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Ng A, Lovat F, Shih AJ, Ma Y, Pekarsky Y, DiCaro F, Crichton L, Sharma E, Yan XJ, Sun D, Song T, Zou YR, Will B, Croce CM, Chiorazzi N. Complete miRNA-15/16 loss in mice promotes hematopoietic progenitor expansion and a myeloid-biased hyperproliferative state. Proc Natl Acad Sci U S A 2023; 120:e2308658120. [PMID: 37844234 PMCID: PMC10614620 DOI: 10.1073/pnas.2308658120] [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: 05/29/2023] [Accepted: 09/13/2023] [Indexed: 10/18/2023] Open
Abstract
Dysregulated apoptosis and proliferation are fundamental properties of cancer, and microRNAs (miRNA) are critical regulators of these processes. Loss of miR-15a/16-1 at chromosome 13q14 is the most common genomic aberration in chronic lymphocytic leukemia (CLL). Correspondingly, the deletion of either murine miR-15a/16-1 or miR-15b/16-2 locus in mice is linked to B cell lymphoproliferative malignancies. However, unexpectedly, when both miR-15/16 clusters are eliminated, most double knockout (DKO) mice develop acute myeloid leukemia (AML). Moreover, in patients with CLL, significantly reduced expression of miR-15a, miR-15b, and miR-16 associates with progression of myelodysplastic syndrome to AML, as well as blast crisis in chronic myeloid leukemia. Thus, the miR-15/16 clusters have a biological relevance for myeloid neoplasms. Here, we demonstrate that the myeloproliferative phenotype in DKO mice correlates with an increase of hematopoietic stem and progenitor cells (HSPC) early in life. Using single-cell transcriptomic analyses, we presented the molecular underpinning of increased myeloid output in the HSPC of DKO mice with gene signatures suggestive of dysregulated hematopoiesis, metabolic activities, and cell cycle stages. Functionally, we found that multipotent progenitors (MPP) of DKO mice have increased self-renewing capacities and give rise to significantly more progeny in the granulocytic compartment. Moreover, a unique transcriptomic signature of DKO MPP correlates with poor outcome in patients with AML. Together, these data point to a unique regulatory role for miR-15/16 during the early stages of hematopoiesis and to a potentially useful biomarker for the pathogenesis of myeloid neoplasms.
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Affiliation(s)
- Anita Ng
- Karches Center for Oncology Research, The Feinstein Institutes for Medical Research Northwell Health, Manhasset, NY11030
| | - Francesca Lovat
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH43210
| | - Andrew J. Shih
- Boas Center for Human Genetics and Genomics, The Feinstein Institutes for Medical Research Northwell Health, Manhasset, NY11030
| | - Yuhong Ma
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY10461
| | - Yuri Pekarsky
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH43210
| | - Frank DiCaro
- Karches Center for Oncology Research, The Feinstein Institutes for Medical Research Northwell Health, Manhasset, NY11030
| | - Lita Crichton
- Karches Center for Oncology Research, The Feinstein Institutes for Medical Research Northwell Health, Manhasset, NY11030
| | - Esha Sharma
- Karches Center for Oncology Research, The Feinstein Institutes for Medical Research Northwell Health, Manhasset, NY11030
| | - Xiao Jie Yan
- Karches Center for Oncology Research, The Feinstein Institutes for Medical Research Northwell Health, Manhasset, NY11030
| | - Daqian Sun
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY10461
| | - Tengfei Song
- The Center for Autoimmune, Musculoskeletal, and Hematopoietic Diseases, The Feinstein Institutes for Medical Research Northwell Health, Manhasset, NY11030
| | - Yong-Rui Zou
- The Center for Autoimmune, Musculoskeletal, and Hematopoietic Diseases, The Feinstein Institutes for Medical Research Northwell Health, Manhasset, NY11030
- Departments of Medicine and Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY11549
| | - Britta Will
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY10461
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH43210
| | - Nicholas Chiorazzi
- Karches Center for Oncology Research, The Feinstein Institutes for Medical Research Northwell Health, Manhasset, NY11030
- Departments of Medicine and Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY11549
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2
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Ramirez De Oleo I, Kim V, Atisha-Fregoso Y, Shih AJ, Lee K, Diamond B, Kim SJ. Phenotypic and functional characteristics of murine CD11c+ B cells which is suppressed by metformin. Front Immunol 2023; 14:1241531. [PMID: 37744368 PMCID: PMC10512061 DOI: 10.3389/fimmu.2023.1241531] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Since the description of age-associated or autoimmune-associated B cells (ABCs), there has been a growing interest in the role of these cells in autoimmunity. ABCs are differently defined depending on the research group and are heterogenous subsets. Here, we sought to characterize ABCs in Sle1/2/3 triple congenic (TC) mice, which is a well accepted mouse model of lupus. Compared to follicular (FO) B cells, ABCs have many distinct functional properties, including antigen presentation. They express key costimulatory molecules for T cell activation and a distinct profile of cytokines. Moreover, they exhibit an increased capacity for antigen uptake. ABCs were also compared with germinal center (GC) B cells, which are antigen activated B cell population. There are several phenotypic similarities between ABCs and GC B cells, but GC B cells do not produce proinflammatory cytokines or take up antigen. While T cell proliferation and activation is induced by both FO B and ABCs in an antigen-dependent manner, ABCs induce stronger T cell receptor signaling in naïve CD4+ T cells and preferentially induce differentiation of T follicular helper (Tfh) cells. We found that ABCs exhibit a distinct transcriptomic profile which is focused on metabolism, cytokine signaling and antigen uptake and processing. ABCs exhibit an increase in both glycolysis and oxidative phosphorylation compared to FO B cells. Treatment of ABCs with metformin suppresses antigen presentation by decreasing antigen uptake, resulting in decreased Tfh differentiation. Taken together, these findings define a fundamental connection between metabolism and function within ABCs.
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Affiliation(s)
- Ivan Ramirez De Oleo
- Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Vera Kim
- Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Yemil Atisha-Fregoso
- Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Andrew J. Shih
- Center for Genomics and Human Genetics, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Kyungwoo Lee
- Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
- Department of Biology at Hofstra University, Hempstead, NY, United States
| | - Betty Diamond
- Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
- Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra University/Northwell, Hempstead, NY, United States
| | - Sun Jung Kim
- Center for Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
- Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra University/Northwell, Hempstead, NY, United States
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3
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Jin H, Aziz M, Murao A, Kobritz M, Shih AJ, Adelson RP, Brenner M, Wang P. Antigen-presenting aged neutrophils induce CD4+ T cells to exacerbate inflammation in sepsis. J Clin Invest 2023; 133:e164585. [PMID: 37463445 DOI: 10.1172/jci164585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 05/26/2023] [Indexed: 07/20/2023] Open
Abstract
Extracellular cold-inducible RNA-binding protein (eCIRP) is a key mediator of severity and mortality in sepsis. We found that stimulation of mouse bone marrow-derived neutrophils (BMDNs) with eCIRP generated a distinct neutrophil subpopulation, characterized by cell surface markers of both antigen-presenting cells and aged neutrophils as well as expression of IL-12, which we named antigen-presenting aged neutrophils (APANs). The frequency of APANs was significantly increased in the blood, spleen, and lungs of WT mice subjected to cecal ligation and puncture-induced sepsis but not in CIRP-/- mice. Patients with sepsis had a significant increase in circulating APAN counts compared with healthy individuals. Compared with non-APAN-transfered mice, APAN-transferred septic mice had increased serum levels of injury and inflammatory markers, exacerbated acute lung injury (ALI), and worsened survival. APANs and CD4+ T cells colocalized in the spleen, suggesting an immune interaction between these cells. APANs cocultured with CD4+ T cells significantly induced the release of IFN-γ via IL-12. BMDNs stimulated with eCIRP and IFN-γ underwent hyper-NETosis. Stimulating human peripheral blood neutrophils with eCIRP also induced APANs, and stimulating human neutrophils with eCIRP and IFN-γ caused hyper-NETosis. Thus, eCIRP released during sepsis induced APANs to aggravate ALI and worsen the survival of septic animals via CD4+ T cell activation, Th1 polarization, and IFN-γ-mediated hyper-NETosis.
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Affiliation(s)
- Hui Jin
- Center for Immunology and Inflammation, Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Monowar Aziz
- Center for Immunology and Inflammation, Feinstein Institutes for Medical Research, Manhasset, New York, USA
- Department of Molecular Medicine and
- Department of Surgery, Zucker School of Medicine at Hofstra/Northwell, Manhasset, New York, USA
| | - Atsushi Murao
- Center for Immunology and Inflammation, Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Molly Kobritz
- Center for Immunology and Inflammation, Feinstein Institutes for Medical Research, Manhasset, New York, USA
- Department of Surgery, Zucker School of Medicine at Hofstra/Northwell, Manhasset, New York, USA
| | - Andrew J Shih
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Robert P Adelson
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Max Brenner
- Center for Immunology and Inflammation, Feinstein Institutes for Medical Research, Manhasset, New York, USA
- Department of Molecular Medicine and
- Department of Surgery, Zucker School of Medicine at Hofstra/Northwell, Manhasset, New York, USA
| | - Ping Wang
- Center for Immunology and Inflammation, Feinstein Institutes for Medical Research, Manhasset, New York, USA
- Department of Molecular Medicine and
- Department of Surgery, Zucker School of Medicine at Hofstra/Northwell, Manhasset, New York, USA
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4
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Shih AJ, Jun T, Skol AD, Bao R, Huang L, Vora S, McNerney ME, Hungate EA, Le Beau MM, Larson RA, Elliott A, Lu HM, Huether R, Hernandez F, Stölzel F, Allan JM, Onel K. Inherited cancer predisposing mutations in patients with therapy-related myeloid neoplasms. Br J Haematol 2023; 200:489-493. [PMID: 36349721 DOI: 10.1111/bjh.18543] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022]
Abstract
Some patients with therapy-related myeloid neoplasms (t-MN) may have unsuspected inherited cancer predisposition syndrome (CPS). We propose a set of clinical criteria to identify t-MN patients with high risk of CPS (HR-CPS). Among 225 t-MN patients with an antecedent non-myeloid malignancy, our clinical criteria identified 52 (23%) HR-CPS patients. Germline whole-exome sequencing identified pathogenic or likely pathogenic variants in 10 of 27 HR-CPS patients compared to 0 of 9 low-risk CPS patients (37% vs. 0%, p = 0.04). These simple clinical criteria identify t-MN patients most likely to benefit from genetic testing for inherited CPS.
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Affiliation(s)
- Andrew J Shih
- The Feinstein Institute for Medical Research, Northwell Health, Manhasset, New York, USA
| | - Tomi Jun
- Sema4, Stamford, Connecticut, USA
| | - Andrew D Skol
- Department of Pediatrics, The University of Chicago, Chicago, Illinois, USA
| | - Riyue Bao
- Department of Medicine, The University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Lei Huang
- Center for Research Informatics, The University of Chicago, Chicago, Illinois, USA
| | - Sapana Vora
- Department of Pediatrics, The University of Chicago, Chicago, Illinois, USA
| | - Megan E McNerney
- Department of Pediatrics, The University of Chicago, Chicago, Illinois, USA.,Department of Pathology, The University of Chicago, Chicago, Illinois, USA
| | - Eric A Hungate
- Department of Pediatrics, The University of Chicago, Chicago, Illinois, USA
| | - Michelle M Le Beau
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Richard A Larson
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | | | | | | | | | - Friedrich Stölzel
- Department of Internal Medicine I, University Hospital Carl Gustav Carus Dresden, Dresden University of Technology, Dresden, Germany
| | - James M Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Kenan Onel
- Sema4, Stamford, Connecticut, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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5
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Shih AJ, Adelson RP, Vashistha H, Khalili H, Nayyar A, Puran R, Herrera R, Chatterjee PK, Lee AT, Truskinovsky AM, Elmaliki K, DeFranco M, Metz CN, Gregersen PK. Single-cell analysis of menstrual endometrial tissues defines phenotypes associated with endometriosis. BMC Med 2022; 20:315. [PMID: 36104692 PMCID: PMC9476391 DOI: 10.1186/s12916-022-02500-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/27/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Endometriosis is a common, complex disorder which is underrecognized and subject to prolonged delays in diagnosis. It is accompanied by significant changes in the eutopic endometrial lining. METHODS We have undertaken the first single-cell RNA-sequencing (scRNA-Seq) comparison of endometrial tissues in freshly collected menstrual effluent (ME) from 33 subjects, including confirmed endometriosis patients (cases) and controls as well as symptomatic subjects (who have chronic symptoms suggestive of endometriosis but have not been diagnosed). RESULTS We identify a unique subcluster of proliferating uterine natural killer (uNK) cells in ME-tissues from controls that is almost absent from endometriosis cases, along with a striking reduction of total uNK cells in the ME of cases (p < 10-16). In addition, an IGFBP1+ decidualized subset of endometrial stromal cells are abundant in the shed endometrium of controls when compared to cases (p < 10-16) confirming findings of compromised decidualization of cultured stromal cells from cases. By contrast, endometrial stromal cells from cases are enriched in cells expressing pro-inflammatory and senescent phenotypes. An enrichment of B cells in the cases (p = 5.8 × 10-6) raises the possibility that some may have chronic endometritis, a disorder which predisposes to endometriosis. CONCLUSIONS We propose that characterization of endometrial tissues in ME will provide an effective screening tool for identifying endometriosis in patients with chronic symptoms suggestive of this disorder. This constitutes a major advance, since delayed diagnosis for many years is a major clinical problem in the evaluation of these patients. Comprehensive analysis of ME is expected to lead to new diagnostic and therapeutic approaches to endometriosis and other associated reproductive disorders such as female infertility.
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Affiliation(s)
- Andrew J Shih
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY, 11030, USA
| | - Robert P Adelson
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY, 11030, USA
| | - Himanshu Vashistha
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY, 11030, USA
| | - Houman Khalili
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY, 11030, USA
| | - Ashima Nayyar
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY, 11030, USA
| | - Radha Puran
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY, 11030, USA
| | - Rixsi Herrera
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY, 11030, USA
| | - Prodyot K Chatterjee
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY, 11030, USA
| | - Annette T Lee
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY, 11030, USA.,Donald and Barbara Zucker School of Medicine, 500 Hofstra Blvd, Hempstead, NY, USA
| | - Alexander M Truskinovsky
- Donald and Barbara Zucker School of Medicine, 500 Hofstra Blvd, Hempstead, NY, USA.,Department of Pathology, North Shore University Hospital, Northwell Health, 300 Community Drive, Manhasset, NY, USA
| | - Kristine Elmaliki
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY, 11030, USA
| | - Margaret DeFranco
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY, 11030, USA
| | - Christine N Metz
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY, 11030, USA. .,Donald and Barbara Zucker School of Medicine, 500 Hofstra Blvd, Hempstead, NY, USA.
| | - Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, 350 Community Drive, Manhasset, NY, 11030, USA. .,Donald and Barbara Zucker School of Medicine, 500 Hofstra Blvd, Hempstead, NY, USA.
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6
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Ghanem MH, Shih AJ, Khalili H, Werth EG, Chakrabarty JK, Brown LM, Simpfendorfer KR, Gregersen PK. Proteomic and Single-Cell Transcriptomic Dissection of Human Plasmacytoid Dendritic Cell Response to Influenza Virus. Front Immunol 2022; 13:814627. [PMID: 35401570 PMCID: PMC8984281 DOI: 10.3389/fimmu.2022.814627] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/24/2022] [Indexed: 12/12/2022] Open
Abstract
Plasmacytoid dendritic cells [pDCs] represent a rare innate immune subset uniquely endowed with the capacity to produce substantial amounts of type-I interferons. This function of pDCs is critical for effective antiviral defenses and has been implicated in autoimmunity. While IFN-I and select cytokines have been recognized as pDC secreted products, a comprehensive agnostic profiling of the pDC secretome in response to a physiologic stimulus has not been reported. We applied LC-MS/MS to catalogue the repertoire of proteins secreted by pDCs in the unperturbed condition and in response to challenge with influenza H1N1. We report the identification of a baseline pDC secretome, and the repertoire of virus-induced proteins including most type-I interferons, various cytokines, chemokines and granzyme B. Additionally, using single-cell RNA-seq [scRNA-seq], we perform multidimensional analyses of pDC transcriptional diversity immediately ex vivo and following stimulation. Our data evidence preexisting pDC heterogeneity, with subsequent highly specialized roles within the pDC population upon stimulation ranging from dedicated cytokine super-producers to cells with APC-like traits. Dynamic expression of transcription factors and surface markers characterize subclusters within activated pDCs. Integrating the proteomic and transcriptomic datasets confirms the pDC-subcluster origin of the proteins identified in the secretome. Our findings represent the most comprehensive molecular characterization of primary human pDCs at baseline, and in response to influenza virus, reported to date.
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Affiliation(s)
- Mustafa H Ghanem
- Department of Molecular Medicine, Donald & Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States.,The Institute of Molecular Medicine at The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Andrew J Shih
- The Institute of Molecular Medicine at The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Houman Khalili
- The Institute of Molecular Medicine at The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Emily G Werth
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Jayanta K Chakrabarty
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Lewis M Brown
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Kim R Simpfendorfer
- Department of Molecular Medicine, Donald & Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States.,The Institute of Molecular Medicine at The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Peter K Gregersen
- Department of Molecular Medicine, Donald & Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States.,The Institute of Molecular Medicine at The Feinstein Institutes for Medical Research, Manhasset, NY, United States
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7
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Hsieh FF, Korsunsky I, Shih AJ, Moss MA, Chatterjee PK, Deshpande J, Xue X, Madankumar S, Kumar G, Rochelson B, Metz CN. Maternal oxytocin administration modulates gene expression in the brains of perinatal mice. J Perinat Med 2022; 50:207-218. [PMID: 34717055 DOI: 10.1515/jpm-2020-0525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 10/01/2021] [Indexed: 01/05/2023]
Abstract
OBJECTIVES Oxytocin (OXT) is widely used to facilitate labor. However, little is known about the effects of perinatal OXT exposure on the developing brain. We investigated the effects of maternal OXT administration on gene expression in perinatal mouse brains. METHODS Pregnant C57BL/6 mice were treated with saline or OXT at term (n=6-7/group). Dams and pups were euthanized on gestational day (GD) 18.5 after delivery by C-section. Another set of dams was treated with saline or OXT (n=6-7/group) and allowed to deliver naturally; pups were euthanized on postnatal day 9 (PND9). Perinatal/neonatal brain gene expression was determined using Illumina BeadChip Arrays and real time quantitative PCR. Differential gene expression analyses were performed. In addition, the effect of OXT on neurite outgrowth was assessed using PC12 cells. RESULTS Distinct and sex-specific gene expression patterns were identified in offspring brains following maternal OXT administration at term. The microarray data showed that female GD18.5 brains exhibited more differential changes in gene expression compared to male GD18.5 brains. Specifically, Cnot4 and Frmd4a were significantly reduced by OXT exposure in male and female GD18.5 brains, whereas Mtap1b, Srsf11, and Syn2 were significantly reduced only in female GD18.5 brains. No significant microarray differences were observed in PND9 brains. By quantitative PCR, OXT exposure reduced Oxtr expression in female and male brains on GD18.5 and PND9, respectively. PC12 cell differentiation assays revealed that OXT induced neurite outgrowth. CONCLUSIONS Prenatal OXT exposure induces sex-specific differential regulation of several nervous system-related genes and pathways with important neural functions in perinatal brains.
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Affiliation(s)
- Frances F Hsieh
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA.,Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology Stamford Hospital, Stamford, CT, USA
| | - Ilya Korsunsky
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA.,Division of Genetics, Department of Medicine at Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrew J Shih
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA
| | - Matthew A Moss
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Prodyot K Chatterjee
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA
| | - Jaai Deshpande
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA.,Providence Community Health Center, Providence, RI, USA
| | - Xiangying Xue
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA
| | - Swati Madankumar
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA
| | - Gopal Kumar
- Elmezzi Graduate School of Molecular Medicine at Northwell Health, Manhasset, NY, USA
| | - Burton Rochelson
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Christine N Metz
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA.,Institute of Molecular Medicine, Feinstein Institutes for Medical Research at Northwell Health, Manhasset, NY, USA.,Elmezzi Graduate School of Molecular Medicine at Northwell Health, Manhasset, NY, USA
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8
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Ghanem MH, Shih AJ, Vashistha H, Coke LN, Li W, Kim SJ, Simpfendorfer KR, Gregersen PK. Investigations into SCAMP5, a candidate lupus risk gene expressed in plasmacytoid dendritic cells. Lupus Sci Med 2021; 8:8/1/e000567. [PMID: 34728555 PMCID: PMC8565557 DOI: 10.1136/lupus-2021-000567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/01/2021] [Indexed: 11/08/2022]
Abstract
Objective We have investigated the molecular function of SCAMP5, a candidate risk gene for SLE exclusively expressed in plasmacytoid dendritic cells (pDCs) among peripheral leucocytes. Methods We tested the independence of the association in SCAMP5 with SLE by performing conditional analyses. We profiled the expression pattern of SCAMP5 among circulating leucocytes at the transcript and protein levels. Using lentiviral vectors, we localised the subcellular distribution of SCAMP5 alongside the interferon secretory pathway. We analysed pDCs for the expression of SCAMP5 and interferon production capacity by SCAMP5 genotype. Finally, we examined pDC-specific SCAMP5 isoforms by total RNAseq analysis and examined for genotype-associated quantitative differences therein. Results A conditional analysis revealed evidence of an independent genetic association of SCAMP5 with SLE. Among circulating leucocytes, SCAMP5 is uniquely expressed in pDCs at the transcript and protein levels, with main presence in the Golgi apparatus and minor presence at the cell periphery. In live cells, SCAMP5 displayed dynamic Golgi-cell surface trafficking and localised with the interferon secretory pathway. SCAMP5 did not differ in expression levels in pDCs between genotyped donors; however, a transient interferon secretory defect was noted in pDCs from donors carrying the risk genotype. Conclusions SCAMP5 constitutes a novel SLE risk gene on the basis of genomic data and expression in a cell type widely implicated in SLE pathogenesis. While we could not find evidence of quantitative expression differences in SCAMP5 between genotyped donors, SCAMP5 remains an attractive gene to explore given its highly restricted expression pattern and colocalisation with interferon secretion.
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Affiliation(s)
- Mustafa H Ghanem
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA.,Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Andrew J Shih
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Himanshu Vashistha
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Latanya N Coke
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Wentian Li
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Sun Jung Kim
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA.,Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Kim R Simpfendorfer
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA .,Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Peter K Gregersen
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA .,Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
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9
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Shih AJ, Murphy N, Kozel Z, Shah P, Yaskiv O, Khalili H, Liew A, Kavoussi L, Hall S, Vira M, Zhu XH, Lee AT. Prognostic Molecular Signatures for Metastatic Potential in Clinically Low-Risk Stage I and II Clear Cell Renal Cell Carcinomas. Front Oncol 2020; 10:1383. [PMID: 32850445 PMCID: PMC7431518 DOI: 10.3389/fonc.2020.01383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/30/2020] [Indexed: 12/20/2022] Open
Abstract
Introduction: For patients with localized node-negative (Stage I and II) clear cell renal cell carcinomas (ccRCC), current clinicopathological staging has limited predictive capability because of their low risk. Analyzing molecular signatures at the time of nephrectomy can aid in understanding future metastatic potential. Objective: Develop a molecular signature that can stratify patients who have clinically low risk ccRCC, but have high risk genetic changes driving an aggressive metastatic phenotype. Patients, Materials, and Methods: Presented is the differential expression of mRNA and miRNA in 44 Stage I and Stage II patients, 21 who developed metastasis within 5 years of nephrectomy, compared to 23 patients who remained disease free for more than 5 years. Extracted RNA from nephrectomy specimens preserved in FFPE blocks was sequenced using RNAseq. MiRNA expression was performed using the TaqMan OpenArray qPCR protocol. Results: One hundred thirty one genes and 2 miRNA were differentially expressed between the two groups. Canonical correlation (CC) analysis was applied and four CCs (CC32, CC20, CC9, and CC7) have an AUC > 0.65 in our dataset with similar predictive power in the TCGA-KIRC dataset. Gene set enrichment showed CC9 as kidney development/adhesion, CC20 as oxidative phosphorylation pathway, CC32 as RNA binding/spindle and CC7 as immune response. In a multivariate Cox model, the four CCs were able to identify high/low risk groups for metastases in the TCGA-KIRC (p < 0.05) with odds ratios of CC32 = 5.7, CC20 = 4.4, CC9 = 3.6, and CC7 = 2.7. Conclusion: These results identify molecular signatures for more aggressive tumors in clinically low risk ccRCC patients who have a higher potential of metastasis than would be expected.
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Affiliation(s)
- Andrew J Shih
- Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Neal Murphy
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States.,Division of Hospital Medicine, LIJ Medical Center, New Hyde Park, NY, United States
| | - Zachary Kozel
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States.,The Smith Institute for Urology, New Hyde Park, NY, United States
| | - Paras Shah
- Department of Urology, Mayo Clinic, Rochester, MN, United States
| | - Oksana Yaskiv
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States.,Northwell Health Department of Pathology, New Hyde Park, NY, United States
| | - Houman Khalili
- Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Anthony Liew
- Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Louis Kavoussi
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States.,The Smith Institute for Urology, New Hyde Park, NY, United States
| | - Simon Hall
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States.,The Smith Institute for Urology, New Hyde Park, NY, United States
| | - Manish Vira
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States.,The Smith Institute for Urology, New Hyde Park, NY, United States
| | - Xin-Hua Zhu
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States.,Northwell Health Cancer Institute, Lake Success, NY, United States
| | - Annette T Lee
- Feinstein Institutes for Medical Research, Manhasset, NY, United States.,Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States
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10
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Nayyar A, Saleem MI, Yilmaz M, DeFranco M, Klein G, Elmaliki KM, Kowalsky E, Chatterjee PK, Xue X, Viswanathan R, Shih AJ, Gregersen PK, Metz CN. Menstrual Effluent Provides a Novel Diagnostic Window on the Pathogenesis of Endometriosis. Front Reprod Health 2020; 2:3. [PMID: 36304708 PMCID: PMC9580670 DOI: 10.3389/frph.2020.00003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/10/2020] [Indexed: 01/17/2023] Open
Abstract
Endometriosis is a chronic inflammatory disorder characterized by the presence of endometrial-like tissue growing outside of the uterus. Although the cause is unknown, retrograde menstruation leads to deposition of endometrial cells into the peritoneal cavity. Lack of disease recognition and long diagnostic delays (6–10 years) lead to substantial personal, social and financial burdens, as well as delayed treatment. A non-invasive diagnostic for endometriosis is a major unmet clinical need. Here, we assessed whether differences in menstrual effluent-derived stromal fibroblast cells (ME-SFCs) from women with and without endometriosis provide the basis for a non-invasive diagnostic for endometriosis. In addition, we investigated whether treatment of control ME-SFCs with inflammatory cytokines (TNF and IL-1β) could induce an endometriosis-like phenotype. ME-SFCs from laparoscopically diagnosed endometriosis patients exhibit reduced decidualization capacity, measured by IGFBP1 production after exposure to cAMP. A receiver operating characteristic (ROC) curve developed using decidualization data from controls and endometriosis subjects yielded an area under the curve of 0.92. In addition, a significant reduction in ALDH1A1 gene expression and increased podoplanin surface expression were also observed in endometriosis ME-SFCs when compared to control ME-SFCs. These endometriosis-like phenotypes can be reproduced in control ME-SFCs by exposure to inflammatory cytokines (TNF and IL-1β) and are associated with increased cell migration. These results are consistent with the hypothesis that chronic intrauterine inflammation influences the development of endometriosis lesions following retrograde menstruation. In conclusion, the analysis of ME-SFCs can provide an accurate, rapid, and non-invasive diagnostic for endometriosis and insight into disease pathogenesis.
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Affiliation(s)
- Ashima Nayyar
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Matthew I. Saleem
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States
| | - Mine Yilmaz
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Margaret DeFranco
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Gila Klein
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Kristine Mae Elmaliki
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Elena Kowalsky
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Prodyot K. Chatterjee
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Xiangying Xue
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Radhika Viswanathan
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Andrew J. Shih
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Peter K. Gregersen
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States
- *Correspondence: Peter K. Gregersen
| | - Christine N. Metz
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, United States
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States
- Christine N. Metz
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11
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Shih AJ, Menzin A, Whyte J, Lovecchio J, Liew A, Khalili H, Bhuiya T, Gregersen PK, Lee AT. Identification of grade and origin specific cell populations in serous epithelial ovarian cancer by single cell RNA-seq. PLoS One 2018; 13:e0206785. [PMID: 30383866 PMCID: PMC6211742 DOI: 10.1371/journal.pone.0206785] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/18/2018] [Indexed: 12/15/2022] Open
Abstract
Here we investigated different cell populations within ovarian cancer using single-cell RNA seq: fourteen samples from nine patients with differing grades (high grade, low grade and benign) as well as different origin sites (primary and metastatic tumor site, ovarian in origin and fallopian in origin). We were able to identify sixteen distinct cell populations with specific cells correlated to high grade tumors, low grade tumors, benign and one population unique to a patient with a breast cancer relapse. Furthermore the proportion of these populations changes from primary to metastatic in a shift from mainly epithelial cells to leukocytes with few cancer epithelial cells in the metastases. Differential gene expression shows myeloid lineage cells are the primary cell group expressing soluble factors in primary samples while fibroblasts do so in metastatic samples. The leukocytes that were captured did not seem to be suppressed through known pro-tumor cytokines from any of the cell populations. Single cell RNA-seq is necessary to de-tangle cellular heterogeneity for better understanding of ovarian cancer progression.
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Affiliation(s)
- Andrew J. Shih
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Manhasset, New York, United States of America
- * E-mail:
| | - Andrew Menzin
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, United States of America
| | - Jill Whyte
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, United States of America
| | - John Lovecchio
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, United States of America
| | - Anthony Liew
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Manhasset, New York, United States of America
| | - Houman Khalili
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Manhasset, New York, United States of America
| | - Tawfiqul Bhuiya
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, United States of America
| | - Peter K. Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Manhasset, New York, United States of America
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, United States of America
| | - Annette T. Lee
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Manhasset, New York, United States of America
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, United States of America
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12
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Shih AJ, Korsunsky I, Guttadauria B, Bhuiya T, Liew A, Khalili H, Gregersen PK, Lee AT. Abstract P2-07-09: Integrative analysis of miRNA and mRNA expression in metastatic versus non-metastatic triple negative breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p2-07-09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Triple Negative Breast Cancer (TNBC) is a subset of breast cancer that is difficult to treat clinically and is characterized by being estrogen receptor (ER) negative, progesterone receptor (PR) negative, and does not overexpress human epidermal growth factor receptor 2 (HER2). Patients with TNBC tend to have a worse prognosis than other breast cancer subtypes.
Methods: We obtained fifteen TNBC sample FFPE tissue blocks with corresponding plasma samples. All samples were from primary tumors; seven samples having metastasized, four samples that had not metastasized and four samples with unknown metastatic status. The total RNA was isolated from FFPE blocks using the RecoverAll Total Nucleic Acid Isolation Protocol. miRNA from plasma was isolated using Ambion's mirVANA kit. The plasma and tissue miRNAs were evaluated using the QuantStudio qPCR platform, capturing ˜750 miRNAs. The mRNA was processed using the TruSeq RNA Access kit and sequenced on the Illumina NextSeq platform. Analysis of the miRNA and mRNA individually was performed using limma and DESeq2 packages, respectively. Gene enrichment analysis of the mRNA expression was done using the GAGE package on KEGG pathways while the integrative analysis was done with sparse Canonical Correlation Analysis (sCCA) using the PMA pacakge.
Results: Analysis of plasma miRNA had four miRNAs with a significant difference in raw p-value (p < 0.05) between metastatic and non-metastatic TNBC; miRNA 708, 483-3p, 518f, and 766; in the tissue there were fifteen miRNA with p < 0.05, with one miR-872 still having significance after adjusting for multiple testing. mRNA had 33 genes being significant after multiple testing correction with several immune KEGG pathways being downregulated in metastatic samples (adjusted p < 0.05). The integrative analysis revealed five microRNA (miR-216, miR-127, miR-370, miR-382, and miR-487b) and 312 gene modules enriched in integrin (Fisher p < 10^-5) and extracellular matrix (Fisher p < 10^-6) signaling.
Conclusions: One of the circulating plasma miRNAs, miR483-3p, has been found to promote tumorigenesis, while miR581f and miR766 have not been reported in cancer to date. Further investigation into these miRNA could provide a feasible biomarker. The downregulation of immune pathways observed within the metastatic TNBC subjects implies immune evasion is of particular importance for metastasis and a targeted immunotherapy may be a viable treatment option. The integrative analysis of the miRNA and mRNA showed an enrichment in pathways previously linked to increased proliferation and chemoresistance, with an increased signal compared to either miRNA or mRNA alone.
Citation Format: Shih AJ, Korsunsky I, Guttadauria B, Bhuiya T, Liew A, Khalili H, Gregersen PK, Lee AT. Integrative analysis of miRNA and mRNA expression in metastatic versus non-metastatic triple negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-07-09.
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Affiliation(s)
- AJ Shih
- The Feinstein Institute for Medical Research, Northwell Health, Manhassett, NY; Hofstra Northwell School of Medicine, Hempstead, NY; Northwell Health, Lake Success, NY
| | - I Korsunsky
- The Feinstein Institute for Medical Research, Northwell Health, Manhassett, NY; Hofstra Northwell School of Medicine, Hempstead, NY; Northwell Health, Lake Success, NY
| | - B Guttadauria
- The Feinstein Institute for Medical Research, Northwell Health, Manhassett, NY; Hofstra Northwell School of Medicine, Hempstead, NY; Northwell Health, Lake Success, NY
| | - T Bhuiya
- The Feinstein Institute for Medical Research, Northwell Health, Manhassett, NY; Hofstra Northwell School of Medicine, Hempstead, NY; Northwell Health, Lake Success, NY
| | - A Liew
- The Feinstein Institute for Medical Research, Northwell Health, Manhassett, NY; Hofstra Northwell School of Medicine, Hempstead, NY; Northwell Health, Lake Success, NY
| | - H Khalili
- The Feinstein Institute for Medical Research, Northwell Health, Manhassett, NY; Hofstra Northwell School of Medicine, Hempstead, NY; Northwell Health, Lake Success, NY
| | - PK Gregersen
- The Feinstein Institute for Medical Research, Northwell Health, Manhassett, NY; Hofstra Northwell School of Medicine, Hempstead, NY; Northwell Health, Lake Success, NY
| | - AT Lee
- The Feinstein Institute for Medical Research, Northwell Health, Manhassett, NY; Hofstra Northwell School of Medicine, Hempstead, NY; Northwell Health, Lake Success, NY
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13
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Chen RK, Shih AJ. Multi-modality gellan gum-based tissue-mimicking phantom with targeted mechanical, electrical, and thermal properties. Phys Med Biol 2013; 58:5511-25. [DOI: 10.1088/0031-9155/58/16/5511] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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14
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15
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Shih AJ, Telesco SE, Choi SH, Lemmon MA, Radhakrishnan R. Molecular dynamics analysis of conserved hydrophobic and hydrophilic bond-interaction networks in ErbB family kinases. Biochem J 2011; 436:241-51. [PMID: 21426301 PMCID: PMC3138537 DOI: 10.1042/bj20101791] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The EGFR (epidermal growth factor receptor)/ErbB/HER (human EGFR) family of kinases contains four homologous receptor tyrosine kinases that are important regulatory elements in key signalling pathways. To elucidate the atomistic mechanisms of dimerization-dependent activation in the ErbB family, we have performed molecular dynamics simulations of the intracellular kinase domains of three members of the ErbB family (those with known kinase activity), namely EGFR, ErbB2 (HER2) and ErbB4 (HER4), in different molecular contexts: monomer against dimer and wild-type against mutant. Using bioinformatics and fluctuation analyses of the molecular dynamics trajectories, we relate sequence similarities to correspondence of specific bond-interaction networks and collective dynamical modes. We find that in the active conformation of the ErbB kinases, key subdomain motions are co-ordinated through conserved hydrophilic interactions: activating bond-networks consisting of hydrogen bonds and salt bridges. The inactive conformations also demonstrate conserved bonding patterns (albeit less extensive) that sequester key residues and disrupt the activating bond network. Both conformational states have distinct hydrophobic advantages through context-specific hydrophobic interactions. We show that the functional (activating) asymmetric kinase dimer interface forces a corresponding change in the hydrophobic and hydrophilic interactions that characterize the inactivating bond network, resulting in motion of the αC-helix through allostery. Several of the clinically identified activating kinase mutations of EGFR act in a similar fashion to disrupt the inactivating bond network. The present molecular dynamics study reveals a fundamental difference in the sequence of events in EGFR activation compared with that described for the Src kinase Hck.
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Affiliation(s)
- Andrew J. Shih
- Department of Bioengineering, University of Pennsylvania, 210 S. 33 Street, 240 Skirkanich Hall, Philadelphia, PA 19104
| | - Shannon E. Telesco
- Department of Bioengineering, University of Pennsylvania, 210 S. 33 Street, 240 Skirkanich Hall, Philadelphia, PA 19104
| | - Sung Hee Choi
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 809C Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, PA 19104
| | - Mark A. Lemmon
- Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 809C Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, PA 19104
| | - Ravi Radhakrishnan
- Department of Bioengineering, University of Pennsylvania, 210 S. 33 Street, 240 Skirkanich Hall, Philadelphia, PA 19104
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16
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Telesco SE, Shih AJ, Jia F, Radhakrishnan R. A multiscale modeling approach to investigate molecular mechanisms of pseudokinase activation and drug resistance in the HER3/ErbB3 receptor tyrosine kinase signaling network. Mol Biosyst 2011; 7:2066-80. [PMID: 21509365 DOI: 10.1039/c0mb00345j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Multiscale modeling provides a powerful and quantitative platform for investigating the complexity inherent in intracellular signaling pathways and rationalizing the effects of molecular perturbations on downstream signaling events and ultimately, on the cell phenotype. Here we describe the application of a multiscale modeling scheme to the HER3/ErbB3 receptor tyrosine kinase (RTK) signaling network, which regulates critical cellular processes including proliferation, migration and differentiation. The HER3 kinase is a topic of current interest and investigation, as it has been implicated in mechanisms of resistance to tyrosine kinase inhibition (TKI) of EGFR and HER2 in the treatment of many human malignancies. Moreover, the commonly regarded status of HER3 as a catalytically inactive 'pseudokinase' has recently been challenged by our previous study, which demonstrated robust residual kinase activity for HER3. Through our multiscale model, we investigate the most significant molecular interactions that contribute to potential mechanisms of HER3 activity and the physiological relevance of this activity to mechanisms of drug resistance in an ErbB-driven tumor cell in silico. The results of our molecular-scale simulations support the characterization of HER3 as a weakly active kinase that, in contrast to its fully-active ErbB family members, depends upon a unique hydrophobic interface to coordinate the alignment of specific catalytic residues required for its activity. Translating our molecular simulation results of the uniquely active behavior of the HER3 kinase into a physiologically relevant environment, our HER3 signaling model demonstrates that even a weak level of HER3 activity may be sufficient to induce AKT signaling and TKI resistance in the context of an ErbB signaling-dependent tumor cell, and therefore therapeutic targeting of HER3 may represent a superior treatment strategy for specific ErbB-driven cancers.
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Affiliation(s)
- Shannon E Telesco
- Department of Bioengineering, University of Pennsylvania, 210 S. 33rd Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
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17
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Shih AJ, Telesco SE, Radhakrishnan R. Analysis of Somatic Mutations in Cancer: Molecular Mechanisms of Activation in the ErbB Family of Receptor Tyrosine Kinases. Cancers (Basel) 2011; 3:1195-231. [PMID: 21701703 PMCID: PMC3119571 DOI: 10.3390/cancers3011195] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 02/28/2011] [Accepted: 03/01/2011] [Indexed: 01/02/2023] Open
Abstract
The ErbB/EGFR/HER family of kinases consists of four homologous receptor tyrosine kinases which are important regulatory elements in many cellular processes, including cell proliferation, differentiation, and migration. Somatic mutations in, or over-expression of, the ErbB family is found in many cancers and is correlated with a poor prognosis; particularly, clinically identified mutations found in non-small-cell lung cancer (NSCLC) of ErbB1 have been shown to increase its basal kinase activity and patients carrying these mutations respond remarkably to the small tyrosine kinase inhibitor gefitinib. Here, we analyze the potential effects of the currently catalogued clinically identified mutations in the ErbB family kinase domains on the molecular mechanisms of kinase activation. Recently, we identified conserved networks of hydrophilic and hydrophobic interactions characteristic to the active and inactive conformation, respectively. Here, we show that the clinically identified mutants influence the kinase activity in distinctive fashion by affecting the characteristic interaction networks.
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Affiliation(s)
- Andrew J. Shih
- Department of Bioengineering, University of Pennsylvania, 210 S. 33 Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA; E-Mails: (A.J.S.); (S.E.T)
| | - Shannon E. Telesco
- Department of Bioengineering, University of Pennsylvania, 210 S. 33 Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA; E-Mails: (A.J.S.); (S.E.T)
| | - Ravi Radhakrishnan
- Department of Bioengineering, University of Pennsylvania, 210 S. 33 Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA; E-Mails: (A.J.S.); (S.E.T)
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18
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Purvis JE, Shih AJ, Liu Y, Radhakrishnan R. Cancer Cell: Linking Oncogenic Signaling to Molecular Structure. Chapman Hall CRC Math Comput Biol Ser 2011; 2011:31-44. [PMID: 25285322 PMCID: PMC4180656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A multiscale strategy is presented for constructing models of intracellular signaling networks in which the oncogenic behavior of the network is encoded through alternate parameterization of the kinetic and structural properties of mutant oncoproteins. The approach uses molecular dynamics and docking simulations to quantify altered topologies of interactions as well as to provide the missing parameters for network models of both wild-type and oncogenic signaling. Through simulation of the resulting signaling networks, the global behavior of these networks may then be compared and functional roles may be assigned to the mutant oncoproteins. An example of this approach is presented in which structural alterations found in a mutant form of the epidermal growth factor receptor are represented as kinetic perturbations in a model of growth factor signaling. Based on network parameters estimated from molecular-level simulations, simulations at the network level show that small perturbations in molecular structure can lead to profoundly altered cellular phenotype.
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Affiliation(s)
- Jeremy E Purvis
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, 210 S. 33 Street, 240 Skirkanich Hall, Philadelphia PA, USA
| | - Andrew J Shih
- Department of Bioengineering, University of Pennsylvania, 210 S. 33 Street, 240 Skirkanich Hall, Philadelphia PA, USA
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Shih AJ, Purvis J, Radhakrishnan R. Molecular systems biology of ErbB1 signaling: bridging the gap through multiscale modeling and high-performance computing. Mol Biosyst 2008; 4:1151-9. [PMID: 19396377 PMCID: PMC2811052 DOI: 10.1039/b803806f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The complexity in intracellular signaling mechanisms relevant for the conquest of many diseases resides at different levels of organization with scales ranging from the subatomic realm relevant to catalytic functions of enzymes to the mesoscopic realm relevant to the cooperative association of molecular assemblies and membrane processes. Consequently, the challenge of representing and quantifying functional or dysfunctional modules within the networks remains due to the current limitations in our understanding of mesoscopic biology, i.e., how the components assemble into functional molecular ensembles. A multiscale approach is necessary to treat a hierarchy of interactions ranging from molecular (nm, ns) to signaling (microm, ms) length and time scales, which necessitates the development and application of specialized modeling tools. Complementary to multiscale experimentation (encompassing structural biology, mechanistic enzymology, cell biology, and single molecule studies) multiscale modeling offers a powerful and quantitative alternative for the study of functional intracellular signaling modules. Here, we describe the application of a multiscale approach to signaling mediated by the ErbB1 receptor which constitutes a network hub for the cell's proliferative, migratory, and survival programs. Through our multiscale model, we mechanistically describe how point-mutations in the ErbB1 receptor can profoundly alter signaling characteristics leading to the onset of oncogenic transformations. Specifically, we describe how the point mutations induce cascading fragility mechanisms at the molecular scale as well as at the scale of the signaling network to preferentially activate the survival factor Akt. We provide a quantitative explanation for how the hallmark of preferential Akt activation in cell-lines harboring the constitutively active mutant ErbB1 receptors causes these cell-lines to be addicted to ErbB1-mediated generation of survival signals. Consequently, inhibition of ErbB1 activity leads to a remarkable therapeutic response in the addicted cell lines.
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Affiliation(s)
- Andrew J. Shih
- Department of Bioengineering, University of Pennsylvania, 210 S 33rd Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
| | - Jeremy Purvis
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, 210 S 33rd Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
| | - Ravi Radhakrishnan
- Department of Bioengineering, University of Pennsylvania, 210 S 33rd Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, 210 S 33rd Street, 240 Skirkanich Hall, Philadelphia, PA 19104, USA
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