1
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Dick JK, Sangala JA, Krishna VD, Khaimraj A, Hamel L, Erickson SM, Hicks D, Soigner Y, Covill LE, Johnson A, Ehrhardt MJ, Ernste K, Brodin P, Koup RA, Khaitan A, Baehr C, Thielen BK, Henzler CM, Skipper C, Miller JS, Bryceson YT, Wu J, John CC, Panoskaltsis-Mortari A, Orioles A, Steiner ME, Cheeran MCJ, Pravetoni M, Hart GT. Antibody-mediated cellular responses are dysregulated in Multisystem Inflammatory Syndrome in Children (MIS-C). bioRxiv 2024:2024.04.16.589585. [PMID: 38659969 PMCID: PMC11042288 DOI: 10.1101/2024.04.16.589585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Multisystem Inflammatory Syndrome in Children (MIS-C) is a severe complication of SARS-CoV-2 infection characterized by multi-organ involvement and inflammation. Testing of cellular function ex vivo to understand the aberrant immune response in MIS-C is limited. Despite strong antibody production in MIS-C, SARS-CoV-2 nucleic acid testing can remain positive for 4-6 weeks after infection. Therefore, we hypothesized that dysfunctional cell-mediated antibody responses downstream of antibody production may be responsible for delayed clearance of viral products in MIS-C. In MIS-C, monocytes were hyperfunctional for phagocytosis and cytokine production, while natural killer (NK) cells were hypofunctional for both killing and cytokine production. The decreased NK cell cytotoxicity correlated with an NK exhaustion marker signature and systemic IL-6 levels. Potentially providing a therapeutic option, cellular engagers of CD16 and SARS-CoV-2 proteins were found to rescue NK cell function in vitro. Together, our results reveal dysregulation in antibody-mediated cellular responses unique to MIS-C that likely contribute to the immune pathology of this disease.
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2
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Tarullo SE, He Y, Daughters C, Knutson TP, Henzler CM, Price MA, Shanley R, Witschen P, Tolg C, Kaspar RE, Hallstrom C, Gittsovich L, Sulciner ML, Zhang X, Forster CL, Lange CA, Shats O, Desler M, Cowan KH, Yee D, Schwertfeger KL, Turley EA, McCarthy JB, Nelson AC. Receptor for hyaluronan-mediated motility (RHAMM) defines an invasive niche associated with tumor progression and predicts poor outcomes in breast cancer patients. J Pathol 2023; 260:289-303. [PMID: 37186300 PMCID: PMC10417882 DOI: 10.1002/path.6082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/13/2023] [Accepted: 03/23/2023] [Indexed: 05/17/2023]
Abstract
Breast cancer invasion and metastasis result from a complex interplay between tumor cells and the tumor microenvironment (TME). Key oncogenic changes in the TME include aberrant synthesis, processing, and signaling of hyaluronan (HA). Hyaluronan-mediated motility receptor (RHAMM, CD168; HMMR) is an HA receptor enabling tumor cells to sense and respond to this aberrant TME during breast cancer progression. Previous studies have associated RHAMM expression with breast tumor progression; however, cause and effect mechanisms are incompletely established. Focused gene expression analysis of an internal breast cancer patient cohort confirmed that increased RHAMM expression correlates with aggressive clinicopathological features. To probe mechanisms, we developed a novel 27-gene RHAMM-related signature (RRS) by intersecting differentially expressed genes in lymph node (LN)-positive patient cases with the transcriptome of a RHAMM-dependent model of cell transformation, which we validated in an independent cohort. We demonstrate that the RRS predicts for poor survival and is enriched for cell cycle and TME-interaction pathways. Further analyses using CRISPR/Cas9-generated RHAMM-/- breast cancer cells provided direct evidence that RHAMM promotes invasion in vitro and in vivo. Immunohistochemistry studies highlighted heterogeneous RHAMM protein expression, and spatial transcriptomics associated the RRS with RHAMM-high microanatomic foci. We conclude that RHAMM upregulation leads to the formation of 'invasive niches', which are enriched in RRS-related pathways that drive invasion and could be targeted to limit invasive progression and improve patient outcomes. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Sarah E Tarullo
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Yuyu He
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Claire Daughters
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Todd P Knutson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Christine M Henzler
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Matthew A Price
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Ryan Shanley
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Patrice Witschen
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Cornelia Tolg
- London Health Sciences Center, Western University, Ontario, Canada
| | - Rachael E Kaspar
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Caroline Hallstrom
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Lyubov Gittsovich
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Megan L Sulciner
- School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Xihong Zhang
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Colleen L Forster
- Clinical and Translational Science Institute, University of Minnesota, Minneapolis, MN, USA
| | - Carol A Lange
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Oleg Shats
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE, USA
| | - Michelle Desler
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE, USA
| | - Kenneth H Cowan
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE, USA
| | - Douglas Yee
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Kathryn L Schwertfeger
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Eva A Turley
- London Health Sciences Center, Western University, Ontario, Canada
| | - James B McCarthy
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
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3
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Geistlinger L, Oh S, Ramos M, Schiffer L, LaRue RS, Henzler CM, Munro SA, Daughters C, Nelson AC, Winterhoff BJ, Chang Z, Talukdar S, Shetty M, Mullany SA, Morgan M, Parmigiani G, Birrer MJ, Qin LX, Riester M, Starr TK, Waldron L. Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian Carcinoma. Cancer Res 2020; 80:4335-4345. [PMID: 32747365 DOI: 10.1158/0008-5472.can-20-0521] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/13/2020] [Accepted: 07/29/2020] [Indexed: 12/15/2022]
Abstract
Multiple studies have identified transcriptome subtypes of high-grade serous ovarian carcinoma (HGSOC), but their interpretation and translation are complicated by tumor evolution and polyclonality accompanied by extensive accumulation of somatic aberrations, varying cell type admixtures, and different tissues of origin. In this study, we examined the chronology of HGSOC subtype evolution in the context of these factors using a novel integrative analysis of absolute copy-number analysis and gene expression in The Cancer Genome Atlas complemented by single-cell analysis of six independent tumors. Tumor purity, ploidy, and subclonality were reliably inferred from different genomic platforms, and these characteristics displayed marked differences between subtypes. Genomic lesions associated with HGSOC subtypes tended to be subclonal, implying subtype divergence at later stages of tumor evolution. Subclonality of recurrent HGSOC alterations was evident for proliferative tumors, characterized by extreme genomic instability, absence of immune infiltration, and greater patient age. In contrast, differentiated tumors were characterized by largely intact genome integrity, high immune infiltration, and younger patient age. Single-cell sequencing of 42,000 tumor cells revealed widespread heterogeneity in tumor cell type composition that drove bulk subtypes but demonstrated a lack of intrinsic subtypes among tumor epithelial cells. Our findings prompt the dismissal of discrete transcriptome subtypes for HGSOC and replacement by a more realistic model of continuous tumor development that includes mixtures of subclones, accumulation of somatic aberrations, infiltration of immune and stromal cells in proportions correlated with tumor stage and tissue of origin, and evolution between properties previously associated with discrete subtypes. SIGNIFICANCE: This study infers whether transcriptome-based groupings of tumors differentiate early in carcinogenesis and are, therefore, appropriate targets for therapy and demonstrates that this is not the case for HGSOC.
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Affiliation(s)
- Ludwig Geistlinger
- Graduate School of Public Health and Health Policy, City University of New York, New York, New York
- Institute for Implementation Science and Population Health, City University of New York, New York, New York
| | - Sehyun Oh
- Graduate School of Public Health and Health Policy, City University of New York, New York, New York
- Institute for Implementation Science and Population Health, City University of New York, New York, New York
| | - Marcel Ramos
- Graduate School of Public Health and Health Policy, City University of New York, New York, New York
- Institute for Implementation Science and Population Health, City University of New York, New York, New York
- Roswell Park Comprehensive Cancer Institute, Buffalo, New York
| | - Lucas Schiffer
- Graduate School of Public Health and Health Policy, City University of New York, New York, New York
- Institute for Implementation Science and Population Health, City University of New York, New York, New York
| | - Rebecca S LaRue
- Minnesota Supercomputing Institute, Minneapolis, Minnesota
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Christine M Henzler
- Minnesota Supercomputing Institute, Minneapolis, Minnesota
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Sarah A Munro
- Minnesota Supercomputing Institute, Minneapolis, Minnesota
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Claire Daughters
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
- University of Minnesota Masonic Cancer Center, Minneapolis, Minnesota
| | - Boris J Winterhoff
- University of Minnesota Masonic Cancer Center, Minneapolis, Minnesota
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota
| | - Zenas Chang
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota
| | - Shobhana Talukdar
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota
| | - Mihir Shetty
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota
| | - Sally A Mullany
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota
| | - Martin Morgan
- Roswell Park Comprehensive Cancer Institute, Buffalo, New York
| | - Giovanni Parmigiani
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Michael J Birrer
- The Winthrop P Rockefeller Cancer Institute, University of Arkansas Medical Sciences, Little Rock, Arkansas
| | - Li-Xuan Qin
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Markus Riester
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Timothy K Starr
- University of Minnesota Masonic Cancer Center, Minneapolis, Minnesota
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, Minnesota
| | - Levi Waldron
- Graduate School of Public Health and Health Policy, City University of New York, New York, New York.
- Institute for Implementation Science and Population Health, City University of New York, New York, New York
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4
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Li Y, Yang R, Henzler CM, Ho Y, Passow C, Auch B, Carreira S, Nava Rodrigues D, Bertan C, Hwang TH, Quigley DA, Dang HX, Morrissey C, Fraser M, Plymate SR, Maher CA, Feng FY, de Bono JS, Dehm SM. Diverse AR Gene Rearrangements Mediate Resistance to Androgen Receptor Inhibitors in Metastatic Prostate Cancer. Clin Cancer Res 2020; 26:1965-1976. [PMID: 31932493 DOI: 10.1158/1078-0432.ccr-19-3023] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 12/04/2019] [Accepted: 01/09/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Prostate cancer is the second leading cause of male cancer deaths. Castration-resistant prostate cancer (CRPC) is a lethal stage of the disease that emerges when endocrine therapies are no longer effective at suppressing activity of the androgen receptor (AR) transcription factor. The purpose of this study was to identify genomic mechanisms that contribute to the development and progression of CRPC. EXPERIMENTAL DESIGN We used whole-genome and targeted DNA-sequencing approaches to identify mechanisms underlying CRPC in an aggregate cohort of 272 prostate cancer patients. We analyzed structural rearrangements at the genome-wide level and carried out a detailed structural rearrangement analysis of the AR locus. We used genome engineering to perform experimental modeling of AR gene rearrangements and long-read RNA sequencing to analyze effects on expression of AR and truncated AR variants (AR-V). RESULTS AR was among the most frequently rearranged genes in CRPC tumors. AR gene rearrangements promoted expression of diverse AR-V species. AR gene rearrangements occurring in the context of AR amplification correlated with AR overexpression. Cell lines with experimentally derived AR gene rearrangements displayed high expression of tumor-specific AR-Vs and were resistant to endocrine therapies, including the AR antagonist enzalutamide. CONCLUSIONS AR gene rearrangements are an important mechanism of resistance to endocrine therapies in CRPC.
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Affiliation(s)
- Yingming Li
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Rendong Yang
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota.,The Hormel Institute, University of Minnesota, Austin, Minnesota
| | - Christine M Henzler
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
| | - Yeung Ho
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Courtney Passow
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, Minnesota
| | - Benjamin Auch
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, Minnesota
| | | | | | - Claudia Bertan
- The Institute for Cancer Research, London, United Kingdom
| | - Tae Hyun Hwang
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Ha X Dang
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri.,Department of Internal Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington
| | - Michael Fraser
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario
| | - Stephen R Plymate
- Division of Gerontology, Geriatric Medicine, University of Washington, Seattle, Washington.,Geriatric Research Education and Clinical Centers, VA Puget Sound Health Care System, Seattle, Washington
| | - Christopher A Maher
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri.,Department of Internal Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California.,Department of Radiation Oncology, University of California, San Francisco, San Francisco, California
| | - Johann S de Bono
- The Institute for Cancer Research, London, United Kingdom.,The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota. .,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota.,Department of Urology, University of Minnesota, Minneapolis, Minnesota
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5
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Owen DL, Mahmud SA, Sjaastad LE, Williams JB, Spanier JA, Simeonov DR, Ruscher R, Huang W, Proekt I, Miller CN, Hekim C, Jeschke JC, Aggarwal P, Broeckel U, LaRue RS, Henzler CM, Alegre ML, Anderson MS, August A, Marson A, Zheng Y, Williams CB, Farrar MA. Thymic regulatory T cells arise via two distinct developmental programs. Nat Immunol 2019; 20:195-205. [PMID: 30643267 PMCID: PMC6650268 DOI: 10.1038/s41590-018-0289-6] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 11/21/2018] [Indexed: 12/14/2022]
Abstract
The developmental programs that generate a broad repertoire of regulatory T cells (Treg cells) able to respond to both self antigens and non-self antigens remain unclear. Here we found that mature Treg cells were generated through two distinct developmental programs involving CD25+ Treg cell progenitors (CD25+ TregP cells) and Foxp3lo Treg cell progenitors (Foxp3lo TregP cells). CD25+ TregP cells showed higher rates of apoptosis and interacted with thymic self antigens with higher affinity than did Foxp3lo TregP cells, and had a T cell antigen receptor repertoire and transcriptome distinct from that of Foxp3lo TregP cells. The development of both CD25+ TregP cells and Foxp3lo TregP cells was controlled by distinct signaling pathways and enhancers. Transcriptomics and histocytometric data suggested that CD25+ TregP cells and Foxp3lo TregP cells arose by coopting negative-selection programs and positive-selection programs, respectively. Treg cells derived from CD25+ TregP cells, but not those derived from Foxp3lo TregP cells, prevented experimental autoimmune encephalitis. Our findings indicate that Treg cells arise through two distinct developmental programs that are both required for a comprehensive Treg cell repertoire capable of establishing immunotolerance.
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Affiliation(s)
- David L Owen
- Center for Immunology, Masonic Cancer Center, and the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Shawn A Mahmud
- Center for Immunology, Masonic Cancer Center, and the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Louisa E Sjaastad
- Center for Immunology, Masonic Cancer Center, and the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Jason B Williams
- Section of Rheumatology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Justin A Spanier
- Center for Immunology, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Dimitre R Simeonov
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.,Diabetes Center, University of California San Francisco, San Francisco, CA, USA.,Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Roland Ruscher
- Center for Immunology, Masonic Cancer Center, and the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Weishan Huang
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.,Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Irina Proekt
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Corey N Miller
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Can Hekim
- Center for Immunology, Masonic Cancer Center, and the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Jonathan C Jeschke
- Section of Rheumatology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Praful Aggarwal
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ulrich Broeckel
- Section of Genomic Pediatrics, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Rebecca S LaRue
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, MN, USA
| | - Christine M Henzler
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, MN, USA
| | - Maria-Luisa Alegre
- Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Mark S Anderson
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Avery August
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.,Diabetes Center, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA.,Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Ye Zheng
- Nomis Foundation Laboratories for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Calvin B Williams
- Section of Rheumatology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michael A Farrar
- Center for Immunology, Masonic Cancer Center, and the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA.
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6
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Burrack KS, Huggins MA, Taras E, Dougherty P, Henzler CM, Yang R, Alter S, Jeng EK, Wong HC, Felices M, Cichocki F, Miller JS, Hart GT, Johnson AJ, Jameson SC, Hamilton SE. Interleukin-15 Complex Treatment Protects Mice from Cerebral Malaria by Inducing Interleukin-10-Producing Natural Killer Cells. Immunity 2018; 48:760-772.e4. [PMID: 29625893 DOI: 10.1016/j.immuni.2018.03.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 11/27/2017] [Accepted: 03/05/2018] [Indexed: 12/21/2022]
Abstract
Cerebral malaria is a deadly complication of Plasmodium infection and involves blood brain barrier (BBB) disruption following infiltration of white blood cells. During experimental cerebral malaria (ECM), mice inoculated with Plasmodium berghei ANKA-infected red blood cells develop a fatal CM-like disease caused by CD8+ T cell-mediated pathology. We found that treatment with interleukin-15 complex (IL-15C) prevented ECM, whereas IL-2C treatment had no effect. IL-15C-expanded natural killer (NK) cells were necessary and sufficient for protection against ECM. IL-15C treatment also decreased CD8+ T cell activation in the brain and prevented BBB breakdown without influencing parasite load. IL-15C induced NK cells to express IL-10, which was required for IL-15C-mediated protection against ECM. Finally, we show that ALT-803, a modified human IL-15C, mediates similar induction of IL-10 in NK cells and protection against ECM. These data identify a regulatory role for cytokine-stimulated NK cells in the prevention of a pathogenic immune response.
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Affiliation(s)
- Kristina S Burrack
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55414, USA
| | - Matthew A Huggins
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55414, USA; Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Emily Taras
- Department of Medicine, University of Minnesota, Minneapolis, MN 55414, USA
| | - Philip Dougherty
- Department of Medicine, University of Minnesota, Minneapolis, MN 55414, USA
| | - Christine M Henzler
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, MN 55414, USA
| | - Rendong Yang
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, MN 55414, USA
| | - Sarah Alter
- Altor BioScience Corporation, Miramar, FL 33025, USA
| | - Emily K Jeng
- Altor BioScience Corporation, Miramar, FL 33025, USA
| | - Hing C Wong
- Altor BioScience Corporation, Miramar, FL 33025, USA
| | - Martin Felices
- Department of Medicine, University of Minnesota, Minneapolis, MN 55414, USA
| | - Frank Cichocki
- Department of Medicine, University of Minnesota, Minneapolis, MN 55414, USA
| | - Jeffrey S Miller
- Department of Medicine, University of Minnesota, Minneapolis, MN 55414, USA
| | - Geoffrey T Hart
- Center for Immunology, Department of Medicine, University of Minnesota, Minneapolis, MN 55414, USA
| | - Aaron J Johnson
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephen C Jameson
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55414, USA
| | - Sara E Hamilton
- Center for Immunology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55414, USA.
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7
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Katerndahl CDS, Heltemes-Harris LM, Willette MJL, Henzler CM, Frietze S, Yang R, Schjerven H, Silverstein KAT, Ramsey LB, Hubbard G, Wells AD, Kuiper RP, Scheijen B, van Leeuwen FN, Müschen M, Kornblau SM, Farrar MA. Antagonism of B cell enhancer networks by STAT5 drives leukemia and poor patient survival. Nat Immunol 2017; 18:694-704. [PMID: 28369050 PMCID: PMC5540372 DOI: 10.1038/ni.3716] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 02/28/2017] [Indexed: 12/14/2022]
Abstract
The transcription factor STAT5 has a critical role in B cell acute lymphoblastic leukemia (B-ALL). How STAT5 mediates this effect is unclear. Here we found that activation of STAT5 worked together with defects in signaling components of the precursor to the B cell antigen receptor (pre-BCR), including defects in BLNK, BTK, PKCβ, NF-κB1 and IKAROS, to initiate B-ALL. STAT5 antagonized the transcription factors NF-κB and IKAROS by opposing regulation of shared target genes. Super-enhancers showed enrichment for STAT5 binding and were associated with an opposing network of transcription factors, including PAX5, EBF1, PU.1, IRF4 and IKAROS. Patients with a high ratio of active STAT5 to NF-κB or IKAROS had more-aggressive disease. Our studies indicate that an imbalance of two opposing transcriptional programs drives B-ALL and suggest that restoring the balance of these pathways might inhibit B-ALL.
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Affiliation(s)
- Casey D S Katerndahl
- Department of Laboratory Medicine and Pathology, Center for Immunology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Lynn M Heltemes-Harris
- Department of Laboratory Medicine and Pathology, Center for Immunology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Mark J L Willette
- Department of Laboratory Medicine and Pathology, Center for Immunology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Christine M Henzler
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Seth Frietze
- MLRS Department, University of Vermont, Burlington, Vermont, USA
| | - Rendong Yang
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Hilde Schjerven
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Kevin A T Silverstein
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Laura B Ramsey
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Gregory Hubbard
- Department of Laboratory Medicine and Pathology, Center for Immunology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Andrew D Wells
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania and The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Roland P Kuiper
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Blanca Scheijen
- Laboratory of Pediatric Oncology Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.,Department of Pathology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Frank N van Leeuwen
- Laboratory of Pediatric Oncology Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Markus Müschen
- Department of Systems Biology, Beckman Research Institute and City of Hope Comprehensive Cancer Center, Pasadena, California, USA
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas Maryland Anderson Cancer Center, Houston, Texas, USA
| | - Michael A Farrar
- Department of Laboratory Medicine and Pathology, Center for Immunology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
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Lee YJ, Starrett GJ, Lee ST, Yang R, Henzler CM, Jameson SC, Hogquist KA. Lineage-Specific Effector Signatures of Invariant NKT Cells Are Shared amongst γδ T, Innate Lymphoid, and Th Cells. J Immunol 2016; 197:1460-70. [PMID: 27385777 DOI: 10.4049/jimmunol.1600643] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/14/2016] [Indexed: 12/17/2022]
Abstract
Invariant NKT cells differentiate into three predominant effector lineages in the steady state. To understand these lineages, we sorted undifferentiated invariant NK T progenitor cells and each effector population and analyzed their transcriptional profiles by RNAseq. Bioinformatic comparisons were made to effector subsets among other lymphocytes, specifically Th cells, innate lymphoid cells (ILC), and γδ T cells. Myc-associated signature genes were enriched in NKT progenitors, like in other hematopoietic progenitors. Only NKT1 cells, but not NKT2 and NKT17 cells, had transcriptome similarity to NK cells and were also similar to other IFN-γ-producing lineages such as Th1, ILC1, and intraepithelial γδ T cells. NKT2 and NKT17 cells were similar to their analogous subsets of γδ T cells and ILCs, but surprisingly, not to Th2 and Th17 cells. We identified a set of genes common to each effector lineage regardless of Ag receptor specificity, suggesting the use of conserved regulatory cores for effector function.
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Affiliation(s)
- You Jeong Lee
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota, Minneapolis, MN 55455;
| | - Gabriel J Starrett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455; and
| | - Seungeun Thera Lee
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota, Minneapolis, MN 55455
| | - Rendong Yang
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, MN 55455
| | - Christine M Henzler
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, MN 55455
| | - Stephen C Jameson
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota, Minneapolis, MN 55455
| | - Kristin A Hogquist
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota, Minneapolis, MN 55455;
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Kren BT, Unger GM, Abedin MJ, Vogel RI, Henzler CM, Ahmed K, Trembley JH. Preclinical evaluation of cyclin dependent kinase 11 and casein kinase 2 survival kinases as RNA interference targets for triple negative breast cancer therapy. Breast Cancer Res 2015; 17:19. [PMID: 25837326 PMCID: PMC4344788 DOI: 10.1186/s13058-015-0524-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 01/27/2015] [Indexed: 12/27/2022] Open
Abstract
Introduction Targeted therapies for aggressive breast cancers like triple negative breast cancer (TNBC) are needed. The use of small interfering RNAs (siRNAs) to disable expression of survival genes provides a tool for killing these cancer cells. Cyclin dependent kinase 11 (CDK11) is a survival protein kinase that regulates RNA transcription, splicing and mitosis. Casein kinase 2 (CK2) is a survival protein kinase that suppresses cancer cell death. Eliminating the expression of these genes has potential therapeutic utility for breast cancer. Methods Expression levels of CDK11 and CK2 mRNAs and associated proteins were examined in breast cancer cell lines and tissue arrays. RNA expression levels of CDC2L1, CDC2L2, CCNL1, CCNL2, CSNK2A1, CSNK2A2, and CSNK2B genes in breast cancer subtypes were analyzed. Effects following transfection of siRNAs against CDK11 and CK2 in cultured cells were examined by viability and clonal survival assays and by RNA and protein measures. Uptake of tenfibgen (TBG) nanocapsules by TNBC cells was analyzed by fluorescence-activated cell sorting. TBG nanocapsules delivered siRNAs targeting CDK11 or CK2 in mice carrying TNBC xenograft tumors. Transcript cleavage and response parameters were evaluated. Results We found strong CDK11 and CK2 mRNA and protein expression in most human breast cancer cells. Immunohistochemical analysis of TNBC patient tissues showed 100% of tumors stained positive for CDK11 with high nuclear intensity compared to normal tissue. The Cancer Genome Atlas analysis comparing basal to other breast cancer subtypes and to normal breast revealed statistically significant differences. Down-regulation of CDK11 and/or CK2 in breast cancer cells caused significant loss of cell viability and clonal survival, reduced relevant mRNA and protein expression, and induced cell death changes. TBG nanocapsules were taken up by TNBC cells both in culture and in xenograft tumors. Treatment with TBG- siRNA to CDK11 or TBG- siRNA to CK2αα’ nanocapsules induced appropriate cleavage of CDK11 and CK2α transcripts in TNBC tumors, and caused MDA-MB-231 tumor reduction, loss of proliferation, and decreased expression of targeted genes. Conclusions CDK11 and CK2 expression are individually essential for breast cancer cell survival, including TNBC. These genes serve as promising new targets for therapeutic development in breast cancer.
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Affiliation(s)
- Betsy T Kren
- Research Service (151), Minneapolis VA Health Care System, One Veterans Drive, Minneapolis, MN 55417 USA ; Department of Laboratory Medicine and Pathology, University of Minnesota, 420 Delaware Street, SE, Minneapolis, MN USA ; Masonic Cancer Center, University of Minnesota, 717 Delaware Street SE Room 130, Minneapolis, MN 55414 USA
| | | | - Md J Abedin
- Research Service (151), Minneapolis VA Health Care System, One Veterans Drive, Minneapolis, MN 55417 USA ; Department of Laboratory Medicine and Pathology, University of Minnesota, 420 Delaware Street, SE, Minneapolis, MN USA
| | - Rachel I Vogel
- Masonic Cancer Center, University of Minnesota, 717 Delaware Street SE Room 130, Minneapolis, MN 55414 USA
| | - Christine M Henzler
- Department of Laboratory Medicine and Pathology, University of Minnesota, 420 Delaware Street, SE, Minneapolis, MN USA ; Minnesota Supercomputing Institute, University of Minnesota, 117 Pleasant Street SE, Minneapolis, MN 55455 USA
| | - Khalil Ahmed
- Research Service (151), Minneapolis VA Health Care System, One Veterans Drive, Minneapolis, MN 55417 USA ; Department of Laboratory Medicine and Pathology, University of Minnesota, 420 Delaware Street, SE, Minneapolis, MN USA ; Masonic Cancer Center, University of Minnesota, 717 Delaware Street SE Room 130, Minneapolis, MN 55414 USA ; Department of Urology, University of Minnesota, 420 Delaware St. SE, Minneapolis, MN 55455 USA
| | - Janeen H Trembley
- Research Service (151), Minneapolis VA Health Care System, One Veterans Drive, Minneapolis, MN 55417 USA ; Department of Laboratory Medicine and Pathology, University of Minnesota, 420 Delaware Street, SE, Minneapolis, MN USA ; Masonic Cancer Center, University of Minnesota, 717 Delaware Street SE Room 130, Minneapolis, MN 55414 USA
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Henzler CM, Li Z, Dang J, Arcila ML, Zhou H, Liu J, Chang KY, Bassett DS, Rana TM, Kosik KS. Staged miRNA re-regulation patterns during reprogramming. Genome Biol 2013; 14:R149. [PMID: 24380417 PMCID: PMC4053856 DOI: 10.1186/gb-2013-14-12-r149] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 12/31/2013] [Indexed: 11/24/2022] Open
Abstract
Background MiRNAs often operate in feedback loops with transcription factors and represent a key mechanism for fine-tuning gene expression. In transcription factor-induced reprogramming, miRNAs play a critical role; however, detailed analyses of miRNA expression changes during reprogramming at the level of deep sequencing have not been previously reported. Results We use four factor reprogramming to induce pluripotent stem cells from mouse fibroblasts and isolate FACS-sorted Thy1- and SSEA1+ intermediates and Oct4-GFP+ induced pluripotent stem cells (iPSCs). Small RNAs from these cells, and two partial-iPSC lines, another iPSC line, and mouse embryonic stem cells (mES cells) were deep sequenced. A comprehensive resetting of the miRNA profile occurs during reprogramming; however, analysis of miRNA co-expression patterns yields only a few patterns of change. Dlk1-Dio3 region miRNAs dominate the large pool of miRNAs experiencing small but significant fold changes early in reprogramming. Overexpression of Dlk1-Dio3 miRNAs early in reprogramming reduces reprogramming efficiency, suggesting the observed downregulation of these miRNAs may contribute to reprogramming. As reprogramming progresses, fewer miRNAs show changes in expression, but those changes are generally of greater magnitude. Conclusions The broad resetting of the miRNA profile during reprogramming that we observe is due to small changes in gene expression in many miRNAs early in the process, and large changes in only a few miRNAs late in reprogramming. This corresponds with a previously observed transition from a stochastic to a more deterministic signal.
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Henzler CM, Ingólfsson A. The biogeography of the beachflea, Orchestia gammarellus (Crustacea, Amphipoda, Talitridae), in the North Atlantic with special reference to Iceland: a morphometric and genetic study. ZOOL SCR 2007. [DOI: 10.1111/j.1463-6409.2007.00307.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Riginos C, Hickerson MJ, Henzler CM, Cunningham CW. Differential patterns of male and female mtDNA exchange across the Atlantic Ocean in the blue mussel, Mytilus edulis. Evolution 2005; 58:2438-51. [PMID: 15612287 DOI: 10.1111/j.0014-3820.2004.tb00873.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Comparisons among loci with differing modes of inheritance can reveal unexpected aspects of population history. We employ a multilocus approach to ask whether two types of independently assorting mitochondrial DNAs (maternally and paternally inherited: F- and M-mtDNA) and a nuclear locus (ITS) yield concordant estimates of gene flow and population divergence. The blue mussel, Mytilus edulis, is distributed on both North American and European coastlines and these populations are separated by the waters of the Atlantic Ocean. Gene flow across the Atlantic Ocean differs among loci, with F-mtDNA and ITS showing an imprint of some genetic interchange and M-mtDNA showing no evidence for gene flow. Gene flow of F-mtDNA and ITS causes trans-Atlantic population divergence times to be greatly underestimated for these loci, although a single trans-Atlantic population divergence time (1.2 MYA) can be accommodated by considering all three loci in combination in a coalescent framework. The apparent lack of gene flow for M-mtDNA is not readily explained by different dispersal capacities of male and female mussels. A genetic barrier to M-mtDNA exchange between North American and European mussel populations is likely to explain the observed pattern, perhaps associated with the double uniparental system of mitochondrial DNA inheritance.
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Affiliation(s)
- Cynthia Riginos
- Department of Biology, Box 90338, Duke University, Durham, North Carolina 27708, USA.
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Riginos C, Hickerson MJ, Henzler CM, Cunningham CW. DIFFERENTIAL PATTERNS OF MALE AND FEMALE MTDNA EXCHANGE ACROSS THE ATLANTIC OCEAN IN THE BLUE MUSSEL, MYTILUS EDULIS. Evolution 2004. [DOI: 10.1554/04-183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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