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Michaud ME, Mota L, Bakhtiari M, Thomas BE, Tomeo J, Pilcher W, Contreras M, Ferran C, Bhasin S, Pradhan-Nabzdyk L, LoGerfo FW, Liang P, Bhasin MK. Integrated single-nuclei and spatial transcriptomic analysis reveals propagation of early acute vein harvest and distension injury signaling pathways following arterial implantation. bioRxiv 2024:2023.10.31.564995. [PMID: 37961724 PMCID: PMC10635041 DOI: 10.1101/2023.10.31.564995] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background Vein graft failure (VGF) following cardiovascular bypass surgery results in significant patient morbidity and cost to the healthcare system. Vein graft injury can occur during autogenous vein harvest and preparation, as well as after implantation into the arterial system, leading to the development of intimal hyperplasia, vein graft stenosis, and, ultimately, bypass graft failure. While previous studies have identified maladaptive pathways that occur shortly after implantation, the specific signaling pathways that occur during vein graft preparation are not well defined and may result in a cumulative impact on VGF. We, therefore, aimed to elucidate the response of the vein conduit wall during harvest and following implantation, probing the key maladaptive pathways driving graft failure with the overarching goal of identifying therapeutic targets for biologic intervention to minimize these natural responses to surgical vein graft injury. Methods Employing a novel approach to investigating vascular pathologies, we harnessed both single-nuclei RNA-sequencing (snRNA-seq) and spatial transcriptomics (ST) analyses to profile the genomic effects of vein grafts after harvest and distension, then compared these findings to vein grafts obtained 24 hours after carotid-cartoid vein bypass implantation in a canine model (n=4). Results Spatial transcriptomic analysis of canine cephalic vein after initial conduit harvest and distention revealed significant enrichment of pathways (P < 0.05) involved in the activation of endothelial cells (ECs), fibroblasts (FBs), and vascular smooth muscle cells (VSMCs), namely pathways responsible for cellular proliferation and migration and platelet activation across the intimal and medial layers, cytokine signaling within the adventitial layer, and extracellular matrix (ECM) remodeling throughout the vein wall. Subsequent snRNA-seq analysis supported these findings and further unveiled distinct EC and FB subpopulations with significant upregulation (P < 0.00001) of markers related to endothelial injury response and cellular activation of ECs, FBs, and VSMCs. Similarly, in vein grafts obtained 24 hours after arterial bypass, there was an increase in myeloid cell, protomyofibroblast, injury-response EC, and mesenchymal-transitioning EC subpopulations with a concomitant decrease in homeostatic ECs and fibroblasts. Among these markers were genes previously implicated in vein graft injury, including VCAN (versican), FBN1 (fibrillin-1), and VEGFC (vascular endothelial growth factor C), in addition to novel genes of interest such as GLIS3 (GLIS family zinc finger 3) and EPHA3 (ephrin-A3). These genes were further noted to be driving the expression of genes implicated in vascular remodeling and graft failure, such as IL-6, TGFBR1, SMAD4, and ADAMTS9. By integrating the ST and snRNA-seq datasets, we highlighted the spatial architecture of the vein graft following distension, wherein activated and mesenchymal-transitioning ECs, myeloid cells, and FBs were notably enriched in the intima and media of distended veins. Lastly, intercellular communication network analysis unveiled the critical roles of activated ECs, mesenchymal transitioning ECs, protomyofibroblasts, and VSMCs in upregulating signaling pathways associated with cellular proliferation (MDK, PDGF, VEGF), transdifferentiation (Notch), migration (ephrin, semaphorin), ECM remodeling (collagen, laminin, fibronectin), and inflammation (thrombospondin), following distension. Conclusions Vein conduit harvest and distension elicit a prompt genomic response facilitated by distinct cellular subpopulations heterogeneously distributed throughout the vein wall. This response was found to be further exacerbated following vein graft implantation, resulting in a cascade of maladaptive gene regulatory networks. Together, these results suggest that distension initiates the upregulation of pathological pathways that may ultimately contribute to bypass graft failure and presents potential early targets warranting investigation for targeted therapies. This work highlights the first applications of single-nuclei and spatial transcriptomic analyses to investigate venous pathologies, underscoring the utility of these methodologies and providing a foundation for future investigations.
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Affiliation(s)
- Marina E. Michaud
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Lucas Mota
- Department of Surgery, Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Mojtaba Bakhtiari
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Beena E. Thomas
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
| | - John Tomeo
- Department of Surgery, Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - William Pilcher
- Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
| | - Mauricio Contreras
- Department of Surgery, Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Christiane Ferran
- Department of Surgery, Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Center for Vascular Biology Research and the Division of Nephrology Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Swati Bhasin
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA
| | - Leena Pradhan-Nabzdyk
- Department of Surgery, Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Frank W. LoGerfo
- Department of Surgery, Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Patric Liang
- Department of Surgery, Division of Vascular and Endovascular Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Manoj K. Bhasin
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA 30322, USA
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA
- Department of Biomedical Engineering, Emory University, Atlanta, GA 30322, USA
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2
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Johnson TS, MacDonald TJ, Pacholczyk R, Aguilera D, Al-Basheer A, Bajaj M, Bandopadhayay P, Berrong Z, Bouffet E, Castellino RC, Dorris K, Eaton BR, Esiashvili N, Fangusaro JR, Foreman N, Fridlyand D, Giller C, Heger IM, Huang C, Kadom N, Kennedy EP, Manoharan N, Martin W, McDonough C, Parker RS, Ramaswamy V, Ring E, Rojiani A, Sadek RF, Satpathy S, Schniederjan M, Smith A, Smith C, Thomas BE, Vaizer R, Yeo KK, Bhasin MK, Munn DH. Indoximod-based chemo-immunotherapy for pediatric brain tumors: A first-in-children phase I trial. Neuro Oncol 2024; 26:348-361. [PMID: 37715730 PMCID: PMC10836763 DOI: 10.1093/neuonc/noad174] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 03/23/2023] [Indexed: 09/18/2023] Open
Abstract
BACKGROUND Recurrent brain tumors are the leading cause of cancer death in children. Indoleamine 2,3-dioxygenase (IDO) is a targetable metabolic checkpoint that, in preclinical models, inhibits anti-tumor immunity following chemotherapy. METHODS We conducted a phase I trial (NCT02502708) of the oral IDO-pathway inhibitor indoximod in children with recurrent brain tumors or newly diagnosed diffuse intrinsic pontine glioma (DIPG). Separate dose-finding arms were performed for indoximod in combination with oral temozolomide (200 mg/m2/day x 5 days in 28-day cycles), or with palliative conformal radiation. Blood samples were collected at baseline and monthly for single-cell RNA-sequencing with paired single-cell T cell receptor sequencing. RESULTS Eighty-one patients were treated with indoximod-based combination therapy. Median follow-up was 52 months (range 39-77 months). Maximum tolerated dose was not reached, and the pediatric dose of indoximod was determined as 19.2 mg/kg/dose, twice daily. Median overall survival was 13.3 months (n = 68, range 0.2-62.7) for all patients with recurrent disease and 14.4 months (n = 13, range 4.7-29.7) for DIPG. The subset of n = 26 patients who showed evidence of objective response (even a partial or mixed response) had over 3-fold longer median OS (25.2 months, range 5.4-61.9, p = 0.006) compared to n = 37 nonresponders (7.3 months, range 0.2-62.7). Four patients remain free of active disease longer than 36 months. Single-cell sequencing confirmed emergence of new circulating CD8 T cell clonotypes with late effector phenotype. CONCLUSIONS Indoximod was well tolerated and could be safely combined with chemotherapy and radiation. Encouraging preliminary evidence of efficacy supports advancing to Phase II/III trials for pediatric brain tumors.
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Affiliation(s)
- Theodore S Johnson
- Georgia Cancer Center, Augusta University, Augusta, Georgia, USA
- Department of Pediatrics, Augusta University, Augusta, Georgia, USA
| | - Tobey J MacDonald
- Aflac Cancer & Blood Disorders Center at Children’s Healthcare of Atlanta and Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Rafal Pacholczyk
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Dolly Aguilera
- Aflac Cancer & Blood Disorders Center at Children’s Healthcare of Atlanta and Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Ahmad Al-Basheer
- Georgia Cancer Center, Augusta University, Augusta, Georgia, USA
- Department of Radiation Oncology, Augusta University, Augusta, Georgia, USA
| | - Manish Bajaj
- Department of Radiology, Augusta University, Augusta, Georgia, USA
| | | | - Zuzana Berrong
- Georgia Cancer Center, Augusta University, Augusta, Georgia, USA
| | - Eric Bouffet
- Department of Paediatrics, The Hospital for Sick Children, Toronto, Canada
| | - Robert C Castellino
- Aflac Cancer & Blood Disorders Center at Children’s Healthcare of Atlanta and Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Kathleen Dorris
- Department of Pediatrics, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Bree R Eaton
- Department of Radiation Oncology and Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - Natia Esiashvili
- Department of Radiation Oncology and Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - Jason R Fangusaro
- Aflac Cancer & Blood Disorders Center at Children’s Healthcare of Atlanta and Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Nicholas Foreman
- Department of Pediatrics, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Diana Fridlyand
- Department of Pediatrics, Augusta University, Augusta, Georgia, USA
| | - Cole Giller
- Department of Neurosurgery, Augusta University, Augusta, Georgia, USA
| | - Ian M Heger
- Department of Neurosurgery, Augusta University, Augusta, Georgia, USA
| | - Chenbin Huang
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
- Department of Biomedical Informatics, Emory University, Atlanta, Georgia, USA
| | - Nadja Kadom
- Department of Radiology and Winship Cancer Institute of Emory University, Atlanta, Georgia, USA
| | - Eugene P Kennedy
- Lumos Pharma, Inc. (formerly NewLink Genetics Corporation), Austin, Texas, USA
| | - Neevika Manoharan
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - William Martin
- Department of Radiation Oncology, Augusta University, Augusta, Georgia, USA
| | - Colleen McDonough
- Georgia Cancer Center, Augusta University, Augusta, Georgia, USA
- Department of Pediatrics, Augusta University, Augusta, Georgia, USA
| | - Rebecca S Parker
- Georgia Cancer Center, Augusta University, Augusta, Georgia, USA
- Department of Pediatrics, Augusta University, Augusta, Georgia, USA
| | - Vijay Ramaswamy
- Department of Paediatrics, The Hospital for Sick Children, Toronto, Canada
| | - Eric Ring
- Georgia Cancer Center, Augusta University, Augusta, Georgia, USA
- Department of Pediatrics, Augusta University, Augusta, Georgia, USA
| | - Amyn Rojiani
- Georgia Cancer Center, Augusta University, Augusta, Georgia, USA
- Department of Pathology, Augusta University, Augusta, Georgia, USA
| | - Ramses F Sadek
- Georgia Cancer Center, Augusta University, Augusta, Georgia, USA
- Department of Population Health Sciences, Augusta University, Augusta, Georgia, USA
| | - Sarthak Satpathy
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
- Department of Biomedical Informatics, Emory University, Atlanta, Georgia, USA
| | - Matthew Schniederjan
- Children’s Healthcare of Atlanta and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - Amy Smith
- Department of Pediatrics, Arnold Palmer Hospital for Children, Orlando, Florida, USA
| | - Christopher Smith
- Lumos Pharma, Inc. (formerly NewLink Genetics Corporation), Austin, Texas, USA
| | - Beena E Thomas
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Rachel Vaizer
- Department of Pediatrics, Augusta University, Augusta, Georgia, USA
| | - Kee Kiat Yeo
- Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Manoj K Bhasin
- Aflac Cancer & Blood Disorders Center at Children’s Healthcare of Atlanta and Department of Pediatrics, Emory University, Atlanta, Georgia, USA
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
- Department of Biomedical Informatics, Emory University, Atlanta, Georgia, USA
| | - David H Munn
- Georgia Cancer Center, Augusta University, Augusta, Georgia, USA
- Department of Pediatrics, Augusta University, Augusta, Georgia, USA
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3
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Satpathy S, Thomas BE, Pilcher WJ, Bakhtiari M, Ponder LA, Pacholczyk R, Prahalad S, Bhasin SS, Munn DH, Bhasin MK. The Simple prEservatioN of Single cElls method for cryopreservation enables the generation of single-cell immune profiles from whole blood. Front Immunol 2023; 14:1271800. [PMID: 38090590 PMCID: PMC10713715 DOI: 10.3389/fimmu.2023.1271800] [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: 08/02/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction Current multistep methods utilized for preparing and cryopreserving single-cell suspensions from blood samples for single-cell RNA sequencing (scRNA-seq) are time-consuming, requiring trained personnel and special equipment, so limiting their clinical adoption. We developed a method, Simple prEservatioN of Single cElls (SENSE), for single-step cryopreservation of whole blood (WB) along with granulocyte depletion during single-cell assay, to generate high quality single-cell profiles (SCP). Methods WB was cryopreserved using the SENSE method and peripheral blood mononuclear cells (PBMCs) were isolated and cryopreserved using the traditional density-gradient method (PBMC method) from the same blood sample (n=6). The SCPs obtained from both methods were processed using a similar pipeline and quality control parameters. Further, entropy calculation, differential gene expression, and cellular communication analysis were performed to compare cell types and subtypes from both methods. Results Highly viable (86.3 ± 1.51%) single-cell suspensions (22,353 cells) were obtained from the six WB samples cryopreserved using the SENSE method. In-depth characterization of the scRNA-seq datasets from the samples processed with the SENSE method yielded high-quality profiles of lymphoid and myeloid cell types which were in concordance with the profiles obtained with classical multistep PBMC method processed samples. Additionally, the SENSE method cryopreserved samples exhibited significantly higher T-cell enrichment, enabling deeper characterization of T-cell subtypes. Overall, the SENSE and PBMC methods processed samples exhibited transcriptional, and cellular communication network level similarities across cell types with no batch effect except in myeloid lineage cells. Discussion Comparative analysis of scRNA-seq datasets obtained with the two cryopreservation methods i.e., SENSE and PBMC methods, yielded similar cellular and molecular profiles, confirming the suitability of the former method's incorporation in clinics/labs for cryopreserving and obtaining high-quality single-cells for conducting critical translational research.
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Affiliation(s)
- Sarthak Satpathy
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA, United States
- Department of Biomedical Informatics, Emory University, Atlanta, GA, United States
| | - Beena E. Thomas
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA, United States
- Department of Pediatrics, Emory University, Atlanta, GA, United States
| | - William J. Pilcher
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA, United States
- Department of Biomedical Informatics, Emory University, Atlanta, GA, United States
| | - Mojtaba Bakhtiari
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA, United States
- Department of Pediatrics, Emory University, Atlanta, GA, United States
| | - Lori A. Ponder
- Division of Rheumatology, Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Rafal Pacholczyk
- Georgia Cancer Center, Augusta University, Augusta, GA, United States
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA, United States
| | - Sampath Prahalad
- Department of Pediatrics, Emory University, Atlanta, GA, United States
- Division of Rheumatology, Children’s Healthcare of Atlanta, Atlanta, GA, United States
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, United States
| | - Swati S. Bhasin
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA, United States
- Department of Biomedical Informatics, Emory University, Atlanta, GA, United States
- Department of Pediatrics, Emory University, Atlanta, GA, United States
| | - David H. Munn
- Georgia Cancer Center, Augusta University, Augusta, GA, United States
- Department of Pediatrics, Augusta University, Augusta, GA, United States
| | - Manoj K. Bhasin
- Aflac Cancer and Blood Disorders Center, Children Healthcare of Atlanta, Atlanta, GA, United States
- Department of Biomedical Informatics, Emory University, Atlanta, GA, United States
- Department of Pediatrics, Emory University, Atlanta, GA, United States
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4
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Ganesan R, Bhasin SS, Bakhtiary M, Krishnan U, Cheemarla NR, Thomas BE, Bhasin MK, Sukhatme VP. Taxane chemotherapy induces stromal injury that leads to breast cancer dormancy escape. PLoS Biol 2023; 21:e3002275. [PMID: 37699010 PMCID: PMC10497165 DOI: 10.1371/journal.pbio.3002275] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 04/04/2023] [Accepted: 07/24/2023] [Indexed: 09/14/2023] Open
Abstract
A major cause of cancer recurrence following chemotherapy is cancer dormancy escape. Taxane-based chemotherapy is standard of care in breast cancer treatment aimed at killing proliferating cancer cells. Here, we demonstrate that docetaxel injures stromal cells, which release protumor cytokines, IL-6 and granulocyte colony stimulating factor (G-CSF), that in turn invoke dormant cancer outgrowth both in vitro and in vivo. Single-cell transcriptomics shows a reprogramming of awakened cancer cells including several survival cues such as stemness, chemoresistance in a tumor stromal organoid (TSO) model, as well as an altered tumor microenvironment (TME) with augmented protumor immune signaling in a syngeneic mouse breast cancer model. IL-6 plays a role in cancer cell proliferation, whereas G-CSF mediates tumor immunosuppression. Pathways and differential expression analyses confirmed MEK as the key regulatory molecule in cancer cell outgrowth and survival. Antibody targeting of protumor cytokines (IL-6, G-CSF) or inhibition of cytokine signaling via MEK/ERK pathway using selumetinib prior to docetaxel treatment prevented cancer dormancy outgrowth suggesting a novel therapeutic strategy to prevent cancer recurrence.
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Affiliation(s)
- Ramya Ganesan
- Department of Medicine—Renal Division, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Swati S. Bhasin
- Department of Pediatrics—Hematology Division, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
| | - Mojtaba Bakhtiary
- Department of Pediatrics—Hematology Division, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
| | - Upaasana Krishnan
- Department of Pediatrics—Hematology Division, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Nagarjuna R. Cheemarla
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Beena E. Thomas
- Department of Pediatrics—Hematology Division, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
| | - Manoj K. Bhasin
- Department of Pediatrics—Hematology Division, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Aflac Cancer and Blood Disorders Center, Children’s Healthcare of Atlanta, Atlanta, Georgia, United States of America
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Department of Biomedical Informatics, Emory University, Atlanta, Georgia, United States of America
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Winship Cancer Institute, Emory University, Atlanta, Georgia, United States of America
| | - Vikas P. Sukhatme
- Department of Medicine—Renal Division, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Winship Cancer Institute, Emory University, Atlanta, Georgia, United States of America
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5
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Bhasin SS, Thomas BE, Summers RJ, Sarkar D, Mumme H, Pilcher W, Emam M, Raikar SS, Park SI, Castellino SM, Graham DK, Bhasin MK, DeRyckere D. Pediatric T-cell acute lymphoblastic leukemia blast signature and MRD associated immune environment changes defined by single cell transcriptomics analysis. Sci Rep 2023; 13:12556. [PMID: 37532715 PMCID: PMC10397284 DOI: 10.1038/s41598-023-39152-z] [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] [Received: 02/28/2023] [Accepted: 07/20/2023] [Indexed: 08/04/2023] Open
Abstract
Different driver mutations and/or chromosomal aberrations and dysregulated signaling interactions between leukemia cells and the immune microenvironment have been implicated in the development of T-cell acute lymphoblastic leukemia (T-ALL). To better understand changes in the bone marrow microenvironment and signaling pathways in pediatric T-ALL, bone marrows collected at diagnosis (Dx) and end of induction therapy (EOI) from 11 patients at a single center were profiled by single cell transcriptomics (10 Dx, 5 paired EOI, 1 relapse). T-ALL blasts were identified by comparison with healthy bone marrow cells. T-ALL blast-associated gene signature included SOX4, STMN1, JUN, HES4, CDK6, ARMH1 among the most significantly overexpressed genes, some of which are associated with poor prognosis in children with T-ALL. Transcriptome profiles of the blast cells exhibited significant inter-patient heterogeneity. Post induction therapy expression profiles of the immune cells revealed significant changes. Residual blast cells in MRD+ EOI samples exhibited significant upregulation (P < 0.01) of PD-1 and RhoGDI signaling pathways. Differences in cellular communication were noted in the presence of residual disease in T cell and hematopoietic stem cell compartments in the bone marrow. Together, these studies generate new insights and expand our understanding of the bone marrow landscape in pediatric T-ALL.
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Affiliation(s)
- Swati S Bhasin
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA.
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
| | - Beena E Thomas
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ryan J Summers
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Debasree Sarkar
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA
| | - Hope Mumme
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA
| | - William Pilcher
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mohamed Emam
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Sunil S Raikar
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Sunita I Park
- Department of Pathology, Children's Healthcare of Atlanta, Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Sharon M Castellino
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Douglas K Graham
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Manoj K Bhasin
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Deborah DeRyckere
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
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6
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Vava A, Paccez JD, Wang Y, Gu X, Bhasin MK, Myers M, Soares NC, Libermann TA, Zerbini LF. DCUN1D1 Is an Essential Regulator of Prostate Cancer Proliferation and Tumour Growth That Acts through Neddylation of Cullin 1, 3, 4A and 5 and Deregulation of Wnt/Catenin Pathway. Cells 2023; 12:1973. [PMID: 37566052 PMCID: PMC10417424 DOI: 10.3390/cells12151973] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/12/2023] Open
Abstract
Defective in cullin neddylation 1 domain containing 1 (DCUN1D1) is an E3 ligase for the neddylation, a post-translational process similar to and occurring in parallel to ubiquitin proteasome pathway. Although established as an oncogene in a variety of squamous cell carcinomas, the precise role of DCUN1D1 in prostate cancer (PCa) has not been previously explored thoroughly. Here, we investigated the role of DCUN1D1 in PCa and demonstrated that DCUN1D1 is upregulated in cell lines as well as human tissue samples. Inhibition of DCUN1D1 significantly reduced PCa cell proliferation and migration and remarkably inhibited xenograft formation in mice. Applying both genomics and proteomics approaches, we provide novel information about the DCUN1D1 mechanism of action. We identified CUL3, CUL4B, RBX1, CAND1 and RPS19 proteins as DCUN1D1 binding partners. Our analysis also revealed the dysregulation of genes associated with cellular growth and proliferation, developmental, cell death and cancer pathways and the WNT/β-catenin pathway as potential mechanisms. Inhibition of DCUN1D1 leads to the inactivation of β-catenin through its phosphorylation and degradation which inhibits the downstream action of β-catenin, reducing its interaction with Lef1 in the Lef1/TCF complex that regulates Wnt target gene expression. Together our data point to an essential role of the DCUN1D1 protein in PCa which can be explored for potential targeted therapy.
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Affiliation(s)
- Akhona Vava
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town 7925, South Africa; (A.V.); (J.D.P.)
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Juliano D. Paccez
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town 7925, South Africa; (A.V.); (J.D.P.)
| | - Yihong Wang
- Department of Pathology and Laboratory Medicine, Warren Alpert School of Medicine, Brown University, Providence, RI 02912, USA;
| | - Xuesong Gu
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA; (X.G.); (T.A.L.)
| | - Manoj K. Bhasin
- Department of Pediatrics Bioinformatics, Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Michael Myers
- Protein Networks Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy;
| | - Nelson C. Soares
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah P.O. Box 26666, United Arab Emirates;
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 26666, United Arab Emirates
- Laboratory of Proteomics, Department of Human Genetics, National Institute of Health, Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
- Centre for Toxicogenomics and Human Health (ToxOmics), NOVA/School/Faculdade de Lisboa, 1169-056 Lisbon, Portugal
| | - Towia A. Libermann
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA; (X.G.); (T.A.L.)
| | - Luiz F. Zerbini
- Cancer Genomics Group, International Centre for Genetic Engineering and Biotechnology, Cape Town 7925, South Africa; (A.V.); (J.D.P.)
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7
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Yao L, Jayasinghe RG, Lee BH, Bhasin SS, Pilcher W, Doxie DB, Gonzalez-Kozlova E, Dasari S, Fiala MA, Pita-Juarez Y, Strausbauch M, Kelly G, Thomas BE, Kumar SK, Cho HJ, Anderson E, Wendl MC, Dawson T, D'Souza D, Oh ST, Cheloni G, Li Y, DiPersio JF, Rahman AH, Dhodapkar KM, Kim-Schulze S, Vij R, Vlachos IS, Mehr S, Hamilton M, Auclair D, Kourelis T, Avigan D, Dhodapkar MV, Gnjatic S, Bhasin MK, Ding L. Comprehensive characterization of the multiple myeloma immune microenvironment using integrated scRNA-seq, CyTOF, and CITE-seq analysis. Cancer Research Communications 2022; 2:1255-1265. [PMID: 36969740 PMCID: PMC10035369 DOI: 10.1158/2767-9764.crc-22-0022] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 06/09/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022]
Abstract
Abstract
As part of the Multiple Myeloma Research Foundation (MMRF) immune atlas pilot project, we compared immune cells of Multiple Myeloma (MM) bone marrow samples from 18 patients assessed by single-cell RNA-seq (scRNA-seq), mass cytometry (CyTOF), and Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) to understand the concordance of measurements among single-cell techniques. Cell type abundances are relatively consistent across the three approaches, while variations are observed in T cells, macrophages, and monocytes. Concordance and correlation analysis of cell type marker gene expression across different modalities highlighted the importance of choosing cell type marker genes best suited to particular modalities. By integrating data from these three assays, we found International Staging System (ISS) stage 3 patients exhibited decreased CD4+ T/ CD8+ T cells ratio. Moreover, we observed upregulation of RAC2 and PSMB9, in NK cells of fast progressors (FP) compared to those of non-progressors (NP), as revealed by both scRNA-seq and CITE-seq RNA measurement. This detailed examination of the immune microenvironment in MM using multiple single cell technologies revealed markers associated with MM rapid progression which will be further characterized by the full-scale immune atlas project.
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Affiliation(s)
- Lijun Yao
- Washington University, St. Louis University School of Medicine, St. Louis, Mo, United States
| | - Reyka G Jayasinghe
- Washington University in St. Louis School of Medicine, Saint Louis, MO, United States
| | - Brian H. Lee
- Icahn School of Medicine at Mt. Sinai, New York, United States
| | - Swati S. Bhasin
- Emory University School of Medicine, Atlanta, GA, United States
| | | | | | | | | | - Mark A Fiala
- Washington University in St. Louis School of Medicine, St. Louis, United States
| | | | | | - Geoffrey Kelly
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Beena E Thomas
- Emory University School of Medicine, Atlanta, Ga, United States
| | | | - Hearn Jay Cho
- Multiple Myeloma Research Foundation, Norwalk, CT, United States
| | | | - Michael C. Wendl
- Washington University, St. Louis University School of Medicine, St. Louis, Mo, United States
| | - Travis Dawson
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Darwin D'Souza
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Stephen T Oh
- Washington University in St. Louis School of Medicine, St. Louis, United States
| | - Giulia Cheloni
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Ying Li
- Mayo Clinic, Rochester, Minnesota, United States
| | | | - Adeeb H. Rahman
- Icahn School of Medicine at Mt. Sinai, New York, United States
| | | | | | - Ravi Vij
- Washington University in St. Louis, Saint Louis, MO, United States
| | | | - Shaadi Mehr
- Multiple Myeloma Research Foundation, Norwalk, CT, United States
| | - Mark Hamilton
- Multiple Myeloma Research Foundation, Norwalk, CT, United States
| | | | | | - David Avigan
- Harvard Medical School, Boston, MA, United States
| | | | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Manoj K. Bhasin
- Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Li Ding
- Washington University School of Medicine in St. Louis, St Louis, MO, United States
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8
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Bekhbat M, Ulukaya GB, Bhasin MK, Felger JC, Miller AH. Cellular and immunometabolic mechanisms of inflammation in depression: Preliminary findings from single cell RNA sequencing and a tribute to Bruce McEwen. Neurobiol Stress 2022; 19:100462. [PMID: 35655933 PMCID: PMC9152104 DOI: 10.1016/j.ynstr.2022.100462] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/03/2022] [Accepted: 05/16/2022] [Indexed: 11/04/2022] Open
Abstract
Inflammation is associated with symptoms of anhedonia, a core feature of major depression (MD). We have shown that MD patients with high inflammation as measured by plasma C-reactive protein (CRP) and anhedonia display gene signatures of metabolic reprograming (e.g., shift to glycolysis) necessary to sustain cellular immune activation. To gain preliminary insight into the immune cell subsets and transcriptomic signatures that underlie increased inflammation and its relationship with behavior in MD at the single-cell (sc) level, herein we conducted scRNA-Seq on peripheral blood mononuclear cells from a subset of medically-stable, unmedicated MD outpatients. Three MD patients with high CRP (>3 mg/L) before and two weeks after anti-inflammatory challenge with the tumor necrosis factor antagonist infliximab and three patients with low CRP (≤3 mg/L) were studied. Cell clusters were identified using a Single Cell Wizard pipeline, followed by pathway analysis. CD14+ and CD16+ monocytes were more abundant in MD patients with high CRP and were reduced by 29% and 55% respectively after infliximab treatment. Within CD14+ and CD16+ monocytes, genes upregulated in high CRP patients were enriched for inflammatory (phagocytosis, complement, leukocyte migration) and immunometabolic (hypoxia-inducible factor [HIF]-1, aerobic glycolysis) pathways. Shifts in CD4+ T cell subsets included ∼30% and ∼10% lower abundance of CD4+ central memory (TCM) and naïve cells and ∼50% increase in effector memory-like (TEM-like) cells in high versus low CRP patients. TCM cells of high CRP patients displayed downregulation of the oxidative phosphorylation (OXPHOS) pathway, a main energy source in this cell type. Following infliximab, changes in the number of CD14+ monocytes and CD4+ TEM-like cells predicted improvements in anhedonia scores (r = 1.0, p < 0.001). In sum, monocytes and CD4+ T cells from MD patients with increased inflammation exhibited immunometabolic reprograming in association with symptoms of anhedonia. These findings are the first step toward determining the cellular and molecular immune pathways associated with inflammatory phenotypes in MD, which may lead to novel immunomodulatory treatments of psychiatric illnesses with increased inflammation.
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9
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Summers RJ, Castellino SM, Porter CC, MacDonald TJ, Basu GD, Szelinger S, Bhasin MK, Cash T, Carter AB, Castellino RC, Fangusaro JR, Mitchell SG, Pauly MG, Pencheva B, Wechsler DS, Graham DK, Goldsmith KC. Comprehensive Genomic Profiling of High-Risk Pediatric Cancer Patients Has a Measurable Impact on Clinical Care. JCO Precis Oncol 2022; 6:e2100451. [PMID: 35544730 DOI: 10.1200/po.21.00451] [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: 11/20/2022] Open
Abstract
PURPOSE Profiling of pediatric cancers through deep sequencing of large gene panels and whole exomes is rapidly being adopted in many clinical settings. However, the most impactful approach to genomic profiling of pediatric cancers remains to be defined. METHODS We conducted a prospective precision medicine trial, using whole-exome sequencing of tumor and germline tissue and whole-transcriptome sequencing (RNA Seq) of tumor tissue to characterize the mutational landscape of 127 tumors from 126 unique patients across the spectrum of pediatric brain tumors, hematologic malignancies, and extracranial solid tumors. RESULTS We identified somatic tumor alterations in 121/127 (95.3%) tumor samples and identified cancer predisposition syndromes on the basis of known pathogenic or likely pathogenic germline mutations in cancer predisposition genes in 9/126 patients (7.1%). Additionally, we developed a novel scoring system for measuring the impact of tumor and germline sequencing, encompassing therapeutically relevant genomic alterations, cancer-related germline findings, recommendations for treatment, and refinement of risk stratification or prognosis. At least one impactful finding from the genomic results was identified in 108/127 (85%) samples sequenced. A recommendation to consider a targeted agent was provided for 82/126 (65.1%) patients. Twenty patients ultimately received therapy with a molecularly targeted agent, representing 24% of those who received a targeted agent recommendation and 16% of the total cohort. CONCLUSION Paired tumor/normal whole-exome sequencing and tumor RNA Seq of de novo or relapsed/refractory tumors was feasible and clinically impactful in high-risk pediatric cancer patients.
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Affiliation(s)
- Ryan J Summers
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Sharon M Castellino
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Christopher C Porter
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Tobey J MacDonald
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | | | | | - Manoj K Bhasin
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA.,Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA
| | - Thomas Cash
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Alexis B Carter
- Department of Pathology and Laboratory Medicine, Children's Healthcare of Atlanta, Atlanta, GA
| | - Robert Craig Castellino
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Jason R Fangusaro
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Sarah G Mitchell
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Melinda G Pauly
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Bojana Pencheva
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Daniel S Wechsler
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Douglas K Graham
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
| | - Kelly C Goldsmith
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta/Emory University, Atlanta, GA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, GA
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10
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Ma F, Arai S, Wang K, Calagua C, Yuan AR, Poluben L, Gu Z, Russo JW, Einstein DJ, Ye H, He MX, Liu Y, Van Allen E, Sowalsky AG, Bhasin MK, Yuan X, Balk SP. Autocrine Canonical Wnt Signaling Primes Noncanonical Signaling through ROR1 in Metastatic Castration-Resistant Prostate Cancer. Cancer Res 2022; 82:1518-1533. [PMID: 35131873 PMCID: PMC9018564 DOI: 10.1158/0008-5472.can-21-1807] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 11/22/2021] [Accepted: 02/02/2022] [Indexed: 11/16/2022]
Abstract
Wnt signaling driven by genomic alterations in genes including APC and CTNNB, which encodes β-catenin, have been implicated in prostate cancer development and progression to metastatic castration-resistant prostate cancer (mCRPC). However, nongenomic drivers and downstream effectors of Wnt signaling in prostate cancer and the therapeutic potential of targeting this pathway in prostate cancer have not been fully established. Here we analyzed Wnt/β-catenin signaling in prostate cancer and identified effectors distinct from those found in other tissues, including aryl hydrocarbon receptor and RUNX1, which are linked to stem cell maintenance, and ROR1, a noncanonical Wnt5a coreceptor. Wnt/β-catenin signaling-mediated increases in ROR1 enhanced noncanonical responses to Wnt5a. Regarding upstream drivers, APC genomic loss, but not its epigenetic downregulation commonly observed in prostate cancer, was strongly associated with Wnt/β-catenin pathway activation in clinical samples. Tumor cell upregulation of the Wnt transporter Wntless (WLS) was strongly associated with Wnt/β-catenin pathway activity in primary prostate cancer but also associated with both canonical and noncanonical Wnt signaling in mCRPC. IHC confirmed tumor cell WLS expression in primary prostate cancer and mCRPC, and patient-derived prostate cancer xenografts expressing WLS were responsive to treatment with Wnt synthesis inhibitor ETC-1922159. These findings reveal that Wnt/β-catenin signaling in prostate cancer drives stem cell maintenance and invasion and primes for noncanonical Wnt signaling through ROR1. They further show that autocrine Wnt production is a nongenomic driver of canonical and noncanonical Wnt signaling in prostate cancer, which can be targeted with Wnt synthesis inhibitors to suppress tumor growth. SIGNIFICANCE This work provides fundamental insights into Wnt signaling and prostate cancer cell biology and indicates that a subset of prostate cancer driven by autocrine Wnt signaling is sensitive to Wnt synthesis inhibitors.
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Affiliation(s)
- Fen Ma
- Department of Medicine and Cancer Center, Beth Israel Deaconess Medical Center and Harvard Medical School; Boston, MA, 02215, USA
| | - Seiji Arai
- Department of Medicine and Cancer Center, Beth Israel Deaconess Medical Center and Harvard Medical School; Boston, MA, 02215, USA
- Department of Urology, Gunma University Hospital; Maebashi, Gunma, Japan
| | - Keshan Wang
- Department of Medicine and Cancer Center, Beth Israel Deaconess Medical Center and Harvard Medical School; Boston, MA, 02215, USA
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology; Wuhan, Hubei 430022, P.R. China
| | - Carla Calagua
- Department of Medicine and Cancer Center, Beth Israel Deaconess Medical Center and Harvard Medical School; Boston, MA, 02215, USA
| | - Amanda R. Yuan
- Department of Medicine and Cancer Center, Beth Israel Deaconess Medical Center and Harvard Medical School; Boston, MA, 02215, USA
| | - Larysa Poluben
- Department of Medicine and Cancer Center, Beth Israel Deaconess Medical Center and Harvard Medical School; Boston, MA, 02215, USA
| | - Zhongkai Gu
- Department of Medicine and Cancer Center, Beth Israel Deaconess Medical Center and Harvard Medical School; Boston, MA, 02215, USA
| | - Joshua W. Russo
- Department of Medicine and Cancer Center, Beth Israel Deaconess Medical Center and Harvard Medical School; Boston, MA, 02215, USA
| | - David J. Einstein
- Department of Medicine and Cancer Center, Beth Israel Deaconess Medical Center and Harvard Medical School; Boston, MA, 02215, USA
| | - Huihui Ye
- Department of Medicine and Cancer Center, Beth Israel Deaconess Medical Center and Harvard Medical School; Boston, MA, 02215, USA
- Department of Pathology, UCLA David Geffen School of Medicine; Los Angeles, CA 90095
| | - Meng Xiao He
- Harvard Graduate Program in Biophysics, Harvard Medical School; Boston, MA 02115, USA
- Department of Medical Oncology, Dana Farber Cancer Institute; Boston, MA 02115
- Broad Institute of Harvard and MIT; Cambridge, MA 02142, USA
| | - Yu Liu
- Program in System Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School; Worcester, MA 01605, USA
| | - Eliezer Van Allen
- Department of Medical Oncology, Dana Farber Cancer Institute; Boston, MA 02115
- Broad Institute of Harvard and MIT; Cambridge, MA 02142, USA
| | - Adam G. Sowalsky
- Laboratory of Genitourinary Cancer Pathogenesis, National Cancer Institute, National Institutes of Health; Bethesda, MD 20892, USA
| | - Manoj K. Bhasin
- Department of Medicine and Cancer Center, Beth Israel Deaconess Medical Center and Harvard Medical School; Boston, MA, 02215, USA
- Departments of Pediatrics and Biomedical Informatics, Emory School of Medicine; Atlanta, GA 30322, USA
| | - Xin Yuan
- Department of Medicine and Cancer Center, Beth Israel Deaconess Medical Center and Harvard Medical School; Boston, MA, 02215, USA
| | - Steven P. Balk
- Department of Medicine and Cancer Center, Beth Israel Deaconess Medical Center and Harvard Medical School; Boston, MA, 02215, USA
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11
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Pal R, Bhasin MK, Bhadada SK. COVID-19 and Type 2 Diabetes Mellitus: HCQ may be the Holy Grail. Infect Disord Drug Targets 2020; 21:e270421186842. [PMID: 33050869 DOI: 10.2174/1871526520666201013160803] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/09/2020] [Accepted: 08/31/2020] [Indexed: 11/22/2022]
Abstract
The novel coronavirus disease (COVID-19) is on the rampage claiming over 297000 lives globally. Disease severity and mortality rates are higher in patients with underlying diabetes mellitus. Till date, there exists no effective vaccine or therapy against COVID-19. However, with limited clinical data, HCQ is being used for treatment and prophylaxis in patients with COVID-19. HCQ is also used as an anti-diabetic drug and has been approved in India as an adjunct to diet and exercise to improve glycemic control of patients with Type 2 Diabetes Mellitus (T2DM) on metformin and sulfonylurea combination in Type 2 Diabetes Mellitus (T2DM). Thus, although indiscriminate use of HCQ is fraught with danger, HCQ can be considered as a third-line add on anti-diabetic agent in people with T2DM amid the ongoing pandemic after having ruled out the contraindications to the use of this drug.
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Affiliation(s)
- Rimesh Pal
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Manoj K Bhasin
- Department of Biomedical Informatics, Emory School of Medicine, Atlanta, GA-30322, United States
| | - Sanjay K Bhadada
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
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12
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Khatri I, Bhasin MK. A Transcriptomics-Based Meta-Analysis Combined With Machine Learning Identifies a Secretory Biomarker Panel for Diagnosis of Pancreatic Adenocarcinoma. Front Genet 2020; 11:572284. [PMID: 33133160 PMCID: PMC7511758 DOI: 10.3389/fgene.2020.572284] [Citation(s) in RCA: 10] [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: 06/13/2020] [Accepted: 08/12/2020] [Indexed: 12/22/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is generally incurable due to the late diagnosis and absence of markers that are concordant with expression in several sample sources (i.e., tissue, blood, plasma) and platforms (i.e., Microarray, sequencing). We optimized meta-analysis of 19 PDAC (tissue and blood) transcriptome studies from multiple platforms. The key biomarkers for PDAC diagnosis with secretory potential were identified and validated in different cohorts. Machine learning approach i.e., support vector machine supported by leave-one-out cross-validation was used to build and test the classifier. We identified a 9-gene panel (IFI27, ITGB5, CTSD, EFNA4, GGH, PLBD1, HTATIP2, IL1R2, CTSA) that achieved ∼0.92 average sensitivity and ∼0.90 average specificity in distinguishing PDAC from healthy samples in five training sets using cross-validation. These markers were also validated in proteomics and single-cell transcriptomics studies suggesting their prognostic role in the diagnosis of PDAC. Our 9-gene classifier can not only clearly discriminate between better and poor survivors but can also precisely discriminate PDAC from chronic pancreatitis (AUC = 0.95), early stages of progression [Stage I and II (AUC = 0.82), IPMA and IPMN (AUC = 1), and IPMC (AUC = 0.81)]. The 9-gene marker outperformed the previously known markers in blood studies particularly (AUC = 0.84). The discrimination of PDAC from early precursor lesions in non-malignant tissue (AUC > 0.81) and peripheral blood (AUC > 0.80) may assist in an early diagnosis of PDAC in blood samples and thus will also facilitate risk stratification upon validation in clinical trials.
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Affiliation(s)
- Indu Khatri
- Division of IMBIO, Department of Medicine, Beth Israel Lahey Health, Harvard Medical School, Boston, MA, United States.,Department of Immunology and Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands
| | - Manoj K Bhasin
- Division of IMBIO, Department of Medicine, Beth Israel Lahey Health, Harvard Medical School, Boston, MA, United States.,Department of Pediatrics and Biomedical Informatics, Children's Healthcare of Atlanta, Emory School of Medicine, Atlanta, GA, United States
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13
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Lynch MR, Tran MT, Ralto KM, Zsengeller ZK, Raman V, Bhasin SS, Sun N, Chen X, Brown D, Rovira II, Taguchi K, Brooks CR, Stillman IE, Bhasin MK, Finkel T, Parikh SM. TFEB-driven lysosomal biogenesis is pivotal for PGC1α-dependent renal stress resistance. JCI Insight 2020; 5:142898. [PMID: 32759500 PMCID: PMC7455057 DOI: 10.1172/jci.insight.142898] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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14
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Abstract
BACKGROUND The complex host response to sepsis is incompletely understood. The aim of this investigation is to use leukocyte RNA sequencing to characterize biological functions, cellular pathways, and key regulatory molecules driving sepsis pathophysiology. METHODS This was a prospective, observational study of emergency department patients with sepsis, at an urban, academic, tertiary care center. In the derivation cohort, we collected blood at enrollment and 90 days after hospital discharge allowing each patient to serve as an internal control. We performed RNA sequencing to quantify transcriptional expression changes during sepsis and non-sepsis states. We then performed unsupervised and supervised analyses, as well as functional and pathway analyses. We selected the top down and upregulated genes and key regulatory molecules for validation. Validation occurred in a cohort of septic and non-septic using real-time PCR. RESULTS The derivation cohort included 5 patients, and RNA sequencing revealed 916 unique mRNA transcripts differentially expressed during sepsis. Among these, 673 (73%) genes were upregulated, and 243 (27%) were downregulated. Functional enrichment analysis revealed a highly dynamic downstream effect of the transcriptional activity during sepsis. Of the 43 functional cellular pathways activated during sepsis, the top pathways were closely associated with inflammation and response to infection. Validation occurred in 18 septic and 25 non-septic control patients, with 34/45 (76%) of identified genes validated. The regulatory analysis identified several key regulators of sepsis. CONCLUSIONS Highly dynamic transcriptional activity occurs in leukocytes during sepsis, activating key cellular pathways and master regulatory molecules that drive the sepsis process.
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Affiliation(s)
- Simon Skibsted
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA
- Center for Emergency Medicine Research, Aarhus University Hospital & Aarhus University, Aarhus, Denmark
| | - Manoj K. Bhasin
- Center for Genomics, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA
| | - Daniel J. Henning
- Division of Emergency Medicine, University of Washington, Seattle, WA, USA
| | - Shou Ching Jaminet
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA
- Department of Pathology, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA
| | - Jeffrey Lewandowski
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA
| | - Hans Kirkegaard
- Center for Emergency Medicine Research, Aarhus University Hospital & Aarhus University, Aarhus, Denmark
| | - William C. Aird
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA
| | - Nathan I. Shapiro
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center & Harvard Medical School, Boston, MA, USA
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15
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Lynch MR, Tran MT, Ralto KM, Zsengeller ZK, Raman V, Bhasin SS, Sun N, Chen X, Brown D, Rovira II, Taguchi K, Brooks CR, Stillman IE, Bhasin MK, Finkel T, Parikh SM. TFEB-driven lysosomal biogenesis is pivotal for PGC1α-dependent renal stress resistance. JCI Insight 2019; 5:126749. [PMID: 30870143 PMCID: PMC6538327 DOI: 10.1172/jci.insight.126749] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Because injured mitochondria can accelerate cell death through the elaboration of oxidative free radicals and other mediators, it is striking that proliferator γ coactivator 1-α (PGC1α), a stimulator of increased mitochondrial abundance, protects stressed renal cells instead of potentiating injury. Here, we report that PGC1α’s induction of lysosomes via transcription factor EB (TFEB) may be pivotal for kidney protection. CRISPR and stable gene transfer showed that PGC1α-KO tubular cells were sensitized to the genotoxic stressor cisplatin, whereas Tg cells were protected. The biosensor mitochondrial-targeted Keima (mtKeima) unexpectedly revealed that cisplatin blunts mitophagy both in cells and mice. PGC1α and its downstream mediator NAD+ counteracted this effect. PGC1α did not consistently affect known autophagy pathways modulated by cisplatin. Instead RNA sequencing identified coordinated regulation of lysosomal biogenesis via TFEB. This effector pathway was sufficiently important that inhibition of TFEB or lysosomes unveiled a striking harmful effect of excess PGC1α in cells and conditional mice. These results uncover an unexpected effect of cisplatin on mitophagy and PGC1α’s reliance on lysosomes for kidney protection. Finally, the data illuminate TFEB as a potentially novel target for renal tubular stress resistance. PGC1α is renoprotective in the setting of platinum-based chemotherapy through the induction of mitophagy and lysosomal biogenesis via transcription factor EB.
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Affiliation(s)
- Matthew R Lynch
- Division of Nephrology.,Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Mei T Tran
- Division of Nephrology.,Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Kenneth M Ralto
- Division of Nephrology.,Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Zsuzsanna K Zsengeller
- Division of Nephrology.,Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Vinod Raman
- Division of Nephrology.,Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Swati S Bhasin
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Nuo Sun
- Center for Molecular Medicine, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland, USA
| | - Xiuying Chen
- Division of Nephrology.,Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel Brown
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Ilsa I Rovira
- Center for Molecular Medicine, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland, USA
| | - Kensei Taguchi
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Craig R Brooks
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Isaac E Stillman
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Manoj K Bhasin
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Toren Finkel
- Center for Molecular Medicine, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland, USA.,Aging Institute of UPMC and the University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Samir M Parikh
- Division of Nephrology.,Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
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16
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Khatri I, Ganguly K, Sharma S, Carmicheal J, Kaur S, Batra SK, Bhasin MK. Systems Biology Approach to Identify Novel Genomic Determinants for Pancreatic Cancer Pathogenesis. Sci Rep 2019; 9:123. [PMID: 30644396 PMCID: PMC6333820 DOI: 10.1038/s41598-018-36328-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 11/05/2018] [Indexed: 02/06/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy with a 5-year survival rate of <8%. Its dismal prognosis stems from inefficient therapeutic modalities owing to the lack of understanding about pancreatic cancer pathogenesis. Considering the molecular complexity and heterogeneity of PDAC, identification of novel molecular contributors involved in PDAC onset and progression using global "omics" analysis will pave the way to improved strategies for disease prevention and therapeutic targeting. Meta-analysis of multiple miRNA microarray datasets containing healthy controls (HC), chronic pancreatitis (CP) and PDAC cases, identified 13 miRNAs involved in the progression of PDAC. These miRNAs showed dysregulation in both tissue as well as blood samples, along with progressive decrease in expression from HC to CP to PDAC. Gene-miRNA interaction analysis further elucidated 5 miRNAs (29a/b, 27a, 130b and 148a) that are significantly downregulated in conjunction with concomitant upregulation of their target genes throughout PDAC progression. Among these, miRNA-29a/b targeted genes were found to be most significantly altered in comparative profiling of HC, CP and PDAC, indicating its involvement in malignant evolution. Further, pathway analysis suggested direct involvement of miRNA-29a/b in downregulating the key pathways associated with PDAC development and metastasis including focal adhesion signaling and extracellular matrix organization. Our systems biology data analysis, in combination with real-time PCR validation indicates direct functional involvement of miRNA-29a in PDAC progression and is a potential prognostic marker and therapeutic candidate for patients with progressive disease.
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Affiliation(s)
- Indu Khatri
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Koelina Ganguly
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Sunandini Sharma
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Joseph Carmicheal
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Sukhwinder Kaur
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA.
| | - Manoj K Bhasin
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, MA, USA.
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17
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Singh PK, Khatri I, Jha A, Pretto CD, Spindler KR, Arumugaswami V, Giri S, Kumar A, Bhasin MK. Determination of system level alterations in host transcriptome due to Zika virus (ZIKV) Infection in retinal pigment epithelium. Sci Rep 2018; 8:11209. [PMID: 30046058 PMCID: PMC6060127 DOI: 10.1038/s41598-018-29329-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/10/2018] [Indexed: 12/26/2022] Open
Abstract
Previously, we reported that Zika virus (ZIKV) causes ocular complications such as chorioretinal atrophy, by infecting cells lining the blood-retinal barrier, including the retinal pigment epithelium (RPE). To understand the molecular basis of ZIKV-induced retinal pathology, we performed a meta-analysis of transcriptome profiles of ZIKV-infected human primary RPE and other cell types infected with either ZIKV or other related flaviviruses (Japanese encephalitis, West Nile, and Dengue). This led to identification of a unique ZIKV infection signature comprising 43 genes (35 upregulated and 8 downregulated). The major biological processes perturbed include SH3/SH2 adaptor activity, lipid and ceramide metabolism, and embryonic organ development. Further, a comparative analysis of some differentially regulated genes (ABCG1, SH2B3, SIX4, and TNFSF13B) revealed that ZIKV induced their expression relatively more than dengue virus did in RPE. Importantly, the pharmacological inhibition of ABCG1, a membrane transporter of cholesterol, resulted in reduced ZIKV infectivity. Interestingly, the ZIKV infection signature revealed the downregulation of ALDH5A1 and CHML, genes implicated in neurological (cognitive impairment, expressive language deficit, and mild ataxia) and ophthalmic (choroideremia) disorders, respectively. Collectively, our study revealed that ZIKV induces differential gene expression in RPE cells, and the identified genes/pathways (e.g., ABCG1) could potentially contribute to ZIKV-associated ocular pathologies.
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Affiliation(s)
- Pawan Kumar Singh
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, Detroit, MI, USA
| | - Indu Khatri
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Centre, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Interdisciplinary Medicine and Biotechnology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Alokkumar Jha
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Centre, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Division of Interdisciplinary Medicine and Biotechnology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Carla D Pretto
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Katherine R Spindler
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | | | - Shailendra Giri
- Department of Neurology, Henry Ford Health System, Detroit, MI, USA
| | - Ashok Kumar
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University, Detroit, MI, USA.
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University, Detroit, MI, USA.
| | - Manoj K Bhasin
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Centre, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Division of Interdisciplinary Medicine and Biotechnology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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18
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Bhasin MK, Denninger JW, Huffman JC, Joseph MG, Niles H, Chad-Friedman E, Goldman R, Buczynski-Kelley B, Mahoney BA, Fricchione GL, Dusek JA, Benson H, Zusman RM, Libermann TA. Specific Transcriptome Changes Associated with Blood Pressure Reduction in Hypertensive Patients After Relaxation Response Training. J Altern Complement Med 2018; 24:486-504. [PMID: 29616846 PMCID: PMC5961875 DOI: 10.1089/acm.2017.0053] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVE Mind-body practices that elicit the relaxation response (RR) have been demonstrated to reduce blood pressure (BP) in essential hypertension (HTN) and may be an adjunct to antihypertensive drug therapy. However, the molecular mechanisms by which the RR reduces BP remain undefined. DESIGN Genomic determinants associated with responsiveness to an 8-week RR-based mind-body intervention for lowering HTN in 13 stage 1 hypertensive patients classified as BP responders and 11 as nonresponders were identified. RESULTS Transcriptome analysis in peripheral blood mononuclear cells identified 1771 genes regulated by the RR in responders. Biological process- and pathway-based analysis of transcriptome data demonstrated enrichment in the following gene categories: immune regulatory pathways and metabolism (among downregulated genes); glucose metabolism, cardiovascular system development, and circadian rhythm (among upregulated genes). Further in silico estimation of cell abundance from the microarray data showed enrichment of the anti-inflammatory M2 subtype of macrophages in BP responders. Nuclear factor-κB, vascular endothelial growth factor, and insulin were critical molecules emerging from interactive network analysis. CONCLUSIONS These findings provide the first insights into the molecular mechanisms that are associated with the beneficial effects of the RR on HTN.
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Affiliation(s)
- Manoj K. Bhasin
- Benson-Henry Institute for Mind Body Medicine, Massachusetts General Hospital, Boston, MA
- Division of Interdisciplinary Medicine and Biotechnology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, MA
| | - John W. Denninger
- Benson-Henry Institute for Mind Body Medicine, Massachusetts General Hospital, Boston, MA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Jeff C. Huffman
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Marie G. Joseph
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, MA
| | - Halsey Niles
- Benson-Henry Institute for Mind Body Medicine, Massachusetts General Hospital, Boston, MA
| | - Emma Chad-Friedman
- Benson-Henry Institute for Mind Body Medicine, Massachusetts General Hospital, Boston, MA
- Division of Interdisciplinary Medicine and Biotechnology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Roberta Goldman
- Benson-Henry Institute for Mind Body Medicine, Massachusetts General Hospital, Boston, MA
| | - Beverly Buczynski-Kelley
- Department of Medicine, Corrigan-Minehan Heart Center, Cardiology Division, Section on Hypertension, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Barbara A. Mahoney
- Department of Medicine, Corrigan-Minehan Heart Center, Cardiology Division, Section on Hypertension, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Gregory L. Fricchione
- Benson-Henry Institute for Mind Body Medicine, Massachusetts General Hospital, Boston, MA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Jeffery A. Dusek
- Benson-Henry Institute for Mind Body Medicine, Massachusetts General Hospital, Boston, MA
- Integrative Health Research Center, Penny George Institute for Health and Healing, Allina Health, Minneapolis, MN
| | - Herbert Benson
- Benson-Henry Institute for Mind Body Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Randall M. Zusman
- Department of Medicine, Corrigan-Minehan Heart Center, Cardiology Division, Section on Hypertension, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Towia A. Libermann
- Benson-Henry Institute for Mind Body Medicine, Massachusetts General Hospital, Boston, MA
- Division of Interdisciplinary Medicine and Biotechnology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, MA
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19
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Wang X, Solban N, Khanna P, Callea M, Song J, Alsop DC, Pearsall RS, Atkins MB, Mier JW, Signoretti S, Alimzhanov M, Kumar R, Bhasin MK, Bhatt RS. Inhibition of ALK1 signaling with dalantercept combined with VEGFR TKI leads to tumor stasis in renal cell carcinoma. Oncotarget 2018; 7:41857-41869. [PMID: 27248821 PMCID: PMC5173101 DOI: 10.18632/oncotarget.9621] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/05/2016] [Indexed: 12/21/2022] Open
Abstract
Treatment of metastatic renal cell carcinoma (mRCC) with agents that block signaling through vascular endothelial growth factor receptor 2 (VEGFR2) induces disease regression or stabilization in some patients; however, these responses tend to be short-lived. Therefore, development of combination therapies that can extend the efficacy of VEGFR antagonists in mRCC remains a priority. We studied murine xenograft models of RCC that become refractory to treatment with the VEGFR tyrosine kinase inhibitor (TKI) sunitinib. Dalantercept is a novel antagonist of Activin receptor-like kinase 1 (ALK1)/Bone morphogenetic protein (BMP) 9 signaling. Dalantercept inhibited growth in the murine A498 xenograft model which correlated with hyperdilation of the tumor vasculature and an increase in tumor hypoxia. When combined with sunitinib, dalantercept induced tumor necrosis and prevented tumor regrowth and revascularization typically seen with sunitinib monotherapy in two RCC models. Combination therapy led to significant downregulation of angiogenic genes as well as downregulation of endothelial specific gene expression particularly of the Notch signaling pathway. We demonstrate that simultaneous targeting of molecules that control distinct phases of angiogenesis, such as ALK1 and VEGFR, is a valid strategy for treatment of mRCC. At the molecular level, combination therapy leads to downregulation of Notch signaling.
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Affiliation(s)
- Xiaoen Wang
- Department of Radiology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - Prateek Khanna
- Division of Hematology-Oncology and Cancer Biology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Marcella Callea
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jiaxi Song
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - David C Alsop
- Department of Radiology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - Michael B Atkins
- Departments of Oncology and Medicine, Georgetown Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - James W Mier
- Division of Hematology-Oncology and Cancer Biology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Ravi Kumar
- Acceleron Pharma, Inc., Cambridge, MA, USA
| | - Manoj K Bhasin
- Division of Interdisciplinary Medicine & Biotechnology, and Genomics, Proteomics, Bioinformatics and Systems Biology Center, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Rupal S Bhatt
- Division of Hematology-Oncology and Cancer Biology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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20
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Jeganathan J, Saraf R, Mahmood F, Pal A, Bhasin MK, Huang T, Mittel A, Knio Z, Simons R, Khabbaz K, Senthilnathan V, Liu D, Sellke F, Matyal R. Mitochondrial Dysfunction in Atrial Tissue of Patients Developing Postoperative Atrial Fibrillation. Ann Thorac Surg 2017; 104:1547-1555. [PMID: 28760472 DOI: 10.1016/j.athoracsur.2017.04.060] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/31/2017] [Accepted: 04/24/2017] [Indexed: 11/15/2022]
Abstract
BACKGROUND Mitochondria are the major site of cellular oxidation. Metabolism and oxidative stress have been implicated as possible mechanisms for postoperative atrial fibrillation (POAF) after cardiac operations. Establishing the precise nature of mitochondrial dysfunction as an etiologic factor for oxidative stress-related cell death and apoptosis could further the understanding of POAF. To establish this relationship, mitochondrial function was studied in patients undergoing cardiac operations that developed POAF and compared it with patients without POAF. METHODS Right atrial tissue and serum samples were collected from 85 patients before and after cardiopulmonary bypass. Microarray analysis (36 patients) and RNA sequencing (5 patients) were performed on serum and atrial tissues, respectively, for identifying significantly altered genes in patients who developed POAF. On the basis of these results, Western blot was performed in 52 patients for the genes that were most altered, and functional pathways were established. RESULTS POAF developed in 30.6% (n = 26) of patients. Serum microarray showed significant fold changes in the expression of 49 genes involved in inflammatory response, oxidative stress, apoptosis, and amyloidosis (p < 0.05) in the POAF group. Similarly, RNA sequencing demonstrated an increased expression of genes associated with inflammatory response, fatty acid metabolism, and apoptosis in the POAF group (false discovery rate > 0.05). Immunoblotting showed a significant increase in TNFAIP6 (tumor necrosis factor, α-induced protein 6; p = 0.02) and transforming growth factor-β (p = 0.04) after cardiopulmonary bypass in the POAF group. There was a significant decrease in PGC-1α (peroxisome proliferator-activated receptor-γ coactivator-1α; p = 0.002) and CPT1 (carnitine palmitoyltransferase I; p < 0.0005) in the POAF group after cardiopulmonary bypass. CONCLUSIONS Compared with patients without POAF, those with POAF demonstrated mitochondrial dysfunction at various levels that are suitable for potential pharmacotherapy.
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Affiliation(s)
- Jelliffe Jeganathan
- Department of Anesthesia, Critical Care & Pain Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Rabya Saraf
- Division of Cardiac Surgery, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Feroze Mahmood
- Department of Anesthesia, Critical Care & Pain Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Anam Pal
- Department of Anesthesia, Critical Care & Pain Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Manoj K Bhasin
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Thomas Huang
- Department of Anesthesia, Critical Care & Pain Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Aaron Mittel
- Department of Anesthesia, Critical Care & Pain Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Ziyad Knio
- Division of Cardiac Surgery, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Russell Simons
- Department of Anesthesia, Critical Care & Pain Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Kamal Khabbaz
- Division of Cardiac Surgery, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Venkatachalam Senthilnathan
- Division of Cardiac Surgery, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - David Liu
- Division of Cardiac Surgery, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Frank Sellke
- Department of Cardiac Surgery, Rhode Island Hospital, Brown University, Providence, Rhode Island
| | - Robina Matyal
- Department of Anesthesia, Critical Care & Pain Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts.
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21
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Bhasin MK, Dusek JA, Chang BH, Joseph MG, Denninger JW, Fricchione GL, Benson H, Libermann TA. Correction: Relaxation Response Induces Temporal Transcriptome Changes in Energy Metabolism, Insulin Secretion and Inflammatory Pathways. PLoS One 2017; 12:e0172873. [PMID: 28222196 PMCID: PMC5319675 DOI: 10.1371/journal.pone.0172873] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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22
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Thomas C, Henry W, Cuiffo BG, Collmann AY, Marangoni E, Benhamo V, Bhasin MK, Fan C, Fuhrmann L, Baldwin AS, Perou C, Vincent-Salomon A, Toker A, Karnoub AE. Pentraxin-3 is a PI3K signaling target that promotes stem cell-like traits in basal-like breast cancers. Sci Signal 2017; 10:10/467/eaah4674. [PMID: 28223411 DOI: 10.1126/scisignal.aah4674] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Basal-like breast cancers (BLBCs) exhibit hyperactivation of the phosphoinositide 3-kinase (PI3K) signaling pathway because of the frequent mutational activation of the PIK3CA catalytic subunit and the genetic loss of its negative regulators PTEN (phosphatase and tensin homolog) and INPP4B (inositol polyphosphate-4-phosphatase type II). However, PI3K inhibitors have had limited clinical efficacy in BLBC management because of compensatory amplification of PI3K downstream signaling loops. Therefore, identification of critical PI3K mediators is paramount to the development of effective BLBC therapeutics. Using transcriptomic analysis of activated PIK3CA-expressing BLBC cells, we identified the gene encoding the humoral pattern recognition molecule pentraxin-3 (PTX3) as a critical target of oncogenic PI3K signaling. We found that PTX3 abundance is stimulated, in part, through AKT- and nuclear factor κB (NF-κB)-dependent pathways and that presence of PTX3 is necessary for PI3K-induced stem cell-like traits. We further showed that PTX3 expression is greater in tumor samples from patients with BLBC and that it is prognostic of poor patient survival. Our results thus reveal PTX3 as a newly identified PI3K-regulated biomarker and a potential therapeutic target in BLBC.
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Affiliation(s)
- Clémence Thomas
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Whitney Henry
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Benjamin G Cuiffo
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Anthony Y Collmann
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | | | | | - Manoj K Bhasin
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Albert S Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Charles Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Alex Toker
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Antoine E Karnoub
- Department of Pathology and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA. .,Harvard Stem Cell Institute, Cambridge, MA 02138, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
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23
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Perry CJ, Blake P, Buettner C, Papavassiliou E, Schain AJ, Bhasin MK, Burstein R. Upregulation of inflammatory gene transcripts in periosteum of chronic migraineurs: Implications for extracranial origin of headache. Ann Neurol 2016; 79:1000-13. [PMID: 27091721 DOI: 10.1002/ana.24665] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 03/29/2016] [Accepted: 04/07/2016] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Chronic migraine (CM) is often associated with chronic tenderness of pericranial muscles. A distinct increase in muscle tenderness prior to onset of occipital headache that eventually progresses into a full-blown migraine attack is common. This experience raises the possibility that some CM attacks originate outside the cranium. The objective of this study was to determine whether there are extracranial pathophysiologies in these headaches. METHODS We biopsied and measured the expression of gene transcripts (mRNA) encoding proteins that play roles in immune and inflammatory responses in affected (ie, where the head hurts) calvarial periosteum of (1) patients whose CMs are associated with muscle tenderness and (2) patients with no history of headache. RESULTS Expression of proinflammatory genes (eg, CCL8, TLR2) in the calvarial periosteum significantly increased in CM patients attesting to muscle tenderness, whereas expression of genes that suppress inflammation and immune cell differentiation (eg, IL10RA, CSF1R) decreased. INTERPRETATION Because the upregulated genes were linked to activation of white blood cells, production of cytokines, and inhibition of NF-κB, and the downregulated genes were linked to prevention of macrophage activation and cell lysis, we suggest that the molecular environment surrounding periosteal pain fibers is inflamed and in turn activates trigeminovascular nociceptors that reach the affected periosteum through suture branches of intracranial meningeal nociceptors and/or somatic branches of the occipital nerve. This study provides the first set of evidence for localized extracranial pathophysiology in CM. Ann Neurol 2016;79:1000-1013.
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Affiliation(s)
| | - Pamela Blake
- Headache Center of Greater Heights, Memorial Hermann Greater Heights Hospital, Houston, TX
| | - Catherine Buettner
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA.,Harvard Medical School, Boston, MA
| | - Efstathios Papavassiliou
- Harvard Medical School, Boston, MA.,Department of Surgery, Beth Israel Deaconess Medical Center, Boston, MA
| | - Aaron J Schain
- Harvard Medical School, Boston, MA.,Department of Anesthesia and Critical Care, Beth Israel Deaconess Medical Center, Boston, MA
| | - Manoj K Bhasin
- Harvard Medical School, Boston, MA.,Division of Genomics, Proteomics, Bioinformatics, and Systems Biology, Beth Israel Deaconess Medical Center, Boston, MA
| | - Rami Burstein
- Harvard Medical School, Boston, MA.,Department of Anesthesia and Critical Care, Beth Israel Deaconess Medical Center, Boston, MA
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24
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Bhasin MK, Ndebele K, Bucur O, Yee EU, Otu HH, Plati J, Bullock A, Gu X, Castan E, Zhang P, Najarian R, Muraru MS, Miksad R, Khosravi-Far R, Libermann TA. Meta-analysis of transcriptome data identifies a novel 5-gene pancreatic adenocarcinoma classifier. Oncotarget 2016; 7:23263-81. [PMID: 26993610 PMCID: PMC5029625 DOI: 10.18632/oncotarget.8139] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 02/28/2016] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Pancreatic ductal adenocarcinoma (PDAC) is largely incurable due to late diagnosis. Superior early detection biomarkers are critical to improving PDAC survival and risk stratification. EXPERIMENTAL DESIGN Optimized meta-analysis of PDAC transcriptome datasets identified and validated key PDAC biomarkers. PDAC-specific expression of a 5-gene biomarker panel was measured by qRT-PCR in microdissected patient-derived FFPE tissues. Cell-based assays assessed impact of two of these biomarkers, TMPRSS4 and ECT2, on PDAC cells. RESULTS A 5-gene PDAC classifier (TMPRSS4, AHNAK2, POSTN, ECT2, SERPINB5) achieved on average 95% sensitivity and 89% specificity in discriminating PDAC from non-tumor samples in four training sets and similar performance (sensitivity = 94%, specificity = 89.6%) in five independent validation datasets. This classifier accurately discriminated PDAC from chronic pancreatitis (AUC = 0.83), other cancers (AUC = 0.89), and non-tumor from PDAC precursors (AUC = 0.92) in three independent datasets. Importantly, the classifier distinguished PanIN from healthy pancreas in the PDX1-Cre;LSL-KrasG12D PDAC mouse model. Discriminatory expression of the PDAC classifier genes was confirmed in microdissected FFPE samples of PDAC and matched surrounding non-tumor pancreas or pancreatitis. Notably, knock-down of TMPRSS4 and ECT2 reduced PDAC soft agar growth and cell viability and TMPRSS4 knockdown also blocked PDAC migration and invasion. CONCLUSIONS This study identified and validated a highly accurate 5-gene PDAC classifier for discriminating PDAC and early precursor lesions from non-malignant tissue that may facilitate early diagnosis and risk stratification upon validation in prospective clinical trials. Cell-based experiments of two overexpressed proteins encoded by the panel, TMPRSS4 and ECT2, suggest a causal link to PDAC development and progression, confirming them as potential therapeutic targets.
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Affiliation(s)
- Manoj K. Bhasin
- Department of Medicine, BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Kenneth Ndebele
- Department of Pathology, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Octavian Bucur
- Department of Pathology, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Molecular Cell Biology, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Eric U. Yee
- Department of Pathology, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Hasan H. Otu
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Jessica Plati
- Department of Pathology, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Andrea Bullock
- Division of Hematology and Oncology, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Xuesong Gu
- Department of Medicine, BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Eduardo Castan
- Department of Medicine, BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Peng Zhang
- Department of Medicine, BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Robert Najarian
- Department of Pathology, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Maria S. Muraru
- Department of Pathology, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Rebecca Miksad
- Division of Hematology and Oncology, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Roya Khosravi-Far
- Department of Pathology, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Towia A. Libermann
- Department of Medicine, BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, MA, USA
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25
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Cea M, Cagnetta A, Adamia S, Acharya C, Tai YT, Fulciniti M, Ohguchi H, Munshi A, Acharya P, Bhasin MK, Zhong L, Carrasco R, Monacelli F, Ballestrero A, Richardson P, Gobbi M, Lemoli RM, Munshi N, Hideshima T, Nencioni A, Chauhan D, Anderson KC. Evidence for a role of the histone deacetylase SIRT6 in DNA damage response of multiple myeloma cells. Blood 2016; 127:1138-50. [PMID: 26675349 PMCID: PMC4778164 DOI: 10.1182/blood-2015-06-649970] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [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: 06/25/2015] [Accepted: 12/02/2015] [Indexed: 12/18/2022] Open
Abstract
Multiple myeloma (MM) is characterized by a highly unstable genome, with aneuploidy observed in nearly all patients. The mechanism causing this karyotypic instability is largely unknown, but recent observations have correlated these abnormalities with dysfunctional DNA damage response. Here, we show that the NAD(+)-dependent deacetylase SIRT6 is highly expressed in MM cells, as an adaptive response to genomic stability, and that high SIRT6 levels are associated with adverse prognosis. Mechanistically, SIRT6 interacts with the transcription factor ELK1 and with the ERK signaling-related gene. By binding to their promoters and deacetylating H3K9 at these sites, SIRT6 downregulates the expression of mitogen-activated protein kinase (MAPK) pathway genes, MAPK signaling, and proliferation. In addition, inactivation of ERK2/p90RSK signaling triggered by high SIRT6 levels increases DNA repair via Chk1 and confers resistance to DNA damage. Using genetic and biochemical studies in vitro and in human MM xenograft models, we show that SIRT6 depletion both enhances proliferation and confers sensitization to DNA-damaging agents. Our findings therefore provide insights into the functional interplay between SIRT6 and DNA repair mechanisms, with implications for both tumorigenesis and the treatment of MM.
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Affiliation(s)
- Michele Cea
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA; Clinic of Hematology, Department of Internal Medicine, University of Genoa, Istituto di Ricovero e Cura a Carattere Scientifico Scientifico Azienda Ospedaliera Universitaria San Martino-Istituto Scientifico Tumori, Genoa, Italy
| | - Antonia Cagnetta
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA; Clinic of Hematology, Department of Internal Medicine, University of Genoa, Istituto di Ricovero e Cura a Carattere Scientifico Scientifico Azienda Ospedaliera Universitaria San Martino-Istituto Scientifico Tumori, Genoa, Italy
| | - Sophia Adamia
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Chirag Acharya
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Yu-Tzu Tai
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Mariateresa Fulciniti
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Hiroto Ohguchi
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Aditya Munshi
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Prakrati Acharya
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Manoj K Bhasin
- Beth Israel Deaconess Medical Center Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, MA; and
| | - Lei Zhong
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA
| | - Ruben Carrasco
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Fiammetta Monacelli
- Clinic of Hematology, Department of Internal Medicine, University of Genoa, Istituto di Ricovero e Cura a Carattere Scientifico Scientifico Azienda Ospedaliera Universitaria San Martino-Istituto Scientifico Tumori, Genoa, Italy
| | - Alberto Ballestrero
- Clinic of Hematology, Department of Internal Medicine, University of Genoa, Istituto di Ricovero e Cura a Carattere Scientifico Scientifico Azienda Ospedaliera Universitaria San Martino-Istituto Scientifico Tumori, Genoa, Italy
| | - Paul Richardson
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Marco Gobbi
- Clinic of Hematology, Department of Internal Medicine, University of Genoa, Istituto di Ricovero e Cura a Carattere Scientifico Scientifico Azienda Ospedaliera Universitaria San Martino-Istituto Scientifico Tumori, Genoa, Italy
| | - Roberto M Lemoli
- Clinic of Hematology, Department of Internal Medicine, University of Genoa, Istituto di Ricovero e Cura a Carattere Scientifico Scientifico Azienda Ospedaliera Universitaria San Martino-Istituto Scientifico Tumori, Genoa, Italy
| | - Nikhil Munshi
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Teru Hideshima
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Alessio Nencioni
- Clinic of Hematology, Department of Internal Medicine, University of Genoa, Istituto di Ricovero e Cura a Carattere Scientifico Scientifico Azienda Ospedaliera Universitaria San Martino-Istituto Scientifico Tumori, Genoa, Italy
| | - Dharminder Chauhan
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Kenneth C Anderson
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Research, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
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26
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Rajamani D, Singh PK, Rottmann BG, Singh N, Bhasin MK, Kumar A. Temporal retinal transcriptome and systems biology analysis identifies key pathways and hub genes in Staphylococcus aureus endophthalmitis. Sci Rep 2016; 6:21502. [PMID: 26865111 PMCID: PMC4749995 DOI: 10.1038/srep21502] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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: 08/24/2015] [Accepted: 01/08/2016] [Indexed: 12/11/2022] Open
Abstract
Bacterial endophthalmitis remains a devastating inflammatory condition associated with permanent vision loss. Hence, assessing the host response in this disease may provide new targets for intervention. Using a mouse model of Staphylococcus aureus (SA) endophthalmitis and performing retinal transcriptome analysis, we discovered progressive changes in the expression of 1,234 genes. Gene ontology (GO) and pathway analyses revealed the major pathways impacted in endophthalmitis includes: metabolism, inflammatory/immune, antimicrobial, cell trafficking, and lipid biosynthesis. Among the immune/inflammation pathways, JAK/Stat and IL-17A signaling were the most significantly affected. Interactive network-based analyses identified 13 focus hub genes (IL-6, IL-1β, CXCL2, STAT3, NUPR1, Jun, CSF1, CYR61, CEBPB, IGF-1, EGFR1, SPP1, and TGM2) within these important pathways. The expression of hub genes confirmed by qRT-PCR, ELISA (IL-6, IL-1β, and CXCL2), and Western blot or immunostaining (CEBP, STAT3, NUPR1, and IGF1) showed strong correlation with transcriptome data. Since TLR2 plays an important role in SA endophthalmitis, counter regulation analysis of TLR2 ligand pretreated retina or the use of retinas from TLR2 knockout mice showed the down-regulation of inflammatory regulatory genes. Collectively, our study provides, for the first time, a comprehensive analysis of the transcriptomic response and identifies key pathways regulating retinal innate responses in staphylococcal endophthalmitis.
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Affiliation(s)
- Deepa Rajamani
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, MA
| | - Pawan Kumar Singh
- Kresge Eye Institute, Wayne State University, Detroit, MI.,Department of Anatomy and Cell Biology, Wayne State University, Detroit, MI
| | - Bruce G Rottmann
- Department of Anatomy and Cell Biology, Wayne State University, Detroit, MI
| | - Natasha Singh
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, MA
| | - Manoj K Bhasin
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, MA.,Department of Medicine, Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Ashok Kumar
- Kresge Eye Institute, Wayne State University, Detroit, MI.,Department of Anatomy and Cell Biology, Wayne State University, Detroit, MI.,Department of Immunology and Microbiology, Wayne State University, Detroit, MI
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27
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Wang F, Kaplan JL, Gold BD, Bhasin MK, Ward NL, Kellermayer R, Kirschner BS, Heyman MB, Dowd SE, Cox SB, Dogan H, Steven B, Ferry GD, Cohen SA, Baldassano RN, Moran CJ, Garnett EA, Drake L, Otu HH, Mirny LA, Libermann TA, Winter HS, Korolev KS. Detecting Microbial Dysbiosis Associated with Pediatric Crohn Disease Despite the High Variability of the Gut Microbiota. Cell Rep 2016; 14:945-955. [PMID: 26804920 DOI: 10.1016/j.celrep.2015.12.088] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 12/03/2015] [Accepted: 12/18/2015] [Indexed: 02/06/2023] Open
Abstract
The relationship between the host and its microbiota is challenging to understand because both microbial communities and their environments are highly variable. We have developed a set of techniques based on population dynamics and information theory to address this challenge. These methods identify additional bacterial taxa associated with pediatric Crohn disease and can detect significant changes in microbial communities with fewer samples than previous statistical approaches required. We have also substantially improved the accuracy of the diagnosis based on the microbiota from stool samples, and we found that the ecological niche of a microbe predicts its role in Crohn disease. Bacteria typically residing in the lumen of healthy individuals decrease in disease, whereas bacteria typically residing on the mucosa of healthy individuals increase in disease. Our results also show that the associations with Crohn disease are evolutionarily conserved and provide a mutual information-based method to depict dysbiosis.
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Affiliation(s)
- Feng Wang
- Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
| | - Jess L Kaplan
- Department of Pediatrics, MassGeneral Hospital for Children, Harvard Medical School, Boston, MA 02114, USA
| | - Benjamin D Gold
- Children's Healthcare of Atlanta, LLC; GI Care for Kids, LLC; Atlanta, GA 30342, USA
| | - Manoj K Bhasin
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center and Department of Medicine, Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115, USA
| | - Naomi L Ward
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Richard Kellermayer
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Barbara S Kirschner
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | - Melvin B Heyman
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Scot E Dowd
- Molecular Research MR DNA, Shallowater, TX 79363, USA
| | - Stephen B Cox
- Molecular Research MR DNA, Shallowater, TX 79363, USA
| | - Haluk Dogan
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Blaire Steven
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - George D Ferry
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stanley A Cohen
- Children's Healthcare of Atlanta, LLC; GI Care for Kids, LLC; Atlanta, GA 30342, USA
| | - Robert N Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christopher J Moran
- Department of Pediatrics, MassGeneral Hospital for Children, Harvard Medical School, Boston, MA 02114, USA
| | - Elizabeth A Garnett
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lauren Drake
- Department of Pediatrics, MassGeneral Hospital for Children, Harvard Medical School, Boston, MA 02114, USA
| | - Hasan H Otu
- Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Leonid A Mirny
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Towia A Libermann
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center and Department of Medicine, Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115, USA
| | - Harland S Winter
- Department of Pediatrics, MassGeneral Hospital for Children, Harvard Medical School, Boston, MA 02114, USA.
| | - Kirill S Korolev
- Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA; Department of Physics, Boston University, Boston, MA 02215, USA.
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28
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Ohguchi H, Hideshima T, Bhasin MK, Gorgun GT, Santo L, Cea M, Samur MK, Mimura N, Suzuki R, Tai YT, Carrasco RD, Raje N, Richardson PG, Munshi NC, Harigae H, Sanda T, Sakai J, Anderson KC. The KDM3A-KLF2-IRF4 axis maintains myeloma cell survival. Nat Commun 2016; 7:10258. [PMID: 26728187 PMCID: PMC4728406 DOI: 10.1038/ncomms10258] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [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: 02/13/2015] [Accepted: 11/23/2015] [Indexed: 12/14/2022] Open
Abstract
KDM3A is implicated in tumorigenesis; however, its biological role in multiple myeloma (MM) has not been elucidated. Here we identify KDM3A–KLF2–IRF4 axis dependence in MM. Knockdown of KDM3A is toxic to MM cells in vitro and in vivo. KDM3A maintains expression of KLF2 and IRF4 through H3K9 demethylation, and knockdown of KLF2 triggers apoptosis. Moreover, KLF2 directly activates IRF4 and IRF4 reciprocally upregulates KLF2, forming a positive autoregulatory circuit. The interaction of MM cells with bone marrow milieu mediates survival of MM cells. Importantly, silencing of KDM3A, KLF2 or IRF4 both decreases MM cell adhesion to bone marrow stromal cells and reduces MM cell homing to the bone marrow, in association with decreased ITGB7 expression in MAF-translocated MM cell lines. Our results indicate that the KDM3A–KLF2–IRF4 pathway plays an essential role in MM cell survival and homing to the bone marrow, and therefore represents a therapeutic target. Several histone modifiers have been implicated in the survival of multiple myeloma cells. Here, the authors reveal a role for the histone demethylase KDM3A in the survival of this haematologic cancer, and show that mechanistically KDM3A removes H3K9 methylation from the promoters of KLF2 and IRF4, genes essential for myeloma cell survival.
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Affiliation(s)
- Hiroto Ohguchi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Teru Hideshima
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Manoj K Bhasin
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA
| | - Gullu T Gorgun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Loredana Santo
- MGH Cancer Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Michele Cea
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Mehmet K Samur
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Naoya Mimura
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Rikio Suzuki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Yu-Tzu Tai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Ruben D Carrasco
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Noopur Raje
- MGH Cancer Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Paul G Richardson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Nikhil C Munshi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.,West Roxbury Division, VA Boston Healthcare System, West Roxbury, MA 02132, USA
| | - Hideo Harigae
- Department of Hematology and Rheumatology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8574, Japan
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, Department of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Juro Sakai
- Division of Metabolic Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904, Japan
| | - Kenneth C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
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29
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de Vasconcellos JF, Laranjeira ABA, Leal PC, Bhasin MK, Zenatti PP, Nunes RJ, Yunes RA, Nowill AE, Libermann TA, Zerbini LF, Yunes JA. SB225002 Induces Cell Death and Cell Cycle Arrest in Acute Lymphoblastic Leukemia Cells through the Activation of GLIPR1. PLoS One 2015; 10:e0134783. [PMID: 26302043 PMCID: PMC4547718 DOI: 10.1371/journal.pone.0134783] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 04/10/2014] [Accepted: 07/14/2015] [Indexed: 01/07/2023] Open
Abstract
Acute Lymphoblastic Leukemia (ALL) is the most frequent childhood malignancy. In the effort to find new anti-leukemic agents, we evaluated the small drug SB225002 (N-(2-hydroxy-4-nitrophenyl)-N’-(2-bromophenyl)urea). Although initially described as a selective antagonist of CXCR2, later studies have identified other cellular targets for SB225002, with potential medicinal use in cancer. We found that SB225002 has a significant pro-apoptotic effect against both B- and T-ALL cell lines. Cell cycle analysis demonstrated that treatment with SB225002 induces G2-M cell cycle arrest. Transcriptional profiling revealed that SB225002-mediated apoptosis triggered a transcriptional program typical of tubulin binding agents. Network analysis revealed the activation of genes linked to the JUN and p53 pathways and inhibition of genes linked to the TNF pathway. Early cellular effects activated by SB225002 included the up-regulation of GLIPR1, a p53-target gene shown to have pro-apoptotic activities in prostate and bladder cancer. Silencing of GLIPR1 in B- and T-ALL cell lines resulted in increased resistance to SB225002. Although SB225002 promoted ROS increase in ALL cells, antioxidant N-Acetyl Cysteine pre-treatment only modestly attenuated cell death, implying that the pro-apoptotic effects of SB225002 are not exclusively mediated by ROS. Moreover, GLIPR1 silencing resulted in increased ROS levels both in untreated and SB225002-treated cells. In conclusion, SB225002 induces cell cycle arrest and apoptosis in different B- and T-ALL cell lines. Inhibition of tubulin function with concurrent activation of the p53 pathway, in particular, its downstream target GLIPR1, seems to underlie the anti-leukemic effect of SB225002.
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Affiliation(s)
- Jaíra Ferreira de Vasconcellos
- Centro Infantil Boldrini, Campinas, SP, Brazil
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, SP, Brazil
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Paulo C. Leal
- Department of Chemistry, Santa Catarina Federal University, Florianopólis, SC, Brazil
| | - Manoj K. Bhasin
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Ricardo J. Nunes
- Department of Chemistry, Santa Catarina Federal University, Florianopólis, SC, Brazil
| | - Rosendo A. Yunes
- Department of Chemistry, Santa Catarina Federal University, Florianopólis, SC, Brazil
| | - Alexandre E. Nowill
- Centro Integrado de Pesquisas Oncohematológicas da Infancia, University of Campinas, Campinas, SP, Brazil
| | - Towia A. Libermann
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Luiz Fernando Zerbini
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
- Cancer Genomics Group, International Center for Genetic Engineering and Biotechnology and Medical Biochemistry Division, University of Cape Town, Cape Town, South Africa
| | - José Andrés Yunes
- Centro Infantil Boldrini, Campinas, SP, Brazil
- Department of Medical Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, SP, Brazil
- * E-mail:
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30
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Cuiffo BG, Campagne A, Bell GW, Lembo A, Orso F, Lien E, Bhasin MK, Raimo M, Hanson SE, Marusyk A, Hematti P, Polyak K, Mariani O, Volinia S, Vincent-Salomon A, Taverna D, Karnoub AE. Abstract P1-07-02: Mesenchymal stem cell regulated microRNAs converge on the speech gene FOXP2 and regulate breast cancer metastasis. Cancer Res 2015. [DOI: 10.1158/1538-7445.sabcs14-p1-07-02] [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
About 90% of breast cancer mortalities are due to the spread of breast cancer cells (BCCs) from a primary tumor to distant organs, a process known as metastasis. However, the molecular mechanisms underlying metastasis remain poorly understood. Substantial evidence now supports a major role for the tumor microenvironment (TME) in catalyzing breast cancer metastasis. Indeed, observations indicate that proximal interactions between BCCs and cells of the TME induce altered gene expression programs in BCCs, allowing for the navigation of the various steps of the metastatic cascade. Our group and others observed that breast tumors recruit mesenchymal stem cells (MSCs): multipotent fibroblasts that normally exert tissue maintenance functions. We and others have observed that physical interactions of MSCs with BCCs are sufficient to drive their metastatic dissemination in murine xenograft models, via the induction of epithelial-mesenchymal transition (EMT) and dedifferentiation into stem cell-like states (cancer stem cells, or CSCs), states tightly associated with the capacity to seed new tumors (for example in foreign tissues) and with chemotherapeutic resistance. However, the TME-induced molecular pathways regulating such mechanisms remain poorly understood.
MicroRNAs (miRNAs, miRs) are small noncoding RNAs that regulate gene expression via base-pair interactions with messenger RNAs (mRNAs), resulting in mRNA degradation or translational inhibition. Due to their ability to interact with large numbers of target mRNAs simultaneously, miRNAs are major regulators of cell identity, and thereby serve critical roles in metastasis.
We performed miRnome-wide screening of MSC-stimulated BCCs to determine if TME interactions might contribute to BCC metastasis via the deregulation of miRNAs. We observed that proximal MSCs induce aberrant expression of a specific set of miRNAs in BCCs, which had not been previously implicated in breast cancer pathogenesis. These miRNAs, led by the transcriptionally co-regulated miR-199a-3p and miR-214, were sufficient to actuate the metastasis of weakly metastatic human BCCs in xenograft models. We observed that exogenous expression of the miRNAs provided BCCs with phenotypes and gene markers characteristic of CSCs, including enhanced tumor initiation capacities. Interestingly, we found that the MSC-induced miRNAs function as an interrelated network, and converge upon a common novel target: the speech associated gene FOXP2. Knockdown of FOXP2 phenocopied the metastatic phenotypes observed in MSC-induced miRNA expressing BCCs. Importantly, elevated levels of the MSC-induced miRNAs or depressed levels of FOXP2 could predict patient prognosis in the clinic. Altogether, our results incriminate FOXP2 and it’s MSC-induced miRNA regulatory network as novel determinants of breast cancer metastasis.
Citation Format: Benjamin G Cuiffo, Antoine Campagne, George W Bell, Antonio Lembo, Francesca Orso, Evan Lien, Manoj K Bhasin, Monica Raimo, Summer E Hanson, Andriy Marusyk, Peiman Hematti, Kornelia Polyak, Odette Mariani, Stefano Volinia, Anne Vincent-Salomon, Daniela Taverna, Antoine E Karnoub. Mesenchymal stem cell regulated microRNAs converge on the speech gene FOXP2 and regulate breast cancer metastasis [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P1-07-02.
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Affiliation(s)
| | - Antoine Campagne
- 1Beth Israel Deaconess Medical Center, Harvard Medical School
- 2Institut Curie
| | | | | | | | - Evan Lien
- 1Beth Israel Deaconess Medical Center, Harvard Medical School
| | - Manoj K Bhasin
- 1Beth Israel Deaconess Medical Center, Harvard Medical School
| | | | - Summer E Hanson
- 5University of Wisconsin-Madison, School of Medicine and Public Health
| | | | - Peiman Hematti
- 5University of Wisconsin-Madison, School of Medicine and Public Health
| | | | | | | | | | | | - Antoine E Karnoub
- 1Beth Israel Deaconess Medical Center, Harvard Medical School
- 8Harvard Stem Cell Institute
- 9Broad Institute of MIT and Harvard
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Jedinak A, Curatolo A, Zurakowski D, Dillon S, Bhasin MK, Libermann TA, Roy R, Sachdev M, Loughlin KR, Moses MA. Novel non-invasive biomarkers that distinguish between benign prostate hyperplasia and prostate cancer. BMC Cancer 2015; 15:259. [PMID: 25884438 PMCID: PMC4433087 DOI: 10.1186/s12885-015-1284-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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: 08/29/2014] [Accepted: 03/30/2015] [Indexed: 11/20/2022] Open
Abstract
Background The objective of this study was to discover and to validate novel noninvasive biomarkers that distinguish between benign prostate hyperplasia (BPH) and localized prostate cancer (PCa), thereby helping to solve the diagnostic dilemma confronting clinicians who treat these patients. Methods Quantitative iTRAQ LC/LC/MS/MS analysis was used to identify proteins that are differentially expressed in the urine of men with BPH compared with those who have localized PCa. These proteins were validated in 173 urine samples from patients diagnosed with BPH (N = 83) and PCa (N = 90). Multivariate logistic regression analysis was used to identify the predictive biomarkers. Results Three proteins, β2M, PGA3, and MUC3 were identified by iTRAQ and validated by immunoblot analyses. Univariate analysis demonstrated significant elevations in urinary β2M (P < 0.001), PGA3 (P = 0.006), and MUC3 (P = 0.018) levels found in the urine of PCa patients. Multivariate logistic regression analysis revealed AUC values ranging from 0.618 for MUC3 (P = 0.009), 0.625 for PGA3 (P < 0.008), and 0.668 for β2M (P < 0.001). The combination of all three demonstrated an AUC of 0.710 (95% CI: 0.631 – 0.788, P < 0.001); diagnostic accuracy improved even more when these data were combined with PSA categories (AUC = 0.812, (95% CI: 0.740 – 0.885, P < 0.001). Conclusions Urinary β2M, PGA3, and MUC3, when analyzed alone or when multiplexed with clinically defined categories of PSA, may be clinically useful in noninvasively resolving the dilemma of effectively discriminating between BPH and localized PCa. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1284-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrej Jedinak
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA.
| | - Adam Curatolo
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Boston, MA, USA.
| | - David Zurakowski
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Boston, MA, USA. .,Department of Anesthesia, Boston Children's Hospital, Boston, MA, USA.
| | - Simon Dillon
- Harvard Medical School, Boston, MA, USA. .,Genomics and Proteomics Center, Beth Israel Deaconess Medical Center, Boston, MA, USA.
| | - Manoj K Bhasin
- Harvard Medical School, Boston, MA, USA. .,Genomics and Proteomics Center, Beth Israel Deaconess Medical Center, Boston, MA, USA.
| | - Towia A Libermann
- Harvard Medical School, Boston, MA, USA. .,Genomics and Proteomics Center, Beth Israel Deaconess Medical Center, Boston, MA, USA.
| | - Roopali Roy
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA.
| | - Monisha Sachdev
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Boston, MA, USA.
| | - Kevin R Loughlin
- Harvard Medical School, Boston, MA, USA. .,Department of Urology, Brigham and Women's Hospital, Boston, MA, USA.
| | - Marsha A Moses
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA.
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Rauh-Hain A, Kim M, Zhang L, Foster R, Rueda B, Bhasin MK, Growdon W. Next-generation sequencing demonstrates genomic signature of resistance patterns following phosphatidylinositol 3-kinase (PI3K) inhibition. Gynecol Oncol 2015. [DOI: 10.1016/j.ygyno.2014.11.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Cuiffo BG, Campagne A, Bell GW, Lembo A, Orso F, Lien EC, Bhasin MK, Raimo M, Hanson SE, Marusyk A, El-Ashry D, Hematti P, Polyak K, Mechta-Grigoriou F, Mariani O, Volinia S, Vincent-Salomon A, Taverna D, Karnoub AE. MSC-regulated microRNAs converge on the transcription factor FOXP2 and promote breast cancer metastasis. Cell Stem Cell 2014; 15:762-74. [PMID: 25515522 DOI: 10.1016/j.stem.2014.10.001] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 06/27/2014] [Accepted: 10/02/2014] [Indexed: 12/17/2022]
Abstract
Mesenchymal stem/stromal cells (MSCs) are progenitor cells shown to participate in breast tumor stroma formation and to promote metastasis. Despite expanding knowledge of their contributions to breast malignancy, the underlying molecular responses of breast cancer cells (BCCs) to MSC influences remain incompletely understood. Here, we show that MSCs cause aberrant expression of microRNAs, which, led by microRNA-199a, provide BCCs with enhanced cancer stem cell (CSC) properties. We demonstrate that such MSC-deregulated microRNAs constitute a network that converges on and represses the expression of FOXP2, a forkhead transcription factor tightly associated with speech and language development. FOXP2 knockdown in BCCs was sufficient in promoting CSC propagation, tumor initiation, and metastasis. Importantly, elevated microRNA-199a and depressed FOXP2 expression levels are prominent features of malignant clinical breast cancer and are associated significantly with poor survival. Our results identify molecular determinants of cancer progression of potential utility in the prognosis and therapy of breast cancer.
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Affiliation(s)
- Benjamin G Cuiffo
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Antoine Campagne
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Institut Curie, 75248 Paris Cedex 05, France
| | - George W Bell
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Antonio Lembo
- Department of Molecular Biotechnology and Health Sciences, University of Turin and MBC, 10126 Torino, Italy
| | - Francesca Orso
- Department of Molecular Biotechnology and Health Sciences, University of Turin and MBC, 10126 Torino, Italy
| | - Evan C Lien
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Manoj K Bhasin
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Monica Raimo
- Department of Molecular Biotechnology and Health Sciences, University of Turin and MBC, 10126 Torino, Italy
| | - Summer E Hanson
- Carbone Cancer Center, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53792, USA
| | - Andriy Marusyk
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Dorraya El-Ashry
- Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Peiman Hematti
- Carbone Cancer Center, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI 53792, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Stefano Volinia
- Department of Morphology, Surgery and Experimental Medicine, Human Anatomy Branch, University of Ferrara, 44121 Ferrara, Italy
| | | | - Daniela Taverna
- Department of Molecular Biotechnology and Health Sciences, University of Turin and MBC, 10126 Torino, Italy
| | - Antoine E Karnoub
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Dahlke C, Angin M, Müller C, Sharma S, Bhasin MK, Zhuang Y, Addo MM. A Distinct Treg Transcriptome Signature in HIV-1 Elite Controllers Might Contribute to Improved Disease Outcome. AIDS Res Hum Retroviruses 2014. [DOI: 10.1089/aid.2014.5383.abstract] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Christine Dahlke
- Universitätsklinikum Hamburg-Eppendorf, Department of Medicine, Emerging Infections, Hamburg, Germany
| | - Mathieu Angin
- Ragon Institute of MIT, MGH and Harvard, Boston, MA, United States
- Institut Pasteur, Virology, Paris, France
| | - Christian Müller
- University Heart Center Hamburg, Clinic for General and Interventional Cardiology, Hamburg, Germany
| | - Siddharta Sharma
- Ragon Institute of MIT, MGH and Harvard, Boston, MA, United States
| | - Manoj K. Bhasin
- Beth Israel Deaconess Medical Center, Genomics & Proteomics Core, Boston, MA, United States
| | - Yan Zhuang
- Ragon Institute of MIT, MGH and Harvard, Boston, MA, United States
| | - Marylyn M. Addo
- Universitätsklinikum Hamburg-Eppendorf, Department of Medicine, Emerging Infections, Hamburg, Germany
- German Center for Infection Research, Emerging Infections, Hamburg, Germany
- Massachusetts General Hospital, Division of Infectious Diseases, Boston, MA, United States
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35
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Zerbini LF, Bhasin MK, de Vasconcellos JF, Paccez JD, Gu X, Kung AL, Libermann TA. Computational repositioning and preclinical validation of pentamidine for renal cell cancer. Mol Cancer Ther 2014; 13:1929-1941. [PMID: 24785412 DOI: 10.1158/1535-7163.mct-13-0750] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although early stages of clear cell renal cell carcinoma (ccRCC) are curable, survival outcome for metastatic ccRCC remains poor. We previously established a highly accurate signature of differentially expressed genes that distinguish ccRCC from normal kidney. The purpose of this study was to apply a new individualized bioinformatics analysis (IBA) strategy to these transcriptome data in conjunction with Gene Set Enrichment Analysis of the Connectivity Map (C-MAP) database to identify and reposition FDA-approved drugs for anticancer therapy. Here, we demonstrate that one of the drugs predicted to revert the RCC gene signature toward normal kidney, pentamidine, is effective against RCC cells in culture and in a RCC xenograft model. ccRCC-specific gene expression signatures of individual patients were used to query the C-MAP software. Eight drugs with negative correlation and P-value <0.05 were analyzed for efficacy against RCC in vitro and in vivo. Our data demonstrate consistency across most patients with ccRCC for the set of high-scoring drugs. Most of the selected high-scoring drugs potently induce apoptosis in RCC cells. Several drugs also demonstrate selectivity for Von Hippel-Lindau negative RCC cells. Most importantly, at least one of these drugs, pentamidine, slows tumor growth in the 786-O human ccRCC xenograft mouse model. Our findings suggest that pentamidine might be a new therapeutic agent to be combined with current standard-of-care regimens for patients with metastatic ccRCC and support our notion that IBA combined with C-MAP analysis enables repurposing of FDA-approved drugs for potential anti-RCC therapy.
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Affiliation(s)
- Luiz Fernando Zerbini
- International Center for Genetic Engineering and Biotechnology (ICGEB), Cancer Genomics Group and Division of Medical Biochemistry, University of Cape Town, Cape Town, South Africa.,BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Manoj K Bhasin
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Jaira F de Vasconcellos
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Juliano D Paccez
- International Center for Genetic Engineering and Biotechnology (ICGEB), Cancer Genomics Group and Division of Medical Biochemistry, University of Cape Town, Cape Town, South Africa
| | - Xuesong Gu
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Andrew L Kung
- Department of Pediatrics, Columbia University Medical Center, New York, NY
| | - Towia A Libermann
- BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
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36
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Angin M, Sharma S, King M, Murooka TT, Ghebremichael M, Mempel TR, Walker BD, Bhasin MK, Addo MM. HIV-1 infection impairs regulatory T-cell suppressive capacity on a per-cell basis. J Infect Dis 2014; 210:899-903. [PMID: 24664171 DOI: 10.1093/infdis/jiu188] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The impact of CD4+ regulatory T cells (Tregs) on human immunodeficiency virus type 1 (HIV-1) pathogenesis remains incompletely understood. Although it has been shown that Tregs can be infected with HIV-1, the consequences of infection on a per-cell basis are still unknown. In vitro HIV-GFP infected and noninfected Tregs were isolated by flow-based cell-sorting to investigate Treg suppressive capacity and gene expression profiles. Our data show that HIV-1-infected Tregs were significantly less suppressive than noninfected Tregs and demonstrated down-regulation of genes critical to Treg function. This impaired function may have detrimental consequences for the control of generalized immune activation and accelerate HIV disease progression.
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Affiliation(s)
| | | | | | | | | | | | | | - Manoj K Bhasin
- BIDMC Genomics and Proteomics Center, Dana Farber/Harvard Cancer Center
| | - Marylyn M Addo
- Ragon Institute of MGH, MIT and Harvard Massachusetts General Hospital, Division of Infectious Diseases, Boston, Massachusetts Department of Medicine I, University Hospital Hamburg-Eppendorf German Center for Infection Research (DZIF), partner site Hamburg/Lübeck/Borstel, Germany
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37
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Niles H, Mehta DH, Corrigan AA, Bhasin MK, Denninger JW. Functional genomics in the study of mind-body therapies. Ochsner J 2014; 14:681-95. [PMID: 25598735 PMCID: PMC4295747] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND Mind-body therapies (MBTs) are used throughout the world in treatment, disease prevention, and health promotion. However, the mechanisms by which MBTs exert their positive effects are not well understood. Investigations into MBTs using functional genomics have revolutionized the understanding of MBT mechanisms and their effects on human physiology. METHODS We searched the literature for the effects of MBTs on functional genomics determinants using MEDLINE, supplemented by a manual search of additional journals and a reference list review. RESULTS We reviewed 15 trials that measured global or targeted transcriptomic, epigenomic, or proteomic changes in peripheral blood. Sample sizes ranged from small pilot studies (n=2) to large trials (n=500). While the reliability of individual genes from trial to trial was often inconsistent, genes related to inflammatory response, particularly those involved in the nuclear factor-kappa B (NF-κB) pathway, were consistently downregulated across most studies. CONCLUSION In general, existing trials focusing on gene expression changes brought about by MBTs have revealed intriguing connections to the immune system through the NF-κB cascade, to telomere maintenance, and to apoptotic regulation. However, these findings are limited to a small number of trials and relatively small sample sizes. More rigorous randomized controlled trials of healthy subjects and specific disease states are warranted. Future research should investigate functional genomics areas both upstream and downstream of MBT-related gene expression changes-from epigenomics to proteomics and metabolomics.
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Affiliation(s)
- Halsey Niles
- Benson-Henry Institute for Mind Body Medicine, Massachusetts General Hospital, Boston, MA
| | - Darshan H. Mehta
- Benson-Henry Institute for Mind Body Medicine, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Alexandra A. Corrigan
- Benson-Henry Institute for Mind Body Medicine, Massachusetts General Hospital, Boston, MA
| | - Manoj K. Bhasin
- Benson-Henry Institute for Mind Body Medicine, Massachusetts General Hospital, Boston, MA
- Genomics and Proteomics Core, Beth Israel Deaconess Medical Center, Boston, MA
| | - John W. Denninger
- Benson-Henry Institute for Mind Body Medicine, Massachusetts General Hospital, Boston, MA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA
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38
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Black KM, Masuzawa A, Hagberg RC, Khabbaz KR, Trovato ME, Rettagliati VM, Bhasin MK, Dillon ST, Libermann TA, Toumpoulis IK, Levitsky S, McCully JD. Preliminary biomarkers for identification of human ascending thoracic aortic aneurysm. J Am Heart Assoc 2013; 2:e000138. [PMID: 24231657 PMCID: PMC3886733 DOI: 10.1161/jaha.113.000138] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Background Human ascending thoracic aortic aneurysms (ATAAs) are life threatening and constitute a leading cause of mortality in the United States. Previously, we demonstrated that collagens α2(V) and α1(XI) mRNA and protein expression levels are significantly increased in ATAAs. Methods and Results In this report, the authors extended these preliminary studies using high‐throughput proteomic analysis to identify additional biomarkers for use in whole blood real‐time RT‐PCR analysis to allow for the identification of ATAAs before dissection or rupture. Human ATAA samples were obtained from male and female patients aged 65±14 years. Both bicuspid and tricuspid aortic valve patients were included and compared with nonaneurysmal aortas (mean diameter 2.3 cm). Five biomarkers were identified as being suitable for detection and identification of ATAAs using qRT‐PCR analysis of whole blood. Analysis of 41 samples (19 small, 13 medium‐sized, and 9 large ATAAs) demonstrated the overexpression of 3 of these transcript biomarkers correctly identified 79.4% of patients with ATAA of ≥4.0 cm (P<0.001, sensitivity 0.79, CI=0.62 to 0.91; specificity 1.00, 95% CI=0.42 to 1.00). Conclusion A preliminary transcript biomarker panel for the identification of ATAAs using whole blood qRT‐PCR analysis in men and women is presented.
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Affiliation(s)
- Kendra M Black
- Division of Cardiothoracic Surgery, Beth Israel Deaconess Medical Center, Boston, MA
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Abstract
The early, accurate diagnosis and risk stratification of sepsis remains an important challenge in the critically ill. Since traditional biomarker strategies have not yielded a gold standard marker for sepsis, focus is shifting towards novel strategies that improve assessment capabilities. The combination of technological advancements and information generated through the human genome project positions systems biology at the forefront of biomarker discovery. While previously available, developments in the technologies focusing on DNA, gene expression, gene regulatory mechanisms, protein and metabolite discovery have made these tools more feasible to implement and less costly, and they have taken on an enhanced capacity such that they are ripe for utilization as tools to advance our knowledge and clinical research. Medicine is in a genome-level era that can leverage the assessment of thousands of molecular signals beyond simply measuring selected circulating proteins. Genomics is the study of the entire complement of genetic material of an individual. Epigenetics is the regulation of gene activity by reversible modifications of the DNA. Transcriptomics is the quantification of the relative levels of messenger RNA for a large number of genes in specific cells or tissues to measure differences in the expression levels of different genes, and the utilization of patterns of differential gene expression to characterize different biological states of a tissue. Proteomics is the large-scale study of proteins. Metabolomics is the study of the small molecule profiles that are the terminal downstream products of the genome and consists of the total complement of all low-molecular-weight molecules that cellular processes leave behind. Taken together, these individual fields of study may be linked during a systems biology approach. There remains a valuable opportunity to deploy these technologies further in human research. The techniques described in this paper not only have the potential to increase the spectrum of diagnostic and prognostic biomarkers in sepsis, but they may also enable the discovery of new disease pathways. This may in turn lead us to improved therapeutic targets. The objective of this paper is to provide an overview and basic framework for clinicians and clinical researchers to better understand the 'omics technologies' to enhance further use of these valuable tools.
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Affiliation(s)
- Simon Skibsted
- Department of Emergency Medicine and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, 99 Brookline Street, Boston, MA 02215, USA
| | - Manoj K Bhasin
- Beth Israel Deaconess Medical Center Genomics and Core, 99 Brookline Avenue, Boston, MA 02115, USA
| | - William C Aird
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, 99 Brookline Street, Boston, MA 02215, USA
| | - Nathan I Shapiro
- Department of Emergency Medicine and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, 99 Brookline Street, Boston, MA 02215, USA
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Dillon ST, Bhasin MK, Feng X, Koh DW, Daoud SS. Quantitative proteomic analysis in HCV-induced HCC reveals sets of proteins with potential significance for racial disparity. J Transl Med 2013; 11:239. [PMID: 24283668 PMCID: PMC3850534 DOI: 10.1186/1479-5876-11-239] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 09/28/2013] [Indexed: 12/18/2022] Open
Abstract
Background The incidence and mortality of hepatitis C virus (HCV)-induced hepatocellular carcinoma (HCC) is higher in African Americans (AA) than other racial/ethnic groups in the U.S., but the reasons for this disparity are unknown. There is an urgent need for the discovery of novel molecular signatures for HCV disease progression to understand the underlying biological basis for this cancer rate disparity to improve the clinical outcome. Methods We performed differential proteomics with isobaric labeling tags for relative and absolute quantitation (iTRAQ) and MS/MS analysis to identify proteins differentially expressed in cirrhotic (CIR) and HCC as compared to normal tissues of Caucasian American (CA) patients. The raw data were analyzed using the ProteinPilot v3.0. Searches were performed against all known sequences populating the Swiss-Prot, Refseq, and TrEMBL databases. Quality control analyses were accomplished using pairwise correlation plots, boxplots, principal component analysis, and unsupervised hierarchical clustering. Supervised analysis was carried out to identify differentially expressed proteins. Candidates were validated in independent cohorts of CA and AA tissues by qRT-PCR or Western blotting. Results A total of 238 unique proteins were identified. Of those, around 15% were differentially expressed between normal, CIR & HCC groups. Target validation demonstrates racially distinct alteration in the expression of certain proteins. For example, the mRNA expression levels of transferrin (TF) were 2 and18-fold higher in CIR and HCC in AA as compared to CA. Similarly; the expression of Apolipoprotein A1 (APOA1) was 7-fold higher in HCC of AA. This increase was mirrored in the protein expression levels. Interestingly, the level of hepatocyte nuclear factor4α (HNF4α) protein was down regulated in AA, whereas repression of transcription is seen more in CA compared to AA. These data suggest that racial disparities in HCC could be a consequence of differential dysregulation of HNF4α transcriptional activity. Conclusion This study identifies novel molecular signatures in HCV-induced HCC using iTRAQ-based tissue proteomics. The proteins identified will further enhance a molecular explanation to the biochemical mechanism(s) that may play a role in HCC racial disparities.
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Bhasin MK, Dusek JA, Chang BH, Joseph MG, Denninger JW, Fricchione GL, Benson H, Libermann TA. Relaxation response induces temporal transcriptome changes in energy metabolism, insulin secretion and inflammatory pathways. PLoS One 2013; 8:e62817. [PMID: 23650531 PMCID: PMC3641112 DOI: 10.1371/journal.pone.0062817] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 03/26/2013] [Indexed: 01/08/2023] Open
Abstract
The relaxation response (RR) is the counterpart of the stress response. Millennia-old practices evoking the RR include meditation, yoga and repetitive prayer. Although RR elicitation is an effective therapeutic intervention that counteracts the adverse clinical effects of stress in disorders including hypertension, anxiety, insomnia and aging, the underlying molecular mechanisms that explain these clinical benefits remain undetermined. To assess rapid time-dependent (temporal) genomic changes during one session of RR practice among healthy practitioners with years of RR practice and also in novices before and after 8 weeks of RR training, we measured the transcriptome in peripheral blood prior to, immediately after, and 15 minutes after listening to an RR-eliciting or a health education CD. Both short-term and long-term practitioners evoked significant temporal gene expression changes with greater significance in the latter as compared to novices. RR practice enhanced expression of genes associated with energy metabolism, mitochondrial function, insulin secretion and telomere maintenance, and reduced expression of genes linked to inflammatory response and stress-related pathways. Interactive network analyses of RR-affected pathways identified mitochondrial ATP synthase and insulin (INS) as top upregulated critical molecules (focus hubs) and NF-κB pathway genes as top downregulated focus hubs. Our results for the first time indicate that RR elicitation, particularly after long-term practice, may evoke its downstream health benefits by improving mitochondrial energy production and utilization and thus promoting mitochondrial resiliency through upregulation of ATPase and insulin function. Mitochondrial resiliency might also be promoted by RR-induced downregulation of NF-κB-associated upstream and downstream targets that mitigates stress.
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Affiliation(s)
- Manoj K. Bhasin
- Benson-Henry Institute for Mind Body Medicine at Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- BIDMC Genomics and Proteomics Center, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Jeffery A. Dusek
- Institute for Health and Healing, Abbott Northwestern Hospital, Minneapolis, Minnesota, United States of America
| | - Bei-Hung Chang
- VA Boston Healthcare System, Boston, Massachusetts, United States of America
- Department of Health Policy and Management, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Marie G. Joseph
- BIDMC Genomics and Proteomics Center, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - John W. Denninger
- Benson-Henry Institute for Mind Body Medicine at Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gregory L. Fricchione
- Benson-Henry Institute for Mind Body Medicine at Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Herbert Benson
- Benson-Henry Institute for Mind Body Medicine at Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Towia A. Libermann
- Benson-Henry Institute for Mind Body Medicine at Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- BIDMC Genomics and Proteomics Center, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- * E-mail:
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Dillon ST, Bhasin MK, Feng X(S, Koh D, Daoud SS. Abstract 1150: Biomarkers discovery and racial disparity in hepatitis C-associated hepatocellular carcinoma. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-1150] [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
Cancer health disparities represent a major public health concern in the US. Even when factors such as socioeconomic status, carcinogen exposure, and access to care are accounted for, disparities persist in the form of higher overall incidence rates and worse clinical outcomes for minority populations than for overall population. A case of point is the racial disparities in liver cancer-related mortality. Hepatitis C virus (HCV) is the most significant contributing factor in the development of hepatocellular carcinoma (HCC). In the US, African Americans (AAs) have twice the prevalence of HCV/genotype 1 infection, and develop HCC at more than twice the rate as Caucasian (CA) counterparts. African Americans are, however, less likely to respond to interferon-based therapy than CAs, and have considerably lower likelihood of receiving liver transplantation. While it is evident that viral infection with HCV is associated with the development of HCC, there are critical gaps in our understanding of the biological basis for this racial disparity. The aim of the current study was to define the molecular signatures of HCV disease progression in liver & tumor tissue samples obtained from AA & CA patients using 8-plex iTRAQ-based proteomics coupled with bioinformatics data analyses. The raw data were analyzed by the ProteinPilot v3.0 using the paragon algorithm. Searches were performed against a comprehensive database generated from SwissPort, Refseq, and Tremble protein sequences. The data were normalized for loading error & background correction. The proteins with confidence score > 90% and with at least 1 peptide of 95% identification confidence were used for further quality control & differential expression analysis. The quality control analysis was performed using pairwise correlation plots, boxplots, principal component analysis (PCA), and unsupervised hierarchical clustering. Supervised analysis was performed to identify differentially expressed proteins (DEP), where the relative protein expression values were compared between groups (Normal vs. Cirrhosis (CIR), Normal vs. HCC, CIR vs. HCC). Based on our experimental design, 787 unique proteins were identified. Of those, 32 were differentially expressed between normal, cirrhosis & HCC groups. Targets validation using real-time PCR (RT-PCR) or western blotting (WB) shows racially distinct alteration in the expression of certain targets. For example, the mRNA expression levels of TF were 2 and18-fold higher in CIR & HCC, respectively in AAs compared to CAs. Similarly, the expression of APOA1 mRNA levels was 7-fold higher in HCC of AAs compared to CAs. This trend was similar to their protein expression levels using WB. However, the level of HNF4α protein was down regulated in AAs compared to CAs. This indicates that HNF4α does not regulate TF & APOA1 expression in HCC of AA samples.
Citation Format: Simon T. Dillon, Manoj K. Bhasin, Xiaoxing (Stella) Feng, David Koh, Sayed Salih Daoud. Biomarkers discovery and racial disparity in hepatitis C-associated hepatocellular carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1150. doi:10.1158/1538-7445.AM2013-1150
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Affiliation(s)
| | | | | | - David Koh
- 2Washington State University, Pullman, WA
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Friehs I, Cowan DB, Choi YH, Black KM, Barnett R, Bhasin MK, Daly C, Dillon SJ, Libermann TA, McGowan FX, del Nido PJ, Levitsky S, McCully JD. Pressure-overload hypertrophy of the developing heart reveals activation of divergent gene and protein pathways in the left and right ventricular myocardium. Am J Physiol Heart Circ Physiol 2012; 304:H697-708. [PMID: 23262132 DOI: 10.1152/ajpheart.00802.2012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Right ventricular (RV) and left ventricular (LV) myocardium differ in their pathophysiological response to pressure-overload hypertrophy. In this report we use microarray and proteomic analyses to identify pathways modulated by LV-aortic banding (AOB) and RV-pulmonary artery banding (PAB) in the immature heart. Newborn New Zealand White rabbits underwent banding of the descending thoracic aorta [LV-AOB; n = 6]. RV-PAB was achieved by banding the pulmonary artery (n = 6). Controls (n = 6 each) were sham-manipulated. After 4 (LV-AOB) and 6 (RV-PAB) wk recovery, the hearts were removed and matched RNA and proteins samples were isolated for microarray and proteomic analysis. Microarray and proteomic data demonstrate that in LV-AOB there is increased transcript expression levels for oxidative phosphorylation, mitochondria energy pathways, actin, ILK, hypoxia, calcium, and protein kinase-A signaling and increased protein expression levels of proteins for cellular macromolecular complex assembly and oxidative phosphorylation. In RV-PAB there is also an increased transcript expression levels for cardiac oxidative phosphorylation but increased protein expression levels for structural constituents of muscle, cardiac muscle tissue development, and calcium handling. These results identify divergent transcript and protein expression profiles in LV-AOB and RV-PAB and provide new insight into the biological basis of ventricular specific hypertrophy. The identification of these pathways should allow for the development of specific therapeutic interventions for targeted treatment and amelioration of LV-AOB and RV-PAB to ameliorate morbidity and mortality.
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Affiliation(s)
- Ingeborg Friehs
- Division of Cardiothoracic Surgery, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
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Wang X, Solban N, Bhasin MK, Bahamon B, Zhang L, Signoretti S, Alsop DC, Atkins MB, Pearsall RS, Mier JW, Kumar R, Bhatt RS. Abstract LB-313: ALK1-Fc inhibits tumor growth in a VEGF pathway resistance model of renal cell carcinoma. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-lb-313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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
Treatment of metastatic RCC with agents that block signaling through VEGFR2 induces disease stabilization or regression in a substantial fraction of patients (pts); however, these responses tend to be short-lived. Mice bearing 786-O and A498 human RCC xenografts treated with sunitinib or sorafenib also exhibit a period of tumor stabilization followed by the resumption of growth and restoration of angiogenesis despite continued drug administration. Thus, alternate angiogenic pathways are of interest in the treatment of RCC. Activin receptor-like kinase 1 (ALK1) is one of 7 type I TGFβ receptors which is predominantly expressed on activated vascular endothelial cells. ALK1-Fc is a soluble receptor fusion protein containing the extracellular domain of ALK1 linked to a human Ig Fc region. ALK1-Fc binds to and neutralizes the activity of bone morphogenetic protein 9 and 10 (BMP9, 10) and has demonstrated antiangiogenic activity in vivo. Currently, ALK1-Fc (ACE-041) is undergoing clinical development. We have found evidence of TGFβ pathway upregulation in tumors that have developed resistance to sunitinib. Thus, to explore the role of ALK signaling in the treatment of RCC we administered ALK1-Fc to mice bearing RCC xenografts. In the treatment naïve A498 model, administration of ALK1-Fc alone delayed tumor growth relative to vehicle: days to grow by 2 mm vehicle- 5.8 +/−0.96 days (n=5) vs ALK1-Fc- 10.8 +/− 1.7 days (n=4, p<0.01). Single agent ALK1-Fc did not show activity in the 786-O model; however combination ALK1-Fc + sunitinib slowed tumor growth to a greater extent than either agent alone or vehicle tumors in both the A498 and the 786-O tumor models. A498 tumors treated with sunitinib took 13.8+/−2.5 days (n=4) to increase by 2 mm vs the ALK1-Fc + sunitinib combination (35 +/− 12.6 days (n=4) (p=0.01)). 786-O derived tumors, treated with sunitinib took 24.7+/−8.3 days (n=3), while tumors treated with combination of ALK1-Fc + sunitinib took 43.7+/−4.2 days (n=3, p<0.03) to grow by 2 mm. Perfusion imaging of these tumors revealed that sunitinib + ALK-Fc lowers perfusion more than sunitinib treated tumors. Our data indicate that ALK1-Fc treatment can act as a single agent to delay tumor growth in at least 1 RCC xenograft model. In addition, combination therapy with ALK1-Fc and sunitinib further delays tumor growth vs either agent administered alone. The effect of the combination therapy on vessel formation and tumor perfusion are currently being investigated. The differential response to ALK1-Fc treatment in the A498 compared to the 786-O cell lines provides an opportunity to explore the molecular and pathological differences between the two models, which may allow for better insight into mechanisms of action and future pt selection. The data demonstrate that blocking ligand signaling through the endogenous ALK1 receptor, either alone or in combination with other antiangiogenic therapies, is a valid strategy for treatment of RCC.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-313. doi:1538-7445.AM2012-LB-313
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Affiliation(s)
- Xiaoen Wang
- 1Beth Israel Deaconess Medical Center, Boston, MA
| | | | | | | | - Liang Zhang
- 1Beth Israel Deaconess Medical Center, Boston, MA
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Damrauer SM, Studer P, da Silva CG, Longo CR, Ramsey HE, Csizmadia E, Shrikhande GV, Scali ST, Libermann TA, Bhasin MK, Ferran C. A20 modulates lipid metabolism and energy production to promote liver regeneration. PLoS One 2011; 6:e17715. [PMID: 21437236 PMCID: PMC3060102 DOI: 10.1371/journal.pone.0017715] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 02/10/2011] [Indexed: 01/18/2023] Open
Abstract
Background Liver Regeneration is clinically of major importance in the setting of liver injury, resection or transplantation. We have demonstrated that the NF-κB inhibitory protein A20 significantly improves recovery of liver function and mass following extended liver resection (LR) in mice. In this study, we explored the Systems Biology modulated by A20 following extended LR in mice. Methodology and Principal Findings We performed transcriptional profiling using Affymetrix-Mouse 430.2 arrays on liver mRNA retrieved from recombinant adenovirus A20 (rAd.A20) and rAd.βgalactosidase treated livers, before and 24 hours after 78% LR. A20 overexpression impacted 1595 genes that were enriched for biological processes related to inflammatory and immune responses, cellular proliferation, energy production, oxidoreductase activity, and lipid and fatty acid metabolism. These pathways were modulated by A20 in a manner that favored decreased inflammation, heightened proliferation, and optimized metabolic control and energy production. Promoter analysis identified several transcriptional factors that implemented the effects of A20, including NF-κB, CEBPA, OCT-1, OCT-4 and EGR1. Interactive scale-free network analysis captured the key genes that delivered the specific functions of A20. Most of these genes were affected at basal level and after resection. We validated a number of A20's target genes by real-time PCR, including p21, the mitochondrial solute carriers SLC25a10 and SLC25a13, and the fatty acid metabolism regulator, peroxisome proliferator activated receptor alpha. This resulted in greater energy production in A20-expressing livers following LR, as demonstrated by increased enzymatic activity of cytochrome c oxidase, or mitochondrial complex IV. Conclusion This Systems Biology-based analysis unravels novel mechanisms supporting the pro-regenerative function of A20 in the liver, by optimizing energy production through improved lipid/fatty acid metabolism, and down-regulated inflammation. These findings support pursuit of A20-based therapies to improve patients’ outcomes in the context of extreme liver injury and extensive LR for tumor treatment or donation.
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Affiliation(s)
- Scott M. Damrauer
- Division of Vascular Surgery, Center for Vascular Biology Research and the Transplant Institute, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter Studer
- Division of Vascular Surgery, Center for Vascular Biology Research and the Transplant Institute, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Cleide G. da Silva
- Division of Vascular Surgery, Center for Vascular Biology Research and the Transplant Institute, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Christopher R. Longo
- Division of Vascular Surgery, Center for Vascular Biology Research and the Transplant Institute, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Haley E. Ramsey
- Division of Vascular Surgery, Center for Vascular Biology Research and the Transplant Institute, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Eva Csizmadia
- Division of Vascular Surgery, Center for Vascular Biology Research and the Transplant Institute, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gautam V. Shrikhande
- Division of Vascular Surgery, Center for Vascular Biology Research and the Transplant Institute, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Salvatore T. Scali
- Division of Vascular Surgery, Center for Vascular Biology Research and the Transplant Institute, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Towia A. Libermann
- Division of Interdisciplinary Medicine and Biotechnology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Manoj K. Bhasin
- Division of Interdisciplinary Medicine and Biotechnology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (MKB) (MB); (CF) (CF)
| | - Christiane Ferran
- Division of Vascular Surgery, Center for Vascular Biology Research and the Transplant Institute, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (MKB) (MB); (CF) (CF)
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Abstract
Data are presented on AB0 and RhD blood groups in 186 patients suffering from carcinoma of cervix uteri and 274 controls from Delhi, India. A strong association is observed between carcinoma patients and blood group A, and a slightly weaker association with blood group B. There is no significant association with RhD blood group. The available data in other populations confirm the association with AB0 blood group.
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Affiliation(s)
- I Kaur
- Department of Anthropology, University of Delhi, India
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Bhasin MK, Shil AP, Sharma MB, Walter H, Danker-Hopfe H, Singh IP, Bhasin V, Bhardwaj V, Sudhakar K, Wadhavan D. Biology of the people of Sikkim, India. 2. Colour blindness, ear lobe attachment, mid-phalangeal hair and behavioural traits. Anthropol Anz 1987; 45:351-60. [PMID: 3501697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
14 population groups of Sikkim (India)--Lepchas (2), Bhutias (2), Sherpas, Tamangs, Gurungs, Mangars, Rais, Limboos/Subbas, Pradhans (Newars), Brahmans, Chhetris, Scheduled Castes--have been studied in regard of the intra- and intergroup variability of colour blindness, ear lobe attachment, mid-phalangeal hair and behavioural traits (tongue folding, hand clapsing, arm folding, leg folding, handedness). Some of these variables show a considerable distribution heterogeneity, which is discussed considering history and marriage patterns of these populations. As most of them are highly endogamous one can assume that this heterogeneity is caused by locally acting factors such as drift and/or founder effects, which could be preserved due to as good as lacking gene flow among the populations under study. Beyond that the Sikkim data are compared briefly with those reported for other Indian and Asiatic populations.
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Affiliation(s)
- M K Bhasin
- Department of Anthropology, University of Delhi, India
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Abstract
One hundred and seventy normal male infants from Delhi were studied using the CBG technique to estimate Y-chromosome length heteromorphisms. The median class in Y/F [Y/F = total length of the Y chromosome/average total length of the F group chromosomes (19 and 20)] distribution was 0.75-0.79. The Y/F index in infants varied from 0.60 to 1.16 with a mean of 0.81 and a standard deviation of 0.09. A high incidence for very small (53.5 percent) and small (41.2 percent) categories of Y-chromosome length heteromorphisms was observed. Data were compared with other available reports; also possible mechanisms of the Y-chromosome length heteromorphisms and their role in ethnic/racial variation as well as in developmental disturbances are discussed. It is suggested there may be a need to redefine the long and short Y chromosome in a given population while studying different clinical disorders.
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Bhasin MK, Singh IP, Walter H, Bhasin V, Chahal SM, Singh R. Genetic studies of Pangwalas, Transhumant and Settled Gaddis. 4. Colour blindness, mid-phalangeal hair, ear lobe attachment and behavioural traits. Anthropol Anz 1986; 44:45-53. [PMID: 3485955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Frequency distributions of colour blindness, midphalangeal hair, ear lobe attachment, hand clasping, arm folding, leg folding and handedness are reported for different population groups from Himachal Pradesh, North India, namely Pangwalas, Transhumant Gaddis (Brahmans, Rajputs and Scheduled Castes) and Settled Gaddis (Brahmans, Rajputs and Schedules Castes). An attempt has been made to compare the results of the present study within and between these groups as well as with the results of other reports from different population groups of India and Asia.
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