Department of Oncology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Aibin Liu
- Department of Geriatrics, Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Zhichao Lin
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Bin Wang
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China; Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, 523808, China; Collaborative Innovation Center for Antitumor Active Substance Research and Development, Guangdong Medical University, Zhanjiang, 524023, China
| | - Xingxing Chai
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, 523808, China; Laboratory Animal Center, Guangdong Medical University, Zhanjiang, 524023, China
| | - Shasha Chen
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China; Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, 523808, China; Collaborative Innovation Center for Antitumor Active Substance Research and Development, Guangdong Medical University, Zhanjiang, 524023, China
| | - Wenjie Lu
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Mingzhu Zheng
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Ting Cao
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Meigong Zhong
- Department of Pharmacy, Jiangmen Maternity and Child Health Care Hospital, Jiangmen, 529030, China
| | - Ronggang Li
- Department of Pathology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Minyan Wu
- Department of Basic Medicine, Guangdong Jiangmen Chinese Medical College, Jiangmen, 529030, China
| | - Zhuming Lu
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Wenguang Pang
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Wenhai Huang
- Department of Thoracic Surgery, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Lin Xiao
- Department of Radiotherapy Center, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Daren Lin
- Department of Oncology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Zhihui Wang
- Department of Oncology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Fangyong Lei
- Department of Oncology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Xiangmeng Chen
- Department of Radiology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Wansheng Long
- Department of Radiology, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Yan Zheng
- Department of Research and Development, Research and Development Center for Molecular Diagnosis Engineering Technology of Human Papillomavirus (HPV) Related Diseases of Guangdong Province, Hybribio Limited, Changzhou, 521021, China
| | - Qiong Chen
- Department of Geriatrics, Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Jincheng Zeng
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, 523808, China; Collaborative Innovation Center for Antitumor Active Substance Research and Development, Guangdong Medical University, Zhanjiang, 524023, China
| | - Dong Ren
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China; Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, 523808, China
| | - Jun Li
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China
| | - Xin Zhang
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China; Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, Dongguan, 523808, China; Collaborative Innovation Center for Antitumor Active Substance Research and Development, Guangdong Medical University, Zhanjiang, 524023, China.
| | - Yanming Huang
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, 529030, China.
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Klein HU, Schäfer M, Bennett DA, Schwender H, De Jager PL. Bayesian integrative analysis of epigenomic and transcriptomic data identifies Alzheimer's disease candidate genes and networks. PLoS Comput Biol 2020; 16:e1007771. [PMID: 32255787 PMCID: PMC7138305 DOI: 10.1371/journal.pcbi.1007771] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 03/03/2020] [Indexed: 12/28/2022] Open
Abstract
Biomedical research studies have generated large multi-omic datasets to study complex diseases like Alzheimer’s disease (AD). An important aim of these studies is the identification of candidate genes that demonstrate congruent disease-related alterations across the different data types measured by the study. We developed a new method to detect such candidate genes in large multi-omic case-control studies that measure multiple data types in the same set of samples. The method is based on a gene-centric integrative coefficient quantifying to what degree consistent differences are observed in the different data types. For statistical inference, a Bayesian hierarchical model is used to study the distribution of the integrative coefficient. The model employs a conditional autoregressive prior to integrate a functional gene network and to share information between genes known to be functionally related. We applied the method to an AD dataset consisting of histone acetylation, DNA methylation, and RNA transcription data from human cortical tissue samples of 233 subjects, and we detected 816 genes with consistent differences between persons with AD and controls. The findings were validated in protein data and in RNA transcription data from two independent AD studies. Finally, we found three subnetworks of jointly dysregulated genes within the functional gene network which capture three distinct biological processes: myeloid cell differentiation, protein phosphorylation and synaptic signaling. Further investigation of the myeloid network indicated an upregulation of this network in early stages of AD prior to accumulation of hyperphosphorylated tau and suggested that increased CSF1 transcription in astrocytes may contribute to microglial activation in AD. Thus, we developed a method that integrates multiple data types and external knowledge of gene function to detect candidate genes, applied the method to an AD dataset, and identified several disease-related genes and processes demonstrating the usefulness of the integrative approach. Recent technological advances have led to a new generation of studies that interrogate multiple molecular levels in the same target tissue of a set of subjects, generating complex multi-omic datasets with which to study disease mechanism. These datasets of genetic, epigenomic, transcriptomic, and other data have the potential to reveal novel biological insights; however, integrative analyses remain challenging and require new computational methods. We developed an integrative Bayesian approach to detect genes with consistent differences between case and control samples across multiple data types. The method further integrates prior knowledge about gene function in the form of a gene functional similarity network to improve statistical inference by sharing information between related genes. We applied our method to an Alzheimer’s disease dataset of epigenomic and transcriptomic data and detected and then validated several novel and known candidate genes as well as three major disease-related biological processes. One of these processes reflected microglial activation and included the cytokine CSF1. Single-nucleus data revealed that CSF1 was primarily upregulated in astrocytes, implicating the involvement of this cell type in microglial activation. Hence, we demonstrated that integrative analysis approaches to multi-omic datasets can improve candidate gene detection and thereby generate new insights into complex diseases.
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Affiliation(s)
- Hans-Ulrich Klein
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, New York, United States of America
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, United States of America
- * E-mail:
| | - Martin Schäfer
- Mathematical Institute, Heinrich Heine University, Düsseldorf, Germany
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University, Düsseldorf, Germany
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, New York, United States of America
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, United States of America
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Huang Y, Mouttet B, Warnatz HJ, Risch T, Rietmann F, Frommelt F, Ngo QA, Dobay MP, Marovca B, Jenni S, Tsai YC, Matzk S, Amstislavskiy V, Schrappe M, Stanulla M, Gstaiger M, Bornhauser B, Yaspo ML, Bourquin JP. The Leukemogenic TCF3-HLF Complex Rewires Enhancers Driving Cellular Identity and Self-Renewal Conferring EP300 Vulnerability. Cancer Cell 2019; 36:630-644.e9. [PMID: 31735627 DOI: 10.1016/j.ccell.2019.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 08/18/2019] [Accepted: 10/14/2019] [Indexed: 01/08/2023]
Abstract
The chimeric transcription factor TCF3-HLF defines an incurable acute lymphoblastic leukemia subtype. Here we decipher the regulome of endogenous TCF3-HLF and dissect its essential transcriptional components and targets by functional genomics. We demonstrate that TCF3-HLF recruits HLF binding sites at hematopoietic stem cell/myeloid lineage associated (super-) enhancers to drive lineage identity and self-renewal. Among direct targets, hijacking an HLF binding site in a MYC enhancer cluster by TCF3-HLF activates a conserved MYC-driven transformation program crucial for leukemia propagation in vivo. TCF3-HLF pioneers the cooperation with ERG and recruits histone acetyltransferase p300 (EP300), conferring susceptibility to EP300 inhibition. Our study provides a framework for targeting driving transcriptional dependencies in this fatal leukemia.
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Affiliation(s)
- Yun Huang
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Brice Mouttet
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Hans-Jörg Warnatz
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Thomas Risch
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Fabian Rietmann
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Quy A Ngo
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Maria Pamela Dobay
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Blerim Marovca
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Silvia Jenni
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Yi-Chien Tsai
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Sören Matzk
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Vyacheslav Amstislavskiy
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Martin Schrappe
- Department of Pediatrics, Christian-Albrecht University of Kiel and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Martin Stanulla
- Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Beat Bornhauser
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Marie-Laure Yaspo
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Jean-Pierre Bourquin
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland.
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Musilova Z, Indermaur A, Bitja‐Nyom AR, Omelchenko D, Kłodawska M, Albergati L, Remišová K, Salzburger W. Evolution of the visual sensory system in cichlid fishes from crater lake Barombi Mbo in Cameroon. Mol Ecol 2019; 28:5010-5031. [DOI: 10.1111/mec.15217] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Zuzana Musilova
- Department of Zoology Charles University in Prague Prague Czech Republic
- Zoological Institute University of Basel Basel Switzerland
| | | | - Arnold Roger Bitja‐Nyom
- Department of Biological Sciences University of Ngaoundéré Ngaoundéré Cameroon
- Department of Management of Fisheries and Aquatic Ecosystems University of Douala Douala Cameroon
| | - Dmytro Omelchenko
- Department of Zoology Charles University in Prague Prague Czech Republic
| | - Monika Kłodawska
- Department of Zoology Charles University in Prague Prague Czech Republic
| | - Lia Albergati
- Zoological Institute University of Basel Basel Switzerland
| | - Kateřina Remišová
- Department of Physiology Charles University in Prague Prague Czech Republic
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Xiang DM, Sun W, Zhou T, Zhang C, Cheng Z, Li SC, Jiang W, Wang R, Fu G, Cui X, Hou G, Jin GZ, Li H, Hou C, Liu H, Wang H, Ding J. Oncofetal HLF transactivates c-Jun to promote hepatocellular carcinoma development and sorafenib resistance. Gut 2019; 68:1858-1871. [PMID: 31118247 DOI: 10.1136/gutjnl-2018-317440] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS The unique expression pattern makes oncofetal proteins ideal diagnostic biomarkers and therapeutic targets in cancer. However, few oncofetal proteins have been identified and entered clinical practice. METHODS Fetal liver, adult liver and hepatocellular carcinoma (HCC) tissues were employed to assess the expression of hepatic leukaemia factor (HLF). The impact of HLF on HCC onset and progression was investigated both in vivo and in vitro. The association between HLF and patient prognosis was determined in patient cohorts. The correlation between HLF expression and sorafenib benefits in HCC was further evaluated in patient cohorts and patient-derived xenografts (PDXs). RESULTS HLF is a novel oncofetal protein which is reactivated in HCC by SOX2 and OCT4. Functional studies revealed that HLF transactivates c-Jun to promote tumour initiating cell (TIC) generation and enhances TIC-like properties of hepatoma cells, thus driving HCC initiation and progression. Consistently, our clinical investigations elucidated the association between HLF and patient prognosis and unravelled the close correlation between HLF levels and c-Jun expression in patient HCCs. Importantly, HLF/c-Jun axis determines the responses of hepatoma cells to sorafenib treatment, and interference of HLF abrogated c-Jun activation and enhanced sorafenib response. Analysis of patient cohorts and PDXs further suggests that HLF/c-Jun axis might serve as a biomarker for sorafenib benefits in HCC patients. CONCLUSIONS Our findings uncovered HLF as a novel oncofetal protein and revealed the crucial role of the HLF/c-Jun axis in HCC development and sorafenib response, rendering HLF as an optimal target for the prevention and intervention of HCC.
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Affiliation(s)
- Dai-Min Xiang
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, the Second Military Medical University, shanghai, China
- National Center for Liver Cancer, shanghai, China
| | - Wen Sun
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, the Second Military Medical University, shanghai, China
| | - Tengfei Zhou
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, the Second Military Medical University, shanghai, China
| | - Cheng Zhang
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, the Second Military Medical University, shanghai, China
| | - Zhuo Cheng
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, the Second Military Medical University, shanghai, China
| | - Shi-Chao Li
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, the Second Military Medical University, shanghai, China
| | - Weiqi Jiang
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, the Second Military Medical University, shanghai, China
| | - Ruoyu Wang
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, the Second Military MedicalUniversity, shanghai, China
| | - Gongbo Fu
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, the Second Military Medical University, shanghai, China
| | - Xiuliang Cui
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, the Second Military Medical University, shanghai, China
| | - Guojun Hou
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, the Second Military MedicalUniversity, shanghai, China
| | - Guang-Zhi Jin
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital/Institute, the Second MilitaryMedical University, shanghai, China
| | - Hengyu Li
- Department of Breast and Thyroid surgery, First Affiliated Hospital of Second Military Medical University, shanghai, China
| | - Caiying Hou
- General Hospital of PLA Rocket Force, Beijing, China
| | - Hui Liu
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, the Second Military MedicalUniversity, shanghai, China
| | - Hongyang Wang
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, the Second Military Medical University, shanghai, China
- National Center for Liver Cancer, shanghai, China
| | - Jin Ding
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, the Second Military Medical University, shanghai, China
- National Center for Liver Cancer, shanghai, China
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39
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Transcription factor Oct1 protects against hematopoietic stress and promotes acute myeloid leukemia. Exp Hematol 2019; 76:38-48.e2. [PMID: 31295506 PMCID: PMC7670548 DOI: 10.1016/j.exphem.2019.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 06/18/2019] [Accepted: 07/03/2019] [Indexed: 01/01/2023]
Abstract
A better understanding of the development and progression of acute myelogenous leukemia (AML) is necessary to improve patient outcome. Here we define roles for the transcription factor Oct1/Pou2f1 in AML and normal hematopoiesis. Inappropriate reactivation of the CDX2 gene is widely observed in leukemia patients and in leukemia mouse models. We show that Oct1 associates with the CDX2 promoter in both normal and AML primary patient samples, but recruits the histone demethylase Jmjd1a/Kdm3a to remove the repressive H3K9me2 mark only in malignant specimens. The CpG DNA immediately adjacent to the Oct1 binding site within the CDX2 promoter exhibits variable DNA methylation in healthy control blood and bone marrow samples, but complete demethylation in AML samples. In MLL-AF9-driven mouse models, partial loss of Oct1 protects from myeloid leukemia. Complete Oct1 loss completely suppresses leukemia but results in lethality from bone marrow failure. Loss of Oct1 in normal hematopoietic transplants results in superficially normal long-term reconstitution; however, animals become acutely sensitive to 5-fluorouracil, indicating that Oct1 is dispensable for normal hematopoiesis but protects blood progenitor cells against external chemotoxic stress. These findings elucidate a novel and important role for Oct1 in AML.
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40
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Jakobsen JS, Laursen LG, Schuster MB, Pundhir S, Schoof E, Ge Y, d’Altri T, Vitting-Seerup K, Rapin N, Gentil C, Jendholm J, Theilgaard-Mönch K, Reckzeh K, Bullinger L, Döhner K, Hokland P, Fitzgibbon J, Porse BT. Mutant CEBPA directly drives the expression of the targetable tumor-promoting factor CD73 in AML. SCIENCE ADVANCES 2019; 5:eaaw4304. [PMID: 31309149 PMCID: PMC6620102 DOI: 10.1126/sciadv.aaw4304] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/31/2019] [Indexed: 05/04/2023]
Abstract
The key myeloid transcription factor (TF), CEBPA, is frequently mutated in acute myeloid leukemia (AML), but the direct molecular effects of this leukemic driver mutation remain elusive. To investigate CEBPA mutant AML, we performed microscale, in vivo chromatin immunoprecipitation sequencing and identified a set of aberrantly activated enhancers, exclusively occupied by the leukemia-associated CEBPA-p30 isoform. Comparing gene expression changes in human CEBPA mutant AML and the corresponding Cebpa Lp30 mouse model, we identified Nt5e, encoding CD73, as a cross-species AML gene with an upstream leukemic enhancer physically and functionally linked to the gene. Increased expression of CD73, mediated by the CEBPA-p30 isoform, sustained leukemic growth via the CD73/A2AR axis. Notably, targeting of this pathway enhanced survival of AML-transplanted mice. Our data thus indicate a first-in-class link between a cancer driver mutation in a TF and a druggable, direct transcriptional target.
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MESH Headings
- 5'-Nucleotidase/genetics
- Animals
- Binding Sites
- CCAAT-Enhancer-Binding Proteins/genetics
- CCAAT-Enhancer-Binding Proteins/metabolism
- Enhancer Elements, Genetic
- Epigenesis, Genetic
- GPI-Linked Proteins/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mutation
- Nucleotide Motifs
- Prognosis
- Promoter Regions, Genetic
- Protein Binding
- Protein Isoforms/genetics
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Affiliation(s)
- Janus S. Jakobsen
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Linea G. Laursen
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel B. Schuster
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sachin Pundhir
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Erwin Schoof
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ying Ge
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Teresa d’Altri
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kristoffer Vitting-Seerup
- The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicolas Rapin
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Coline Gentil
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Johan Jendholm
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kim Theilgaard-Mönch
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Hematology, Rigshospitalet, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Reckzeh
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Bullinger
- Department of Hematology, Oncology, and Tumor Immunology, Charité University Medicine, Berlin, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany
| | - Peter Hokland
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | - Jude Fitzgibbon
- Centre for Haemato-Oncology, Queen Mary University of London, London, UK
| | - Bo T. Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Corresponding author.
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Yokomizo T, Watanabe N, Umemoto T, Matsuo J, Harai R, Kihara Y, Nakamura E, Tada N, Sato T, Takaku T, Shimono A, Takizawa H, Nakagata N, Mori S, Kurokawa M, Tenen DG, Osato M, Suda T, Komatsu N. Hlf marks the developmental pathway for hematopoietic stem cells but not for erythro-myeloid progenitors. J Exp Med 2019; 216:1599-1614. [PMID: 31076455 PMCID: PMC6605751 DOI: 10.1084/jem.20181399] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/21/2018] [Accepted: 04/19/2019] [Indexed: 12/26/2022] Open
Abstract
Hematopoietic stem cells (HSCs) and HSC-independent progenitors are generated from hemogenic endothelium. Yokomizo et al. show that Hlf expression distinguishes nascent HSCs from HSC-independent progenitors. HSC specification, regulated by the Evi-1/Hlf axis, is activated only within Hlf+ nascent hematopoietic clusters. Before the emergence of hematopoietic stem cells (HSCs), lineage-restricted progenitors, such as erythro-myeloid progenitors (EMPs), are detected in the embryo or in pluripotent stem cell cultures in vitro. Although both HSCs and EMPs are derived from hemogenic endothelium, it remains unclear how and when these two developmental programs are segregated during ontogeny. Here, we show that hepatic leukemia factor (Hlf) expression specifically marks a developmental continuum between HSC precursors and HSCs. Using the Hlf-tdTomato reporter mouse, we found that Hlf is expressed in intra-aortic hematopoietic clusters and fetal liver HSCs. In contrast, EMPs and yolk sac hematopoietic clusters before embryonic day 9.5 do not express Hlf. HSC specification, regulated by the Evi-1/Hlf axis, is activated only within Hlf+ nascent hematopoietic clusters. These results strongly suggest that HSCs and EMPs are generated from distinct cohorts of hemogenic endothelium. Selective induction of the Hlf+ lineage pathway may lead to the in vitro generation of HSCs from pluripotent stem cells.
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Affiliation(s)
- Tomomasa Yokomizo
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan .,Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Naoki Watanabe
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Terumasa Umemoto
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Junichi Matsuo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ryota Harai
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshihiko Kihara
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Leading Center for the Development and Research of Cancer Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Eri Nakamura
- Laboratory of Genome Research, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Norihiro Tada
- Laboratory of Genome Research, Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tomohiko Sato
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoiku Takaku
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Akihiko Shimono
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Hitoshi Takizawa
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Naomi Nakagata
- Division of Reproductive Engineering, Center for Animal Resources and Development, Kumamoto University, Kumamoto, Japan
| | - Seiichi Mori
- Division of Cancer Genomics, Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Mineo Kurokawa
- Department of Hematology and Oncology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Harvard Stem Cell Institute, Boston, MA
| | - Motomi Osato
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Toshio Suda
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan .,Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Norio Komatsu
- Department of Hematology, Juntendo University Graduate School of Medicine, Tokyo, Japan
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42
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Hepatic leukemia factor is a novel leukemic stem cell regulator in DNMT3A, NPM1, and FLT3-ITD triple-mutated AML. Blood 2019; 134:263-276. [PMID: 31076446 DOI: 10.1182/blood.2018862383] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 05/02/2019] [Indexed: 12/20/2022] Open
Abstract
FLT3, DNMT3A, and NPM1 are the most frequently mutated genes in cytogenetically normal acute myeloid leukemia (AML), but little is known about how these mutations synergize upon cooccurrence. Here we show that triple-mutated AML is characterized by high leukemia stem cell (LSC) frequency, an aberrant leukemia-specific GPR56 highCD34low immunophenotype, and synergistic upregulation of Hepatic Leukemia Factor (HLF). Cell sorting based on the LSC marker GPR56 allowed isolation of triple-mutated from DNMT3A/NPM1 double-mutated subclones. Moreover, in DNMT3A R882-mutated patients, CpG hypomethylation at the HLF transcription start site correlated with high HLF mRNA expression, which was itself associated with poor survival. Loss of HLF via CRISPR/Cas9 significantly reduced the CD34+GPR56+ LSC compartment of primary human triple-mutated AML cells in serial xenotransplantation assays. HLF knockout cells were more actively cycling when freshly harvested from mice, but rapidly exhausted when reintroduced in culture. RNA sequencing of primary human triple-mutated AML cells after shRNA-mediated HLF knockdown revealed the NOTCH target Hairy and Enhancer of Split 1 (HES1) and the cyclin-dependent kinase inhibitor CDKN1C/p57 as novel targets of HLF, potentially mediating these effects. Overall, our data establish HLF as a novel LSC regulator in this genetically defined high-risk AML subgroup.
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43
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Komorowska K, Doyle A, Wahlestedt M, Subramaniam A, Debnath S, Chen J, Soneji S, Van Handel B, Mikkola HKA, Miharada K, Bryder D, Larsson J, Magnusson M. Hepatic Leukemia Factor Maintains Quiescence of Hematopoietic Stem Cells and Protects the Stem Cell Pool during Regeneration. Cell Rep 2018; 21:3514-3523. [PMID: 29262330 DOI: 10.1016/j.celrep.2017.11.084] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/19/2017] [Accepted: 11/22/2017] [Indexed: 01/06/2023] Open
Abstract
The transcription factor hepatic leukemia factor (HLF) is strongly expressed in hematopoietic stem cells (HSCs) and is thought to influence both HSC self-renewal and leukemogenesis. However, the physiological role of HLF in hematopoiesis and HSC function is unclear. Here, we report that mice lacking Hlf are viable with essentially normal hematopoietic parameters, including an intact HSC pool during steady-state hematopoiesis. In contrast, when challenged through transplantation, Hlf-deficient HSCs showed an impaired ability to reconstitute hematopoiesis and became gradually exhausted upon serial transplantation. Transcriptional profiling of Hlf-deficient HSCs revealed changes associated with enhanced cellular activation, and cell-cycle analysis demonstrated a significant reduction of quiescent HSCs. Accordingly, toxic insults targeting dividing cells completely eradicated the HSC pool in Hlf-deficient mice. In summary, our findings point to HLF as a critical regulator of HSC quiescence and as an essential factor for maintaining the HSC pool during regeneration.
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Affiliation(s)
- Karolina Komorowska
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Alexander Doyle
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Martin Wahlestedt
- Molecular Hematology, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Agatheeswaran Subramaniam
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Shubhranshu Debnath
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Jun Chen
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Shamit Soneji
- Molecular Hematology, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Ben Van Handel
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; CarthroniX, Inc., Tarzana, CA 91356, USA
| | - Hanna K A Mikkola
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kenichi Miharada
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
| | - David Bryder
- Molecular Hematology, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Jonas Larsson
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden
| | - Mattias Magnusson
- Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, BMC A12, 221 84, Lund, Sweden.
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