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Tanwar H, Gnanasekaran JM, Allison D, Chuang LS, He X, Aimetti M, Baima G, Costalonga M, Cross RK, Sears C, Mehandru S, Cho J, Colombel JF, Raufman JP, Thumbigere-Math V. Unravelling the Oral-Gut Axis: Interconnection Between Periodontitis and Inflammatory Bowel Disease, Current Challenges, and Future Perspective. J Crohns Colitis 2024; 18:1319-1341. [PMID: 38417137 PMCID: PMC11324343 DOI: 10.1093/ecco-jcc/jjae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/04/2023] [Accepted: 02/27/2024] [Indexed: 03/01/2024]
Abstract
As the opposite ends of the orodigestive tract, the oral cavity and the intestine share anatomical, microbial, and immunological ties that have bidirectional health implications. A growing body of evidence suggests an interconnection between oral pathologies and inflammatory bowel disease [IBD], implying a shift from the traditional concept of independent diseases to a complex, reciprocal cycle. This review outlines the evidence supporting an 'oral-gut' axis, marked by a higher prevalence of periodontitis and other oral conditions in IBD patients and vice versa. We present an in-depth examination of the interconnection between oral pathologies and IBD, highlighting the shared microbiological and immunological pathways, and proposing a 'multi-hit' hypothesis in the pathogenesis of periodontitis-mediated intestinal inflammation. Furthermore, the review underscores the critical need for a collaborative approach between dentists and gastroenterologists to provide holistic oral-systemic healthcare.
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Affiliation(s)
- Himanshi Tanwar
- Division of Periodontology, University of Maryland School of Dentistry, Baltimore, MD, USA
| | | | - Devon Allison
- Division of Periodontology, University of Maryland School of Dentistry, Baltimore, MD, USA
| | - Ling-shiang Chuang
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Mario Aimetti
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Giacomo Baima
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Massimo Costalonga
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, USA
| | - Raymond K Cross
- Division of Gastroenterology & Hepatology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Cynthia Sears
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Saurabh Mehandru
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy Cho
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Pierre Raufman
- Division of Gastroenterology & Hepatology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Vivek Thumbigere-Math
- Division of Periodontology, University of Maryland School of Dentistry, Baltimore, MD, USA
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA
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2
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Wu Z, Xu J, Hu Y, Peng X, Zhang Z, Yao X, Peng Q. The roles of IRF8 in nonspecific orbital inflammation: an integrated analysis by bioinformatics and machine learning. J Ophthalmic Inflamm Infect 2024; 14:29. [PMID: 38900395 PMCID: PMC11190126 DOI: 10.1186/s12348-024-00410-4] [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: 12/09/2023] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Nonspecific Orbital Inflammation (NSOI) represents a persistent and idiopathic proliferative inflammatory disorder, characterized by polymorphous lymphoid infiltration within the orbit. The transcription factor Interferon Regulatory Factor 8 (IRF8), integral to the IRF protein family, was initially identified as a pivotal element for the commitment and differentiation of myeloid cell lineage. Serving as a central regulator of innate immune receptor signaling, IRF8 orchestrates a myriad of functions in hematopoietic cell development. However, the intricate mechanisms underlying IRF8 production remain to be elucidated, and its potential role as a biomarker for NSOI is yet to be resolved. METHODS IRF8 was extracted from the intersection analysis of common DEGs of GSE58331 and GSE105149 from the GEO and immune- related gene lists in the ImmPort database using The Lasso regression and SVM-RFE analysis. We performed GSEA and GSVA with gene sets coexpressed with IRF8, and observed that gene sets positively related to IRF8 were enriched in immune-related pathways. To further explore the correlation between IRF8 and immune-related biological process, the CIBERSORT algorithm and ESTIMATE method were employed to evaluate TME characteristics of each sample and confirmed that high IRF8 expression might give rise to high immune cell infiltration. Finally, the GSE58331 was utilized to confirm the levels of expression of IRF8. RESULTS Among the 314 differentially expressed genes (DEGs), some DEGs were found to be significantly different. With LASSO and SVM-RFE algorithms, we obtained 15 hub genes. For biological function analysis in IRF8, leukocyte mediated immunity, leukocyte cell-cell adhesion, negative regulation of immune system process were emphasized. B cells naive, Macrophages M0, Macrophages M1, T cells CD4 memory activated, T cells CD4 memory resting, T cells CD4 naive, and T cells gamma delta were shown to be positively associated with IRF8. While, Mast cells resting, Monocytes, NK cells activated, Plasma cells, T cells CD8, and T cells regulatory (Tregs) were shown to be negatively linked with IRF8. The diagnostic ability of the IRF8 in differentiating NSOI exhibited a good value. CONCLUSIONS This study discovered IRF8 that are linked to NSOI. IRF8 shed light on potential new biomarkers for NSOI and tracking its progression.
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Affiliation(s)
- Zixuan Wu
- Hunan University of Traditional Chinese Medicine, Changsha, 410208, Hunan Province, China
| | - Jinfeng Xu
- Dongying People's Hospital (Dongying Hospital of Shandong Provincial Hospital Group), Dongying, Shandong, 257091, PR China
| | - Yi Hu
- Hunan University of Traditional Chinese Medicine, Changsha, 410208, Hunan Province, China
| | - Xin Peng
- Hunan University of Traditional Chinese Medicine, Changsha, 410208, Hunan Province, China
| | - Zheyuan Zhang
- Hunan University of Traditional Chinese Medicine, Changsha, 410208, Hunan Province, China
| | - Xiaolei Yao
- Department of Ophthalmology, the First Affiliated Hospital of Hunan University of Traditional Chinese Medicine, Changsha, 410007, Hunan Province, China
- Ophthalmology Department, The First Hospital of Hunan University of Chinese Medicine, Changsha, 410011, China
| | - Qinghua Peng
- Hunan University of Traditional Chinese Medicine, Changsha, 410208, Hunan Province, China.
- Department of Ophthalmology, the First Affiliated Hospital of Hunan University of Traditional Chinese Medicine, Changsha, 410007, Hunan Province, China.
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Li N, Steiger S, Zhong M, Lu M, Lei Y, Tang C, Chen J, Guo Y, Li J, Zhang D, Li J, Zhu E, Zheng Z, Lichtnekert J, Chen Y, Wang X. IRF8 maintains mononuclear phagocyte and neutrophil function in acute kidney injury. Heliyon 2024; 10:e31818. [PMID: 38845872 PMCID: PMC11153194 DOI: 10.1016/j.heliyon.2024.e31818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 06/09/2024] Open
Abstract
Immune cells are key players in acute tissue injury and inflammation, including acute kidney injury (AKI). Their development, differentiation, activation status, and functions are mediated by a variety of transcription factors, such as interferon regulatory factor 8 (IRF8) and IRF4. We speculated that IRF8 has a pathophysiologic impact on renal immune cells in AKI and found that IRF8 is highly expressed in blood type 1 conventional dendritic cells (cDC1s), monocytes, monocyte-derived dendritic cells (moDCs) and kidney biopsies from patients with AKI. In a mouse model of ischemia‒reperfusion injury (IRI)-induced AKI, Irf8 -/- mice displayed increased tubular cell necrosis and worsened kidney dysfunction associated with the recruitment of a substantial amount of monocytes and neutrophils but defective renal infiltration of cDC1s and moDCs. Mechanistically, global Irf8 deficiency impaired moDC and cDC1 maturation and activation, as well as cDC1 proliferation, antigen uptake, and trafficking to lymphoid organs for T-cell priming in ischemic AKI. Moreover, compared with Irf8 +/+ mice, Irf8 -/- mice exhibited increased neutrophil recruitment and neutrophil extracellular trap (NET) formation following AKI. IRF8 primarily regulates cDC1 and indirectly neutrophil functions, and thereby protects mice from kidney injury and inflammation following IRI. Our results demonstrate that IRF8 plays a predominant immunoregulatory role in cDC1 function and therefore represents a potential therapeutic target in AKI.
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Affiliation(s)
- Na Li
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, 518107, Shenzhen, China
- Scientific Research Center, Edmond H. Fischer Translational Medical Research Laboratory, The Seventh Affiliated Hospital, Sun Yat-Sen University, 518107, Shenzhen, China
| | - Stefanie Steiger
- Renal Division, Department of Medicine IV, Ludwig-Maximilians-University Hospital, Ludwig-Maximilian-University Munich, 80336, Munich, Bavaria, Germany
| | - Ming Zhong
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, 518107, Shenzhen, China
| | - Meihua Lu
- Department of Geriatrics, People's Hospital of Banan District, 401320, Chongqing, China
| | - Yan Lei
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, 518107, Shenzhen, China
| | - Chun Tang
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, 518107, Shenzhen, China
| | - Jiasi Chen
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, 518107, Shenzhen, China
| | - Yao Guo
- Scientific Research Center, Edmond H. Fischer Translational Medical Research Laboratory, The Seventh Affiliated Hospital, Sun Yat-Sen University, 518107, Shenzhen, China
| | - Jinhong Li
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, 518107, Shenzhen, China
| | - Dengyang Zhang
- Scientific Research Center, Edmond H. Fischer Translational Medical Research Laboratory, The Seventh Affiliated Hospital, Sun Yat-Sen University, 518107, Shenzhen, China
| | - Jingyi Li
- Department of Pulmonary & Critical Care Medicine, Shenzhen Hospital of Southern Medical University, 518107, Shenzhen, China
| | - Enyi Zhu
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, 518107, Shenzhen, China
| | - Zhihua Zheng
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, 518107, Shenzhen, China
| | - Julia Lichtnekert
- Renal Division, Department of Medicine IV, Ludwig-Maximilians-University Hospital, Ludwig-Maximilian-University Munich, 80336, Munich, Bavaria, Germany
| | - Yun Chen
- Scientific Research Center, Edmond H. Fischer Translational Medical Research Laboratory, The Seventh Affiliated Hospital, Sun Yat-Sen University, 518107, Shenzhen, China
| | - Xiaohua Wang
- Department of Nephrology, Center of Kidney and Urology, The Seventh Affiliated Hospital, Sun Yat-Sen University, 518107, Shenzhen, China
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4
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Huh HD, Park HW. Emerging paradigms in cancer cell plasticity. BMB Rep 2024; 57:273-280. [PMID: 38627950 PMCID: PMC11214895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/09/2024] [Accepted: 04/05/2024] [Indexed: 06/28/2024] Open
Abstract
Cancer cells metastasize to distant organs by altering their characteristics within the tumor microenvironment (TME) to effectively overcome challenges during the multistep tumorigenesis. Plasticity endows cancer cell with the capacity to shift between different morphological states to invade, disseminate, and seed metastasis. The epithelial-to-mesenchymal transition (EMT) is a theory derived from tissue biopsy, which explains the acquisition of EMT transcription factors (TFs) that convey mesenchymal features during cancer migration and invasion. On the other hand, adherent-to-suspension transition (AST) is an emerging theory derived from liquid biopsy, which describes the acquisition of hematopoietic features by AST-TFs that reprograms anchorage dependency during the dissemination of circulating tumor cells (CTCs). The induction and plasticity of EMT and AST dynamically reprogram cell-cell interaction and cell-matrix interaction during cancer dissemination and colonization. Here, we review the mechanisms governing cellular plasticity of AST and EMT during the metastatic cascade and discuss therapeutic challenges posed by these two morphological adaptations to provide insights for establishing new therapeutic interventions. [BMB Reports 2024; 57(6): 273-280].
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Affiliation(s)
- Hyunbin D. Huh
- Department of Biochemistry, Brain Korea 21 Project, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hyun Woo Park
- Department of Biochemistry, Brain Korea 21 Project, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
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5
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Weinand K, Sakaue S, Nathan A, Jonsson AH, Zhang F, Watts GFM, Al Suqri M, Zhu Z, Rao DA, Anolik JH, Brenner MB, Donlin LT, Wei K, Raychaudhuri S. The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis. Nat Commun 2024; 15:4650. [PMID: 38821936 PMCID: PMC11143375 DOI: 10.1038/s41467-024-48620-7] [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: 03/29/2023] [Accepted: 05/02/2024] [Indexed: 06/02/2024] Open
Abstract
Synovial tissue inflammation is a hallmark of rheumatoid arthritis (RA). Recent work has identified prominent pathogenic cell states in inflamed RA synovial tissue, such as T peripheral helper cells; however, the epigenetic regulation of these states has yet to be defined. Here, we examine genome-wide open chromatin at single-cell resolution in 30 synovial tissue samples, including 12 samples with transcriptional data in multimodal experiments. We identify 24 chromatin classes and predict their associated transcription factors, including a CD8 + GZMK+ class associated with EOMES and a lining fibroblast class associated with AP-1. By integrating with an RA tissue transcriptional atlas, we propose that these chromatin classes represent 'superstates' corresponding to multiple transcriptional cell states. Finally, we demonstrate the utility of this RA tissue chromatin atlas through the associations between disease phenotypes and chromatin class abundance, as well as the nomination of classes mediating the effects of putatively causal RA genetic variants.
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Affiliation(s)
- Kathryn Weinand
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Saori Sakaue
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Fan Zhang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine Division of Rheumatology and Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Gerald F M Watts
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Majd Al Suqri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zhu Zhu
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jennifer H Anolik
- Division of Allergy, Immunology and Rheumatology, Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura T Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
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6
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Yamasaki T, Nishiyama A, Kurogi N, Nishimura K, Nishida S, Kurotaki D, Ban T, Ramilowski JA, Ozato K, Toyoda A, Tamura T. Physical and functional interaction among Irf8 enhancers during dendritic cell differentiation. Cell Rep 2024; 43:114107. [PMID: 38613785 DOI: 10.1016/j.celrep.2024.114107] [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: 09/30/2023] [Revised: 02/28/2024] [Accepted: 03/28/2024] [Indexed: 04/15/2024] Open
Abstract
The production of type 1 conventional dendritic cells (cDC1s) requires high expression of the transcription factor IRF8. Three enhancers at the Irf8 3' region function in a differentiation stage-specific manner. However, whether and how these enhancers interact physically and functionally remains unclear. Here, we show that the Irf8 3' enhancers directly interact with each other and contact the Irf8 gene body during cDC1 differentiation. The +56 kb enhancer, which functions from multipotent progenitor stages, activates the other 3' enhancers through an IRF8-dependent transcription factor program, that is, in trans. Then, the +32 kb enhancer, which operates in cDC1-committed cells, reversely acts in cis on the other 3' enhancers to maintain the high expression of Irf8. Indeed, mice with compound heterozygous deletion of the +56 and +32 kb enhancers are unable to generate cDC1s. These results illustrate how multiple enhancers cooperate to induce a lineage-determining transcription factor gene during cell differentiation.
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Affiliation(s)
- Takaya Yamasaki
- Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Akira Nishiyama
- Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Nagomi Kurogi
- Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Koutarou Nishimura
- Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Shion Nishida
- Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan; Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, Sagamihara, Kanagawa, Japan
| | - Daisuke Kurotaki
- Laboratory of Chromatin Organization in Immune Cell Development, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Tatsuma Ban
- Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Jordan A Ramilowski
- Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Keiko Ozato
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan; Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tomohiko Tamura
- Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan; Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa, Japan.
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7
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Swarnkar G, Semenkovich NP, Arra M, Mims DK, Naqvi SK, Peterson T, Mbalaviele G, Wu CL, Abu-Amer Y. DNA hypomethylation ameliorates erosive inflammatory arthritis by modulating interferon regulatory factor-8. Proc Natl Acad Sci U S A 2024; 121:e2310264121. [PMID: 38319963 PMCID: PMC10873594 DOI: 10.1073/pnas.2310264121] [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: 06/22/2023] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
Epigenetic regulation plays a crucial role in the pathogenesis of autoimmune diseases such as inflammatory arthritis. DNA hypomethylating agents, such as decitabine (DAC), have been shown to dampen inflammation and restore immune homeostasis. In the present study, we demonstrate that DAC elicits potent anti-inflammatory effects and attenuates disease symptoms in several animal models of arthritis. Transcriptomic and epigenomic profiling show that DAC-mediated hypomethylation regulates a wide range of cell types in arthritis, altering the differentiation trajectories of anti-inflammatory macrophage populations, regulatory T cells, and tissue-protective synovial fibroblasts (SFs). Mechanistically, DAC-mediated demethylation of intragenic 5'-Cytosine phosphate Guanine-3' (CpG) islands of the transcription factor Irf8 (interferon regulatory factor 8) induced its re-expression and promoted its repressor activity. As a result, DAC restored joint homeostasis by resetting the transcriptomic signature of negative regulators of inflammation in synovial macrophages (MerTK, Trem2, and Cx3cr1), TREGs (Foxp3), and SFs (Pdpn and Fapα). In conclusion, we found that Irf8 is necessary for the inhibitory effect of DAC in murine arthritis and that direct expression of Irf8 is sufficient to significantly mitigate arthritis.
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Affiliation(s)
- Gaurav Swarnkar
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO63110
| | | | - Manoj Arra
- Department of Emergency Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Dorothy K. Mims
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO63110
| | - Syeda Kanwal Naqvi
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO63110
| | - Timothy Peterson
- Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
- HealthSpan Technologies, Inc, St. Louis, MO63110
| | - Gabriel Mbalaviele
- Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Chia-Lung Wu
- Department of Orthopedics and Physical Performance, University of Rochester, Rochester, NY14642
| | - Yousef Abu-Amer
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO63110
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO63110
- Shriners Hospital for Children, St. Louis, MO63110
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8
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Zhang P, Lu R. The Molecular and Biological Function of MEF2D in Leukemia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:379-403. [PMID: 39017853 DOI: 10.1007/978-3-031-62731-6_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Myocyte enhancer factor 2 (MEF2) is a key transcription factor (TF) in skeletal, cardiac, and neural tissue development and includes four isoforms: MEF2A, MEF2B, MEF2C, and MEF2D. These isoforms significantly affect embryonic development, nervous system regulation, muscle cell differentiation, B- and T-cell development, thymocyte selection, and effects on tumorigenesis and leukemia. This chapter describes the multifaceted roles of MEF2 family proteins, covering embryonic development, nervous system regulation, and muscle cell differentiation. It further elucidates the contribution of MEF2 to various blood and immune cell functions. Specifically, in B-cell precursor acute lymphoblastic leukemia (BCP-ALL), MEF2D is aberrantly expressed and forms a fusion protein with BCL9, CSF1R, DAZAP1, HNRNPUL1, and SS18. These fusion proteins are closely related to the pathogenesis of leukemia. In addition, it specifically introduces the regulatory effect of MEF2D fusion protein on the proliferation and growth of B-cell acute lymphoblastic leukemia (B-ALL) cells. Finally, we detail the positive feedback loop between MEF2D and IRF8 that significantly promotes the progression of acute myeloid leukemia (AML) and the importance of the ZMYND8-BRD4 interaction in regulating the IRF8 and MYC transcriptional programs. The MEF2D-CEBPE axis is highlighted as a key transcriptional mechanism controlling the block of leukemic cell self-renewal and differentiation in AML. This chapter starts with the structure and function of MEF2 family proteins, specifically summarizing and analyzing the role of MEF2D in B-ALL and AML, mediating the complex molecular mechanisms of transcriptional regulation and exploring their implications for human health and disease.
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Affiliation(s)
- Pengcheng Zhang
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA
| | - Rui Lu
- Department of Medicine, Division of Hematology/Oncology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL, USA.
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9
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Al Qaryoute A, Fallatah W, Dhinoja S, Raman R, Jagadeeswaran P. Role of microRNAs and their downstream target transcription factors in zebrafish thrombopoiesis. Sci Rep 2023; 13:16066. [PMID: 37752184 PMCID: PMC10522587 DOI: 10.1038/s41598-023-42868-7] [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: 04/12/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Previous studies have shown that human platelets and megakaryocytes carry microRNAs suggesting their role in platelet function and megakaryocyte development, respectively. However, a comprehensive study on the microRNAs and their targets has not been undertaken. Zebrafish thrombocytes could be used as a model to study their role in megakaryocyte maturation and platelet function because thrombocytes have both megakaryocyte features and platelet properties. In our laboratory, we identified 15 microRNAs in thrombocytes using single-cell RNA sequencing. We knocked down each of these 15 microRNAs by the piggyback method and found knockdown of three microRNAs, mir-7148, let-7b, and mir-223 in adult zebrafish led to an increase in the percentage of thrombocytes. Functional thrombocyte analysis using plate tilt assay showed no modulatory effect of the three microRNAs on thrombocyte aggregation/agglutination. We also found enhanced thrombosis using arterial laser thrombosis assay in a group of zebrafish larvae after mir-7148, let-7b, and mir-223 knockdowns. These results suggested mir-7148, let-7b, and mir-223 are repressors for thrombocyte production. We then explored miRWalk database for let-7b downstream targets and then selected those that are expressed in thrombocytes, and from this list based on their role in differentiation selected 14 genes, rorca, tgif1, rfx1a, deaf1, zbtb18, mafba, cebpa, spi1a, spi1b, fhl3b, ikzf1, irf5, irf8, and lbx1b that encode transcriptional regulators. The qRT-PCR analysis of expression levels of the above genes following let-7b knockdown showed changes in the expression of 13 targets. We then studied the effect of the 13 targets on thrombocyte production and identified 5 genes, irf5, tgif1, irf8, cebpa, and rorca that showed thrombocytosis and one gene, ikzf1 that showed thrombocytopenia. Furthermore, we tested whether mir-223 regulates any of the above 13 transcription factors after mir-223 knockdown using qRT-PCR. Six of the 13 genes showed similar gene expression as observed with let-7b knockdown and 7 genes showed opposing results. Thus, our results suggested a possible regulatory network in common with both let-7b and mir-223. We also identified that tgif1, cebpa, ikzf1, irf5, irf8, and ikzf1 play a role in thrombopoiesis. Since the ikzf1 gene showed a differential expression profile in let-7b and mir-223 knockdowns but resulted in thrombocytopenia in ikzf1 knockdown in both adults and larvae we also studied an ikzf1 mutant and showed the mutant had thrombocytopenia. Taken together, these studies showed that thrombopoiesis is controlled by a network of transcription regulators that are regulated by multiple microRNAs in both positive and negative manner resulting in overall inhibition of thrombopoiesis.
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Affiliation(s)
- Ayah Al Qaryoute
- Department of Biological Sciences, University of North Texas, 1511 West Sycamore Street, Denton, TX, 76203, USA
| | - Weam Fallatah
- Department of Biological Sciences, University of North Texas, 1511 West Sycamore Street, Denton, TX, 76203, USA
| | - Sanchi Dhinoja
- Department of Biological Sciences, University of North Texas, 1511 West Sycamore Street, Denton, TX, 76203, USA
| | - Revathi Raman
- Department of Biological Sciences, University of North Texas, 1511 West Sycamore Street, Denton, TX, 76203, USA
| | - Pudur Jagadeeswaran
- Department of Biological Sciences, University of North Texas, 1511 West Sycamore Street, Denton, TX, 76203, USA.
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10
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Friebus-Kardash J, Kuang F, Peitz T, Hamdan TA, Eisenberger U, Boss K, Kribben A, Lang KS, Jahn M. Expression of Interferon Regulatory Factor 8 (IRF8) and Its Association with Infections in Dialysis Patients. Cells 2023; 12:1892. [PMID: 37508555 PMCID: PMC10378315 DOI: 10.3390/cells12141892] [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: 06/24/2023] [Revised: 07/08/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Patients on dialysis have dysfunctions of innate and adaptive immune system responses. The transcriptional factor IRF8 (interferon regulatory factor 8) is primarily expressed in plasmacytoid cells (pDCs) and myeloid dendritic cells (mDCs), playing a crucial role in the maturation of dendritic cells, monocytes, and macrophages, and contributing to protection against bacterial infections. The current study analyzed the expression patterns of IRF8 and assessed its association with the risk of infections in 79 dialysis patients compared to 44 healthy controls. Different subsets of leukocytes and the intracellular expression of IRF8 were measured using flow cytometry. Compared to the healthy controls, the dialysis patients showed significantly reduced numbers of pDCs and significantly increased numbers of natural killer cells and classical and intermediate monocytes. The dialysis patients exhibited decreased numbers of IRF8-positive dendritic cells (pDC p < 0.001, mDC1 p < 0.001, mDC2 p = 0.005) and increased numbers of IRF8-positive monocytes (p < 0.001). IRF8 expression in pDC, mDC, and classical monocytes was lower in the dialysis patients than in the controls. Dialysis patients who required hospitalization due to infections within one year of follow-up displayed significantly reduced IRF8 expression levels in pDCs compared to patients without such infections (p = 0.04). Our results suggest that reduced IRF8 expression in pDCs is a potential risk factor predisposing dialysis patients to serious infections.
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Affiliation(s)
- Justa Friebus-Kardash
- Department of Nephrology, University Hospital Essen, University of Duisburg-Essen, 47057 Essen, Germany
| | - Fei Kuang
- Institute of Immunology, University Hospital Essen, University of Duisburg-Essen, 47057 Essen, Germany
| | - Tobias Peitz
- Department of Nephrology, University Hospital Essen, University of Duisburg-Essen, 47057 Essen, Germany
| | - Thamer A Hamdan
- Institute of Immunology, University Hospital Essen, University of Duisburg-Essen, 47057 Essen, Germany
| | - Ute Eisenberger
- Department of Nephrology, University Hospital Essen, University of Duisburg-Essen, 47057 Essen, Germany
| | - Kristina Boss
- Department of Nephrology, University Hospital Essen, University of Duisburg-Essen, 47057 Essen, Germany
| | - Andreas Kribben
- Department of Nephrology, University Hospital Essen, University of Duisburg-Essen, 47057 Essen, Germany
| | - Karl Sebastian Lang
- Institute of Immunology, University Hospital Essen, University of Duisburg-Essen, 47057 Essen, Germany
| | - Michael Jahn
- Department of Nephrology, University Hospital Essen, University of Duisburg-Essen, 47057 Essen, Germany
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11
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Johnson KD, Jung MM, Tran VL, Bresnick EH. Interferon regulatory factor-8-dependent innate immune alarm senses GATA2 deficiency to alter hematopoietic differentiation and function. Curr Opin Hematol 2023; 30:117-123. [PMID: 37254854 PMCID: PMC10236032 DOI: 10.1097/moh.0000000000000763] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PURPOSE OF REVIEW Recent discoveries have provided evidence for mechanistic links between the master regulator of hematopoiesis GATA2 and the key component of interferon and innate immunity signaling pathways, interferon-regulatory factor-8 (IRF8). These links have important implications for the control of myeloid differentiation in physiological and pathological states. RECENT FINDINGS GATA2 deficiency resulting from loss of the Gata2 -77 enhancer in progenitors triggers an alarm that instigates the transcriptional induction of innate immune signaling and distorts a myeloid differentiation program. This pathological alteration renders progenitors hyperresponsive to interferon γ, toll-like receptor and interleukin-6 signaling and impaired in granulocyte-macrophage colony-stimulating factor signaling. IRF8 upregulation in -77-/- progenitors promotes monocyte and dendritic cell differentiation while suppressing granulocytic differentiation. As PU.1 promotes transcription of Irf8 and other myeloid and B-lineage genes, GATA2-mediated repression of these genes opposes the PU.1-dependent activating mechanism. SUMMARY As GATA2 deficiency syndrome is an immunodeficiency disorder often involving myelodysplastic syndromes and acute myeloid leukemia, elucidating how GATA2 commissions and decommissions genome activity and developmental regulatory programs will unveil mechanisms that go awry when GATA2 levels and/or activities are disrupted.
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Affiliation(s)
- Kirby D Johnson
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
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12
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Qaryoute AA, Fallatah W, Dhinoja S, Raman R, Jagadeeswaran P. Role of MicroRNAs and their Downstream Target Transcription Factors in Zebrafish Thrombopoiesis. RESEARCH SQUARE 2023:rs.3.rs-2807790. [PMID: 37162944 PMCID: PMC10168436 DOI: 10.21203/rs.3.rs-2807790/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Previous studies have shown that human platelets and megakaryocytes carry microRNAs suggesting their role in platelet function and megakaryocyte development, respectively. However, a comprehensive study on the microRNAs and their targets has not been undertaken. Zebrafish thrombocytes could be used as a model to study their role in megakaryocyte maturation and platelet function because thrombocytes have both megakaryocyte features and platelet properties. In our laboratory, we identified 15 microRNAs in thrombocytes using single-cell RNA sequencing. We knocked down each of these 15 microRNAs by the piggyback method and found knockdown of three microRNAs, mir-7148, let-7b , and mir-223 in adult zebrafish led to an increase in the percentage of thrombocytes. Functional thrombocyte analysis using plate tilt assay showed no modulatory effect of the three microRNAs on thrombocyte aggregation/agglutination. We also found enhanced thrombosis using arterial laser thrombosis assay in a group of zebrafish larvae after mir-7148, let-7b , and mir-223 knockdowns. These results suggested mir-7148, let-7b , and mir-223 are repressors for thrombocyte production. We then explored miRWalk database for let-7b downstream targets and then selected those that are expressed in thrombocytes, and from this list based on their role in differentiation selected 14 genes, rorca, tgif1, rfx1a, deaf1, zbtb18, mafba, cebpa, spi1a, spi1b, fhl3b, ikzf1, irf5, irf8 , and lbx1b that encode transcriptional regulators. The qRT-PCR analysis of expression levels of the above genes following let-7b knockdown showed changes in the expression of 13 targets. We then studied the effect of the 13 targets on thrombocyte production and identified 5 genes, irf5, tgif1, irf8, cebpa , and rorca that showed thrombocytosis and one gene, ikzf1 that showed thrombocytopenia. Furthermore, we tested whether mir-223 regulates any of the above 13 transcription factors after mir-223 knockdown using qRT-PCR. Six of the 13 genes showed similar gene expression as observed with let-7b knockdown and 7 genes showed opposing results. Thus, our results suggested a possible regulatory network in common with both let-7b and mir-223 . We also identified that tgif1, cebpa, ikzf1, irf5 , irf8 , and ikzf1 play a role in thrombopoiesis. Since the ikzf1 gene showed a differential expression profile in let-7b and mir-223 knockdowns but resulted in thrombocytopenia in ikzf1 knockdown in both adults and larvae we also studied an ikzf1 mutant and showed the mutant had thrombocytopenia. Taken together, these studies showed that thrombopoiesis is controlled by a network of transcription regulators that are regulated by multiple microRNAs in both positive and negative manner resulting in overall inhibition of thrombopoiesis.
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13
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Weinand K, Sakaue S, Nathan A, Jonsson AH, Zhang F, Watts GFM, Zhu Z, Rao DA, Anolik JH, Brenner MB, Donlin LT, Wei K, Raychaudhuri S. The Chromatin Landscape of Pathogenic Transcriptional Cell States in Rheumatoid Arthritis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.536026. [PMID: 37066336 PMCID: PMC10104143 DOI: 10.1101/2023.04.07.536026] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Synovial tissue inflammation is the hallmark of rheumatoid arthritis (RA). Recent work has identified prominent pathogenic cell states in inflamed RA synovial tissue, such as T peripheral helper cells; however, the epigenetic regulation of these states has yet to be defined. We measured genome-wide open chromatin at single cell resolution from 30 synovial tissue samples, including 12 samples with transcriptional data in multimodal experiments. We identified 24 chromatin classes and predicted their associated transcription factors, including a CD8+ GZMK+ class associated with EOMES and a lining fibroblast class associated with AP-1. By integrating an RA tissue transcriptional atlas, we found that the chromatin classes represented 'superstates' corresponding to multiple transcriptional cell states. Finally, we demonstrated the utility of this RA tissue chromatin atlas through the associations between disease phenotypes and chromatin class abundance as well as the nomination of classes mediating the effects of putatively causal RA genetic variants.
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Affiliation(s)
- Kathryn Weinand
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Saori Sakaue
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Fan Zhang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology and the Center for Health Artificial Intelligence, University of Colorado School of Medicine, Aurora, CO, USA
| | - Gerald F. M. Watts
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhu Zhu
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Deepak A. Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Jennifer H. Anolik
- Division of Allergy, Immunology and Rheumatology; Department of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Michael B. Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura T. Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
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14
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Hartung EE, Singh K, Berg T. LSD1 inhibition modulates transcription factor networks in myeloid malignancies. Front Oncol 2023; 13:1149754. [PMID: 36969082 PMCID: PMC10036816 DOI: 10.3389/fonc.2023.1149754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
Acute Myeloid Leukemia (AML) is a type of cancer of the blood system that is characterized by an accumulation of immature hematopoietic cells in the bone marrow and blood. Its pathogenesis is characterized by an increase in self-renewal and block in differentiation in hematopoietic stem and progenitor cells. Underlying its pathogenesis is the acquisition of mutations in these cells. As there are many different mutations found in AML that can occur in different combinations the disease is very heterogeneous. There has been some progress in the treatment of AML through the introduction of targeted therapies and a broader application of the stem cell transplantation in its treatment. However, many mutations found in AML are still lacking defined interventions. These are in particular mutations and dysregulation in important myeloid transcription factors and epigenetic regulators that also play a crucial role in normal hematopoietic differentiation. While a direct targeting of the partial loss-of-function or change in function observed in these factors is very difficult to imagine, recent data suggests that the inhibition of LSD1, an important epigenetic regulator, can modulate interactions in the network of myeloid transcription factors and restore differentiation in AML. Interestingly, the impact of LSD1 inhibition in this regard is quite different between normal and malignant hematopoiesis. The effect of LSD1 inhibition involves transcription factors that directly interact with LSD1 such as GFI1 and GFI1B, but also transcription factors that bind to enhancers that are modulated by LSD1 such as PU.1 and C/EBPα as well as transcription factors that are regulated downstream of LSD1 such as IRF8. In this review, we are summarizing the current literature on the impact of LSD1 modulation in normal and malignant hematopoietic cells and the current knowledge how the involved transcription factor networks are altered. We are also exploring how these modulation of transcription factors play into the rational selection of combination partners with LSD1 inhibitors, which is an intense area of clinical investigation.
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Affiliation(s)
- Emily E. Hartung
- Centre for Discovery in Cancer Research, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Kanwaldeep Singh
- Centre for Discovery in Cancer Research, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Department of Oncology, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
| | - Tobias Berg
- Centre for Discovery in Cancer Research, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Department of Oncology, Faculty of Health Sciences, McMaster University, Hamilton, ON, Canada
- Escarpment Cancer Research Institute, McMaster University, Hamilton Health Sciences, Hamilton, ON, Canada
- *Correspondence: Tobias Berg,
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15
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Guglietta S, Krieg C. Phenotypic and functional heterogeneity of monocytes in health and cancer in the era of high dimensional technologies. Blood Rev 2023; 58:101012. [PMID: 36114066 DOI: 10.1016/j.blre.2022.101012] [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: 08/28/2021] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/23/2022]
Abstract
Monocytes have been traditionally classified in three discrete subsets, which can participate in the immune responses as effector cells or as precursors of myeloid-derived cells in circulation and tissues. However, recent advances in single-cell omics have revealed unprecedented phenotypic and functional heterogeneity that goes well beyond the three conventional monocytic subsets and propose a more fluid differentiation model. This novel concept does not only apply to the monocytes in circulation but also at the tissue site. Consequently, the binary model proposed for differentiating monocyte into M1 and M2 macrophages has been recently challenged by a spectrum model that more realistically mirrors the heterogeneous cues in inflammatory conditions. This review describes the latest results on the high dimensional characterization of monocytes and monocyte-derived myeloid cells in steady state and cancer. We discuss how environmental cues and monocyte-intrinsic properties may affect their differentiation toward specific functional and phenotypic subsets, the causes of monocyte expansion and reduction in cancer, their metabolic requirements, and the potential effect on tumor immunity.
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Affiliation(s)
- Silvia Guglietta
- Hollings Cancer Center, 86 Jonathan Lucas Street, Charleston, SC 29425, USA; Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina (MUSC), 173 Ashley Avenue, CRI609, Charleston, SC 29425, USA.
| | - Carsten Krieg
- Department of Pathology & Laboratory Medicine, Medical University of South Carolina (MUSC), 68 President Street, BE415, Charleston, SC 29425, USA; Hollings Cancer Center, 86 Jonathan Lucas Street, Charleston, SC 29425, USA.
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16
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Van Goor A, Pasternak A, Walugembe M, Chehab N, Hamonic G, Dekkers JCM, Harding JCS, Lunney JK. Genome wide association study of thyroid hormone levels following challenge with porcine reproductive and respiratory syndrome virus. Front Genet 2023; 14:1110463. [PMID: 36845393 PMCID: PMC9947478 DOI: 10.3389/fgene.2023.1110463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction: Porcine reproductive and respiratory syndrome virus (PRRSV) causes respiratory disease in piglets and reproductive disease in sows. Piglet and fetal serum thyroid hormone (i.e., T3 and T4) levels decrease rapidly in response to Porcine reproductive and respiratory syndrome virus infection. However, the genetic control of T3 and T4 levels during infection is not completely understood. Our objective was to estimate genetic parameters and identify quantitative trait loci (QTL) for absolute T3 and/or T4 levels of piglets and fetuses challenged with Porcine reproductive and respiratory syndrome virus. Methods: Sera from 5-week-old pigs (N = 1792) at 11 days post inoculation (DPI) with Porcine reproductive and respiratory syndrome virus were assayed for T3 levels (piglet_T3). Sera from fetuses (N = 1,267) at 12 or 21 days post maternal inoculation (DPMI) with Porcine reproductive and respiratory syndrome virus of sows (N = 145) in late gestation were assayed for T3 (fetal_T3) and T4 (fetal_T4) levels. Animals were genotyped using 60 K Illumina or 650 K Affymetrix single nucleotide polymorphism (SNP) panels. Heritabilities, phenotypic correlations, and genetic correlations were estimated using ASREML; genome wide association studies were performed for each trait separately using Julia for Whole-genome Analysis Software (JWAS). Results: All three traits were low to moderately heritable (10%-16%). Phenotypic and genetic correlations of piglet_T3 levels with weight gain (0-42 DPI) were 0.26 ± 0.03 and 0.67 ± 0.14, respectively. Nine significant quantitative trait loci were identified for piglet_T3, on Sus scrofa chromosomes (SSC) 3, 4, 5, 6, 7, 14, 15, and 17, and collectively explaining 30% of the genetic variation (GV), with the largest quantitative trait loci identified on SSC5, explaining 15% of the genetic variation. Three significant quantitative trait loci were identified for fetal_T3 on SSC1 and SSC4, which collectively explained 10% of the genetic variation. Five significant quantitative trait loci were identified for fetal_T4 on SSC1, 6, 10, 13, and 15, which collectively explained 14% of the genetic variation. Several putative immune-related candidate genes were identified, including CD247, IRF8, and MAPK8. Discussion: Thyroid hormone levels following Porcine reproductive and respiratory syndrome virus infection were heritable and had positive genetic correlations with growth rate. Multiple quantitative trait loci with moderate effects were identified for T3 and T4 levels during challenge with Porcine reproductive and respiratory syndrome virus and candidate genes were identified, including several immune-related genes. These results advance our understanding of growth effects of both piglet and fetal response to Porcine reproductive and respiratory syndrome virus infection, revealing factors associated with genomic control of host resilience.
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Affiliation(s)
- Angelica Van Goor
- Animal Parasitic Diseases Laboratory, United States Department of Agriculture, Agricultural Research Services, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Alex Pasternak
- Department of Animal Science, Purdue University, West Lafayette, IN, United States
| | - Muhammed Walugembe
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Nadya Chehab
- Animal Parasitic Diseases Laboratory, United States Department of Agriculture, Agricultural Research Services, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Glenn Hamonic
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jack C. M. Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - John C. S. Harding
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Joan K. Lunney
- Animal Parasitic Diseases Laboratory, United States Department of Agriculture, Agricultural Research Services, Beltsville Agricultural Research Center, Beltsville, MD, United States,*Correspondence: Joan K. Lunney,
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Souza COS, Elias-Oliveira J, Pastore MR, Fontanari C, Rodrigues VF, Rodriguez V, Gardinassi LG, Faccioli LH. CD18 controls the development and activation of monocyte-to-macrophage axis during chronic schistosomiasis. Front Immunol 2022; 13:929552. [PMID: 36263057 PMCID: PMC9574367 DOI: 10.3389/fimmu.2022.929552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Schistosomiasis is a neglected tropical disease caused by worms of the genus Schistosoma spp. The progression of disease results in intense tissue fibrosis and high mortality rate. After egg deposition by adult worms, the inflammatory response is characterized by the robust activation of type 2 immunity. Monocytes and macrophages play critical roles during schistosomiasis. Inflammatory Ly6Chigh monocytes are recruited from the blood to the inflammatory foci and differentiate into alternatively activated macrophages (AAMs), which promote tissue repair. The common chain of β2-integrins (CD18) regulates monocytopoiesis and mediates resistance to experimental schistosomiasis. There is still limited knowledge about mechanisms controlled by CD18 that impact monocyte development and effector cells such as macrophages during schistosomiasis. Here, we show that CD18low mice chronically infected with S. mansoni display monocyte progenitors with reduced proliferative capacity, resulting in the accumulation of the progenitor cell denominated proliferating-monocyte (pMo). Consequently, inflammatory Ly6Chigh and patrolling Ly6Clow monocytes are reduced in the bone marrow and blood. Mechanistically, low CD18 expression decreases Irf8 gene expression in pMo progenitor cells, whose encoded transcription factor regulates CSFR1 (CD115) expression on the cell surface. Furthermore, low CD18 expression affects the accumulation of inflammatory Ly6Chigh CD11b+ monocytes in the liver while the adoptive transference of these cells to infected-CD18low mice reduced the inflammatory infiltrate and fibrosis in the liver. Importantly, expression of Il4, Chil3l3 and Arg1 was downregulated, CD206+PD-L2+ AAMs were reduced and there were lower levels of IL-10 in the liver of CD18low mice chronically infected with S. mansoni. Overall, these findings suggest that CD18 controls the IRF8-CD115 axis on pMo progenitor cells, affecting their proliferation and maturation of monocytes. At the same time, CD18 is crucial for the appropriate polarization and function of AAMs and tissue repair during chronic schistosomiasis.
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Affiliation(s)
- Camila O. S. Souza
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Jefferson Elias-Oliveira
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Marcella R. Pastore
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Programa de Pós-Graduação em Biociências e Biotecnologia Aplicadas à Farmácia, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Ribeirão Preto, Brazil
| | - Caroline Fontanari
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Vanessa F. Rodrigues
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Vanderlei Rodriguez
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Luiz G. Gardinassi
- Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás, Goiânia, Brazil
| | - Lúcia H. Faccioli
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- *Correspondence: Lúcia H. Faccioli,
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18
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Grzelak L, Roesch F, Vaysse A, Biton A, Legendre R, Porrot F, Commère PH, Planchais C, Mouquet H, Vignuzzi M, Bruel T, Schwartz O. IRF8 regulates efficacy of therapeutic anti-CD20 monoclonal antibodies. Eur J Immunol 2022; 52:1648-1661. [PMID: 36030374 DOI: 10.1002/eji.202250037] [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: 06/07/2022] [Revised: 07/29/2022] [Accepted: 08/25/2022] [Indexed: 12/14/2022]
Abstract
Anti-CD20 monoclonal antibodies such as Rituximab, Ofatumumab, and Obinutuzumab are widely used to treat lymphomas and autoimmune diseases. They act by depleting B cells, mainly through Fc-dependent effectors functions. Some patients develop resistance to treatment but the underlying mechanisms are poorly understood. Here, we performed a genome-wide CRISPR/Cas9 screen to identify genes regulating the efficacy of anti-CD20 antibodies. We used as a model the killing of RAJI B cells by Rituximab through complement-dependent-cytotoxicity (CDC). As expected, the screen identified MS4A1, encoding CD20, the target of Rituximab. Among other identified genes, the role of Interferon Regulatory Factor 8 (IRF8) was validated in two B-cell lines. IRF8 KO also decreased the efficacy of antibody-dependent cellular cytotoxicity and phagocytosis (ADCC and ADCP) induced by anti-CD20 antibodies. We further show that IRF8 is necessary for efficient CD20 transcription. Levels of IRF8 and CD20 RNA or proteins correlated in normal B cells and in hundreds of malignant B cells. Therefore, IRF8 regulates CD20 expression and controls the depleting capacity of anti-CD20 antibodies. Our results bring novel insights into the pathways underlying resistance to CD20-targeting immunotherapies.
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Affiliation(s)
- Ludivine Grzelak
- Unité Virus et Immunité, Département de Virologie, Institut Pasteur & Université Paris Cité, Paris, France.,École Doctorale Bio Sorbonne Paris Cité (BioSPC), Université Paris Cité, France
| | | | - Amaury Vaysse
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Anne Biton
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Rachel Legendre
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Françoise Porrot
- Unité Virus et Immunité, Département de Virologie, Institut Pasteur & Université Paris Cité, Paris, France
| | | | - Cyril Planchais
- Laboratoire Immunologie Humorale, Institut Pasteur, Paris, France
| | - Hugo Mouquet
- Laboratoire Immunologie Humorale, Institut Pasteur, Paris, France
| | - Marco Vignuzzi
- Unité des Populations virales et pathogenèse, Département de Virologie, Institut Pasteur, Paris, France
| | - Timothée Bruel
- Unité Virus et Immunité, Département de Virologie, Institut Pasteur & Université Paris Cité, Paris, France
| | - Olivier Schwartz
- Unité Virus et Immunité, Département de Virologie, Institut Pasteur & Université Paris Cité, Paris, France
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19
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Pingul BY, Huang H, Chen Q, Alikarami F, Zhang Z, Qi J, Bernt KM, Berger SL, Cao Z, Shi J. Dissection of the MEF2D-IRF8 transcriptional circuit dependency in acute myeloid leukemia. iScience 2022; 25:105139. [PMID: 36193052 PMCID: PMC9526175 DOI: 10.1016/j.isci.2022.105139] [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: 10/25/2021] [Revised: 08/05/2022] [Accepted: 09/10/2022] [Indexed: 11/26/2022] Open
Abstract
Transcriptional dysregulation is a prominent feature in leukemia. Here, we systematically surveyed transcription factor (TF) vulnerabilities in leukemia and uncovered TF clusters that exhibit context-specific vulnerabilities within and between different subtypes of leukemia. Among these TF clusters, we demonstrated that acute myeloid leukemia (AML) with high IRF8 expression was addicted to MEF2D. MEF2D and IRF8 form an autoregulatory loop via direct binding to mutual enhancer elements. One important function of this circuit in AML is to sustain PU.1/MEIS1 co-regulated transcriptional outputs via stabilizing PU.1’s chromatin occupancy. We illustrated that AML could acquire dependency on this circuit through various oncogenic mechanisms that results in the activation of their enhancers. In addition to forming a circuit, MEF2D and IRF8 can also separately regulate gene expression, and dual perturbation of these two TFs leads to a more robust inhibition of AML proliferation. Collectively, our results revealed a TF circuit essential for AML survival. MEF2D is a context-specific vulnerability in IRF8hi AML MEF2D and IRF8 form a transcriptional circuit via binding to each other’s enhancers MEF2D-IRF8 circuit supports PU.1’s chromatin occupancy and transcriptional output MEF2D and IRF8 can regulate separate gene expression programs alongside the circuit
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20
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Zheng L, Guo Y, Zhai X, Zhang Y, Chen W, Zhu Z, Xuan W, Li P. Perivascular macrophages in the CNS: From health to neurovascular diseases. CNS Neurosci Ther 2022; 28:1908-1920. [PMID: 36128654 PMCID: PMC9627394 DOI: 10.1111/cns.13954] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/15/2022] [Accepted: 07/22/2022] [Indexed: 02/06/2023] Open
Abstract
Brain perivascular macrophages (PVMs) are attracting increasing attention as this emerging cell population in the brain has multifaced roles in supporting the central nervous system structure, brain development, and maintaining physiological functions. They also widely participate in neurological diseases such as neurodegeneration and ischemic stroke. Moreover, PVMs have been reported to have both beneficial and detrimental effects under different pathological contexts. Advanced research technologies allowed the further in-depth study of PVMs and revealed novel concepts in their origins, differentiation, and regulatory mechanisms. Deepened understanding of the roles of PVMs in different brain pathological conditions can reveal novel phenotypic changes and regulatory signaling, which might pave the way for the development of novel treatment strategies targeting PVMs.
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Affiliation(s)
- Li Zheng
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related GenesShanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yunlu Guo
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related GenesShanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xiaozhu Zhai
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related GenesShanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yueman Zhang
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related GenesShanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Weijie Chen
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related GenesShanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Ziyu Zhu
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related GenesShanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Wei Xuan
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related GenesShanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Peiying Li
- Department of Anesthesiology, State Key Laboratory of Oncogenes and Related GenesShanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
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21
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Eagle K, Harada T, Kalfon J, Perez MW, Heshmati Y, Ewers J, Koren JV, Dempster JM, Kugener G, Paralkar VR, Lin CY, Dharia NV, Stegmaier K, Orkin SH, Pimkin M. Transcriptional Plasticity Drives Leukemia Immune Escape. Blood Cancer Discov 2022; 3:394-409. [PMID: 35709529 PMCID: PMC9897290 DOI: 10.1158/2643-3230.bcd-21-0207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/21/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022] Open
Abstract
Relapse of acute myeloid leukemia (AML) after allogeneic bone marrow transplantation has been linked to immune evasion due to reduced expression of major histocompatibility complex class II (MHCII) genes through unknown mechanisms. In this work, we developed CORENODE, a computational algorithm for genome-wide transcription network decomposition that identified a transcription factor (TF) tetrad consisting of IRF8, MYB, MEF2C, and MEIS1, regulating MHCII expression in AML cells. We show that reduced MHCII expression at relapse is transcriptionally driven by combinatorial changes in the expression of these TFs, where MYB and IRF8 play major opposing roles, acting independently of the IFNγ/CIITA pathway. Beyond the MHCII genes, MYB and IRF8 antagonistically regulate a broad genetic program responsible for cytokine signaling and T-cell stimulation that displays reduced expression at relapse. A small number of cells with altered TF abundance and silenced MHCII expression are present at the time of initial leukemia diagnosis, likely contributing to eventual relapse. SIGNIFICANCE Our findings point to an adaptive transcriptional mechanism of AML evolution after allogeneic transplantation whereby combinatorial fluctuations of TF expression under immune pressure result in the selection of cells with a silenced T-cell stimulation program. This article is highlighted in the In This Issue feature, p. 369.
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Affiliation(s)
- Kenneth Eagle
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Ken Eagle Consulting, Houston, Texas
| | - Taku Harada
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jérémie Kalfon
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Monika W. Perez
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yaser Heshmati
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jazmin Ewers
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jošt Vrabič Koren
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | | | - Vikram R. Paralkar
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Charles Y. Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Neekesh V. Dharia
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Kimberly Stegmaier
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Stuart H. Orkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston, Massachusetts
| | - Maxim Pimkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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22
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Bono C, Guerrero P, Erades A, Jordán-Pla A, Yáñez A, Gil ML. Direct TLR2 signaling through mTOR and TBK1 induces C/EBPβ and IRF7-dependent macrophage differentiation in hematopoietic stem and progenitor cells. Stem Cells 2022; 40:949-962. [PMID: 35861517 DOI: 10.1093/stmcls/sxac053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022]
Abstract
During an infection, hematopoiesis is altered to increase the output of mature myeloid cells to fight off the pathogen. Despite convincing evidence that hematopoietic stem and progenitor cells (HSPCs) can sense pathogens directly, more mechanistic studies are needed to reveal whether pattern recognition receptor (PRR) signaling initiates myeloid development directly, or indirectly through the production of cytokines by HSPCs that can act in an autocrine/paracrine manner, or by a combination of both direct and indirect mechanisms. In this study, we have used an in vitro model of murine HSPCs to study myeloid differentiation in response to the TLR2 ligand Pam3CSK4 and showed that, besides indirect mechanisms, TLR2 stimulation of HSPCs promotes myelopoiesis directly by initiating a MyD88-dependent signaling. This direct differentiation program involves a combined activation of the transcription factors PU.1, C/EBPβ and IRF7 driven by TBK1 and PI3K/mTOR. Notably, downstream of MyD88, the activated TBK1 kinase can activate mTOR directly and IRF7 induction is mediated by both TBK1 and mTOR. TLR2 signaling also induces NF-κB dependent IL-6 production that may further induce indirect myeloid differentiation. Our results have identified the direct signaling pathways and the transcription factors involved in macrophage development from HSPCs in response to TLR2 engagement, a critical process to trigger a rapid immune response during infection.
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Affiliation(s)
- Cristina Bono
- Departamento de Microbiología y Ecología, Facultad de Ciencias Biológicas and Instituto de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
| | - Paula Guerrero
- Departamento de Microbiología y Ecología, Facultad de Ciencias Biológicas and Instituto de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
| | - Ana Erades
- Departamento de Microbiología y Ecología, Facultad de Ciencias Biológicas and Instituto de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
| | - Antonio Jordán-Pla
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Facultad de Ciencias Biológicas and Instituto de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
| | - Alberto Yáñez
- Departamento de Microbiología y Ecología, Facultad de Ciencias Biológicas and Instituto de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
| | - María Luisa Gil
- Departamento de Microbiología y Ecología, Facultad de Ciencias Biológicas and Instituto de Biotecnología y Biomedicina (BIOTECMED), Universitat de València, Burjassot, Spain
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23
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Pulmonary Alveolar Proteinosis and Multiple Infectious Diseases in a Child with Autosomal Recessive Complete IRF8 Deficiency. J Clin Immunol 2022; 42:975-985. [PMID: 35338423 PMCID: PMC8956456 DOI: 10.1007/s10875-022-01250-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/09/2022] [Indexed: 10/26/2022]
Abstract
BACKGROUND Autosomal recessive (AR) complete IRF8 deficiency is a rare severe inborn error of immunity underlying an absence of blood myeloid mononuclear cells, intracerebral calcifications, and multiple infections. Only three unrelated patients have been reported. MATERIALS AND METHODS We studied an Argentinian child with multiple infectious diseases and severe pulmonary alveolar proteinosis (PAP). We performed whole-exome sequencing (WES) and characterized his condition by genetic, immunological, and clinical means. RESULTS The patient was born and lived in Argentina. He had a history of viral pulmonary diseases, disseminated disease due to bacillus Calmette-Guérin (BCG), PAP, and cerebral calcifications. He died at the age of 10 months from refractory PAP. WES identified two compound heterozygous variants in IRF8: c.55del and p.R111*. In an overexpression system, the p.R111* cDNA was loss-of-expression, whereas the c.55del cDNA yielded a protein with a slightly lower molecular weight than the wild-type protein. The mutagenesis of methionine residues downstream from c.55del revealed a re-initiation of translation. However, both variants were loss-of-function in a luciferase assay, suggesting that the patient had AR complete IRF8 deficiency. The patient had no blood monocytes or dendritic cells, associated with neutrophilia, and normal counts of NK and other lymphoid cell subsets. CONCLUSION We describe the fourth patient with AR complete IRF8 deficiency. This diagnosis should be considered in children with PAP, which is probably due to the defective development or function of alveolar macrophages.
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24
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Harada T, Heshmati Y, Kalfon J, Perez MW, Xavier Ferrucio J, Ewers J, Hubbell Engler B, Kossenkov A, Ellegast JM, Yi JS, Bowker A, Zhu Q, Eagle K, Liu T, Kai Y, Dempster JM, Kugener G, Wickramasinghe J, Herbert ZT, Li CH, Vrabič Koren J, Weinstock DM, Paralkar VR, Nabet B, Lin CY, Dharia NV, Stegmaier K, Orkin SH, Pimkin M. A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia. Genes Dev 2022; 36:368-389. [PMID: 35301220 PMCID: PMC8973843 DOI: 10.1101/gad.349284.121] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/22/2022] [Indexed: 12/12/2022]
Abstract
In this study, Harada et al. identified the transcription factors MEF2D and IRF8 as selective transcriptional dependencies of KMT2A-rearranged AML, where MEF2D displays partially redundant functions with its paralog, MEF2C. This study illustrates a mechanism of context-specific transcriptional addiction whereby a specific AML subclass depends on a highly specialized core regulatory module to directly enforce expression of common leukemia oncogenes. Acute myeloid leukemia with KMT2A (MLL) rearrangements is characterized by specific patterns of gene expression and enhancer architecture, implying unique core transcriptional regulatory circuitry. Here, we identified the transcription factors MEF2D and IRF8 as selective transcriptional dependencies of KMT2A-rearranged AML, where MEF2D displays partially redundant functions with its paralog, MEF2C. Rapid transcription factor degradation followed by measurements of genome-wide transcription rates and superresolution microscopy revealed that MEF2D and IRF8 form a distinct core regulatory module with a narrow direct transcriptional program that includes activation of the key oncogenes MYC, HOXA9, and BCL2. Our study illustrates a mechanism of context-specific transcriptional addiction whereby a specific AML subclass depends on a highly specialized core regulatory module to directly enforce expression of common leukemia oncogenes.
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Affiliation(s)
- Taku Harada
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Yaser Heshmati
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Jérémie Kalfon
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Monika W Perez
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Juliana Xavier Ferrucio
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Jazmin Ewers
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Benjamin Hubbell Engler
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | | | - Jana M Ellegast
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Joanna S Yi
- Baylor College of Medicine, Houston, Texas 77030, USA
| | - Allyson Bowker
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Qian Zhu
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Kenneth Eagle
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Ken Eagle Consulting, Houston, Texas 77494, USA
| | - Tianxin Liu
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Yan Kai
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Joshua M Dempster
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Guillaume Kugener
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Zachary T Herbert
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Charles H Li
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | | | - David M Weinstock
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Vikram R Paralkar
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Behnam Nabet
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Charles Y Lin
- Baylor College of Medicine, Houston, Texas 77030, USA
| | - Neekesh V Dharia
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kimberly Stegmaier
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Stuart H Orkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Howard Hughes Medical Institute, Boston, Massachusetts 02215, USA
| | - Maxim Pimkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
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25
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Ma X, Somasundaram A, Qi Z, Hartman D, Singh H, Osmanbeyoglu H. SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators. Nucleic Acids Res 2021; 49:9633-9647. [PMID: 34500467 PMCID: PMC8464045 DOI: 10.1093/nar/gkab745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 08/09/2021] [Accepted: 09/06/2021] [Indexed: 12/22/2022] Open
Abstract
The identity and functions of specialized cell types are dependent on the complex interplay between signaling and transcriptional networks. Recently single-cell technologies have been developed that enable simultaneous quantitative analysis of cell-surface receptor expression with transcriptional states. To date, these datasets have not been used to systematically develop cell-context-specific maps of the interface between signaling and transcriptional regulators orchestrating cellular identity and function. We present SPaRTAN (Single-cell Proteomic and RNA based Transcription factor Activity Network), a computational method to link cell-surface receptors to transcription factors (TFs) by exploiting cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) datasets with cis-regulatory information. SPaRTAN is applied to immune cell types in the blood to predict the coupling of signaling receptors with cell context-specific TFs. Selected predictions are validated by prior knowledge and flow cytometry analyses. SPaRTAN is then used to predict the signaling coupled TF states of tumor infiltrating CD8+ T cells in malignant peritoneal and pleural mesotheliomas. SPaRTAN enhances the utility of CITE-seq datasets to uncover TF and cell-surface receptor relationships in diverse cellular states.
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Affiliation(s)
- Xiaojun Ma
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Ashwin Somasundaram
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Zengbiao Qi
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Douglas J Hartman
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Harinder Singh
- Center for Systems Immunology and Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Hatice Ulku Osmanbeyoglu
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15206, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
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26
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Zhang P, Schlecht A, Wolf J, Boneva S, Laich Y, Koch J, Ludwig F, Boeck M, Thien A, Härdtner C, Kierdorf K, Agostini H, Schlunck G, Prinz M, Hilgendorf I, Wieghofer P, Lange C. The role of interferon regulatory factor 8 for retinal tissue homeostasis and development of choroidal neovascularisation. J Neuroinflammation 2021; 18:215. [PMID: 34544421 PMCID: PMC8454118 DOI: 10.1186/s12974-021-02230-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microglia cells represent the resident innate immune cells of the retina and are important for retinal development and tissue homeostasis. However, dysfunctional microglia can have a negative impact on the structural and functional integrity of the retina under native and pathological conditions. METHODS In this study, we examined interferon-regulatory factor 8 (Irf8)-deficient mice to determine the transcriptional profile, morphology, and temporospatial distribution of microglia lacking Irf8 and to explore the effects on retinal development, tissue homeostasis, and formation of choroidal neovascularisation (CNV). RESULTS Our study shows that Irf8-deficient MG exhibit a considerable loss of microglial signature genes accompanied by a severely altered MG morphology. An in-depth characterisation by fundus photography, fluorescein angiography, optical coherence tomography and electroretinography revealed no major retinal abnormalities during steady state. However, in the laser-induced CNV model, Irf8-deficient microglia showed an increased activity of biological processes critical for inflammation and cell adhesion and a reduced MG cell density near the lesions, which was associated with significantly increased CNV lesion size. CONCLUSIONS Our results suggest that loss of Irf8 in microglia has negligible effects on retinal homeostasis in the steady state. However, under pathological conditions, Irf8 is crucial for the transformation of resident microglia into a reactive phenotype and thus for the suppression of retinal inflammation and CNV formation.
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Affiliation(s)
- Peipei Zhang
- Medical Faculty, Eye Center, University Hospital, University of Freiburg, Freiburg im Breisgau, Germany
| | - Anja Schlecht
- Medical Faculty, Eye Center, University Hospital, University of Freiburg, Freiburg im Breisgau, Germany.,Institute of Anatomy, Wuerzburg University, Wuerzburg, Germany
| | - Julian Wolf
- Medical Faculty, Eye Center, University Hospital, University of Freiburg, Freiburg im Breisgau, Germany
| | - Stefaniya Boneva
- Medical Faculty, Eye Center, University Hospital, University of Freiburg, Freiburg im Breisgau, Germany
| | - Yannik Laich
- Medical Faculty, Eye Center, University Hospital, University of Freiburg, Freiburg im Breisgau, Germany
| | - Jana Koch
- Medical Faculty, Eye Center, University Hospital, University of Freiburg, Freiburg im Breisgau, Germany
| | - Franziska Ludwig
- Medical Faculty, Eye Center, University Hospital, University of Freiburg, Freiburg im Breisgau, Germany
| | - Myriam Boeck
- Medical Faculty, Eye Center, University Hospital, University of Freiburg, Freiburg im Breisgau, Germany
| | - Adrian Thien
- Medical Faculty, Eye Center, University Hospital, University of Freiburg, Freiburg im Breisgau, Germany
| | - Carmen Härdtner
- Cardiology and Angiology, University Heart Center, University of Freiburg, Freiburg im Breisgau, Germany.,Medical Center and Faculty of Medicine, Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, Freiburg, Germany
| | - Katrin Kierdorf
- Medical Faculty, Institute of Neuropathology, University Hospital, University of Freiburg, Freiburg im Breisgau, Germany.,CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,Medical Faculty, Center for Basics in NeuroModulation (NeuroModulBasics), University of Freiburg, Freiburg im Breisgau, Germany
| | - Hansjürgen Agostini
- Medical Faculty, Eye Center, University Hospital, University of Freiburg, Freiburg im Breisgau, Germany
| | - Günther Schlunck
- Medical Faculty, Eye Center, University Hospital, University of Freiburg, Freiburg im Breisgau, Germany
| | - Marco Prinz
- Medical Faculty, Institute of Neuropathology, University Hospital, University of Freiburg, Freiburg im Breisgau, Germany.,Medical Faculty, Center for Basics in NeuroModulation (NeuroModulBasics), University of Freiburg, Freiburg im Breisgau, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, Germany
| | - Ingo Hilgendorf
- Cardiology and Angiology, University Heart Center, University of Freiburg, Freiburg im Breisgau, Germany.,Medical Center and Faculty of Medicine, Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg Bad Krozingen, University of Freiburg, Freiburg, Germany
| | - Peter Wieghofer
- Medical Faculty, Institute of Neuropathology, University Hospital, University of Freiburg, Freiburg im Breisgau, Germany. .,Institute of Anatomy, Leipzig University, Leipzig, Germany.
| | - Clemens Lange
- Medical Faculty, Eye Center, University Hospital, University of Freiburg, Freiburg im Breisgau, Germany.
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27
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Smith NC, Umasuthan N, Kumar S, Woldemariam NT, Andreassen R, Christian SL, Rise ML. Transcriptome Profiling of Atlantic Salmon Adherent Head Kidney Leukocytes Reveals That Macrophages Are Selectively Enriched During Culture. Front Immunol 2021; 12:709910. [PMID: 34484211 PMCID: PMC8415484 DOI: 10.3389/fimmu.2021.709910] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/05/2021] [Indexed: 01/23/2023] Open
Abstract
The Atlantic salmon (Salmo salar) is an economically important fish, both in aquaculture and in the wild. In vertebrates, macrophages are some of the first cell types to respond to pathogen infection and disease. While macrophage biology has been characterized in mammals, less is known in fish. Our previous work identified changes in the morphology, phagocytic ability, and miRNA profile of Atlantic salmon adherent head kidney leukocytes (HKLs) from predominantly “monocyte-like” at Day 1 of in vitro culture to predominantly “macrophage-like” at Day 5 of culture. Therefore, to further characterize these two cell populations, we examined the mRNA transcriptome profile in Day 1 and Day 5 HKLs using a 44K oligonucleotide microarray. Large changes in the transcriptome were revealed, including changes in the expression of macrophage and immune-related transcripts (e.g. csf1r, arg1, tnfa, mx2), lipid-related transcripts (e.g. fasn, dhcr7, fabp6), and transcription factors involved in macrophage differentiation and function (e.g. klf2, klf9, irf7, irf8, stat1). The in silico target prediction analysis of differentially expressed genes (DEGs) using miRNAs known to change expression in Day 5 HKLs, followed by gene pathway enrichment analysis, supported that these miRNAs may be involved in macrophage maturation by targeting specific DEGs. Elucidating how immune cells, such as macrophages, develop and function is a key step in understanding the Atlantic salmon immune system. Overall, the results indicate that, without the addition of exogenous factors, the adherent HKL cell population differentiates in vitro to become macrophage-like.
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Affiliation(s)
- Nicole C Smith
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | | | - Surendra Kumar
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Nardos T Woldemariam
- Department of Life Sciences and Health, OsloMet-Oslo Metropolitan University, Oslo, Norway
| | - Rune Andreassen
- Department of Life Sciences and Health, OsloMet-Oslo Metropolitan University, Oslo, Norway
| | - Sherri L Christian
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
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28
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Patel A, Oba T, Kajihara R, Yokoi T, Abrams SI, Ito F. Multimodal Intralesional Therapy for Reshaping the Myeloid Compartment of Tumors Resistant to Anti-PD-L1 Therapy via IRF8 Expression. THE JOURNAL OF IMMUNOLOGY 2021; 207:1298-1309. [PMID: 34362833 DOI: 10.4049/jimmunol.2100281] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/23/2021] [Indexed: 12/29/2022]
Abstract
Intralesional therapy is a promising approach for remodeling the immunosuppressive tumor microenvironment while minimizing systemic toxicities. A combinatorial in situ immunomodulation (ISIM) regimen with intratumoral administration of Fms-like tyrosine kinase 3 ligand (Flt3L), local irradiation, and TLR3/CD40 stimulation induces and activates conventional type 1 dendritic cells in the tumor microenvironment and elicits de novo adaptive T cell immunity in poorly T cell-inflamed tumors. However, the impact of ISIM on myeloid-derived suppressor cells (MDSCs), which may promote treatment resistance, remains unknown. In this study, we examined changes in the frequencies and heterogeneity of CD11b+Ly-6CloLy-6G+ polymorphonuclear (PMN)-MDSCs and CD11b+Ly-6ChiLy-6G- monocytic (M)-MDSCs in ISIM-treated tumors using mouse models of triple-negative breast cancer. We found that ISIM treatment decreased intratumoral PMN-MDSCs, but not M-MDSCs. Although the frequency of M-MDSCs remained unchanged, ISIM caused a substantial reduction of CX3CR1+ M-MDSCs that express F4/80. Importantly, these ISIM-induced changes in tumor-residing MDSCs were not observed in Batf3-/- mice. ISIM upregulated PD-L1 expression in both M-MDSCs and PMN-MDSCs and synergized with anti-PD-L1 therapy. Furthermore, ISIM increased the expression of IFN regulatory factor 8 (IRF8) in myeloid cells, a known negative regulator of MDSCs, indicating a potential mechanism by which ISIM decreases PMN-MDSC levels. Accordingly, ISIM-mediated reduction of PMN-MDSCs was not observed in mice with conditional deletion of IRF8 in myeloid cells. Altogether, these findings suggest that ISIM holds promise as a multimodal intralesional therapy to alter both lymphoid and myeloid compartments of highly aggressive poorly T cell-inflamed, myeloid-enriched tumors resistant to anti-PD-L1 therapy.
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Affiliation(s)
- Ankit Patel
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Takaaki Oba
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Ryutaro Kajihara
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Toshihiro Yokoi
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Scott I Abrams
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY; and
| | - Fumito Ito
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY; .,Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY.,Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY; and.,Department of Surgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, The State University of New York, Buffalo, NY
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29
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Yashiro T, Yamamoto M, Araumi S, Hara M, Yogo K, Uchida K, Kasakura K, Nishiyama C. PU.1 and IRF8 Modulate Activation of NLRP3 Inflammasome via Regulating Its Expression in Human Macrophages. Front Immunol 2021; 12:649572. [PMID: 33897697 PMCID: PMC8058198 DOI: 10.3389/fimmu.2021.649572] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/18/2021] [Indexed: 11/26/2022] Open
Abstract
NLRP3 inflammasomes play crucial roles in the initiation of host defense by converting pro-Caspase-1 to mature Caspase-1, which in turn processes immature IL-1β and IL-18 into their biologically active forms. Although NLRP3 expression is restricted to monocytic lineages such as monocytes, macrophages, and dendritic cells, the mechanisms determining the lineage-specific expression of NLRP3 remain largely unknown. In this study, we investigated the transcription factors involved in cell-type-specific transcription of NLRP3. We found that a distal, rather than a proximal, promoter of human NLRP3 was predominantly used in the human monocytic cell lines and macrophages. Reporter analysis showed that an Ets/IRF composite element (EICE) at -309/-300 and an Ets motif at +5/+8 were critical for transcriptional activity of the distal promoter. Electrophoretic mobility shift assays and chromatin immunoprecipitation assays demonstrated that two transcription factors, PU.1 and IRF8, both of which play essential roles in development and gene expression of the monocytic lineage, were bound to the EICE site, whereas PU.1 alone was bound to the Ets site. Knockdown of PU.1 and/or IRF8 mediated by small interfering RNA downregulated expression of NLRP3 and related molecules and markedly diminished the LPS-induced release of IL-1β in THP-1, suggesting that activity of the NLRP3 inflammasome was suppressed by knockdown of PU.1 and IRF8. Taken together, these results indicate that PU.1 and IRF8 are involved in the monocytic lineage-specific expression of NLRP3 by binding to regulatory elements within its promoter and that PU.1 and IRF8 are potential targets for regulating the activity of the NLRP3 inflammasome.
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Affiliation(s)
- Takuya Yashiro
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Katsushika-Ku, Japan
| | - Machiko Yamamoto
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Katsushika-Ku, Japan
| | - Sanae Araumi
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Katsushika-Ku, Japan
| | - Mutsuko Hara
- Atopy (Allergy) Research Center, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
| | - Kyoko Yogo
- Juntendo University Advanced Research Institute for Health Science, Bunkyo-ku, Japan
| | - Koichiro Uchida
- Juntendo University Advanced Research Institute for Health Science, Bunkyo-ku, Japan
| | - Kazumi Kasakura
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Katsushika-Ku, Japan
| | - Chiharu Nishiyama
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Katsushika-Ku, Japan
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30
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Jassinskaja M, Pimková K, Arh N, Johansson E, Davoudi M, Pereira CF, Sitnicka E, Hansson J. Ontogenic shifts in cellular fate are linked to proteotype changes in lineage-biased hematopoietic progenitor cells. Cell Rep 2021; 34:108894. [PMID: 33761361 DOI: 10.1016/j.celrep.2021.108894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/16/2020] [Accepted: 03/02/2021] [Indexed: 12/16/2022] Open
Abstract
The process of hematopoiesis is subject to substantial ontogenic remodeling that is accompanied by alterations in cellular fate during both development and disease. We combine state-of-the-art mass spectrometry with extensive functional assays to gain insight into ontogeny-specific proteomic mechanisms regulating hematopoiesis. Through deep coverage of the cellular proteome of fetal and adult lympho-myeloid multipotent progenitors (LMPPs), common lymphoid progenitors (CLPs), and granulocyte-monocyte progenitors (GMPs), we establish that features traditionally attributed to adult hematopoiesis are conserved across lymphoid and myeloid lineages, whereas generic fetal features are suppressed in GMPs. We reveal molecular and functional evidence for a diminished granulocyte differentiation capacity in fetal LMPPs and GMPs relative to their adult counterparts. Our data indicate an ontogeny-specific requirement of myosin activity for myelopoiesis in LMPPs. Finally, we uncover an ontogenic shift in the monocytic differentiation capacity of GMPs, partially driven by a differential expression of Irf8 during fetal and adult life.
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Affiliation(s)
- Maria Jassinskaja
- Lund Stem Cell Center, Division of Molecular Hematology, Lund University, 221 84 Lund, Sweden
| | - Kristýna Pimková
- Lund Stem Cell Center, Division of Molecular Hematology, Lund University, 221 84 Lund, Sweden
| | - Nejc Arh
- Lund Stem Cell Center, Division of Molecular Medicine and Gene Therapy, Lund University, 221 84 Lund, Sweden; Wallenberg Centre for Molecular Medicine, Lund University, 221 84 Lund, Sweden
| | - Emil Johansson
- Lund Stem Cell Center, Division of Molecular Hematology, Lund University, 221 84 Lund, Sweden; Department of Laboratory Medicine, Lund University, 221 84 Lund, Sweden
| | - Mina Davoudi
- Lund Stem Cell Center, Division of Molecular Hematology, Lund University, 221 84 Lund, Sweden
| | - Carlos-Filipe Pereira
- Lund Stem Cell Center, Division of Molecular Medicine and Gene Therapy, Lund University, 221 84 Lund, Sweden; Wallenberg Centre for Molecular Medicine, Lund University, 221 84 Lund, Sweden
| | - Ewa Sitnicka
- Lund Stem Cell Center, Division of Molecular Hematology, Lund University, 221 84 Lund, Sweden
| | - Jenny Hansson
- Lund Stem Cell Center, Division of Molecular Hematology, Lund University, 221 84 Lund, Sweden.
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31
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Murakami K, Sasaki H, Nishiyama A, Kurotaki D, Kawase W, Ban T, Nakabayashi J, Kanzaki S, Sekita Y, Nakajima H, Ozato K, Kimura T, Tamura T. A RUNX-CBFβ-driven enhancer directs the Irf8 dose-dependent lineage choice between DCs and monocytes. Nat Immunol 2021; 22:301-311. [PMID: 33603226 DOI: 10.1038/s41590-021-00871-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 01/11/2021] [Indexed: 01/30/2023]
Abstract
The transcription factor IRF8 is essential for the development of monocytes and dendritic cells (DCs), whereas it inhibits neutrophilic differentiation. It is unclear how Irf8 expression is regulated and how this single transcription factor supports the generation of both monocytes and DCs. Here, we identified a RUNX-CBFβ-driven enhancer 56 kb downstream of the Irf8 transcription start site. Deletion of this enhancer in vivo significantly decreased Irf8 expression throughout the myeloid lineage from the progenitor stages, thus resulting in loss of common DC progenitors and overproduction of Ly6C+ monocytes. We demonstrated that high, low or null expression of IRF8 in hematopoietic progenitor cells promotes differentiation toward type 1 conventional DCs, Ly6C+ monocytes or neutrophils, respectively, via epigenetic regulation of distinct sets of enhancers in cooperation with other transcription factors. Our results illustrate the mechanism through which IRF8 controls the lineage choice in a dose-dependent manner within the myeloid cell system.
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Affiliation(s)
- Koichi Murakami
- Department of Immunology, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan
| | - Haruka Sasaki
- Department of Immunology, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Akira Nishiyama
- Department of Immunology, Yokohama City University Graduate School of Medicine, Kanagawa, Japan.
| | - Daisuke Kurotaki
- Department of Immunology, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Wataru Kawase
- Department of Immunology, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Tatsuma Ban
- Department of Immunology, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Jun Nakabayashi
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan
| | - Satoko Kanzaki
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, Kanagawa, Japan
| | - Yoichi Sekita
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, Kanagawa, Japan
| | - Hideaki Nakajima
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Kanagawa, Japan
| | - Keiko Ozato
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Tohru Kimura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, Kanagawa, Japan
| | - Tomohiko Tamura
- Department of Immunology, Yokohama City University Graduate School of Medicine, Kanagawa, Japan.
- Advanced Medical Research Center, Yokohama City University, Kanagawa, Japan.
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32
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Ortutay Z, Grönholm A, Laitinen M, Keresztes-Andrei M, Hermelo I, Pesu M. Identification of Novel Genetic Regulatory Region for Proprotein Convertase FURIN and Interferon Gamma in T Cells. Front Immunol 2021; 12:630389. [PMID: 33679774 PMCID: PMC7930619 DOI: 10.3389/fimmu.2021.630389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/22/2021] [Indexed: 12/30/2022] Open
Abstract
The proprotein convertase enzyme FURIN promotes the proteolytic maturation of pro-proteins and thereby it serves as an important factor for maintaining cellular homeostasis. In T cells, FURIN is critical for maintaining the T regulatory cell dependent peripheral immune tolerance and intact T helper cell polarization. The enzymatic activity of FURIN is directly associated with its expression levels, but genetic determinants for cell-type specific Furin gene regulation have remained elusive. By exploring the histone acetyltransferase p300 binding patterns in T helper cells, a putative regulatory region at ca. 20kB upstream of Furin gene was identified. When this region was deleted with CRISPR/Cas9 the production of Furin mRNA was significantly reduced in activated mouse T cells. Genome-wide RNA profiling by sequencing revealed that the novel Furin regulator region also impacted the expression of several genes that have previously been associated with the Th1 type hall mark cytokine IFNγ regulation or function. Finally, Furin genetic regulatory region was found to specifically promote the secretion of IFNγ by activated T cells. In sum, our data unravels the presence of Furin expression regulatory region in T cells that has characteristics of a super-enhancer for Th1 cell fate.
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Affiliation(s)
- Zsuzsanna Ortutay
- Immunoregulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anna Grönholm
- Immunoregulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Melina Laitinen
- Immunoregulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Melinda Keresztes-Andrei
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Ismail Hermelo
- Computational Biology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Marko Pesu
- Immunoregulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Fimlab Laboratories, Tampere, Finland
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33
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Liss F, Frech M, Wang Y, Giel G, Fischer S, Simon C, Weber LM, Nist A, Stiewe T, Neubauer A, Burchert A, Liefke R. IRF8 Is an AML-Specific Susceptibility Factor That Regulates Signaling Pathways and Proliferation of AML Cells. Cancers (Basel) 2021; 13:cancers13040764. [PMID: 33673123 PMCID: PMC7917770 DOI: 10.3390/cancers13040764] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/06/2021] [Accepted: 02/09/2021] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Despite progress, acute myeloid leukemia (AML) remains one of the deadliest cancer diseases. The identification of novel molecular targets may allow developing innovative and alternative treatment options for AML. Using public data from genome-edited cancer cells, we identified factors that are specifically essential for AML cell growth. We validated the critical role of the transcription factor IRF8 and demonstrated that it modulates the function of the cells by regulating important signaling molecules. These results support that IRF8 may be a suitable molecular target for the treatment of AML. Abstract Personalized treatment of acute myeloid leukemia (AML) that target individual aberrations strongly improved the survival of AML patients. However, AML is still one of the most lethal cancer diseases of the 21st century, demonstrating the need to find novel drug targets and to explore alternative treatment strategies. Upon investigation of public perturbation data, we identified the transcription factor IRF8 as a novel AML-specific susceptibility gene in humans. IRF8 is upregulated in a subset of AML cells and its deletion leads to impaired proliferation in those cells. Consistently, high IRF8 expression is associated with poorer patients’ prognoses. Combining gene expression changes upon IRF8 deletion and the genome-wide localization of IRF8 in the AML cell line MV4-11, we demonstrate that IRF8 directly regulates key signaling molecules, such as the kinases SRC and FAK, the transcription factors RUNX1 and IRF5, and the cell cycle regulator Cyclin D1. IRF8 loss impairs AML-driving signaling pathways, including the WNT, Chemokine, and VEGF signaling pathways. Additionally, many members of the focal adhesion pathway showed reduced expression, providing a putative link between high IRF8 expression and poor prognosis. Thus, this study suggests that IRF8 could serve as a biomarker and potential molecular target in a subset of human AMLs.
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Affiliation(s)
- Franziska Liss
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043 Marburg, Germany; (F.L.); (S.F.); (C.S.); (L.M.W.)
| | - Miriam Frech
- Clinic for Hematology, Oncology, Immunology and Center for Tumor Biology and Immunology, Philipps University of Marburg, 35037 Marburg, Germany; (M.F.); (Y.W.); (G.G.); (A.N.); (A.B.)
| | - Ying Wang
- Clinic for Hematology, Oncology, Immunology and Center for Tumor Biology and Immunology, Philipps University of Marburg, 35037 Marburg, Germany; (M.F.); (Y.W.); (G.G.); (A.N.); (A.B.)
| | - Gavin Giel
- Clinic for Hematology, Oncology, Immunology and Center for Tumor Biology and Immunology, Philipps University of Marburg, 35037 Marburg, Germany; (M.F.); (Y.W.); (G.G.); (A.N.); (A.B.)
| | - Sabrina Fischer
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043 Marburg, Germany; (F.L.); (S.F.); (C.S.); (L.M.W.)
| | - Clara Simon
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043 Marburg, Germany; (F.L.); (S.F.); (C.S.); (L.M.W.)
| | - Lisa Marie Weber
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043 Marburg, Germany; (F.L.); (S.F.); (C.S.); (L.M.W.)
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, 35043 Marburg, Germany; (A.N.); (T.S.)
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, 35043 Marburg, Germany; (A.N.); (T.S.)
| | - Andreas Neubauer
- Clinic for Hematology, Oncology, Immunology and Center for Tumor Biology and Immunology, Philipps University of Marburg, 35037 Marburg, Germany; (M.F.); (Y.W.); (G.G.); (A.N.); (A.B.)
| | - Andreas Burchert
- Clinic for Hematology, Oncology, Immunology and Center for Tumor Biology and Immunology, Philipps University of Marburg, 35037 Marburg, Germany; (M.F.); (Y.W.); (G.G.); (A.N.); (A.B.)
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043 Marburg, Germany; (F.L.); (S.F.); (C.S.); (L.M.W.)
- Clinic for Hematology, Oncology, Immunology and Center for Tumor Biology and Immunology, Philipps University of Marburg, 35037 Marburg, Germany; (M.F.); (Y.W.); (G.G.); (A.N.); (A.B.)
- Correspondence: ; Tel.: +49-6421-28-66697
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34
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Developmental pathways of myeloid-derived suppressor cells in neoplasia. Cell Immunol 2020; 360:104261. [PMID: 33373817 DOI: 10.1016/j.cellimm.2020.104261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 02/07/2023]
Abstract
Immunotherapy has become a major weapon against the war on cancer. This has culminated from decades of seminal work that led to the discovery of innovative approaches to drive adaptive immunity. Notably, was the discovery of immune checkpoint inhibitory receptors on T cells, and the subsequent development of monoclonal antibodies that target those receptors, known as immune checkpoint inhibitors (ICIs). Blocking those receptors using ICIs leads to sustained effector function, which has translated to enhanced antitumor responses across multiple human cancer types. However, these treatments are effective in subsets of patients, implicating significant barriers limiting therapeutic potential. While numerous mechanisms may hinder immunotherapy potency, one prominent mechanism is the production of myeloid-derived suppressor cells (MDSCs). MDSCs comprise monocytic and granulocytic cell types and mediate pro-tumorigenic and immune suppressive activities. Here, we summarize several pathways by which MDSCs arise in cancer, providing a conceptual framework for identifying unique combination therapeutic interventions.
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Nagel S, Pommerenke C, Meyer C, MacLeod RAF, Drexler HG. Aberrant expression of NKL homeobox genes HMX2 and HMX3 interferes with cell differentiation in acute myeloid leukemia. PLoS One 2020; 15:e0240120. [PMID: 33048949 PMCID: PMC7553312 DOI: 10.1371/journal.pone.0240120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/18/2020] [Indexed: 12/30/2022] Open
Abstract
The NKL-code describes normal expression patterns of NKL homeobox genes in hematopoiesis. Aberrant expression of NKL homeobox gene subclass members have been reported in several hematopoietic malignancies including acute myeloid leukemia (AML). Here, we analyzed the oncogenic role of the HMX-group of NKL homeobox genes in AML. Public expression profiling data–available for HMX1 and HMX2—indicate aberrant activity of HMX2 in circa 2% AML patients overall, rising to 31% in those with KMT2A/MLL rearrangements whereas HMX1 expression remains inconspicuous. AML cell lines EOL-1, MV4-11 and MOLM-13 expressed both, HMX2 and neighboring HMX3 genes, and harbored KMT2A aberrations, suggesting their potential functional association. Surprisingly, knockdown experiments in these cell lines demonstrated that KMT2A inhibited HMX2/3 which, in turn, did not regulate KMT2A expression. Furthermore, karyotyping and genomic profiling analysis excluded rearrangements of the HMX2/3 locus in these cell lines. However, comparative expression profiling and subsequent functional analyses revealed that IRF8, IL7- and WNT-signalling activated HMX2/3 expression while TNFa/NFkB- signalling proved inhibitory. Whole genome sequencing of EOL-1 identified two mutations in the regulatory upstream regions of HMX2/3 resulting in generation of a consensus ETS-site and transformation of a former NFkB-site into an SP1-site. Reporter-gene assays demonstrated that both mutations contributed to HMX2/3 activation, modifying ETS1/ELK1- and TNFalpha-mediated gene regulation. Moreover, DMSO-induced eosinophilic differentiation of EOL-1 cells coincided with HMX2/3 downregulation while knockdown of HMX2 induced cell differentiation, collectively supporting a fundamental role for these genes in myeloid differentiation arrest. Finally, target genes of HMX2/3 were identified in EOL-1 and included suppression of differentiation gene EPX, and activation of fusion gene FIP1L1-PDGFRA and receptor-encoding gene HTR7, both of which enhanced oncogenic ERK-signalling. Taken together, our study documents a leukemic role for deregulated NKL homeobox genes HMX2 and HMX3 in AML, revealing molecular mechanisms of myeloid differentiation arrest.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- * E-mail:
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A. F. MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Xia X, Wang W, Yin K, Wang S. Interferon regulatory factor 8 governs myeloid cell development. Cytokine Growth Factor Rev 2020; 55:48-57. [DOI: 10.1016/j.cytogfr.2020.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/23/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023]
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Kiss M, Caro AA, Raes G, Laoui D. Systemic Reprogramming of Monocytes in Cancer. Front Oncol 2020; 10:1399. [PMID: 33042791 PMCID: PMC7528630 DOI: 10.3389/fonc.2020.01399] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 07/02/2020] [Indexed: 01/09/2023] Open
Abstract
Monocytes influence multiple aspects of tumor progression, including antitumor immunity, angiogenesis, and metastasis, primarily by infiltrating tumors, and differentiating into tumor-associated macrophages. Emerging evidence suggests that the tumor-induced systemic environment influences the development and phenotype of monocytes before their arrival to the tumor site. As a result, circulating monocytes show functional alterations in cancer, such as the acquisition of immunosuppressive activity and reduced responsiveness to inflammatory stimuli. In this review, we summarize available evidence about cancer-induced changes in monopoiesis and its impact on the abundance and function of monocytes in the periphery. In addition, we describe the phenotypical alterations observed in tumor-educated peripheral blood monocytes and highlight crucial gaps in our knowledge about additional cellular functions that may be affected based on transcriptomic studies. We also highlight emerging therapeutic strategies that aim to reverse cancer-induced changes in monopoiesis and peripheral monocytes to inhibit tumor progression and improve therapy responses. Overall, we suggest that an in-depth understanding of systemic monocyte reprogramming will have implications for cancer immunotherapy and the development of clinical biomarkers.
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Affiliation(s)
- Máté Kiss
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium.,Lab of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Aarushi Audhut Caro
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium.,Lab of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Geert Raes
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium.,Lab of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Damya Laoui
- Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium.,Lab of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
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38
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Kramer ED, Abrams SI. Granulocytic Myeloid-Derived Suppressor Cells as Negative Regulators of Anticancer Immunity. Front Immunol 2020; 11:1963. [PMID: 32983128 PMCID: PMC7481329 DOI: 10.3389/fimmu.2020.01963] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/21/2020] [Indexed: 12/24/2022] Open
Abstract
The immune system plays a critical role in cancer progression and response to therapy. However, the immune system can be compromised during the neoplastic process. Notably, the myeloid lineage, which gives rise to granulocytic cells, including neutrophils, is a well-recognized target of tumor-mediated immune suppression. Ordinarily, granulocytic cells are integral for host defense, but in neoplasia the normal process of granulocyte differentiation (i.e., granulopoiesis) can be impaired leading instead to the formation of granulocytic (or PMN)-myeloid-derived suppressor cells (MDSCs). Such cells comprise various stages of myeloid differentiation and are defined functionally by their highly pro-tumorigenic and immune suppressive activities. Thus, considerable interest has been devoted to impeding the negative contributions of PMN-MDSCs to the antitumor response. Understanding their biology has the potential to unveil novel therapeutic opportunities to hamper PMN-MDSC production in the bone marrow, their mobilization, or their effector functions within the tumor microenvironment and, therefore, bolster anticancer therapies that require a competent myeloid compartment. In this review, we will highlight mechanisms by which the neoplastic process skews granulopoiesis to produce PMN-MDSCs, summarize mechanisms by which they execute their pro-tumorigenic activities and, lastly, underscore strategies to obstruct their role as negative regulators of antitumor immunity.
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Affiliation(s)
- Elliot D Kramer
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Scott I Abrams
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
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39
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Pham TN, Spaulding C, Munshi HG. Controlling TIME: How MNK Kinases Function to Shape Tumor Immunity. Cancers (Basel) 2020; 12:cancers12082096. [PMID: 32731503 PMCID: PMC7465005 DOI: 10.3390/cancers12082096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/20/2020] [Accepted: 07/26/2020] [Indexed: 12/16/2022] Open
Abstract
A number of studies have clearly established the oncogenic role for MAPK-interacting protein kinases (MNK) in human malignancies. Modulation of MNK activity affects translation of mRNAs involved in cancer development, progression, and resistance to therapies. As a result, there are ongoing efforts to develop and evaluate MNK inhibitors for cancer treatment. However, it is important to recognize that MNK activity also plays an important role in regulating the innate and adaptive immune systems. A better understanding of the role of MNK kinases and MNK-mediated signals in regulating the immune system could help mitigate undesired side effects while maximizing therapeutic efficacy of MNK inhibitors. Here, we provide a systematic review on the function of MNK kinases and their substrates in immune cells.
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Affiliation(s)
- Thao N.D. Pham
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
- Correspondence: (T.N.D.P.); (H.G.M.); Tel.: +312-503-0312 (T.N.D.P.); +312-503-2301 (H.G.M.)
| | - Christina Spaulding
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Hidayatullah G. Munshi
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
- Robert H. Lurie Comprehensive Cancer Center, Chicago, IL 60611, USA
- Correspondence: (T.N.D.P.); (H.G.M.); Tel.: +312-503-0312 (T.N.D.P.); +312-503-2301 (H.G.M.)
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40
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Fourier N, Zolty M, Azriel A, Tedesco D, Levi BZ. MafK Mediates Chromatin Remodeling to Silence IRF8 Expression in Non-immune Cells in a Cell Type-SpecificManner. J Mol Biol 2020; 432:4544-4560. [PMID: 32534063 DOI: 10.1016/j.jmb.2020.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/02/2020] [Accepted: 06/05/2020] [Indexed: 11/17/2022]
Abstract
The regulation of gene expression is a result of a complex interplay between chromatin remodeling, transcription factors, and signaling molecules. Cell differentiation is accompanied by chromatin remodeling of specific loci to permanently silence genes that are not essential for the differentiated cell activity. The molecular cues that recruit the chromatin remodeling machinery are not well characterized. IRF8 is an immune-cell specific transcription factor and its expression is augmented by interferon-γ. Therefore, it serves as a model gene to elucidate the molecular mechanisms governing its silencing in non-immune cells. Ahigh-throughput shRNA library screen in IRF8 expression-restrictive cells enabled the identification of MafK as modulator of IRF8 silencing, affecting chromatin architecture. ChIP-Seq analysis revealed three MafK binding regions (-25 kb, -20 kb, and IRF8 6th intron) within the IRF8 locus. These MafK binding sites are sufficient to repress a reporter gene when cloned in genome-integrated lentiviral reporter constructs in only expression-restrictive cells. Conversely, plasmid-based constructs do not demonstrate such repressive effect. These results highlight the role of these MafK binding sites in mediating repressed chromatin assembly. Finally, a more thorough genomic analysis was performed, using CRISPR-Cas9 to delete MafK-int6 binding region in IRF8 expression-restrictive cells. Deleted clones exhibited an accessible chromatin conformation within the IRF8 locus that was accompanied by a significant increase in basal expression of IRF8 that was further induced by interferon-γ. Taken together, we identified and characterized several MafK binding elements within the IRF8 locus that mediate repressive chromatin conformation resulting in the silencing of IRF8 expression in a celltype-specific manner.
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Affiliation(s)
- Nitsan Fourier
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Maya Zolty
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Aviva Azriel
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | | | - Ben-Zion Levi
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel.
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41
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Kuwahara-Ota S, Shimura Y, Steinebach C, Isa R, Yamaguchi J, Nishiyama D, Fujibayashi Y, Takimoto-Shimomura T, Mizuno Y, Matsumura-Kimoto Y, Tsukamoto T, Chinen Y, Kobayashi T, Horiike S, Taniwaki M, Gütschow M, Kuroda J. Lenalidomide and pomalidomide potently interfere with induction of myeloid-derived suppressor cells in multiple myeloma. Br J Haematol 2020; 191:784-795. [PMID: 32558939 DOI: 10.1111/bjh.16881] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/22/2020] [Indexed: 12/15/2022]
Abstract
An increase in immunosuppressive myeloid-derived suppressor cells (MDSCs) is associated with disease progression and treatment resistance in multiple myeloma (MM). We investigated the mechanisms underlying MDSC induction, and sought to discover a strategy for prevention of MDSC induction in MM. Using a transwell co-culture system, four of nine examined human myeloma-derived cell lines (HMCLs) were potent in inducing monocytic (M)-MDSCs from normal peripheral blood mononuclear cells (PBMCs). As the results, we identified that secretion of C-C motif chemokine ligand 5 (CCL5) and macrophage migration inhibitory factor (MIF) by myeloma cells is a prerequisite for induction of MDSCs in MM. The immunomodulatory drug (IMiD) compounds, such as lenalidomide (LEN) and pomalidomide (POM), were identified as potent inhibitors of MDSC induction through bidirectional molecular effects of cereblon (CRBN)-dependent and -independent downregulation of CCL5 and MIF in myeloma cells; and downregulation of C-C motif chemokine receptor 5, a receptor for CCL5, and induction of interferon regulatory factor 8, a critical transcription factor for monocytic differentiation, in PBMCs. In the present study of the molecular mechanisms underlying MDSC induction, we identified a novel effect of LEN and POM of inhibiting MDSC induction via overlapping regulatory effects in myeloma cells and normal PBMCs.
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Affiliation(s)
- Saeko Kuwahara-Ota
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuji Shimura
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Christian Steinebach
- Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, Pharmaceutical Institute, Bonn, Germany
| | - Reiko Isa
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Junko Yamaguchi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Daichi Nishiyama
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuto Fujibayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomoko Takimoto-Shimomura
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshimi Mizuno
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yayoi Matsumura-Kimoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Taku Tsukamoto
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshiaki Chinen
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Hematology, Fukuchiyama City Hospital, Kyoto, Japan
| | - Tsutomu Kobayashi
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shigeo Horiike
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masafumi Taniwaki
- Center for Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Michael Gütschow
- Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, Pharmaceutical Institute, Bonn, Germany
| | - Junya Kuroda
- Division of Hematology and Oncology, Department of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
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42
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Zheng ZM, Yang HL, Lai ZZ, Wang CJ, Yang SL, Li MQ, Shao J. Myeloid-derived suppressor cells in obstetrical and gynecological diseases. Am J Reprod Immunol 2020; 84:e13266. [PMID: 32418253 DOI: 10.1111/aji.13266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
Myeloid-derived suppressor cells (MDSCs) are a heterogeneous group of myeloid-origin cells which have immunosuppressive activities in several conditions, such as cancer and inflammation. Recent research has also associated MDSCs with numerous obstetrical and gynecological diseases. During pregnancy, MDSCs accumulate to ensure maternal-fetal immune tolerance, whereas they are decreased in patients who suffer from early miscarriage or pre-eclampsia. While the etiology of endometriosis is still unknown, abnormal accumulation of MDSCs in the peripheral blood and peritoneal fluid, alongside an increased level of reactive oxygen species (ROS), has been observed in these patients, which is central to the cellular immune regulations by MDSCs. Additionally, the regulation of MDSCs observed in tumours is also applicable to gynecologic neoplasms, including ovarian cancer and cervical cancer. More recently, emerging evidence has shown that there are high levels of MDSCs in premature ovarian failure (POF) and in vitro fertilization (IVF), but the underlying mechanisms are unknown. In this review, the generation and mechanisms of MDSCs are summarized. In particular, the modulation of these cells in immune-related obstetrical and gynecological diseases is discussed, including potential treatment options targeting MDSCs.
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Affiliation(s)
- Zi-Meng Zheng
- Insitute of Obstetrics and Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China.,NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Hui-Li Yang
- Insitute of Obstetrics and Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China.,NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Zhen-Zhen Lai
- Insitute of Obstetrics and Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China.,NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Cheng-Jie Wang
- Insitute of Obstetrics and Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Shao-Liang Yang
- Insitute of Obstetrics and Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China.,NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Ming-Qing Li
- Insitute of Obstetrics and Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China.,NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
| | - Jun Shao
- Insitute of Obstetrics and Gynecology, Hospital of Obstetrics and Gynecology, Fudan University, Shanghai, China
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43
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Bigley V, Collin M. Insights from Patients with Dendritic Cell Immunodeficiency. Mol Immunol 2020; 122:116-123. [PMID: 32344243 DOI: 10.1016/j.molimm.2020.04.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/27/2020] [Accepted: 04/16/2020] [Indexed: 12/15/2022]
Abstract
Dendritic Cells (DCs), derived from haematopoietic stem cells, are critical to the dynamic and balanced functioning of the intact immune system and are of great interest as vehicles of immunotherapy. Genetically modified mouse models have proved powerful tools to map DC development and function in vivo but human studies have previously relied heavily on in vitro systems. Human dendritic cell immunodeficiency, resulting from single gene mutations, offers new opportunities to dissect the role of human DCs in vivo, determine the genetic requirements for their development and map their haematopoietic differentiation pathways. This review will summarise the clinical phenotypes of mutations in GATA2, IRF8 and IKZF1 genes which result in global or subset specific dendritic cell deficiencies, discuss the functional consequences of these cytopenias and how these syndromes have informed our knowledge of DC differentiation and human haematopoiesis.
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Affiliation(s)
- Venetia Bigley
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK; NIHR Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
| | - Matthew Collin
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK; NIHR Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
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44
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Role of IRF8 in immune cells functions, protection against infections, and susceptibility to inflammatory diseases. Hum Genet 2020; 139:707-721. [DOI: 10.1007/s00439-020-02154-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/24/2020] [Indexed: 12/13/2022]
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45
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Qiu X, Rahimzamani A, Wang L, Ren B, Mao Q, Durham T, McFaline-Figueroa JL, Saunders L, Trapnell C, Kannan S. Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe. Cell Syst 2020; 10:265-274.e11. [PMID: 32135093 PMCID: PMC7223477 DOI: 10.1016/j.cels.2020.02.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 06/08/2019] [Accepted: 02/05/2020] [Indexed: 01/13/2023]
Abstract
Here, we present Scribe (https://github.com/aristoteleo/Scribe-py), a toolkit for detecting and visualizing causal regulatory interactions between genes and explore the potential for single-cell experiments to power network reconstruction. Scribe employs restricted directed information to determine causality by estimating the strength of information transferred from a potential regulator to its downstream target. We apply Scribe and other leading approaches for causal network reconstruction to several types of single-cell measurements and show that there is a dramatic drop in performance for "pseudotime"-ordered single-cell data compared with true time-series data. We demonstrate that performing causal inference requires temporal coupling between measurements. We show that methods such as "RNA velocity" restore some degree of coupling through an analysis of chromaffin cell fate commitment. These analyses highlight a shortcoming in experimental and computational methods for analyzing gene regulation at single-cell resolution and suggest ways of overcoming it.
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Affiliation(s)
- Xiaojie Qiu
- Molecular & Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Arman Rahimzamani
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA
| | - Li Wang
- Department of Mathematics, University of Texas at Arlington, Arlington, TX, USA
| | - Bingcheng Ren
- College of Information Science and Engineering, Hunan Normal University, Changsha, China
| | - Qi Mao
- HERE company, Chicago, IL 60606, USA
| | - Timothy Durham
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Lauren Saunders
- Molecular & Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Cole Trapnell
- Molecular & Cellular Biology Program, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA, USA.
| | - Sreeram Kannan
- Department of Electrical Engineering, University of Washington, Seattle, WA, USA.
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46
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Wang L, Gao S, Wang H, Xue C, Liu X, Yuan H, Wang Z, Chen S, Chen Z, de Thé H, Zhang Y, Zhang W, Zhu J, Zhou J. Interferon regulatory factor 2 binding protein 2b regulates neutrophil versus macrophage fate during zebrafish definitive myelopoiesis. Haematologica 2020; 105:325-337. [PMID: 31123027 PMCID: PMC7012491 DOI: 10.3324/haematol.2019.217596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/20/2019] [Indexed: 12/15/2022] Open
Abstract
Aproper choice of neutrophil-macrophage progenitor cell fate is essential for the generation of adequate myeloid subpopulations during embryonic development and in adulthood. The network governing neutrophil-macrophage progenitor cell fate has several key determinants, such as myeloid master regulators CCAAT enhancer binding protein alpha (C/EBPα) and spleen focus forming virus proviral integration oncogene (PU.1). Nevertheless, more regulators remain to be identified and characterized. To ensure balanced commitment of neutrophil-macrophage progenitors toward each lineage, the interplay among these determinants is not only synergistic, but also antagonistic. Depletion of interferon regulatory factor 2 binding protein 2b (Irf2bp2b), a well-known negative transcription regulator, results in a bias in neutrophil-macrophage progenitor cell fate in favor of macrophages at the expense of neutrophils during the stage of definitive myelopoiesis in zebrafish embryos. Mechanistic studies indicate that Irf2bp2b acts as a downstream target of C/EBPα, repressing PU.1 expression, and that SUMOylation confers the repressive function of Irf2bp2b. Thus, Irf2bp2b is a novel determinant in the choice of fate of neutrophil-macrophage progenitor cells.
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Affiliation(s)
- Luxiang Wang
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuo Gao
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haihong Wang
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chang Xue
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohui Liu
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Yuan
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zixuan Wang
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Saijuan Chen
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhu Chen
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hugues de Thé
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Université de Paris 7/INSERM/CNRS UMR 944/7212, Equipe Labellisée No. 11 Ligue Nationale Contre le Cancer, Hôpital St. Louis, Paris, France
| | - Yiyue Zhang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Wenqing Zhang
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jun Zhu
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China .,Université de Paris 7/INSERM/CNRS UMR 944/7212, Equipe Labellisée No. 11 Ligue Nationale Contre le Cancer, Hôpital St. Louis, Paris, France
| | - Jun Zhou
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Remethylation of Dnmt3a -/- hematopoietic cells is associated with partial correction of gene dysregulation and reduced myeloid skewing. Proc Natl Acad Sci U S A 2020; 117:3123-3134. [PMID: 31996479 PMCID: PMC7022185 DOI: 10.1073/pnas.1918611117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mutations that reduce the function of the de novo DNA methyltransferase, DNMT3A, are very common in patients with clonal hematopoiesis and hematopoietic malignancies. Restoring the function of DNMT3A in mouse hematopoietic cells deficient for this protein corrects the DNA methylation defect in an ordered fashion, and partially restores abnormalities in gene expression and myeloid population skewing. These data may be relevant for therapeutic strategies designed to restore DNMT3A activity in patients with diseases caused by mutations in this gene. Mutations in the DNA methyltransferase 3A (DNMT3A) gene are the most common cause of age-related clonal hematopoiesis (ARCH) in older individuals, and are among the most common initiating events for acute myeloid leukemia (AML). The most frequent DNMT3A mutation in AML patients (R882H) encodes a dominant-negative protein that reduces methyltransferase activity by ∼80% in cells with heterozygous mutations, causing a focal, canonical DNA hypomethylation phenotype; this phenotype is partially recapitulated in murine Dnmt3a−/− bone marrow cells. To determine whether the hypomethylation phenotype of Dnmt3a−/− hematopoietic cells is reversible, we developed an inducible transgene to restore expression of DNMT3A in transplanted bone marrow cells from Dnmt3a−/− mice. Partial remethylation was detected within 1 wk, but near-complete remethylation required 6 mo. Remethylation was accurate, dynamic, and highly ordered, suggesting that differentially methylated regions have unique properties that may be relevant for their functions. Importantly, 22 wk of DNMT3A addback partially corrected dysregulated gene expression, and mitigated the expansion of myeloid cells. These data show that restoring DNMT3A expression can alter the epigenetic “state” created by loss of Dnmt3a activity; this genetic proof-of-concept experiment suggests that this approach could be relevant for patients with ARCH or AML caused by loss-of-function DNMT3A mutations.
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Silva J, Chang CS, Hu T, Qin H, Kitamura E, Hawthorn L, Ren M, Cowell JK. Distinct signaling programs associated with progression of FGFR1 driven leukemia in a mouse model of stem cell leukemia lymphoma syndrome. Genomics 2019; 111:1566-1573. [DOI: 10.1016/j.ygeno.2018.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 10/31/2018] [Indexed: 12/16/2022]
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Amon L, Lehmann CHK, Baranska A, Schoen J, Heger L, Dudziak D. Transcriptional control of dendritic cell development and functions. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 349:55-151. [PMID: 31759434 DOI: 10.1016/bs.ircmb.2019.10.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dendritic cells (DCs) are major regulators of adaptive immunity, as they are not only capable to induce efficient immune responses, but are also crucial to maintain peripheral tolerance and thereby inhibit autoimmune reactions. DCs bridge the innate and the adaptive immune system by presenting peptides of self and foreign antigens as peptide MHC complexes to T cells. These properties render DCs as interesting target cells for immunomodulatory therapies in cancer, but also autoimmune diseases. Several subsets of DCs with special properties and functions have been described. Recent achievements in understanding transcriptional programs on single cell level, together with the generation of new murine models targeting specific DC subsets, advanced our current understanding of DC development and function. Thus, DCs arise from precursor cells in the bone marrow with distinct progenitor cell populations splitting the monocyte populations and macrophage populations from the DC lineage, which upon lineage commitment can be separated into conventional cDC1, cDC2, and plasmacytoid DCs (pDCs). The DC populations harbor intrinsic programs enabling them to react for specific pathogens in dependency on the DC subset, and thereby orchestrate T cell immune responses. Similarities, but also varieties, between human and murine DC subpopulations are challenging, and will require further investigation of human specimens under consideration of the influence of the tissue micromilieu and DC subset localization in the future.
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Affiliation(s)
- Lukas Amon
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Christian H K Lehmann
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Anna Baranska
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Janina Schoen
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Lukas Heger
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Diana Dudziak
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.
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Inkpen SM, Solbakken MH, Jentoft S, Eslamloo K, Rise ML. Full characterization and transcript expression profiling of the interferon regulatory factor (IRF) gene family in Atlantic cod (Gadus morhua). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 98:166-180. [PMID: 30928323 DOI: 10.1016/j.dci.2019.03.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/22/2019] [Accepted: 03/22/2019] [Indexed: 06/09/2023]
Abstract
Atlantic cod (Gadus morhua) represents a unique immune system among teleost fish, making it a species of interest for immunological studies, and especially for investigating the evolutionary history of immune gene families. The interferon regulatory factor (IRF) gene family encodes transcription factors which function in the interferon pathway, but also in areas including leukocyte differentiation, cell growth, autoimmunity, and development. We previously characterized several IRF family members in Atlantic cod (Irf4a, Irf4b, Irf7, Irf8, and two Irf10 splice variants) at the cDNA and putative amino acid levels, and in the current study we took advantage of the new and improved Atlantic cod genome assembly in combination with rapid amplification of cDNA ends (RACE) to characterize the remaining family members (i.e. Irf3, Irf5, Irf6, Irf9, and two Irf2 splice variants). Real-time quantitative PCR (QPCR) was used to investigate constitutive expression of all IRF transcripts during embryonic development, suggesting several putative maternal transcripts, and potential stage-specific roles. QPCR studies also showed 11 of 13 transcripts were responsive to stimulation with poly(I:C), while 6 of 13 transcripts were responsive to lipopolysaccharide (LPS) in Atlantic cod head kidney macrophages, indicating roles for cod IRF family members in both antiviral and antibacterial responses. This study is the first to investigate expression of the complete IRF family in Atlantic cod, and suggests potential novel roles for several of these transcription factors within immunity as well as in early development of this species.
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Affiliation(s)
- Sabrina M Inkpen
- Department of Ocean Sciences, Memorial University of Newfoundland, NL, A1C 5S7, Canada.
| | - Monica H Solbakken
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Khalil Eslamloo
- Department of Ocean Sciences, Memorial University of Newfoundland, NL, A1C 5S7, Canada.
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, NL, A1C 5S7, Canada.
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