1
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Liu D, Hsieh CL, Lieber MR. The RNA tether model for human chromosomal translocation fragile zones. Trends Biochem Sci 2024; 49:391-400. [PMID: 38490833 PMCID: PMC11069435 DOI: 10.1016/j.tibs.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/06/2024] [Accepted: 02/16/2024] [Indexed: 03/17/2024]
Abstract
One of the two chromosomal breakage events in recurring translocations in B cell neoplasms is often due to the recombination-activating gene complex (RAG complex) releasing DNA ends before end joining. The other break occurs in a fragile zone of 20-600 bp in a non-antigen receptor gene locus, with a more complex and intriguing set of mechanistic factors underlying such narrow fragile zones. These factors include activation-induced deaminase (AID), which acts only at regions of single-stranded DNA (ssDNA). Recent work leads to a model involving the tethering of AID to the nascent RNA as it emerges from the RNA polymerase. This mechanism may have relevance in class switch recombination (CSR) and somatic hypermutation (SHM), as well as broader relevance for other DNA enzymes.
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Affiliation(s)
- Di Liu
- Institute of Molecular and Translational Medicine (IMTM), and Department of Biochemistry and Molecular Biology, Xi'an Jiaotong University Health Science Center, and Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi 710061, China
| | - Chih-Lin Hsieh
- USC Norris Comprehensive Cancer Center, Department of Urology, University of Southern California, Los Angeles, CA 90089-9176, USA
| | - Michael R Lieber
- USC Norris Comprehensive Cancer Center, Departments of Pathology and Laboratory Medicine, of Molecular Microbiology and Immunology, of Biochemistry and Molecular Medicine, and in the Section of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089-9176, USA.
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2
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Huang X, Li Y, Zhang J, Yan L, Zhao H, Ding L, Bhatara S, Yang X, Yoshimura S, Yang W, Karol SE, Inaba H, Mullighan C, Litzow M, Zhu X, Zhang Y, Stock W, Jain N, Jabbour E, Kornblau SM, Konopleva M, Pui CH, Paietta E, Evans W, Yu J, Yang JJ. Single-cell systems pharmacology identifies development-driven drug response and combination therapy in B cell acute lymphoblastic leukemia. Cancer Cell 2024; 42:552-567.e6. [PMID: 38593781 PMCID: PMC11008188 DOI: 10.1016/j.ccell.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/19/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024]
Abstract
Leukemia can arise at various stages of the hematopoietic differentiation hierarchy, but the impact of developmental arrest on drug sensitivity is unclear. Applying network-based analyses to single-cell transcriptomes of human B cells, we define genome-wide signaling circuitry for each B cell differentiation stage. Using this reference, we comprehensively map the developmental states of B cell acute lymphoblastic leukemia (B-ALL), revealing its strong correlation with sensitivity to asparaginase, a commonly used chemotherapeutic agent. Single-cell multi-omics analyses of primary B-ALL blasts reveal marked intra-leukemia heterogeneity in asparaginase response: resistance is linked to pre-pro-B-like cells, with sensitivity associated with the pro-B-like population. By targeting BCL2, a driver within the pre-pro-B-like cell signaling network, we find that venetoclax significantly potentiates asparaginase efficacy in vitro and in vivo. These findings demonstrate a single-cell systems pharmacology framework to predict effective combination therapies based on intra-leukemia heterogeneity in developmental state, with potentially broad applications beyond B-ALL.
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Affiliation(s)
- Xin Huang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, Anhui 230601, China
| | - Yizhen Li
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Hematology, Children's Hospital of Soochow University, Suzhou, Jiangsu 215003, China
| | - Jingliao Zhang
- Department of Pediatrics Blood Diseases Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Lei Yan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Huanbin Zhao
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Liang Ding
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Sheetal Bhatara
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xu Yang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Satoshi Yoshimura
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wenjian Yang
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Seth E Karol
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Charles Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mark Litzow
- Division of Hematology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaofan Zhu
- Department of Pediatrics Blood Diseases Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Yingchi Zhang
- Department of Pediatrics Blood Diseases Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Wendy Stock
- Department of Medicine Section of Hematology-Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Nitin Jain
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elias Jabbour
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Steven M Kornblau
- Department of Leukemia, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marina Konopleva
- Department of Oncology and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Elisabeth Paietta
- Cancer Center, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - William Evans
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Jun J Yang
- Division of Pharmaceutical Sciences, Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Hematological Malignancies Program, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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3
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Urnikyte A, Masiulyte A, Pranckeniene L, Kučinskas V. Disentangling archaic introgression and genomic signatures of selection at human immunity genes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105528. [PMID: 37977419 DOI: 10.1016/j.meegid.2023.105528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/04/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Pathogens and infectious diseases have imposed exceptionally strong selective pressure on ancient and modern human genomes and contributed to the current variation in many genes. There is evidence that modern humans acquired immune variants through interbreeding with ancient hominins, but the impact of such variants on human traits is not fully understood. The main objectives of this research were to infer the genetic signatures of positive selection that may be involved in adaptation to infectious diseases and to investigate the function of Neanderthal alleles identified within a set of 50 Lithuanian genomes. Introgressed regions were identified using the machine learning tool ArchIE. Recent positive selection signatures were analysed using iHS. We detected high-scoring signals of positive selection at innate immunity genes (EMB, PARP8, HLAC, and CDSN) and evaluated their interactions with the structural proteins of pathogens. Interactions with human immunodeficiency virus (HIV) 1 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified. Overall, genomic regions introgressed from Neanderthals were shown to be enriched in genes related to immunity, keratinocyte differentiation, and sensory perception.
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Affiliation(s)
- Alina Urnikyte
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Santariskiu Street 2, Vilnius LT-08661, Lithuania.
| | - Abigaile Masiulyte
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Santariskiu Street 2, Vilnius LT-08661, Lithuania
| | - Laura Pranckeniene
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Santariskiu Street 2, Vilnius LT-08661, Lithuania.
| | - Vaidutis Kučinskas
- Faculty of Medicine, Department of Human and Medical Genetics, Institute of Biomedical Sciences, Vilnius University, Santariskiu Street 2, Vilnius LT-08661, Lithuania.
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4
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Li W, Morgan R, Nieder R, Habeebu SSM, Myers GD. CD19-negative B-cell precursors in bone marrow: A potential mimicker for CD19-negative B-lymphoblastic leukemia by flow cytometry in patients with anti-CD19 treatment. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2023; 104:392-396. [PMID: 37497861 DOI: 10.1002/cyto.b.22135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/16/2023] [Accepted: 06/20/2023] [Indexed: 07/28/2023]
Affiliation(s)
- Weijie Li
- Pathology and Laboratory Medicine, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Ruth Morgan
- Pathology and Laboratory Medicine, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Roxanne Nieder
- Pathology and Laboratory Medicine, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - Sahibu Sultan M Habeebu
- Pathology and Laboratory Medicine, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
| | - G Doug Myers
- Hematology and Oncology, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, Missouri, USA
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5
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Masih KE, Gardner RA, Chou HC, Abdelmaksoud A, Song YK, Mariani L, Gangalapudi V, Gryder BE, Wilson AL, Adebola SO, Stanton BZ, Wang C, Milewski D, Kim YY, Tian M, Cheuk ATC, Wen X, Zhang Y, Altan-Bonnet G, Kelly MC, Wei JS, Bulyk ML, Jensen MC, Orentas RJ, Khan J. A stem cell epigenome is associated with primary nonresponse to CD19 CAR T cells in pediatric acute lymphoblastic leukemia. Blood Adv 2023; 7:4218-4232. [PMID: 36607839 PMCID: PMC10440404 DOI: 10.1182/bloodadvances.2022008977] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/07/2023] Open
Abstract
CD19 chimeric antigen receptor T-cell therapy (CD19-CAR) has changed the treatment landscape and outcomes for patients with pre-B-cell acute lymphoblastic leukemia (B-ALL). Unfortunately, primary nonresponse (PNR), sustained CD19+ disease, and concurrent expansion of CD19-CAR occur in 20% of the patients and is associated with adverse outcomes. Although some failures may be attributable to CD19 loss, mechanisms of CD19-independent, leukemia-intrinsic resistance to CD19-CAR remain poorly understood. We hypothesize that PNR leukemias are distinct compared with primary sensitive (PS) leukemias and that these differences are present before treatment. We used a multiomic approach to investigate this in 14 patients (7 with PNR and 7 with PS) enrolled in the PLAT-02 trial at Seattle Children's Hospital. Long-read PacBio sequencing helped identify 1 PNR in which 47% of CD19 transcripts had exon 2 skipping, but other samples lacked CD19 transcript abnormalities. Epigenetic profiling discovered DNA hypermethylation at genes targeted by polycomb repressive complex 2 (PRC2) in embryonic stem cells. Similarly, assays of transposase-accessible chromatin-sequencing revealed reduced accessibility at these PRC2 target genes, with a gain in accessibility of regions characteristic of hematopoietic stem cells and multilineage progenitors in PNR. Single-cell RNA sequencing and cytometry by time of flight analyses identified leukemic subpopulations expressing multilineage markers and decreased antigen presentation in PNR. We thus describe the association of a stem cell epigenome with primary resistance to CD19-CAR therapy. Future trials incorporating these biomarkers, with the addition of multispecific CAR T cells targeting against leukemic stem cell or myeloid antigens, and/or combined epigenetic therapy to disrupt this distinct stem cell epigenome may improve outcomes of patients with B-ALL.
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Affiliation(s)
- Katherine E. Masih
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, Cambridge, England
- Medical Scientist Training Program, University of Miami Leonard M. Miller School of Medicine, Miami, FL
| | - Rebecca A. Gardner
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
- Center for Clinical and Translational Research, Seattle Children’s Research Institute, Seattle, WA
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Hsien-Chao Chou
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Abdalla Abdelmaksoud
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Young K. Song
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Luca Mariani
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Vineela Gangalapudi
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Berkley E. Gryder
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH
| | - Ashley L. Wilson
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Serifat O. Adebola
- Immunodynamics Group, Cancer and Inflammation Program, Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Benjamin Z. Stanton
- Center for Childhood Cancer and Blood Diseases, Nationwide Children’s Hospital, Columbus, OH
| | - Chaoyu Wang
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - David Milewski
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yong Yean Kim
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Meijie Tian
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Adam Tai-Chi Cheuk
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Xinyu Wen
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yue Zhang
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Grégoire Altan-Bonnet
- Immunodynamics Group, Cancer and Inflammation Program, Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Michael C. Kelly
- Center for Cancer Research Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Bethesda, MD
| | - Jun S. Wei
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Martha L. Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Michael C. Jensen
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Rimas J. Orentas
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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6
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Kim JC, Chan-Seng-Yue M, Ge S, Zeng AGX, Ng K, Gan OI, Garcia-Prat L, Flores-Figueroa E, Woo T, Zhang AXW, Arruda A, Chithambaram S, Dobson SM, Khoo A, Khan S, Ibrahimova N, George A, Tierens A, Hitzler J, Kislinger T, Dick JE, McPherson JD, Minden MD, Notta F. Transcriptomic classes of BCR-ABL1 lymphoblastic leukemia. Nat Genet 2023:10.1038/s41588-023-01429-4. [PMID: 37337105 DOI: 10.1038/s41588-023-01429-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 05/17/2023] [Indexed: 06/21/2023]
Abstract
In BCR-ABL1 lymphoblastic leukemia, treatment heterogeneity to tyrosine kinase inhibitors (TKIs), especially in the absence of kinase domain mutations in BCR-ABL1, is poorly understood. Through deep molecular profiling, we uncovered three transcriptomic subtypes of BCR-ABL1 lymphoblastic leukemia, each representing a maturation arrest at a stage of B-cell progenitor differentiation. An earlier arrest was associated with lineage promiscuity, treatment refractoriness and poor patient outcomes. A later arrest was associated with lineage fidelity, durable leukemia remissions and improved patient outcomes. Each maturation arrest was marked by specific genomic events that control different transition points in B-cell development. Interestingly, these events were absent in BCR-ABL1+ preleukemic stem cells isolated from patients regardless of subtype, which supports that transcriptomic phenotypes are determined downstream of the leukemia-initialing event. Overall, our data indicate that treatment response and TKI efficacy are unexpected outcomes of the differentiation stage at which this leukemia transforms.
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Affiliation(s)
- Jaeseung C Kim
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | | | - Sabrina Ge
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Karen Ng
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | | | - Tristan Woo
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | | | - Andrea Arruda
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Shivapriya Chithambaram
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Amanda Khoo
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Shahbaz Khan
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Ann George
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Anne Tierens
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Johann Hitzler
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John E Dick
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John D McPherson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Mark D Minden
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Faiyaz Notta
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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7
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Ding L, Zhang Y, Wang Y, Wang Y, Tong Z, Li P, Chen C, Wang B, Yue X, Li C, Wu Z, Liang X, Ma C, Gao L. Zhx2 maintains islet β-cell mass and function by transcriptionally regulating Pax6. iScience 2023; 26:106871. [PMID: 37275527 PMCID: PMC10232729 DOI: 10.1016/j.isci.2023.106871] [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: 11/18/2022] [Revised: 04/05/2023] [Accepted: 05/09/2023] [Indexed: 06/07/2023] Open
Abstract
Emerging evidence shows that pancreatic β-cell function and quality are key determinants in the progression of type 2 diabetes (T2D). The transcription factor zinc finger homeobox 2 (Zhx2) is involved in proliferation and development of multiple cells. However, the exact role of Zhx2 in β-cells and T2D remains completely unknown. Here, we report that Zhx2 orchestrates β-cell mass and function by regulating paired box protein pax-6 (Pax6). We found that β-cell-specific knockout Zhx2 (Zhx2BKO) mice showed a decrease in β-cell proliferation and glucose homeostasis. Under prediabetic and diabetic conditions, we discovered glucose intolerance in both Zhx2BKO-HFD mice and Zhx2BKO-db/db mice, with reduced β-cell mass and insulin secretion. Mechanistically, we demonstrated that Zhx2 targeted the Pax6 promoter region (-1740∼-1563; -862∼-559; -251∼+75), enhanced promoter activity. Overall, Zhx2 maintains β-cell function by transcriptionally regulating Pax6, which provides a therapeutic target for diabetes intervention.
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Affiliation(s)
- Lu Ding
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Infection and Immunity, and Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Yankun Zhang
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Infection and Immunity, and Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Yingchun Wang
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Infection and Immunity, and Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Yuzhen Wang
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Infection and Immunity, and Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Zheng Tong
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Infection and Immunity, and Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Pengfei Li
- Department of Endocrinology, Yucheng People’s Hospital, Dezhou, Shandong 251200, P. R. China
| | - Chaojia Chen
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Infection and Immunity, and Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Bo Wang
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Infection and Immunity, and Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Xuetian Yue
- Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Chunyang Li
- Key Laboratory for Experimental Teratology of Ministry of Education and Department of Histology and Embryology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Zhuanchang Wu
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Infection and Immunity, and Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Xiaohong Liang
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Infection and Immunity, and Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Chunhong Ma
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Infection and Immunity, and Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P. R. China
| | - Lifen Gao
- Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Key Laboratory of Infection and Immunity, and Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, P. R. China
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8
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In Vitro Human Haematopoietic Stem Cell Expansion and Differentiation. Cells 2023; 12:cells12060896. [PMID: 36980237 PMCID: PMC10046976 DOI: 10.3390/cells12060896] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
The haematopoietic system plays an essential role in our health and survival. It is comprised of a range of mature blood and immune cell types, including oxygen-carrying erythrocytes, platelet-producing megakaryocytes and infection-fighting myeloid and lymphoid cells. Self-renewing multipotent haematopoietic stem cells (HSCs) and a range of intermediate haematopoietic progenitor cell types differentiate into these mature cell types to continuously support haematopoietic system homeostasis throughout life. This process of haematopoiesis is tightly regulated in vivo and primarily takes place in the bone marrow. Over the years, a range of in vitro culture systems have been developed, either to expand haematopoietic stem and progenitor cells or to differentiate them into the various haematopoietic lineages, based on the use of recombinant cytokines, co-culture systems and/or small molecules. These approaches provide important tractable models to study human haematopoiesis in vitro. Additionally, haematopoietic cell culture systems are being developed and clinical tested as a source of cell products for transplantation and transfusion medicine. This review discusses the in vitro culture protocols for human HSC expansion and differentiation, and summarises the key factors involved in these biological processes.
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9
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Crosstalk of Transcriptional Regulators of Adaptive Immune System and microRNAs: An Insight into Differentiation and Development. Cells 2023; 12:cells12040635. [PMID: 36831302 PMCID: PMC9953855 DOI: 10.3390/cells12040635] [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: 12/14/2022] [Revised: 01/27/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
MicroRNAs (miRNAs), as small regulatory RNA molecules, are involved in gene expression at the post-transcriptional level. Hence, miRNAs contribute to gene regulation of various steps of different cell subsets' differentiation, maturation, and activation. The adaptive immune system arm, which exhibits the most specific immune responses, is also modulated by miRNAs. The generation and maturation of various T-cell subsets concomitant with B-cells is under precise regulation of miRNAs which function directly on the hallmark genes of each cell subset or indirectly through regulation of signaling pathway mediators and/or transcription factors involved in this maturation journey. In this review, we first discussed the origination process of common lymphocyte progenitors from hematopoietic stem cells, which further differentiate into various T-cell subsets under strict regulation of miRNAs and transcription factors. Subsequently, the differentiation of B-cells from common lymphocyte progenitors in bone marrow and periphery were discussed in association with a network of miRNAs and transcription factors.
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10
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Abstract
As a transcriptional factor and the negative regulator of alpha fetal protein (AFP), Zinc fingers and homeoboxes 2 (ZHX2) has a well-established role in protection against hepatocellular carcinoma (HCC). However, recent studies have suggested ZHX2 as an oncogene in clear cell renal cell carcinoma (ccRCC) and triple-negative breast cancer (TNBC). Moreover, mounting evidence has illustrated a much broader role of ZHX2 in multiple cellular processes, including cell proliferation, cell differentiation, lipid metabolism, and immunoregulation. This comprehensive review emphasizes the role of ZHX2 in health and diseases which have been more recently uncovered.
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Affiliation(s)
- Na Li
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Zhuanchang Wu
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
| | - Chunhong Ma
- Key Laboratory for Experimental Teratology of Ministry of Education and Dept. Immunology, School of Basic Medical Sciences, Cheeloo Medical College, Shandong University, Jinan, Shandong, China
- Key Laboratory of Infection and Immunity of Shandong Province, Shandong University, Jinan, Shandong, China
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11
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Brady SW, Roberts KG, Gu Z, Shi L, Pounds S, Pei D, Cheng C, Dai Y, Devidas M, Qu C, Hill AN, Payne-Turner D, Ma X, Iacobucci I, Baviskar P, Wei L, Arunachalam S, Hagiwara K, Liu Y, Flasch DA, Liu Y, Parker M, Chen X, Elsayed AH, Pathak O, Li Y, Fan Y, Michael JR, Rusch M, Wilkinson MR, Foy S, Hedges D, Newman S, Zhou X, Wang J, Reilly C, Sioson E, Rice SV, Loyola VP, Wu G, Rampersaud E, Reshmi SC, Gastier-Foster J, Guidry-Auvil JM, Gesuwan P, Smith MA, Winick N, Carroll AJ, Heerema NA, Harvey RC, Willman CL, Larsen E, Raetz EA, Borowitz MJ, Wood BL, Carroll WL, Zweidler-McKay PA, Rabin KR, Mattano LA, Maloney KW, Winter SS, Burke MJ, Salzer W, Dunsmore KP, Angiolillo AL, Crews KR, Downing JR, Jeha S, Pui CH, Evans WE, Yang JJ, Relling MV, Gerhard DS, Loh ML, Hunger SP, Zhang J, Mullighan C. The genomic landscape of pediatric acute lymphoblastic leukemia. Nat Genet 2022; 54:1376-1389. [PMID: 36050548 PMCID: PMC9700506 DOI: 10.1038/s41588-022-01159-z] [Citation(s) in RCA: 110] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 07/13/2022] [Indexed: 12/13/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Here, using whole-genome, exome and transcriptome sequencing of 2,754 childhood patients with ALL, we find that, despite a generally low mutation burden, ALL cases harbor a median of four putative somatic driver alterations per sample, with 376 putative driver genes identified varying in prevalence across ALL subtypes. Most samples harbor at least one rare gene alteration, including 70 putative cancer driver genes associated with ubiquitination, SUMOylation, noncoding transcripts and other functions. In hyperdiploid B-ALL, chromosomal gains are acquired early and synchronously before ultraviolet-induced mutation. By contrast, ultraviolet-induced mutations precede chromosomal gains in B-ALL cases with intrachromosomal amplification of chromosome 21. We also demonstrate the prognostic significance of genetic alterations within subtypes. Intriguingly, DUX4- and KMT2A-rearranged subtypes separate into CEBPA/FLT3- or NFATC4-expressing subgroups with potential clinical implications. Together, these results deepen understanding of the ALL genomic landscape and associated outcomes.
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Affiliation(s)
- Samuel W. Brady
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Kathryn G. Roberts
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Zhaohui Gu
- Department of Computational and Quantitative Medicine & Systems Biology, Beckman Research Institute of City of Hope, Duarte CA, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Stanley Pounds
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Yunfeng Dai
- Department of Biostatistics, University of Florida, Gainesville FL, USA
| | - Meenakshi Devidas
- Department of Global Pediatric Medicine, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Chunxu Qu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Ashley N. Hill
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Debbie Payne-Turner
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Pradyuamna Baviskar
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Lei Wei
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Sasi Arunachalam
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Kohei Hagiwara
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Diane A. Flasch
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Yu Liu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Matthew Parker
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Xiaolong Chen
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Abdelrahman H. Elsayed
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA,Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Omkar Pathak
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Yongjin Li
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - J. Robert Michael
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Mark R. Wilkinson
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Scott Foy
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Dale Hedges
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Scott Newman
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Jian Wang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Colleen Reilly
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Edgar Sioson
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Stephen V. Rice
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Victor Pastor Loyola
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Evadnie Rampersaud
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Shalini C. Reshmi
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus OH, USA
| | | | - Jaime M. Guidry-Auvil
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda MD, USA
| | - Patee Gesuwan
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda MD, USA
| | - Malcolm A. Smith
- Cancer Therapeutics Evaluation Program, National Cancer Institute, National Institutes of Health, Bethesda MD, USA
| | - Naomi Winick
- Department of Pediatric Hematology Oncology and Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas TX, USA
| | - Andrew J. Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham AL, USA
| | | | - Richard C. Harvey
- Department of Pathology, University of New Mexico Cancer Center, Albuquerque NM, USA
| | | | - Eric Larsen
- Department of Pediatrics, Maine Children’s Cancer Program, Scarborough ME, USA
| | - Elizabeth A. Raetz
- Department of Pediatrics and Perlmutter Cancer Center, New York University Langone Medical Center, New York NY, USA
| | - Michael J. Borowitz
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore MD, USA
| | - Brent L. Wood
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, University of Southern California, CA, USA
| | - William L. Carroll
- Department of Pediatrics and Perlmutter Cancer Center, New York University Langone Medical Center, New York NY, USA
| | | | - Karen R. Rabin
- Department of Pediatrics, Baylor College of Medicine, Houston TX, USA
| | | | - Kelly W. Maloney
- Department of Pediatrics and Children’s Hospital Colorado, University of Colorado, Aurora CO, USA
| | - Stuart S. Winter
- Children’s Minnesota Research Institute and Cancer and Blood Disorders Program, Minneapolis MN, USA
| | - Michael J. Burke
- Division of Pediatric Hematology-Oncology, Medical College of Wisconsin, Milwaukee WI, USA
| | - Wanda Salzer
- Uniformed Services University, School of Medicine, Bethesda, MD, USA
| | | | | | - Kristine R. Crews
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - James R. Downing
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Sima Jeha
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - William E. Evans
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Jun J. Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Mary V. Relling
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Daniela S. Gerhard
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda MD, USA
| | - Mignon L. Loh
- Department of Pediatrics, Benioff Children’s Hospital and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco CA, USA
| | - Stephen P. Hunger
- Department of Pediatrics and the Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia PA, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Charles Mullighan
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis TN, USA
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12
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Nagaharu K, Kojima Y, Hirose H, Minoura K, Hinohara K, Minami H, Kageyama Y, Sugimoto Y, Masuya M, Nii S, Seki M, Suzuki Y, Tawara I, Shimamura T, Katayama N, Nishikawa H, Ohishi K. A bifurcation concept for B-lymphoid/plasmacytoid dendritic cells with largely fluctuating transcriptome dynamics. Cell Rep 2022; 40:111260. [PMID: 36044861 DOI: 10.1016/j.celrep.2022.111260] [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: 10/19/2021] [Revised: 06/02/2022] [Accepted: 08/04/2022] [Indexed: 11/24/2022] Open
Abstract
Hematopoiesis was considered a hierarchical stepwise process but was revised to a continuous process following single-cell RNA sequencing. However, the uncertainty or fluctuation of single-cell transcriptome dynamics during differentiation was not considered, and the dendritic cell (DC) pathway in the lymphoid context remains unclear. Here, we identify human B-plasmacytoid DC (pDC) bifurcation as large fluctuating transcriptome dynamics in the putative B/NK progenitor region by dry and wet methods. By converting splicing kinetics into diffusion dynamics in a deep generative model, our original computational methodology reveals strong fluctuation at B/pDC bifurcation in IL-7Rα+ regions, and LFA-1 fluctuates positively in the pDC direction at the bifurcation. These expectancies are validated by the presence of B/pDC progenitors in the IL-7Rα+ fraction and preferential expression of LFA-1 in pDC-biased progenitors with a niche-like culture system. We provide a model of fluctuation-based differentiation, which reconciles continuous and discrete models and is applicable to other developmental systems.
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Affiliation(s)
- Keiki Nagaharu
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Yasuhiro Kojima
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Haruka Hirose
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Kodai Minoura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Kunihiko Hinohara
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan; Institute for Advanced Research, Nagoya University, Nagoya, Japan
| | - Hirohito Minami
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Yuki Kageyama
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Yuka Sugimoto
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Masahiro Masuya
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Shigeru Nii
- Shiroko Women's Hospital, Suzuka 510-0235, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa 277-8561, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa 277-8561, Japan
| | - Isao Tawara
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan; Institute for Advanced Research, Nagoya University, Nagoya, Japan
| | - Naoyuki Katayama
- Department of Hematology and Oncology, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Hiroyoshi Nishikawa
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan; Institute for Advanced Research, Nagoya University, Nagoya, Japan; Division of Cancer Immunology, Research Institute, National Cancer Center, Tokyo 104-0045, Japan; Division of Cancer Immunology, Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Chiba 277-8577, Japan.
| | - Kohshi Ohishi
- Department of Transfusion Medicine and Cell Therapy, Mie University Hospital, Tsu 514-8507, Japan.
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13
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Casazza A, Van Helleputte L, Van Renterghem B, Pokreisz P, De Geest N, De Petrini M, Janssens T, Pellens M, Diricx M, Riera-Domingo C, Wozniak A, Mazzone M, Schöffski P, Defert O, Reyns G, Kindt N. PhAc-ALGP-Dox, a Novel Anticancer Prodrug with Targeted Activation and Improved Therapeutic Index. Mol Cancer Ther 2022; 21:568-581. [PMID: 35149549 PMCID: PMC9377749 DOI: 10.1158/1535-7163.mct-21-0518] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/13/2021] [Accepted: 02/08/2022] [Indexed: 01/07/2023]
Abstract
Clinical use of doxorubicin (Dox) is limited by cumulative myelo- and cardiotoxicity. This research focuses on the detailed characterization of PhAc-ALGP-Dox, a targeted tetrapeptide prodrug with a unique dual-step activation mechanism, designed to circumvent Dox-related toxicities and is ready for upcoming clinical investigation. Coupling Dox to a phosphonoacetyl (PhAc)-capped tetrapeptide forms the cell-impermeable, inactive compound, PhAc-ALGP-Dox. After extracellular cleavage by tumor-enriched thimet oligopeptidase-1 (THOP1), a cell-permeable but still biologically inactive dipeptide-conjugate is formed (GP-Dox), which is further processed intracellularly to Dox by fibroblast activation protein-alpha (FAPα) and/or dipeptidyl peptidase-4 (DPP4). In vitro, PhAc-ALGP-Dox is effective in various 2D- and 3D-cancer models, while showing improved safety toward normal epithelium, hematopoietic progenitors, and cardiomyocytes. In vivo, these results translate into a 10-fold higher tolerability and 5-fold greater retention of Dox in the tumor microenvironment compared with the parental drug. PhAc-ALGP-Dox demonstrates 63% to 96% tumor growth inhibition in preclinical models, an 8-fold improvement in efficacy in patient-derived xenograft (PDX) models, and reduced metastatic burden in a murine model of experimental lung metastasis, improving survival by 30%. The current findings highlight the potential clinical benefit of PhAc-ALGP-Dox, a targeted drug-conjugate with broad applicability, favorable tissue biodistribution, significantly improved tolerability, and tumor growth inhibition at primary and metastatic sites in numerous solid tumor models.
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Affiliation(s)
- Andrea Casazza
- CoBioRes NV, Campus Gasthuisberg University of Leuven, Leuven, Belgium
| | | | - Britt Van Renterghem
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Peter Pokreisz
- CoBioRes NV, Campus Gasthuisberg University of Leuven, Leuven, Belgium
| | - Natalie De Geest
- CoBioRes NV, Campus Gasthuisberg University of Leuven, Leuven, Belgium
| | - Marzia De Petrini
- CoBioRes NV, Campus Gasthuisberg University of Leuven, Leuven, Belgium
| | - Tom Janssens
- CoBioRes NV, Campus Gasthuisberg University of Leuven, Leuven, Belgium
| | - Marijke Pellens
- CoBioRes NV, Campus Gasthuisberg University of Leuven, Leuven, Belgium
| | - Marjan Diricx
- CoBioRes NV, Campus Gasthuisberg University of Leuven, Leuven, Belgium
| | - Carla Riera-Domingo
- Laboratory of Tumor Inflammation and Angiogenesis, Vesalius Research Center, VIB, Leuven, Belgium.,Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Agnieszka Wozniak
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and Angiogenesis, Vesalius Research Center, VIB, Leuven, Belgium.,Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Patrick Schöffski
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, Leuven, Belgium.,Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Olivier Defert
- CoBioRes NV, Campus Gasthuisberg University of Leuven, Leuven, Belgium
| | - Geert Reyns
- CoBioRes NV, Campus Gasthuisberg University of Leuven, Leuven, Belgium
| | - Nele Kindt
- CoBioRes NV, Campus Gasthuisberg University of Leuven, Leuven, Belgium.,Corresponding Author: Nele Kindt, CoBioRes NV, Campus Gasthuisberg, CDG, bus 913 Herestraat 49, Leuven, Flanders B-3000, Belgium. E-mail:
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14
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Guo Q, Zhong Y, Wang Z, Cao T, Zhang M, Zhang P, Huang W, Bi J, Yuan Y, Ou M, Zou X, Xiao G, Yang Y, Liu S, Liu L, Wang Z, Zhang G, Wu L. Single-cell transcriptomic landscape identifies the expansion of peripheral blood monocytes as an indicator of HIV-1-TB co-infection. CELL INSIGHT 2022; 1:100005. [PMID: 37192986 PMCID: PMC10120323 DOI: 10.1016/j.cellin.2022.100005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/27/2021] [Accepted: 01/18/2022] [Indexed: 05/18/2023]
Abstract
Certain circulating cell subsets are involved in immune dysregulation in human immunodeficiency virus type 1 (HIV-1) and tuberculosis (TB) co-infection; however, the characteristics and role of these subclusters are unknown. Peripheral blood mononuclear cells (PBMCs) of patients with HIV-1 infection alone (HIV-pre) and those with HIV-1-TB co-infection without anti-TB treatment (HIV-pre & TB-pre) and with anti-TB treatment for 2 weeks (HIV-pre & TB-pos) were subjected to single-cell RNA sequencing (scRNA-seq) to characterize the transcriptome of different immune cell subclusters. We obtained > 60,000 cells and identified 32 cell subclusters based on gene expression. The proportion of immune-cell subclusters was altered in HIV-1-TB co-infected individuals compared with that in HIV-pre-group, indicating immune dysregulation corresponding to different disease states. The proportion of an inflammatory CD14+CD16+ monocyte subset was higher in the HIV-pre & TB-pre group than in the HIV-pre group; this was validated in an additional cohort (n = 80) via a blood cell differential test, which also demonstrated a good discriminative performance (area under the curve, 0.8046). These findings depicted the atlas of immune PBMC subclusters in HIV-1-TB co-infection and demonstrate that monocyte subsets in peripheral blood might serve as a discriminating biomarker for diagnosis of HIV-1-TB co-infection.
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Affiliation(s)
- Qinglong Guo
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Yu Zhong
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
| | - Zhifeng Wang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
| | - Tingzhi Cao
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Mingyuan Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
| | - Peiyan Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Waidong Huang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Bi
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Yue Yuan
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Ou
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Xuanxuan Zou
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guohui Xiao
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Yuan Yang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
| | - Shiping Liu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Single-cell Omics, BGI-Shenzhen, Shenzhen, 518100, China
| | - Longqi Liu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
| | - Zhaoqin Wang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Liang Wu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Single-cell Omics, BGI-Shenzhen, Shenzhen, 518100, China
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15
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Single-cell analysis identifies dynamic gene expression networks that govern B cell development and transformation. Nat Commun 2021; 12:6843. [PMID: 34824268 PMCID: PMC8617197 DOI: 10.1038/s41467-021-27232-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022] Open
Abstract
Integration of external signals and B-lymphoid transcription factor activities organise B cell lineage commitment through alternating cycles of proliferation and differentiation, producing a diverse repertoire of mature B cells. We use single-cell transcriptomics/proteomics to identify differentially expressed gene networks across B cell development and correlate these networks with subtypes of B cell leukemia. Here we show unique transcriptional signatures that refine the pre-B cell expansion stages into pre-BCR-dependent and pre-BCR-independent proliferative phases. These changes correlate with reciprocal changes in expression of the transcription factor EBF1 and the RNA binding protein YBX3, that are defining features of the pre-BCR-dependent stage. Using pseudotime analysis, we further characterize the expression kinetics of different biological modalities across B cell development, including transcription factors, cytokines, chemokines, and their associated receptors. Our findings demonstrate the underlying heterogeneity of developing B cells and characterise developmental nodes linked to B cell transformation.
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16
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Tan S, Guo X, Li M, Wang T, Wang Z, Li C, Wu Z, Li N, Gao L, Liang X, Ma C. Transcription factor Zhx2 restricts NK cell maturation and suppresses their antitumor immunity. J Exp Med 2021; 218:e20210009. [PMID: 34279541 PMCID: PMC8292132 DOI: 10.1084/jem.20210009] [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: 01/02/2021] [Revised: 05/05/2021] [Accepted: 06/17/2021] [Indexed: 02/03/2023] Open
Abstract
The maturation and functional competence of natural killer (NK) cells is a tightly controlled process that relies on transcription factors (TFs). Here, we identify transcriptional repressor zinc fingers and homeoboxes 2 (Zhx2) as a novel regulator that restricts NK cell maturation and function. Mice with Zhx2 conditional deletion in NK cells (Zhx2Δ/Δ) showed accumulation of matured NK cells. Loss of Zhx2 enhanced NK cell survival and NK cell response to IL-15. Transcriptomic analysis revealed Zeb2, a key TF in NK cell terminal maturation, as a direct downstream target of Zhx2. Therapeutically, transfer of Zhx2-deficient NK cells resulted in inhibition of tumor growth and metastasis in different murine models. Our findings collectively unmask a previously unrecognized role of Zhx2 as a novel negative regulator in NK cell maturation and highlight its therapeutic potential as a promising strategy to enhance NK cell-mediated tumor surveillance.
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Affiliation(s)
- Siyu Tan
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Xiaowei Guo
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Mengzhen Li
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Tixiao Wang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Zehua Wang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Chunyang Li
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Histology and Embryology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Zhuanchang Wu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
| | - Nailin Li
- Clinical Pharmacology Group, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
| | - Lifen Gao
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Jinan, Shandong, China
| | - Xiaohong Liang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Jinan, Shandong, China
| | - Chunhong Ma
- Key Laboratory for Experimental Teratology of the Ministry of Education, Key Laboratory of Infection and Immunity of Shandong Province, and Department of Immunology, School of Basic Medical Sciences, Cheeloo Medical College of Shandong University, Jinan, Shandong, China
- Advanced Medical Research Institute, Shandong University, Jinan, Shandong, China
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Jinan, Shandong, China
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17
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Pilat N, Lefsihane K, Brouard S, Kotsch K, Falk C, Steiner R, Thaunat O, Fusil F, Montserrat N, Amarelli C, Casiraghi F. T- and B-cell therapy in solid organ transplantation: current evidence and future expectations. Transpl Int 2021; 34:1594-1606. [PMID: 34448274 DOI: 10.1111/tri.13972] [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: 07/01/2021] [Accepted: 07/08/2021] [Indexed: 01/13/2023]
Abstract
Cell therapy has emerged as an attractive therapeutic option in organ transplantation. During the last decade, the therapeutic potency of Treg immunotherapy has been shown in various preclinical animal models and safety was demonstrated in first clinical trials. However, there are still critical open questions regarding specificity, survival, and migration to the target tissue so the best Treg population for infusion into patients is still under debate. Recent advances in CAR technology hold the promise for Treg-functional superiority. Another exciting strategy is the generation of B-cell antibody receptor (BAR) Treg/cytotoxic T cells to specifically regulate or deplete alloreactive memory B cells. Finally, B cells are also capable of immune regulation, making them promising candidates for immunomodulatory therapeutic strategies. This article summarizes available literature on cell-based innovative therapeutic approaches aiming at modulating alloimmune response for transplantation. Crucial areas of investigation that need a joined effort of the transplant community for moving the field toward successful achievement of tolerance are highlighted.
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Affiliation(s)
- Nina Pilat
- Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Katia Lefsihane
- International Center of Infectiology Research (CIRI), French Institute of Health and Medical Research (INSERM) Unit 1111, Claude Bernard University Lyon I, National Center for Scientific Research (CNRS) Mixed University Unit (UMR) 5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Sophie Brouard
- CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Université de Nantes, Nantes, France
| | - Katja Kotsch
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Department for General and Visceral Surgery, Berlin Institute of Health, Berlin, Germany
| | - Christine Falk
- Institute of Transplant Immunology, Hannover Medical School, MHH, Hannover, Germany
| | - Romy Steiner
- Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Olivier Thaunat
- International Center of Infectiology Research (CIRI), French Institute of Health and Medical Research (INSERM) Unit 1111, Claude Bernard University Lyon I, National Center for Scientific Research (CNRS) Mixed University Unit (UMR) 5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France.,Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France.,Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
| | - Floriane Fusil
- International Center of Infectiology Research (CIRI), French Institute of Health and Medical Research (INSERM) Unit 1111, Claude Bernard University Lyon I, National Center for Scientific Research (CNRS) Mixed University Unit (UMR) 5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Nuria Montserrat
- Pluripotency for Organ Regeneration, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Cristiano Amarelli
- Department of Cardiac Surgery and Transplants Monaldi, A.O. dei Colli, Naples, Italy
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18
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Haas OA. Somatic Sex: On the Origin of Neoplasms With Chromosome Counts in Uneven Ploidy Ranges. Front Cell Dev Biol 2021; 9:631946. [PMID: 34422788 PMCID: PMC8373647 DOI: 10.3389/fcell.2021.631946] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 06/22/2021] [Indexed: 01/09/2023] Open
Abstract
Stable aneuploid genomes with nonrandom numerical changes in uneven ploidy ranges define distinct subsets of hematologic malignancies and solid tumors. The idea put forward herein suggests that they emerge from interactions between diploid mitotic and G0/G1 cells, which can in a single step produce all combinations of mono-, di-, tri-, tetra- and pentasomic paternal/maternal homologue configurations that define such genomes. A nanotube-mediated influx of interphase cell cytoplasm into mitotic cells would thus be responsible for the critical nondisjunction and segregation errors by physically impeding the proper formation of the cell division machinery, whereas only a complete cell fusion can simultaneously generate pentasomies, uniparental trisomies as well as biclonal hypo- and hyperdiploid cell populations. The term "somatic sex" was devised to accentuate the similarities between germ cell and somatic cell fusions. A somatic cell fusion, in particular, recapitulates many processes that are also instrumental in the formation of an abnormal zygote that involves a diploid oocyte and a haploid sperm, which then may further develop into a digynic triploid embryo. Despite their somehow deceptive differences and consequences, the resemblance of these two routes may go far beyond of what has hitherto been appreciated. Based on the arguments put forward herein, I propose that embryonic malignancies of mesenchymal origin with these particular types of aneuploidies can thus be viewed as the kind of flawed somatic equivalent of a digynic triploid embryo.
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Affiliation(s)
- Oskar A Haas
- St. Anna Children's Cancer Research Institute, Vienna, Austria
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19
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Dietary carbohydrate, particularly glucose, drives B cell lymphopoiesis and function. iScience 2021; 24:102835. [PMID: 34381967 PMCID: PMC8333167 DOI: 10.1016/j.isci.2021.102835] [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: 11/16/2020] [Revised: 06/15/2021] [Accepted: 07/07/2021] [Indexed: 01/14/2023] Open
Abstract
While diet modulates immunity, its impact on B cell ontogeny remains unclear. Using mixture modeling, a large-scale isocaloric dietary cohort mouse study identified carbohydrate as a major driver of B cell development and function. Increasing dietary carbohydrate increased B cell proportions in spleen, mesenteric lymph node and Peyer's patches, and increased antigen-specific immunoglobulin G production after immunization. This was linked to increased B lymphopoiesis in the bone marrow. Glucose promoted early B lymphopoiesis and higher total B lymphocyte numbers than fructose. It drove B cell development through glycolysis and oxidative phosphorylation, independently of fatty acid oxidation in vitro and reduced B cell apoptosis in early development via mTOR activation, independently of interleukin-7. Ours is the first comprehensive study showing the impact of macronutrients on B cell development and function. It shows the quantitative and qualitative interplay between dietary carbohydrate and B cells and argues for dietary modulation in B cell-targeting strategies.
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20
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Le Coz C, Nguyen DN, Su C, Nolan BE, Albrecht AV, Xhani S, Sun D, Demaree B, Pillarisetti P, Khanna C, Wright F, Chen PA, Yoon S, Stiegler AL, Maurer K, Garifallou JP, Rymaszewski A, Kroft SH, Olson TS, Seif AE, Wertheim G, Grant SFA, Vo LT, Puck JM, Sullivan KE, Routes JM, Zakharova V, Shcherbina A, Mukhina A, Rudy NL, Hurst ACE, Atkinson TP, Boggon TJ, Hakonarson H, Abate AR, Hajjar J, Nicholas SK, Lupski JR, Verbsky J, Chinn IK, Gonzalez MV, Wells AD, Marson A, Poon GMK, Romberg N. Constrained chromatin accessibility in PU.1-mutated agammaglobulinemia patients. J Exp Med 2021; 218:212070. [PMID: 33951726 PMCID: PMC8105723 DOI: 10.1084/jem.20201750] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 02/09/2021] [Accepted: 03/16/2021] [Indexed: 12/19/2022] Open
Abstract
The pioneer transcription factor (TF) PU.1 controls hematopoietic cell fate by decompacting stem cell heterochromatin and allowing nonpioneer TFs to enter otherwise inaccessible genomic sites. PU.1 deficiency fatally arrests lymphopoiesis and myelopoiesis in mice, but human congenital PU.1 disorders have not previously been described. We studied six unrelated agammaglobulinemic patients, each harboring a heterozygous mutation (four de novo, two unphased) of SPI1, the gene encoding PU.1. Affected patients lacked circulating B cells and possessed few conventional dendritic cells. Introducing disease-similar SPI1 mutations into human hematopoietic stem and progenitor cells impaired early in vitro B cell and myeloid cell differentiation. Patient SPI1 mutations encoded destabilized PU.1 proteins unable to nuclear localize or bind target DNA. In PU.1-haploinsufficient pro–B cell lines, euchromatin was less accessible to nonpioneer TFs critical for B cell development, and gene expression patterns associated with the pro– to pre–B cell transition were undermined. Our findings molecularly describe a novel form of agammaglobulinemia and underscore PU.1’s critical, dose-dependent role as a hematopoietic euchromatin gatekeeper.
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Affiliation(s)
- Carole Le Coz
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - David N Nguyen
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA.,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA.,Diabetes Center, University of California San Francisco, San Francisco, CA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA.,Gladstone-University of California San Francisco Institute of Genomic Immunology, San Francisco, CA
| | - Chun Su
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA.,Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Brian E Nolan
- Division of Rheumatology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL.,Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Amanda V Albrecht
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA
| | - Suela Xhani
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA
| | - Di Sun
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Benjamin Demaree
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA.,University of California Berkeley-University of California San Francisco Graduate Program in Bioengineering, University of California, San Francisco, CA
| | - Piyush Pillarisetti
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Caroline Khanna
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Francis Wright
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA.,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA
| | - Peixin Amy Chen
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA.,Diabetes Center, University of California San Francisco, San Francisco, CA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA.,Gladstone-University of California San Francisco Institute of Genomic Immunology, San Francisco, CA
| | - Samuel Yoon
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Amy L Stiegler
- Departments of Pharmacology, Yale University, New Haven, CT
| | - Kelly Maurer
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - James P Garifallou
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Amy Rymaszewski
- Division of Allergy and Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Steven H Kroft
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI
| | - Timothy S Olson
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA
| | - Alix E Seif
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA
| | - Gerald Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Struan F A Grant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA.,Division of Diabetes and Endocrinology, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Linda T Vo
- Diabetes Center, University of California San Francisco, San Francisco, CA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA
| | - Jennifer M Puck
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, CA.,University of California San Francsico Institute for Human Genetics and Smith Cardiovascular Research Institute, University of California, San Francisco, CA.,UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Kathleen E Sullivan
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - John M Routes
- Division of Allergy and Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Viktoria Zakharova
- Laboratory of Molecular Biology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anna Shcherbina
- Department of Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anna Mukhina
- Department of Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Natasha L Rudy
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL
| | - T Prescott Atkinson
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL
| | - Titus J Boggon
- Departments of Pharmacology, Yale University, New Haven, CT.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA.,University of California Berkeley-University of California San Francisco Graduate Program in Bioengineering, University of California, San Francisco, CA.,Chan Zuckerberg Biohub, San Francisco, CA
| | - Joud Hajjar
- William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX.,Department of Immunology, Allergy and Rheumatology, Baylor College of Medicine, Houston, TX
| | - Sarah K Nicholas
- William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX.,Department of Immunology, Allergy and Rheumatology, Baylor College of Medicine, Houston, TX
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Texas Children's Hospital, Houston, TX.,Baylor-Hopkins Center for Mendelian Genomics, Houston, TX
| | - James Verbsky
- Division of Allergy and Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Ivan K Chinn
- William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX.,Department of Immunology, Allergy and Rheumatology, Baylor College of Medicine, Houston, TX
| | - Michael V Gonzalez
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Alex Marson
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA.,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA.,Diabetes Center, University of California San Francisco, San Francisco, CA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA.,Gladstone-University of California San Francisco Institute of Genomic Immunology, San Francisco, CA.,Chan Zuckerberg Biohub, San Francisco, CA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA
| | - Gregory M K Poon
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA
| | - Neil Romberg
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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21
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Xie Y, Luo X, He H, Pan T, He Y. Identification of an individualized RNA binding protein-based prognostic signature for diffuse large B-cell lymphoma. Cancer Med 2021; 10:2703-2713. [PMID: 33749163 PMCID: PMC8026940 DOI: 10.1002/cam4.3859] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/19/2021] [Accepted: 03/08/2021] [Indexed: 12/19/2022] Open
Abstract
RNA binding proteins (RBPs) are increasingly appreciated as being essential for normal hematopoiesis and have a critical role in the progression of hematological malignancies. However, their functional consequences and clinical significance in diffuse large B‐cell lymphoma (DLBCL) remain unknown. Here, we conducted a systematic analysis to identify RBP‐related genes affecting DLBCL prognosis based on the Gene Expression Omnibus database. By univariate and multivariate Cox proportional hazards regression (CPHR) methods, six RBPs‐related genes (CMSS1, MAEL, THOC5, PSIP1, SNIP1, and ZCCHC7) were identified closely related to the overall survival (OS) of DLBCL patients. The RBPs signature could efficiently distinguished low‐risk from high‐risk patients and could serve as an independent and reliable factor for predicting OS. Moreover, Gene Set Enrichment Analysis revealed 17 significantly enriched pathways between high‐ versus low‐risk group, including the regulation of autophagy, chronic myeloid leukemia, NOTCH signaling pathway, and B cell receptor signaling pathway. Then we developed an RBP‐based nomogram combining other clinical risk factors. The receiver operating characteristic curve analysis demonstrated high prognostic predictive efficiency of this model with the area under the curve values were 0.820 and 0.780, respectively, in the primary set and entire set. In summary, our RBP‐based model could be a novel prognostic predictor and had the potential for developing treatment targets for DLBCL.
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Affiliation(s)
- Yongzhi Xie
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ximei Luo
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Haiqing He
- Department of Urology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Tao Pan
- Department of Lymphoma & Hematology, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Yizi He
- Department of Lymphoma & Hematology, The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, China
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22
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Mikhailova E, Semchenkova A, Illarionova O, Kashpor S, Brilliantova V, Zakharova E, Zerkalenkova E, Zangrando A, Bocharova N, Shelikhova L, Diakonova Y, Zhogov V, Khismatullina R, Molostova O, Buldini B, Raykina E, Larin S, Olshanskaya Y, Miakova N, Novichkova G, Maschan M, Popov AM. Relative expansion of CD19-negative very-early normal B-cell precursors in children with acute lymphoblastic leukaemia after CD19 targeting by blinatumomab and CAR-T cell therapy: implications for flow cytometric detection of minimal residual disease. Br J Haematol 2021; 193:602-612. [PMID: 33715150 DOI: 10.1111/bjh.17382] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/05/2021] [Indexed: 12/13/2022]
Abstract
CD19-directed treatment in B-cell precursor acute lymphoblastic leukaemia (BCP-ALL) frequently leads to the downmodulation of targeted antigens. As multicolour flow cytometry (MFC) application for minimal/measurable residual disease (MRD) assessment in BCP-ALL is based on B-cell compartment study, CD19 loss could hamper MFC-MRD monitoring after blinatumomab or chimeric antigen receptor T-cell (CAR-T) therapy. The use of other antigens (CD22, CD10, CD79a, etc.) as B-lineage gating markers allows the identification of CD19-negative leukaemia, but it could also lead to misidentification of normal very-early CD19-negative BCPs as tumour blasts. In the current study, we summarized the results of the investigation of CD19-negative normal BCPs in 106 children with BCP-ALL who underwent CD19 targeting (blinatumomab, n = 64; CAR-T, n = 25; or both, n = 17). It was found that normal CD19-negative BCPs could be found in bone marrow after CD19-directed treatment more frequently than in healthy donors and children with BCP-ALL during chemotherapy or after stem cell transplantation. Analysis of the antigen expression profile revealed that normal CD19-negative BCPs could be mixed up with residual leukaemic blasts, even in bioinformatic analyses of MFC data. The results of our study should help to investigate MFC-MRD more accurately in patients who have undergone CD19-targeted therapy, even in cases with normal CD19-negative BCP expansion.
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Affiliation(s)
- Ekaterina Mikhailova
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Alexandra Semchenkova
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Olga Illarionova
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Svetlana Kashpor
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Varvara Brilliantova
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Elena Zakharova
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Elena Zerkalenkova
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Andrea Zangrando
- Maternal and Child Health Department, University of Padua, Padua, Italy.,Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padua, Italy
| | | | - Larisa Shelikhova
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Yulia Diakonova
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Vladimir Zhogov
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Rimma Khismatullina
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Olga Molostova
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Barbara Buldini
- Maternal and Child Health Department, University of Padua, Padua, Italy
| | - Elena Raykina
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Sergey Larin
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Yulia Olshanskaya
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Natalia Miakova
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Galina Novichkova
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Michael Maschan
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Alexander M Popov
- National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
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23
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Jackson TR, Ling RE, Roy A. The Origin of B-cells: Human Fetal B Cell Development and Implications for the Pathogenesis of Childhood Acute Lymphoblastic Leukemia. Front Immunol 2021; 12:637975. [PMID: 33679795 PMCID: PMC7928347 DOI: 10.3389/fimmu.2021.637975] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/28/2021] [Indexed: 12/27/2022] Open
Abstract
Human B-lymphopoiesis is a dynamic life-long process that starts in utero by around six post-conception weeks. A detailed understanding of human fetal B-lymphopoiesis and how it changes in postnatal life is vital for building a complete picture of normal B-lymphoid development through ontogeny, and its relevance in disease. B-cell acute lymphoblastic leukemia (B-ALL) is one of the most common cancers in children, with many of the leukemia-initiating events originating in utero. It is likely that the biology of B-ALL, including leukemia initiation, maintenance and progression depends on the developmental stage and type of B-lymphoid cell in which it originates. This is particularly important for early life leukemias, where specific characteristics of fetal B-cells might be key to determining how the disease behaves, including response to treatment. These cellular, molecular and/or epigenetic features are likely to change with age in a cell intrinsic and/or microenvironment directed manner. Most of our understanding of fetal B-lymphopoiesis has been based on murine data, but many recent studies have focussed on characterizing human fetal B-cell development, including functional and molecular assays at a single cell level. In this mini-review we will give a short overview of the recent advances in the understanding of human fetal B-lymphopoiesis, including its relevance to infant/childhood leukemia, and highlight future questions in the field.
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Affiliation(s)
- Thomas R Jackson
- Department of Paediatrics and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Rebecca E Ling
- Department of Paediatrics and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Anindita Roy
- Department of Paediatrics and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, United Kingdom
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24
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Garis M, Garrett-Sinha LA. Notch Signaling in B Cell Immune Responses. Front Immunol 2021; 11:609324. [PMID: 33613531 PMCID: PMC7892449 DOI: 10.3389/fimmu.2020.609324] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/23/2020] [Indexed: 12/22/2022] Open
Abstract
The Notch signaling pathway is highly evolutionarily conserved, dictating cell fate decisions and influencing the survival and growth of progenitor cells that give rise to the cells of the immune system. The roles of Notch signaling in hematopoietic stem cell maintenance and in specification of T lineage cells have been well-described. Notch signaling also plays important roles in B cells. In particular, it is required for specification of marginal zone type B cells, but Notch signaling is also important in other stages of B cell development and activation. This review will focus on established and new roles of Notch signaling during B lymphocyte lineage commitment and describe the function of Notch within mature B cells involved in immune responses.
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Affiliation(s)
- Matthew Garis
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, United States
| | - Lee Ann Garrett-Sinha
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, United States
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25
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Dubois F, Gaignerie A, Flippe L, Heslan JM, Tesson L, Chesneau M, Haspot F, Conchon S, David L, Brouard S. Toward a better definition of hematopoietic progenitors suitable for B cell differentiation. PLoS One 2020; 15:e0243769. [PMID: 33320872 PMCID: PMC7737978 DOI: 10.1371/journal.pone.0243769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/29/2020] [Indexed: 01/10/2023] Open
Abstract
The success of inducing human pluripotent stem cells (hIPSC) offers new opportunities for cell-based therapy. Since B cells exert roles as effector and as regulator of immune responses in different clinical settings, we were interested in generating B cells from hIPSC. We differentiated human embryonic stem cells (hESC) and hIPSC into B cells onto OP9 and MS-5 stromal cells successively. We overcame issues in generating CD34+CD43+ hematopoietic progenitors with appropriate cytokine conditions and emphasized the difficulties to generate proper hematopoietic progenitors. We highlight CD31intCD45int phenotype as a possible marker of hematopoietic progenitors suitable for B cell differentiation. Defining precisely proper lymphoid progenitors will improve the study of their lineage commitment and the signals needed during the in vitro process.
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Affiliation(s)
- Florian Dubois
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Anne Gaignerie
- Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, FED 4203, Inserm UMS 016, CNRS UMS 3556, Nantes, France
| | - Léa Flippe
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Jean-Marie Heslan
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
- Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, FED 4203, Inserm UMS 016, CNRS UMS 3556, Nantes, France
| | - Laurent Tesson
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Mélanie Chesneau
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Fabienne Haspot
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Sophie Conchon
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Laurent David
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
- Université de Nantes, CHU Nantes, Inserm, CNRS, SFR Santé, FED 4203, Inserm UMS 016, CNRS UMS 3556, Nantes, France
| | - Sophie Brouard
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
- * E-mail:
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26
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Wang J, Xu Y, Chen Z, Liang J, Lin Z, Liang H, Xu Y, Wu Q, Guo X, Nie J, Lu B, Huang B, Xian H, Wang X, Wu Q, Zeng J, Chai C, Zhang M, Lin Y, Zhang L, Zhao S, Tong Y, Zeng L, Gu X, Chen ZG, Yi S, Zhang T, Delfouneso D, Zhang Y, Nutt SL, Lew AM, Lu L, Bai F, Xia H, Wen Z, Zhang Y. Liver Immune Profiling Reveals Pathogenesis and Therapeutics for Biliary Atresia. Cell 2020; 183:1867-1883.e26. [PMID: 33248023 DOI: 10.1016/j.cell.2020.10.048] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 09/01/2020] [Accepted: 10/28/2020] [Indexed: 02/06/2023]
Abstract
Biliary atresia (BA) is a severe cholangiopathy that leads to liver failure in infants, but its pathogenesis remains to be fully characterized. By single-cell RNA profiling, we observed macrophage hypo-inflammation, Kupffer cell scavenger function defects, cytotoxic T cell expansion, and deficiency of CX3CR1+effector T and natural killer (NK) cells in infants with BA. More importantly, we discovered that hepatic B cell lymphopoiesis did not cease after birth and that tolerance defects contributed to immunoglobulin G (IgG)-autoantibody accumulation in BA. In a rhesus-rotavirus induced BA model, depleting B cells or blocking antigen presentation ameliorated liver damage. In a pilot clinical study, we demonstrated that rituximab was effective in depleting hepatic B cells and restoring the functions of macrophages, Kupffer cells, and T cells to levels comparable to those of control subjects. In summary, our comprehensive immune profiling in infants with BA had educed that B-cell-modifying therapies may alleviate liver pathology.
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Affiliation(s)
- Jun Wang
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Yanhui Xu
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Zhanghua Chen
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics (IGS), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jiankun Liang
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Zefeng Lin
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Huiying Liang
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Yiping Xu
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Qi Wu
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Xuanjie Guo
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Junli Nie
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Bingtai Lu
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Bing Huang
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Huifang Xian
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Xiaohui Wang
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hongkong; Chongqing International Institute for Immunology, Hongkong, China
| | - Qiang Wu
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Jixiao Zeng
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Chengwei Chai
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Meixue Zhang
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Yuzhen Lin
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Li Zhang
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Shanmeizi Zhao
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Yanlu Tong
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Liang Zeng
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Xiaoqiong Gu
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Zhuang-Gui Chen
- Department of Pediatrics and Hepatic Surgery, Liver Transplant Center, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510630, China
| | - Shuhong Yi
- Department of Pediatrics and Hepatic Surgery, Liver Transplant Center, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510630, China
| | - Tong Zhang
- Department of Pediatrics and Hepatic Surgery, Liver Transplant Center, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510630, China
| | - David Delfouneso
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Yan Zhang
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China
| | - Stephen L Nutt
- Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC 3052, Australia
| | - Andrew M Lew
- Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC 3052, Australia
| | - Liwei Lu
- Department of Pathology and Shenzhen Institute of Research and Innovation, The University of Hongkong; Chongqing International Institute for Immunology, Hongkong, China
| | - Fan Bai
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics (IGS), School of Life Sciences, Peking University, Beijing, 100871, China; Center for Translational Cancer Research, First Hospital, Peking University, Beijing 100871, China.
| | - Huimin Xia
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China.
| | - Zhe Wen
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China.
| | - Yuxia Zhang
- Department of Pediatric Surgery, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Children's Medical Research Center, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, State Key Laboratory of Respiratory Diseases, Guangzhou Medical University, Guangzhou, 510623, Guangdong, China; The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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27
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Karagiannis P, Alsdorf W, Tallarek AC, Blohm ME, Oelrich J, Waizenegger JS, Wolschke C, Hecher K, Singer D, Bokemeyer C, Fiedler W. Treatment of refractory acute myeloid leukaemia during pregnancy with venetoclax, high-dose cytarabine and mitoxantrone. Br J Haematol 2020; 192:e60-e63. [PMID: 33222152 DOI: 10.1111/bjh.17220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Panagiotis Karagiannis
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section of Pneumology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Winfried Alsdorf
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section of Pneumology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Ann-Christin Tallarek
- Department of Obstetrics and Fetal Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Martin E Blohm
- Division of Neonatology and Paediatric Intensive Care, University Children's Hospital, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Jennyfer Oelrich
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section of Pneumology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Jonas S Waizenegger
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section of Pneumology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Christine Wolschke
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section of Pneumology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Kurt Hecher
- Department of Obstetrics and Fetal Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Dominique Singer
- Division of Neonatology and Paediatric Intensive Care, University Children's Hospital, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Carsten Bokemeyer
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section of Pneumology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Walter Fiedler
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section of Pneumology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
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28
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Mehtonen J, Teppo S, Lahnalampi M, Kokko A, Kaukonen R, Oksa L, Bouvy-Liivrand M, Malyukova A, Mäkinen A, Laukkanen S, Mäkinen PI, Rounioja S, Ruusuvuori P, Sangfelt O, Lund R, Lönnberg T, Lohi O, Heinäniemi M. Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities. Genome Med 2020; 12:99. [PMID: 33218352 PMCID: PMC7679990 DOI: 10.1186/s13073-020-00799-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Tight regulatory loops orchestrate commitment to B cell fate within bone marrow. Genetic lesions in this gene regulatory network underlie the emergence of the most common childhood cancer, acute lymphoblastic leukemia (ALL). The initial genetic hits, including the common translocation that fuses ETV6 and RUNX1 genes, lead to arrested cell differentiation. Here, we aimed to characterize transcription factor activities along the B-lineage differentiation trajectory as a reference to characterize the aberrant cell states present in leukemic bone marrow, and to identify those transcription factors that maintain cancer-specific cell states for more precise therapeutic intervention. METHODS We compared normal B-lineage differentiation and in vivo leukemic cell states using single cell RNA-sequencing (scRNA-seq) and several complementary genomics profiles. Based on statistical tools for scRNA-seq, we benchmarked a workflow to resolve transcription factor activities and gene expression distribution changes in healthy bone marrow lymphoid cell states. We compared these to ALL bone marrow at diagnosis and in vivo during chemotherapy, focusing on leukemias carrying the ETV6-RUNX1 fusion. RESULTS We show that lymphoid cell transcription factor activities uncovered from bone marrow scRNA-seq have high correspondence with independent ATAC- and ChIP-seq data. Using this comprehensive reference for regulatory factors coordinating B-lineage differentiation, our analysis of ETV6-RUNX1-positive ALL cases revealed elevated activity of multiple ETS-transcription factors in leukemic cells states, including the leukemia genome-wide association study hit ELK3. The accompanying gene expression changes associated with natural killer cell inactivation and depletion in the leukemic immune microenvironment. Moreover, our results suggest that the abundance of G1 cell cycle state at diagnosis and lack of differentiation-associated regulatory network changes during induction chemotherapy represent features of chemoresistance. To target the leukemic regulatory program and thereby overcome treatment resistance, we show that inhibition of ETS-transcription factors reduced cell viability and resolved pathways contributing to this using scRNA-seq. CONCLUSIONS Our data provide a detailed picture of the transcription factor activities characterizing both normal B-lineage differentiation and those acquired in leukemic bone marrow and provide a rational basis for new treatment strategies targeting the immune microenvironment and the active regulatory network in leukemia.
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Affiliation(s)
- Juha Mehtonen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 1, FI-70211, Kuopio, Finland
| | - Susanna Teppo
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
| | - Mari Lahnalampi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 1, FI-70211, Kuopio, Finland
| | - Aleksi Kokko
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 1, FI-70211, Kuopio, Finland
| | - Riina Kaukonen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | - Laura Oksa
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
| | - Maria Bouvy-Liivrand
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 1, FI-70211, Kuopio, Finland
| | - Alena Malyukova
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Artturi Mäkinen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
| | - Saara Laukkanen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
| | - Petri I Mäkinen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Yliopistonranta 1, FI-70211, Kuopio, Finland
| | | | - Pekka Ruusuvuori
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
| | - Olle Sangfelt
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Riikka Lund
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | - Tapio Lönnberg
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | - Olli Lohi
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, FI-33014, Tampere, Finland
- Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Yliopistonranta 1, FI-70211, Kuopio, Finland.
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29
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Peng Y, Guo F, Liao S, Liao H, Xiao H, Yang L, Liu H, Pan Q. Altered frequency of peripheral B-cell subsets and their correlation with disease activity in patients with systemic lupus erythematosus: A comprehensive analysis. J Cell Mol Med 2020; 24:12044-12053. [PMID: 32918534 PMCID: PMC7579696 DOI: 10.1111/jcmm.15836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/12/2020] [Accepted: 08/17/2020] [Indexed: 02/05/2023] Open
Abstract
Alternations of peripheral B-cell subsets are closely related to disease activity in systemic lupus erythematosus (SLE) and may also predict the relapse of SLE. In this study, we aimed to comprehensively analyse the frequency of peripheral B-cell subsets, and their correlation with disease activity in patients with SLE. The results showed that for B-cell subsets in the antigen-independent differentiation stage, the frequency of the peripheral hematopoietic stem cell (HSC) subset in all patients with SLE was significantly higher than that of control patients. Surprisingly, several significant correlations were noted in newly diagnosed patients with SLE including a positive correlation in the frequency of the common lymphoid progenitor cell (CLP) with cholesterol serum levels. For B-cell subsets in the antigen-dependent differentiation stage, the frequency of naïve B-cell (N-B) subsets in all patients with SLE was significantly higher than that in the control patients. Moreover, the frequency of plasmablasts positively correlated with the SLEDAI score in the newly diagnosed patients. For memory B-cell (M-B) subtypes in the antigen-dependent differentiation stage, the frequency of the class-switched memory B-cell (CSM-B) subsets was positively correlated with the serum levels of complement C3. Notably, the frequency of the CSM-B subset also negatively correlated with the SLEDAI score, whereas the non-class-switched memory B-cell (NSM-B) subset was positively correlated with the serum levels of haemoglobin. Collectively, these findings may contribute to a better understanding of the role played by different B-cell subsets in the pathogenesis of SLE.
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Affiliation(s)
- Yanxia Peng
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang CityInstitute of NephrologyAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
- Central Laboratory and Department of NeurologyShunde HospitalSouthern Medical University (The First People’s Hospital of Shunde Foshan)FoshanChina
| | - Fengbiao Guo
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang CityInstitute of NephrologyAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
- Department of Histology and EmbryologyShantou University Medical CollegeShantouChina
| | - Shuzhen Liao
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang CityInstitute of NephrologyAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Huanjin Liao
- Department of Laboratory MedicineShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Haiyan Xiao
- Department of Cellular Biology and AnatomyAugusta UniversityAugustaGAUSA
| | - Lawei Yang
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang CityInstitute of NephrologyAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Hua‐feng Liu
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang CityInstitute of NephrologyAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Qingjun Pan
- Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang CityInstitute of NephrologyAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
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30
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Transcriptome Profiling across Five Tissues of Giant Panda. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3852586. [PMID: 32851066 PMCID: PMC7436357 DOI: 10.1155/2020/3852586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/03/2020] [Accepted: 06/01/2020] [Indexed: 11/18/2022]
Abstract
Gene differential expression studies can serve to explore and understand the laws and characteristics of animal life activities, and the difference in gene expression between different animal tissues has been well demonstrated and studied. However, for the world-famous rare and protected species giant panda (Ailuropoda melanoleuca), only the transcriptome of the blood and spleen has been reported separately. Here, in order to explore the transcriptome differences between the different tissues of the giant panda, transcriptome profiles of the heart, liver, spleen, lung, and kidney from five captive giant pandas were constructed with Illumina HiSeq 2500 platform. The comparative analysis of the intertissue gene expression patterns was carried out based on the generated RNA sequencing datasets. Analyses of Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network were performed according to the identified differentially expressed genes (DEGs). We generated 194.52 GB clean base data from twenty-five sequencing libraries and identified 18,701 genes, including 3492 novel genes. With corrected p value <0.05 and |log2FoldChange| >2, we finally obtained 921, 553, 574, 457, and 638 tissue-specific DEGs in the heart, liver, spleen, lung, and kidney, respectively. In addition, we identified TTN, CAV3, LDB3, TRDN, and ACTN2 in the heart; FGA, AHSG, and SERPINC1 in the liver; CD19, CD79B, and IL21R in the spleen; NKX2-4 and SFTPB in the lung; GC and HRG in the kidney as hub genes in the PPI network. The results of the analyses showed a similar gene expression pattern between the spleen and lung. This study provided for the first time the heart, liver, lung, and kidney's transcriptome resources of the giant panda, and it provided a valuable resource for further genetic research or other potential research.
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31
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Cascino K, Roederer M, Liechti T. OMIP-068: High-Dimensional Characterization of Global and Antigen-Specific B Cells in Chronic Infection. Cytometry A 2020; 97:1037-1043. [PMID: 32741082 DOI: 10.1002/cyto.a.24204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/01/2020] [Accepted: 07/22/2020] [Indexed: 12/15/2022]
Abstract
This 24-color flow cytometry panel focuses on characterizing antigen-specific B cells and precise delineation of B-cell subsets in chronic infections and is applicable to other chronic diseases such as autoimmunity. The panel was optimized for human cryopreserved peripheral blood mononuclear cells (PBMCs). Markers were chosen to extensively distinguish B-cell lineages (CD19, CD20, CD10, CD38, CD24, IgM, IgD, CD27, CD21, CD43, CD5). Inclusion of antigen-specific probes was of high priority in order to assess hepatitis B virus (HBV) antigen-specific B cells for our purposes. These probes can be readily exchanged for other pathogen-specific probes or additional markers for the panel to be tailored to desired research questions beyond HBV. In addition, we included a comprehensive and unique set of functional markers such as chemokine receptors (CXCR3, CXCR5), co-stimulatory molecule (CD86), Fc receptor (CD32), regulatory molecules (BTLA, CD39), and inhibitory markers associated with chronic infections (PD-1, FcRL5, CD11c, CD22) to enable in-depth analysis of global and antigen-specific B cells during chronic infection. © 2020 International Society for Advancement of Cytometry.
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Affiliation(s)
- Katherine Cascino
- Viral Hepatitis Center, Department of Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, 20892, USA
| | - Thomas Liechti
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, 20892, USA
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32
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Wang C, Sun D, Huang X, Wan C, Li Z, Han Y, Qin Q, Fan J, Qiu X, Xie Y, Meyer CA, Brown M, Tang M, Long H, Liu T, Liu XS. Integrative analyses of single-cell transcriptome and regulome using MAESTRO. Genome Biol 2020; 21:198. [PMID: 32767996 PMCID: PMC7412809 DOI: 10.1186/s13059-020-02116-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO), a comprehensive open-source computational workflow ( http://github.com/liulab-dfci/MAESTRO ) for the integrative analyses of single-cell RNA-seq (scRNA-seq) and ATAC-seq (scATAC-seq) data from multiple platforms. MAESTRO provides functions for pre-processing, alignment, quality control, expression and chromatin accessibility quantification, clustering, differential analysis, and annotation. By modeling gene regulatory potential from chromatin accessibilities at the single-cell level, MAESTRO outperforms the existing methods for integrating the cell clusters between scRNA-seq and scATAC-seq. Furthermore, MAESTRO supports automatic cell-type annotation using predefined cell type marker genes and identifies driver regulators from differential scRNA-seq genes and scATAC-seq peaks.
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Affiliation(s)
- Chenfei Wang
- Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Dongqing Sun
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Xin Huang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Changxin Wan
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Ziyi Li
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Ya Han
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Qian Qin
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Jingyu Fan
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Yingtian Xie
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Clifford A Meyer
- Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Ming Tang
- Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Henry Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Tao Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA.
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
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Savage P. Chemotherapy Curability in Leukemia, Lymphoma, Germ Cell Tumors and Gestational Malignancies: A Reflection of the Unique Physiology of Their Cells of Origin. Front Genet 2020; 11:426. [PMID: 32582272 PMCID: PMC7295948 DOI: 10.3389/fgene.2020.00426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/06/2020] [Indexed: 11/21/2022] Open
Abstract
Cytotoxic DNA damaging chemotherapy brings clinical benefits in the treatment of many metastatic malignancies. However routine curative treatment remains restricted to a small number of malignancies including acute leukemia, high grade lymphoma, germ cell tumors, gestational malignancies and some of the rare childhood cancers. The detailed explanation for this dramatic divergence in outcomes remains to be elucidated. However, we have previously argued that there is a strong correlation between presence of the unique genetic events of immunoglobulin gene variable/diversity/joining (VDJ) recombination, somatic hypermutation (SHM), meiosis, nuclear fusion and gastrulation occurring in cells of origin of these malignancies and their high sensitivity to DNA damaging chemotherapy. In this study we have reviewed some of the basic physiological information relating to the specialized activity and sensitivity to DNA damage mediated apoptosis of normal cells undergoing these processes. In each of unique genetic events there are dramatic changes in apoptotic sensitivity. In VDJ recombination and somatic hypermutation over 95% of the cells involved undergo apoptosis, whilst in meiosis and nuclear fusion there are dramatic short term increases in the apoptotic sensitivity to DNA damage. It is apparent that each of the malignancies arising during these processes retains some of the unique phenotype associated with it. The impact of the physiological differences is most clearly seen in the two non-mutational malignancies. Gestational choriocarcinoma which arises shortly after nuclear fusion is routinely curable with chemotherapy whilst CIMP-positive ependymomas which is not linked to any of the unique genetic events is highly resistant. A similar pattern is found in a pair of malignancies driven by a single driver mutation. Infantile acute lymphoblastic leukemia (ALL) arises in a cell undergoing the early stages of VDJ recombination and has a 40% cure rate in contrast pediatric rhabdoid malignancy which is not linked to a unique genetic event responds very poorly to chemotherapy treatment. The physiological changes occurring in cancer cells at the time of the malignant transformation appear to have a major impact on the subsequent sensitivity to chemotherapy and curability. New therapies that impact on these pathways may be of therapeutic value.
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Affiliation(s)
- Philip Savage
- Department of Oncology, Brighton and Sussex University Hospitals, Brighton, United Kingdom
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34
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Ahmad I, Valverde A, Ahmad F, Naqvi AR. Long Noncoding RNA in Myeloid and Lymphoid Cell Differentiation, Polarization and Function. Cells 2020; 9:cells9020269. [PMID: 31979061 PMCID: PMC7072530 DOI: 10.3390/cells9020269] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNA (lncRNA) are a class of endogenous, non-protein coding RNAs that are increasingly being associated with various cellular functions and diseases. Yet, despite their ubiquity and abundance, only a minute fraction of these molecules has an assigned function. LncRNAs show tissue-, cell-, and developmental stage-specific expression, and are differentially expressed under physiological or pathological conditions. The role of lncRNAs in the lineage commitment of immune cells and shaping immune responses is becoming evident. Myeloid cells and lymphoid cells are two major classes of immune systems that work in concert to initiate and amplify innate and adaptive immunity in vertebrates. In this review, we provide mechanistic roles of lncRNA through which these noncoding RNAs can directly participate in the differentiation, polarization, and activation of myeloid (monocyte, macrophage, and dendritic cells) and lymphoid cells (T cells, B cells, and NK cells). While our knowledge on the role of lncRNA in immune cell differentiation and function has improved in the past decade, further studies are required to unravel the biological role of lncRNAs and identify novel mechanisms of lncRNA functions in immune cells. Harnessing the regulatory potential of lncRNAs can provide novel diagnostic and therapeutic targets in treating immune cell related diseases.
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35
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Camarillo JM, Swaminathan S, Abshiru NA, Sikora JW, Thomas PM, Kelleher NL. Coupling Fluorescence-Activated Cell Sorting and Targeted Analysis of Histone Modification Profiles in Primary Human Leukocytes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2526-2534. [PMID: 31286445 PMCID: PMC6917871 DOI: 10.1007/s13361-019-02255-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 05/17/2019] [Accepted: 05/20/2019] [Indexed: 05/24/2023]
Abstract
Histone posttranslational modifications (PTMs) are essential for regulating chromatin and maintaining gene expression throughout cell differentiation. Despite the deep level of understanding of immunophenotypic differentiation pathways in hematopoietic cells, few studies have investigated global levels of histone PTMs required for differentiation and maintenance of these distinct cell types. Here, we describe an approach to couple fluorescence-activated cell sorting (FACS) with targeted mass spectrometry to define global "epi-proteomic" signatures for primary leukocytes. FACS was used to sort closely and distantly related leukocytes from normal human peripheral blood for quantitation of histone PTMs with a multiple reaction monitoring LC-MS/MS method measuring histone PTMs on histones H3 and H4. We validate cell sorting directly into H2SO4 for immediate histone extraction to decrease time and number of steps after FACS to analyze histone PTMs. Relative histone PTM levels vary in T cells across healthy donors, and the majority of PTMs remain stable up to 2 days following initial blood draw. Large differences in the levels of histone PTMs are observed across the mature lymphoid and myeloid lineages, as well as between different types within the same lineage, though no differences are observed in closely related T cell subtypes. The results show a streamlined approach for quantifying global changes in histone PTMs in cell types separated by FACS that is poised for clinical deployment.
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Affiliation(s)
- Jeannie M Camarillo
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Suchitra Swaminathan
- Department of Medicine, Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Nebiyu A Abshiru
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Jacek W Sikora
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA
| | - Paul M Thomas
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA.
| | - Neil L Kelleher
- Department of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, 2170 Campus Drive, Evanston, IL, 60208, USA.
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36
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Schraven AL, Stannard HJ, Ong OTW, Old JM. Immunogenetics of marsupial B-cells. Mol Immunol 2019; 117:1-11. [PMID: 31726269 DOI: 10.1016/j.molimm.2019.10.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 10/17/2019] [Accepted: 10/30/2019] [Indexed: 11/19/2022]
Abstract
Marsupials and eutherians are mammals that differ in their physiological traits, predominately their reproductive and developmental strategies; eutherians give birth to well-developed young, while marsupials are born highly altricial after a much shorter gestation. These developmental traits also result in differences in the development of the immune system of eutherian and marsupial species. In eutherians, B-cells are the key to humoral immunity as they are found in multiple lymphoid organs and have the unique ability to mediate the production of antigen-specific antibodies in the presence of extracellular pathogens. The development of B-cells in marsupials has been reported and hypothesised to be similar to that of eutherians, except that haematopoiesis occurs in the liver, postpartum, until the bone marrow fully matures. In eutherians, specific genes are linked to specific stages in B-cell development, maturation, and differentiation processes, and have been identified including immunoglobulins (heavy and light chains), cluster of differentiation markers (CD10, 19, 34 and CD79α/β), signal transduction molecules (BTK, Lyn and Syk) and transcriptional regulators (EBF1, E2A, and Pax5). This review aims to discuss the known similarities and differences between marsupial and eutherian B-cells, in regards to their genetic presence, homology, and developmental stages, as well as to highlight the areas requiring further investigation. By enhancing our understanding of the genes that are involved with B-cells in the marsupial lineage, it will, in turn, aid our understanding of the marsupial immune system and support the development of specific immunological reagents for research and wildlife conservation purposes.
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Affiliation(s)
- Andrea L Schraven
- School of Science and Health, Hawkesbury Campus, Western Sydney University, Locked bag 1797, Penrith, NSW 2751, Australia
| | - Hayley J Stannard
- Charles Sturt University, School of Animal and Veterinary Sciences, Wagga Wagga, NSW 2678, Australia
| | - Oselyne T W Ong
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Julie M Old
- School of Science and Health, Hawkesbury Campus, Western Sydney University, Locked bag 1797, Penrith, NSW 2751, Australia.
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37
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Gaffo E, Boldrin E, Dal Molin A, Bresolin S, Bonizzato A, Trentin L, Frasson C, Debatin KM, Meyer LH, Te Kronnie G, Bortoluzzi S. Circular RNA differential expression in blood cell populations and exploration of circRNA deregulation in pediatric acute lymphoblastic leukemia. Sci Rep 2019; 9:14670. [PMID: 31605010 PMCID: PMC6789028 DOI: 10.1038/s41598-019-50864-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/19/2019] [Indexed: 12/21/2022] Open
Abstract
Circular RNAs (circRNAs) are abundantly expressed in the haematopoietic compartment, but knowledge on their diversity among blood cell types is still limited. Nevertheless, emerging data indicate an array of circRNA functions exerted through interactions with other RNAs and proteins, by translation into peptides, and circRNA involvement as regulatory molecules in many biological processes and cancer mechanisms. Interestingly, the role of specific circRNAs in leukemogenesis has been disclosed by a few studies, mostly in acute myeloid leukemia. In this study, circRNA expression in B-cells, T-cells and monocytes of healthy subjects is described, including putative new circRNA genes. Expression comparison considered 6,228 circRNAs and highlighted cell population-specific expression and exon usage patterns. Differential expression has been confirmed by qRT-PCR for circRNAs specific of B-cells (circPAX5, circAFF3, circIL4R, and circSETBP1) or T-cells (circIKZF1, circTNIK, circTXK, and circFBXW7), and for circRNAs from intronic (circBCL2) and intergenic regions that were overexpressed in lymphocytes. Starting from this resource of circRNA expression in mature blood cell populations, targeted examination identified striking and generalized upregulated expression of circPAX5, circPVT1 and circHIPK3 in pediatric B-precursor acute lymphoblastic leukemia, and disclosed circRNAs with variable expression across cytogenetic subtypes.
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Affiliation(s)
- Enrico Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Elena Boldrin
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Anna Dal Molin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Silvia Bresolin
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Annagiulia Bonizzato
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Luca Trentin
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Chiara Frasson
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Klaus-Michael Debatin
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Lueder H Meyer
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm, Germany
| | - Geertruij Te Kronnie
- Department of Women's and Children's Health, University of Padova, Padova, Italy
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Witkowski MT, Lasry A, Carroll WL, Aifantis I. Immune-Based Therapies in Acute Leukemia. Trends Cancer 2019; 5:604-618. [PMID: 31706508 PMCID: PMC6859901 DOI: 10.1016/j.trecan.2019.07.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/24/2019] [Accepted: 07/26/2019] [Indexed: 12/31/2022]
Abstract
Treatment resistance remains a leading cause of acute leukemia-related deaths. Thus, there is an unmet need to develop novel approaches to improve outcome. New immune-based therapies with chimeric antigen receptor (CAR) T cells, bi-specific T cell engagers (BiTEs), and immune checkpoint blockers (ICBs) have emerged as effective treatment options for chemoresistant B cell acute lymphoblastic leukemia (B-ALL) and acute myeloid leukemia (AML). However, many patients show resistance to these immune-based approaches. This review describes crucial lessons learned from immune-based approaches targeting high-risk B-ALL and AML, such as the leukemia-intrinsic (e.g., target antigen loss, tumor heterogeneity) and -extrinsic (e.g., immunosuppressive microenvironment) mechanisms that drive treatment resistance, and discusses alternative approaches to enhance the effectiveness of these immune-based treatment regimens.
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MESH Headings
- Animals
- Antineoplastic Agents, Immunological/pharmacology
- Antineoplastic Agents, Immunological/therapeutic use
- Disease Susceptibility
- Humans
- Immunity
- Immunotherapy/methods
- Immunotherapy, Adoptive
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/therapy
- Molecular Targeted Therapy
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/immunology
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/therapy
- Receptors, Antigen, T-Cell/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Tumor Microenvironment/drug effects
- Tumor Microenvironment/immunology
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Affiliation(s)
- Matthew T Witkowski
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA.
| | - Audrey Lasry
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - William L Carroll
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA; Department of Pediatrics, New York University School of Medicine, New York, NY 10016, USA
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
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39
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Whole transcriptome targeted gene quantification provides new insights on pulmonary sarcomatoid carcinomas. Sci Rep 2019; 9:3536. [PMID: 30837581 PMCID: PMC6401130 DOI: 10.1038/s41598-019-40016-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/22/2019] [Indexed: 02/08/2023] Open
Abstract
Pulmonary sarcomatoid carcinomas (PSC) are a rare group of lung cancer with a median overall survival of 9–12 months. PSC are divided into five histotypes, challenging to diagnose and treat. The identification of PSC biomarkers is warranted, but PSC molecular profile remains to be defined. Herein, a targeted whole transcriptome analysis was performed on 14 PSC samples, evaluated also for the presence of the main oncogene mutations and rearrangements. PSC expression data were compared with transcriptome data of lung adenocarcinomas (LUAD) and squamous cell carcinomas (LUSC) from The Cancer Genome Atlas. Deregulated genes were used for pathway enrichment analysis; the most representative genes were tested by immunohistochemistry (IHC) in an independent cohort (30 PSC, 31 LUAD, 31 LUSC). All PSC cases were investigated for PD-L1 expression. Thirty-eight genes deregulated in PSC were identified, among these IGJ and SLMAP were confirmed by IHC. Moreover, Forkhead box signaling and Fanconi anemia pathways were specifically enriched in PSC. Finally, some PSC harboured alterations in genes targetable by tyrosine kinase inhibitors, as EGFR and MET. We provide a deep molecular characterization of PSC; the identification of specific molecular profiles, besides increasing our knowledge on PSC biology, might suggest new strategies to improve patients management.
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40
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Hart MR, Anderson DJ, Porter CC, Neff T, Levin M, Horwitz MS. Activating PAX gene family paralogs to complement PAX5 leukemia driver mutations. PLoS Genet 2018; 14:e1007642. [PMID: 30216339 PMCID: PMC6157899 DOI: 10.1371/journal.pgen.1007642] [Citation(s) in RCA: 3] [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: 03/05/2018] [Revised: 09/26/2018] [Accepted: 08/17/2018] [Indexed: 12/15/2022] Open
Abstract
PAX5, one of nine members of the mammalian paired box (PAX) family of transcription factors, plays an important role in B cell development. Approximately one-third of individuals with pre-B acute lymphoblastic leukemia (ALL) acquire heterozygous inactivating mutations of PAX5 in malignant cells, and heterozygous germline loss-of-function PAX5 mutations cause autosomal dominant predisposition to ALL. At least in mice, Pax5 is required for pre-B cell maturation, and leukemic remission occurs when Pax5 expression is restored in a Pax5-deficient mouse model of ALL. Together, these observations indicate that PAX5 deficiency reversibly drives leukemogenesis. PAX5 and its two most closely related paralogs, PAX2 and PAX8, which are not mutated in ALL, exhibit overlapping expression and function redundantly during embryonic development. However, PAX5 alone is expressed in lymphocytes, while PAX2 and PAX8 are predominantly specific to kidney and thyroid, respectively. We show that forced expression of PAX2 or PAX8 complements PAX5 loss-of-function mutation in ALL cells as determined by modulation of PAX5 target genes, restoration of immunophenotypic and morphological differentiation, and, ultimately, reduction of replicative potential. Activation of PAX5 paralogs, PAX2 or PAX8, ordinarily silenced in lymphocytes, may therefore represent a novel approach for treating PAX5-deficient ALL. In pursuit of this strategy, we took advantage of the fact that, in kidney, PAX2 is upregulated by extracellular hyperosmolarity. We found that hyperosmolarity, at potentially clinically achievable levels, transcriptionally activates endogenous PAX2 in ALL cells via a mechanism dependent on NFAT5, a transcription factor coordinating response to hyperosmolarity. We also found that hyperosmolarity upregulates residual wild type PAX5 expression in ALL cells and modulates gene expression, including in PAX5-mutant primary ALL cells. These findings specifically demonstrate that osmosensing pathways may represent a new therapeutic target for ALL and more broadly point toward the possibility of using gene paralogs to rescue mutations driving cancer and other diseases.
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Affiliation(s)
- Matthew R. Hart
- Allen Discovery Center and Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Donovan J. Anderson
- Allen Discovery Center and Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Christopher C. Porter
- University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Tobias Neff
- University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Michael Levin
- Allen Discovery Center and Biology Department, Tufts University, Medford, Massachusetts, United States of America
| | - Marshall S. Horwitz
- Allen Discovery Center and Department of Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
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Tanaka Y, Kawazu M, Yasuda T, Tamura M, Hayakawa F, Kojima S, Ueno T, Kiyoi H, Naoe T, Mano H. Transcriptional activities of DUX4 fusions in B-cell acute lymphoblastic leukemia. Haematologica 2018; 103:e522-e526. [PMID: 29773604 DOI: 10.3324/haematol.2017.183152] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Yosuke Tanaka
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo
| | - Masahito Kawazu
- Department of Medical Genomics, Graduate School of Medicine, The University of Tokyo
| | - Takahiko Yasuda
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo.,Division of Biological Information Analysis, Department of Clinical Research Management, Clinical Research Center, National Hospital Organization Nagoya Medical Center, Aichi
| | - Miki Tamura
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo
| | - Fumihiko Hayakawa
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Aichi
| | - Shinya Kojima
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo
| | - Toshihide Ueno
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo
| | - Hitoshi Kiyoi
- Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Aichi
| | - Tomoki Naoe
- National Hospital Organization Nagoya Medical Center, Aichi
| | - Hiroyuki Mano
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo.,National Cancer Center Research Institute, Tokyo, Japan
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42
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Li Z, Li SP, Li RY, Zhu H, Liu X, Guo XL, Mu LL, Cai JJ, Bai F, Chen GQ, Hong DL. Leukaemic alterations of IKZF1 prime stemness and malignancy programs in human lymphocytes. Cell Death Dis 2018; 9:526. [PMID: 29743561 PMCID: PMC5943605 DOI: 10.1038/s41419-018-0600-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 01/12/2023]
Abstract
Somatic cells acquire stem cell-like properties during cancerous transformation; however, mechanisms through which committed cells develop stemness and malignancy remain largely unknown. Here we uncovered upregulated stem cell program in leukaemic lymphoblasts of patients with IKZF1 alterations by analysing the archived gene-expression profiling datasets. We then used a frequent IKZF1 deletion, IK6, as a model via transduction into human primitive haematopoietic cells, followed by xenotransplantation in mice. Immunophenotypically defined stem, pro-B, and immature/mature (IM/M)-B cells were collected from primary recipients for functional assay and transcriptome profiling. Successful reconstitution in secondary recipient mice revealed the stemness of IK6+ pro-B and IM/M-B cells. Upregulated stemness and malignancy programs in IK6+ cells confirmed IK6 effects. Interestingly, these programs corresponded to distinct canonical pathways. Remarkably, the pathway profile mapped in the modelled cells well mirrored that in patients’ leukaemic cells; therefore, our study provides a seminal insight into the cancerous reprogramming of somatic cells.
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Affiliation(s)
- Zhen Li
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology and Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Shui-Ping Li
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology and Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Ruo-Yan Li
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Hua Zhu
- Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology/Oncology, Shanghai Children's Medical Center, SJTU-SM, Shanghai, China
| | - Xia Liu
- Department of gynaecology and obstetrics, Huangshi Aikang Hospital of Hubei Province, Huangshi, China
| | - Xiao-Lin Guo
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology and Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Li-Li Mu
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology and Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Jie-Jing Cai
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology and Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Fan Bai
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China.
| | - Guo-Qiang Chen
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology and Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China.
| | - Deng-Li Hong
- Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Department of Pathophysiology and Ruijin Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China. .,Shanghai Key Laboratory of Reproductive Medicine, SJTU-SM, Shanghai, China.
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43
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Computational de novo discovery of distinguishing genes for biological processes and cell types in complex tissues. PLoS One 2018; 13:e0193067. [PMID: 29494600 PMCID: PMC5832224 DOI: 10.1371/journal.pone.0193067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/02/2018] [Indexed: 11/30/2022] Open
Abstract
Bulk tissue samples examined by gene expression studies are usually heterogeneous. The data gained from these samples display the confounding patterns of mixtures consisting of multiple cell types or similar cell types in various functional states, which hinders the elucidation of the molecular mechanisms underlying complex biological phenomena. A realistic approach to compensate for the limitations of experimentally separating homogenous cell populations from mixed tissues is to computationally identify cell-type specific patterns from bulk, heterogeneous measurements. We designed the CellDistinguisher algorithm to analyze the gene expression data of mixed samples, identifying genes that best distinguish biological processes and cell types. Coupled with a deconvolution algorithm that takes cell type specific gene lists as input, we show that CellDistinguisher performs as well as partial deconvolution algorithms in predicting cell type composition without the need for prior knowledge of cell type signatures. This approach is also better in predicting cell type signatures than the one-step traditional complete deconvolution methods. To illustrate its wide applicability, the algorithm was tested on multiple publicly available data sets. In each case, CellDistinguisher identified genes reflecting biological processes typical for the tissues and development stages of interest and estimated the sample compositions accurately.
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Böiers C, Richardson SE, Laycock E, Zriwil A, Turati VA, Brown J, Wray JP, Wang D, James C, Herrero J, Sitnicka E, Karlsson S, Smith AJH, Jacobsen SEW, Enver T. A Human IPS Model Implicates Embryonic B-Myeloid Fate Restriction as Developmental Susceptibility to B Acute Lymphoblastic Leukemia-Associated ETV6-RUNX1. Dev Cell 2017; 44:362-377.e7. [PMID: 29290585 PMCID: PMC5807056 DOI: 10.1016/j.devcel.2017.12.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 08/04/2017] [Accepted: 12/01/2017] [Indexed: 12/15/2022]
Abstract
ETV6-RUNX1 is associated with childhood acute B-lymphoblastic leukemia (cALL) functioning as a first-hit mutation that initiates a clinically silent pre-leukemia in utero. Because lineage commitment hierarchies differ between embryo and adult, and the impact of oncogenes is cell-context dependent, we hypothesized that the childhood affiliation of ETV6-RUNX1 cALL reflects its origins in a progenitor unique to embryonic life. We characterize the first emerging B cells in first-trimester human embryos, identifying a developmentally restricted CD19-IL-7R+ progenitor compartment, which transitions from a myeloid to lymphoid program during ontogeny. This developmental series is recapitulated in differentiating human pluripotent stem cells (hPSCs), thereby providing a model for the initiation of cALL. Genome-engineered hPSCs expressing ETV6-RUNX1 from the endogenous ETV6 locus show expansion of the CD19-IL-7R+ compartment, show a partial block in B lineage commitment, and produce proB cells with aberrant myeloid gene expression signatures and potential: features (collectively) consistent with a pre-leukemic state.
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Affiliation(s)
- Charlotta Böiers
- Department of Cancer Biology, UCL Cancer Institute, UCL, London, UK; Lund Stem Cell Center, Lund University, Lund, Sweden
| | | | - Emma Laycock
- Department of Cancer Biology, UCL Cancer Institute, UCL, London, UK
| | - Alya Zriwil
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | | | - John Brown
- Department of Cancer Biology, UCL Cancer Institute, UCL, London, UK
| | - Jason P Wray
- Department of Cancer Biology, UCL Cancer Institute, UCL, London, UK
| | - Dapeng Wang
- Department of Cancer Biology, UCL Cancer Institute, UCL, London, UK
| | - Chela James
- Department of Cancer Biology, UCL Cancer Institute, UCL, London, UK
| | - Javier Herrero
- Department of Cancer Biology, UCL Cancer Institute, UCL, London, UK
| | - Ewa Sitnicka
- Lund Stem Cell Center, Lund University, Lund, Sweden
| | | | - Andrew J H Smith
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK; MRC Molecular Haematology Unit, University of Oxford, Oxford, UK
| | - Sten Erik W Jacobsen
- MRC Molecular Haematology Unit, University of Oxford, Oxford, UK; Departments of Cell and Molecular Biology and Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden; Haematopoietic Stem Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Karolinska University Hospital, Stockholm, Sweden
| | - Tariq Enver
- Department of Cancer Biology, UCL Cancer Institute, UCL, London, UK; Lund Stem Cell Center, Lund University, Lund, Sweden.
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45
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Coffre M, Koralov SB. miRNAs in B Cell Development and Lymphomagenesis. Trends Mol Med 2017; 23:721-736. [PMID: 28694140 DOI: 10.1016/j.molmed.2017.06.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/06/2017] [Accepted: 06/08/2017] [Indexed: 12/22/2022]
Abstract
B lymphocytes are essential for an efficient immune response against a variety of pathogens. A large fraction of hematologic malignancies is of B cell origin, suggesting that the development and activation of B cells need to be tightly regulated. In recent years, increasing evidence has emerged demonstrating that microRNAs (miRNAs) - a class of non-coding RNAs that control gene expression - are involved in the regulation of B cell development and function. We provide here an overview of the current knowledge on the role of miRNAs and their relevant targets in B cell development, B cell activation, and B cell malignant transformation.
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Affiliation(s)
- Maryaline Coffre
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
| | - Sergei B Koralov
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA.
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46
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Human haematopoietic stem cell lineage commitment is a continuous process. Nat Cell Biol 2017; 19:271-281. [PMID: 28319093 PMCID: PMC5496982 DOI: 10.1038/ncb3493] [Citation(s) in RCA: 606] [Impact Index Per Article: 86.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/20/2017] [Indexed: 12/11/2022]
Abstract
Blood formation is believed to occur through step-wise progression of haematopoietic stem cells (HSCs) following a tree-like hierarchy of oligo-, bi- and unipotent progenitors. However, this model is based on the analysis of predefined flow-sorted cell populations. Here we integrated flow cytometric, transcriptomic and functional data at single-cell resolution to quantitatively map early differentiation of human HSCs towards lineage commitment. During homeostasis, individual HSCs gradually acquire lineage biases along multiple directions without passing through discrete hierarchically organized progenitor populations. Instead, unilineage-restricted cells emerge directly from a “Continuum of LOw primed UnDifferentiated hematopoietic stem- and progenitor cells” (CLOUD-HSPCs). Distinct gene expression modules operate in a combinatorial manner to control stemness, early lineage priming and the subsequent progression into all major branches of haematopoiesis. These data reveal a continuous landscape of human steady state haematopoiesis downstream of HSCs and provide a basis for the understanding of hematopoietic malignancies.
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Influence of Plasma Cell Niche Factors on the Recruitment and Maintenance of IRF4hi Plasma Cells and Plasmablasts in Vaccinated, Simian Immunodeficiency Virus-Infected Rhesus Macaques with Low and High Viremia. J Virol 2017; 91:JVI.01727-16. [PMID: 27928009 DOI: 10.1128/jvi.01727-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 11/29/2016] [Indexed: 12/30/2022] Open
Abstract
In a recent study, we found that protection following simian immunodeficiency virus (SIV) exposure correlated with rectal plasma cell frequency in vaccinated female rhesus macaques. We sought to determine if the same macaques maintained high mucosal plasma cell frequencies postinfection and if this translated to reduced viremia. Although delayed SIV acquisition did not predict subsequent viral control, alterations existed in the distribution of plasma cells and plasmablasts between macaques that exhibited high or low viremia. Flow cytometric analysis of cells from rectal biopsy specimens, bone marrow, and mesenteric lymph nodes of vaccinated infected, unvaccinated infected, and uninfected macaques identified two main IRF4hi subsets of interest: CD138+ plasma cells, and CD138- plasmablasts. In rectal tissue, plasma cell frequency positively correlated with plasma viremia and unvaccinated macaques had increased plasma cells and plasmablasts compared to vaccinated animals. Likewise, plasmablast frequency in the mesenteric lymph node correlated with viremia. However, in bone marrow, plasmablast frequency negatively correlated with viremia. Accordingly, low-viremic macaques had a higher frequency of both bone marrow IRF4hi subsets than did animals with high viremia. Significant reciprocal relationships between rectal and bone marrow plasmablasts suggested that efficient trafficking to the bone marrow as opposed to the rectal mucosa was linked to viral control. mRNA expression analysis of proteins involved in establishment of plasma cell niches in sorted bone marrow and rectal cell populations further supported this model and revealed differential mRNA expression patterns in these tissues. IMPORTANCE As key antibody producers, plasma cells and plasmablasts are critical components of vaccine-induced immunity to human immunodeficiency virus type 1 (HIV-1) in humans and SIV in the macaque model; however, few have attempted to examine the role of these cells in viral suppression postinfection. Our results suggest that plasmablast trafficking to and retention in the bone marrow play a previously unappreciated role in viral control and contrast the potential contribution of mucosal plasma cells to mediate protection at sites of infection with that of bone marrow plasmablasts and plasma cells to control viremia during chronic infection. Manipulation of niche factors influencing the distribution and maintenance of these critical antibody-secreting cells may serve as potential therapeutic targets to enhance antiviral responses postvaccination and postinfection.
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48
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Global gene regulation during activation of immunoglobulin class switching in human B cells. Sci Rep 2016; 6:37988. [PMID: 27897229 PMCID: PMC5126563 DOI: 10.1038/srep37988] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/03/2016] [Indexed: 02/06/2023] Open
Abstract
Immunoglobulin class switch recombination (CSR) to IgE is a tightly regulated process central to atopic disease. To profile the B-cell transcriptional responses underlying the activation of the germinal centre activities leading to the generation of IgE, naïve human B-cells were stimulated with IL-4 and anti-CD40. Gene expression and alternative splicing were profiled over 12 days using the Affymetrix Human Exon 1.0 ST Array. A total of 1,399 genes, forming 13 temporal profiles were differentially expressed. CCL22 and CCL17 were dramatically induced but followed a temporal trajectory distinct from classical mediators of isotype switching. AICDA, NFIL3, IRF4, XBP1 and BATF3 shared a profile with several genes involved in innate immunity, but with no recognised role in CSR. A transcription factor BHLHE40 was identified at the core of this profile. B-cell activation was also accompanied by variation in exon retention affecting >200 genes including CCL17. The data indicate a circadian component and central roles for the Th2 chemokines CCL22 and CCL17 in the activation of CSR.
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49
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Lin S, Luo RT, Ptasinska A, Kerry J, Assi SA, Wunderlich M, Imamura T, Kaberlein JJ, Rayes A, Althoff MJ, Anastasi J, O'Brien MM, Meetei AR, Milne TA, Bonifer C, Mulloy JC, Thirman MJ. Instructive Role of MLL-Fusion Proteins Revealed by a Model of t(4;11) Pro-B Acute Lymphoblastic Leukemia. Cancer Cell 2016; 30:737-749. [PMID: 27846391 DOI: 10.1016/j.ccell.2016.10.008] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/21/2016] [Accepted: 10/12/2016] [Indexed: 01/11/2023]
Abstract
The t(4;11)(q21;q23) fuses mixed-lineage leukemia (MLL) to AF4, the most common MLL-fusion partner. Here we show that MLL fused to murine Af4, highly conserved with human AF4, produces high-titer retrovirus permitting efficient transduction of human CD34+ cells, thereby generating a model of t(4;11) pro-B acute lymphoblastic leukemia (ALL) that fully recapitulates the immunophenotypic and molecular aspects of the disease. MLL-Af4 induces a B ALL distinct from MLL-AF9 through differential genomic target binding of the fusion proteins leading to specific gene expression patterns. MLL-Af4 cells can assume a myeloid state under environmental pressure but retain lymphoid-lineage potential. Such incongruity was also observed in t(4;11) patients in whom leukemia evaded CD19-directed therapy by undergoing myeloid-lineage switch. Our model provides a valuable tool to unravel the pathogenesis of MLL-AF4 leukemogenesis.
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Affiliation(s)
- Shan Lin
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Roger T Luo
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Anetta Ptasinska
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Jon Kerry
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, Oxford OX3 9DS, UK
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Mark Wunderlich
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Toshihiko Imamura
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Joseph J Kaberlein
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Ahmad Rayes
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Mark J Althoff
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - John Anastasi
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Maureen M O'Brien
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Amom Ruhikanta Meetei
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Thomas A Milne
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, Oxford OX3 9DS, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - James C Mulloy
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Michael J Thirman
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL 60637, USA.
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50
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Role of B Cell Development Marker CD10 in Cancer Progression and Prognosis. Mol Biol Int 2016; 2016:4328697. [PMID: 27965895 PMCID: PMC5124668 DOI: 10.1155/2016/4328697] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/07/2016] [Accepted: 10/17/2016] [Indexed: 12/03/2022] Open
Abstract
The human CD10 antigen is a single pass, type II transmembrane, 100 kD cell surface glycoprotein belonging to peptidase M13 family. Identified in common acute lymphoblastic leukemia as a cancer specific antigen, CD10 is a cell surface ectoenzyme widely expressed on different types of cells. Earlier, it was used only as a cell surface marker to identify and differentiate between haematological malignancies. Later, reported to be present in various malignancies, it is thought to play significant role in cancer development and progression. Regulated expression of CD10 is necessary for angiogenesis and so forth. However its expression level is found to be deregulated in different cancers. In some cancers, it acts as tumor suppressor and inhibits tumor progression whereas in others it has tumor promoting tendency. However, its role in tumorigenesis remains unclear. This review summarises structural features, functions, and probable role of CD10 in cancer development.
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