1
|
Fernández JJ, Mancebo C, Garcinuño S, March G, Alvarez Y, Alonso S, Inglada L, Blanco J, Orduña A, Montero O, Sandoval TA, Cubillos-Ruiz JR, Bustamante-Munguira E, Fernández N, Crespo MS. Innate IRE1α-XBP1 activation by viral single-stranded RNA and its influence on lung cytokine production during SARS-CoV-2 pneumonia. Genes Immun 2024; 25:43-54. [PMID: 38146001 DOI: 10.1038/s41435-023-00243-6] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 12/27/2023]
Abstract
The utilization of host-cell machinery during SARS-CoV-2 infection can overwhelm the protein-folding capacity of the endoplasmic reticulum and activate the unfolded protein response (UPR). The IRE1α-XBP1 arm of the UPR could also be activated by viral RNA via Toll-like receptors. Based on these premises, a study to gain insight into the pathogenesis of COVID-19 disease was conducted using nasopharyngeal exudates and bronchioloalveolar aspirates. The presence of the mRNA of spliced XBP1 and a high expression of cytokine mRNAs were observed during active infection. TLR8 mRNA showed an overwhelming expression in comparison with TLR7 mRNA in bronchioloalveolar aspirates of COVID-19 patients, thus suggesting the presence of monocytes and monocyte-derived dendritic cells (MDDCs). In vitro experiments in MDDCs activated with ssRNA40, a synthetic mimic of SARS-CoV-2 RNA, showed induction of XBP1 splicing and the expression of proinflammatory cytokines. These responses were blunted by the IRE1α inhibitor MKC8866, the TLR8 antagonist CU-CPT9a, and knockdown of TLR8 receptor. In contrast, the IRE1α-XBP1 activator IXA4 enhanced these responses. Based on these findings, the TLR8/IRE1α system seems to play a significant role in the induction of the proinflammatory cytokines associated with severe COVID-19 disease and might be a druggable target to control cytokine storm.
Collapse
Affiliation(s)
- José J Fernández
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003, Valladolid, Spain
| | - Cristina Mancebo
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003, Valladolid, Spain
- Departamento de Bioquímica, Biología Molecular y Fisiología, Universidad de Valladolid, 47003, Valladolid, Spain
| | - Sonsoles Garcinuño
- Servicio de Microbiología, Hospital Clínico Universitario de Valladolid, Universidad de Valladolid, 47003, Valladolid, Spain
| | - Gabriel March
- Servicio de Microbiología, Hospital Clínico Universitario de Valladolid, Universidad de Valladolid, 47003, Valladolid, Spain
| | - Yolanda Alvarez
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003, Valladolid, Spain
- Departamento de Bioquímica, Biología Molecular y Fisiología, Universidad de Valladolid, 47003, Valladolid, Spain
| | - Sara Alonso
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003, Valladolid, Spain
| | - Luis Inglada
- Servicio de Medicina Interna, Hospital Universitario Rio-Hortega, 47012, Valladolid, Spain
| | - Jesús Blanco
- Servicio de Medicina Intensiva, Hospital Universitario Rio-Hortega, 47012, Valladolid, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Antonio Orduña
- Servicio de Microbiología, Hospital Clínico Universitario de Valladolid, Universidad de Valladolid, 47003, Valladolid, Spain
| | - Olimpio Montero
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003, Valladolid, Spain
| | - Tito A Sandoval
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, 10065, USA
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Juan R Cubillos-Ruiz
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, 10065, USA
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Elena Bustamante-Munguira
- Servicio de Medicina Intensiva, Hospital Clínico Universitario de Valladolid, 47003, Valladolid, Spain
| | - Nieves Fernández
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003, Valladolid, Spain
- Departamento de Bioquímica, Biología Molecular y Fisiología, Universidad de Valladolid, 47003, Valladolid, Spain
| | - Mariano Sánchez Crespo
- Unidad de Excelencia Instituto de Biomedicina y Genética Molecular, CSIC-Universidad de Valladolid, 47003, Valladolid, Spain.
| |
Collapse
|
2
|
Hwang SM, Awasthi D, Jeong J, Sandoval TA, Chae CS, Ramos Y, Tan C, Falco MM, McBain IT, Mishra B, Ivashkiv LB, Zamarin D, Cantillo E, Chapman-Davis E, Holcomb K, Morales DK, Rodriguez PC, Conejo-Garcia JR, Kaczocha M, Vähärautio A, Song M, Cubillos-Ruiz JR. Transgelin 2 guards T cell lipid metabolic programming and anti-tumor function. Res Sq 2023:rs.3.rs-3683989. [PMID: 38168227 PMCID: PMC10760247 DOI: 10.21203/rs.3.rs-3683989/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Mounting effective immunity against pathogens and tumors relies on the successful metabolic programming of T cells by extracellular fatty acids1-3. During this process, fatty-acid-binding protein 5 (FABP5) imports lipids that fuel mitochondrial respiration and sustain the bioenergetic requirements of protective CD8+ T cells4,5. Importantly, however, the mechanisms governing this crucial immunometabolic axis remain unexplored. Here we report that the cytoskeletal organizer Transgelin 2 (TAGLN2) is necessary for optimal CD8+ T cell fatty acid uptake, mitochondrial respiration, and anti-cancer function. We found that TAGLN2 interacts with FABP5, enabling the surface localization of this lipid importer on activated CD8+ T cells. Analysis of ovarian cancer specimens revealed that endoplasmic reticulum (ER) stress responses elicited by the tumor microenvironment repress TAGLN2 in infiltrating CD8+ T cells, enforcing their dysfunctional state. Restoring TAGLN2 expression in ER-stressed CD8+ T cells bolstered their lipid uptake, mitochondrial respiration, and cytotoxic capacity. Accordingly, chimeric antigen receptor T cells overexpressing TAGLN2 bypassed the detrimental effects of tumor-induced ER stress and demonstrated superior therapeutic efficacy in mice with metastatic ovarian cancer. Our study unveils the role of cytoskeletal TAGLN2 in T cell lipid metabolism and highlights the potential to enhance cellular immunotherapy in solid malignancies by preserving the TAGLN2-FABP5 axis.
Collapse
Affiliation(s)
- Sung-Min Hwang
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Deepika Awasthi
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Jieun Jeong
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Tito A. Sandoval
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Chang-Suk Chae
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Yusibeska Ramos
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
| | - Chen Tan
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Matías Marin Falco
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ian T. McBain
- Weill Cornell Graduate School of Medical Sciences. New York, NY 10065. USA
| | - Bikash Mishra
- Weill Cornell Graduate School of Medical Sciences. New York, NY 10065. USA
- HSS Research Institute and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Lionel B. Ivashkiv
- Weill Cornell Graduate School of Medical Sciences. New York, NY 10065. USA
- HSS Research Institute and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Dmitriy Zamarin
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Evelyn Cantillo
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Eloise Chapman-Davis
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Kevin Holcomb
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Diana K. Morales
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
| | - Paulo C. Rodriguez
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute. Tampa, FL, USA
| | - Jose R. Conejo-Garcia
- Department of Integrated Immunobiology, Duke School of Medicine, Durham, NC 27710, USA
- Duke Cancer Institute, Duke School of Medicine, Durham, NC 27710, USA
| | - Martin Kaczocha
- Department of Anesthesiology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, USA
- Stony Brook University Pain and Analgesia Research Center (SPARC), Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Anna Vähärautio
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Minkyung Song
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
| | - Juan R. Cubillos-Ruiz
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine. New York, NY 10065, USA
- Weill Cornell Graduate School of Medical Sciences. New York, NY 10065. USA
| |
Collapse
|
3
|
Markowitz GJ, Ban Y, Tavarez DA, Yoffe L, Podaza E, He Y, Martin MT, Crowley MJP, Sandoval TA, Gao D, Martin ML, Elemento O, Cubillos-Ruiz JR, McGraw TE, Altorki NK, Mittal V. Deficiency of metabolic regulator PKM2 activates the pentose phosphate pathway and generates TCF1+ progenitor CD8+ T cells to improve checkpoint blockade. Res Sq 2023:rs.3.rs-3356477. [PMID: 37790365 PMCID: PMC10543315 DOI: 10.21203/rs.3.rs-3356477/v1] [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: 10/05/2023]
Abstract
TCF1high progenitor CD8+ T cells mediate the efficacy of PD-1 blockade, however the mechanisms that govern their generation and maintenance are poorly understood. Here, we show that targeting glycolysis through deletion of pyruvate kinase muscle 2 (PKM2) results in elevated pentose phosphate pathway (PPP) activity, leading to enrichment of a TCF1high central memory-like phenotype and increased responsiveness to PD-1 blockade in vivo. PKM2KO CD8+ T cells showed reduced glycolytic flux, accumulation of glycolytic intermediates and PPP metabolites, and increased PPP cycling as determined by 1,2 13C glucose carbon tracing. Small molecule agonism of the PPP without acute glycolytic impairment skewed CD8+ T cells towards a TCF1high population, generated a unique transcriptional landscape, enhanced tumor control in mice in combination with PD-1 blockade, and promoted tumor killing in patient-derived tumor organoids. Our study demonstrates a new metabolic reprogramming that contributes to a progenitor-like T cell state amenable to checkpoint blockade.
Collapse
|
4
|
Awasthi D, Chopra S, Cho BA, Emmanuelli A, Sandoval TA, Hwang SM, Chae CS, Salvagno C, Tan C, Vasquez-Urbina L, Fernandez Rodriguez JJ, Santagostino SF, Iwawaki T, Romero-Sandoval EA, Crespo MS, Morales DK, Iliev ID, Hohl TM, Cubillos-Ruiz JR. Inflammatory ER stress responses dictate the immunopathogenic progression of systemic candidiasis. J Clin Invest 2023; 133:e167359. [PMID: 37432737 PMCID: PMC10471176 DOI: 10.1172/jci167359] [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: 11/22/2022] [Accepted: 07/06/2023] [Indexed: 07/12/2023] Open
Abstract
Recognition of pathogen-associated molecular patterns can trigger the inositol-requiring enzyme 1 α (IRE1α) arm of the endoplasmic reticulum (ER) stress response in innate immune cells. This process maintains ER homeostasis and also coordinates diverse immunomodulatory programs during bacterial and viral infections. However, the role of innate IRE1α signaling in response to fungal pathogens remains elusive. Here, we report that systemic infection with the human opportunistic fungal pathogen Candida albicans induced proinflammatory IRE1α hyperactivation in myeloid cells that led to fatal kidney immunopathology. Mechanistically, simultaneous activation of the TLR/IL-1R adaptor protein MyD88 and the C-type lectin receptor dectin-1 by C. albicans induced NADPH oxidase-driven generation of ROS, which caused ER stress and IRE1α-dependent overexpression of key inflammatory mediators such as IL-1β, IL-6, chemokine (C-C motif) ligand 5 (CCL5), prostaglandin E2 (PGE2), and TNF-α. Selective ablation of IRE1α in leukocytes, or treatment with an IRE1α pharmacological inhibitor, mitigated kidney inflammation and prolonged the survival of mice with systemic C. albicans infection. Therefore, controlling IRE1α hyperactivation may be useful for impeding the immunopathogenic progression of disseminated candidiasis.
Collapse
Affiliation(s)
| | - Sahil Chopra
- Department of Obstetrics and Gynecology, and
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York, USA
| | - Byuri A. Cho
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alexander Emmanuelli
- Department of Obstetrics and Gynecology, and
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York, USA
| | | | | | | | | | - Chen Tan
- Department of Obstetrics and Gynecology, and
| | | | - Jose J. Fernandez Rodriguez
- Unit of Excellence, Institute of Biology and Molecular Genetics, CSIC–Universidad de Valladolid, Valladolid, Spain
| | - Sara F. Santagostino
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, The Rockefeller University, and Weill Cornell Medicine, New York, New York, USA
| | - Takao Iwawaki
- Division of Cell Medicine, Medical Research Institute, Kanazawa Medical University, Ishikawa, Japan
| | - E. Alfonso Romero-Sandoval
- Department of Anesthesiology, Pain Mechanisms Laboratory, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Mariano Sanchez Crespo
- Unit of Excellence, Institute of Biology and Molecular Genetics, CSIC–Universidad de Valladolid, Valladolid, Spain
| | | | - Iliyan D. Iliev
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York, USA
- Department of Medicine and
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, New York, USA
| | - Tobias M. Hohl
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York, USA
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Juan R. Cubillos-Ruiz
- Department of Obstetrics and Gynecology, and
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York, USA
| |
Collapse
|
5
|
Markowitz GJ, Ban Y, Tavarez DA, Crowley MJ, Yoffe L, Martin MT, Sandoval TA, Gao D, Cubillos-Ruiz JR, McGraw TE, Altorki NK, Mittal V. Abstract 603: Deficiency of metabolic regulator PKM2 activates the pentose phosphate pathway to generate TCF1+ progenitor CD8+ T cells to improve checkpoint blockade. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-603] [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: 04/07/2023]
Abstract
Abstract
Background: TCF1high progenitor CD8+ T cells have been shown to mediate the efficacy of PD-1 checkpoint blockade. However, the mechanisms that govern generation of TCF1high cells are poorly understood.
Methods: We sequenced bulk RNA from tumor-infiltrating lymphocytes to identify differentially expressed genes based on tumor progression. We utilized in vitro co-cultures of tumor-specific T cells tumor cells to examine differentiation, effector function, and metabolism of T cells with different genetic and pharmacologic manipulations by flow cytometry, metabolic flux analyses, and metabolomic profiling. We performed in vivo adoptive transfers of control and manipulated tumor-specific T cells into tumor-bearing mice from both a non-small cell lung cancer and a melanoma model to examine effects of genetic manipulation on differentiation and effector function, as well as determine tumor burden and overall mouse survival both in the treatment-naïve and anti-PD-1 treated contexts.
Results: RNA Sequencing demonstrated a metabolically active response in tumor-infiltrating CD8+ T cells isolated from large and late-stage tumors. Using a genetic screen targeting glycolytic enzymes up-regulated in tumor-infiltrating CD8+ T cells, we demonstrate that PKM2 deficiency (PKM2KO) enriched for TCF1high progenitor cells. Antigen-specific PKM2KO CD8+ T cells from draining lymph nodes and tumors exhibited a central memory-like phenotype with reduced effector cytokine production, increased CD44/CD62L expression, and increased TCF1 and Eomes in non-small cell lung cancer and melanoma. Adoptive transfer of PKM2KO CD8+ T cells in combination with PD-1 blockade impaired tumor growth and improved survival. PKM2KO CD8+ T cells showed reduced glycolytic flux and accumulation of glycolytic intermediates with concomitant increases in pentose phosphate pathway (PPP) metabolites. Importantly, small molecule agonism of PPP was sufficient to skew activated CD8+ T cells towards the TCF1high population, which combined with PD-1 blockade to impair tumor growth and improve survival.
Conclusions: Here we show that targeting glycolytic flux by deletion of pyruvate kinase muscle 2 (PKM2) results in elevated pentose phosphate pathway activity, leading to generation of an altered differentiation state responsive to PD-1 blockade. Our study demonstrates a novel metabolic reprogramming that contributes to a memory-like T cell state amenable to checkpoint blockade.
Citation Format: Geoffrey J. Markowitz, Yi Ban, Diamile A. Tavarez, Michael J. Crowley, Liron Yoffe, Mitchell T. Martin, Tito A. Sandoval, Dingcheng Gao, Juan R. Cubillos-Ruiz, Timothy E. McGraw, Nasser K. Altorki, Vivek Mittal. Deficiency of metabolic regulator PKM2 activates the pentose phosphate pathway to generate TCF1+ progenitor CD8+ T cells to improve checkpoint blockade [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 603.
Collapse
Affiliation(s)
| | - Yi Ban
- 1Weill Cornell Medicine, New York, NY
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Crowley MJP, Bhinder B, Markowitz GJ, Martin M, Verma A, Sandoval TA, Chae CS, Yomtoubian S, Hu Y, Chopra S, Tavarez DA, Giovanelli P, Gao D, McGraw TE, Altorki NK, Elemento O, Cubillos-Ruiz JR, Mittal V. Tumor-intrinsic IRE1α signaling controls protective immunity in lung cancer. Nat Commun 2023; 14:120. [PMID: 36624093 PMCID: PMC9829901 DOI: 10.1038/s41467-022-35584-9] [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: 09/24/2021] [Accepted: 12/13/2022] [Indexed: 01/11/2023] Open
Abstract
IRE1α-XBP1 signaling is emerging as a central orchestrator of malignant progression and immunosuppression in various cancer types. Employing a computational XBP1s detection method applied to TCGA datasets, we demonstrate that expression of the XBP1s mRNA isoform predicts poor survival in non-small cell lung cancer (NSCLC) patients. Ablation of IRE1α in malignant cells delays tumor progression and extends survival in mouse models of NSCLC. This protective effect is accompanied by alterations in intratumoral immune cell subsets eliciting durable adaptive anti-cancer immunity. Mechanistically, cancer cell-intrinsic IRE1α activation sustains mPGES-1 expression, enabling production of the immunosuppressive lipid mediator prostaglandin E2. Accordingly, restoring mPGES-1 expression in IRE1αKO cancer cells rescues normal tumor progression. We have developed an IRE1α gene signature that predicts immune cell infiltration and overall survival in human NSCLC. Our study unveils an immunoregulatory role for cancer cell-intrinsic IRE1α activation and suggests that targeting this pathway may help enhance anti-tumor immunity in NSCLC.
Collapse
Affiliation(s)
- Michael J P Crowley
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
| | - Bhavneet Bhinder
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
| | - Geoffrey J Markowitz
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, 525 East 68th street, New York, NYk, 10065, USA
| | - Mitchell Martin
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
| | - Akanksha Verma
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Volastra Therapeutics, New York, NY, 10027, USA
| | - Tito A Sandoval
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
| | - Chang-Suk Chae
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
| | - Shira Yomtoubian
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Salk Institute for Biological Studies, San Diego, CA, USA
| | - Yang Hu
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
| | - Sahil Chopra
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Vertex Ventures HC, 345 California Avenue, Palo Alto, CA, 94306, USA
| | - Diamile A Tavarez
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Regeneron Pharmaceuticals, 777 Old Saw Mill River Rd, Tarrytown, NY, 10591, USA
| | - Paolo Giovanelli
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
| | - Dingcheng Gao
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, 525 East 68th street, New York, NYk, 10065, USA
| | - Timothy E McGraw
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
- Department of Biochemistry, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
| | - Nasser K Altorki
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA
| | - Juan R Cubillos-Ruiz
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA.
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA.
| | - Vivek Mittal
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA.
- Neuberger Berman Lung Cancer Center, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA.
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, 525 East 68th street, New York, NY, 10065, USA.
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA.
- Department of Cell and Developmental Biology, Weill Cornell Medicine, 525 East 68th street, New York, NYk, 10065, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 413 East 69th street, New York, NY, 10065, USA.
| |
Collapse
|
7
|
Chae CS, Sandoval TA, Hwang SM, Park ES, Giovanelli P, Awasthi D, Salvagno C, Emmanuelli A, Tan C, Chaudhary V, Casado J, Kossenkov AV, Song M, Barrat FJ, Holcomb K, Romero-Sandoval EA, Zamarin D, Pépin D, D’Andrea AD, Färkkilä A, Cubillos-Ruiz JR. Tumor-Derived Lysophosphatidic Acid Blunts Protective Type I Interferon Responses in Ovarian Cancer. Cancer Discov 2022; 12:1904-1921. [PMID: 35552618 PMCID: PMC9357054 DOI: 10.1158/2159-8290.cd-21-1181] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 04/05/2022] [Accepted: 05/09/2022] [Indexed: 02/07/2023]
Abstract
Lysophosphatidic acid (LPA) is a bioactive lipid enriched in the tumor microenvironment of immunosuppressive malignancies such as ovarian cancer. Although LPA enhances the tumorigenic attributes of cancer cells, the immunomodulatory activity of this phospholipid messenger remains largely unexplored. Here, we report that LPA operates as a negative regulator of type I interferon (IFN) responses in ovarian cancer. Ablation of the LPA-generating enzyme autotaxin (ATX) in ovarian cancer cells reprogrammed the tumor immune microenvironment, extended host survival, and improved the effects of therapies that elicit protective responses driven by type I IFN. Mechanistically, LPA sensing by dendritic cells triggered PGE2 biosynthesis that suppressed type I IFN signaling via autocrine EP4 engagement. Moreover, we identified an LPA-controlled, immune-derived gene signature associated with poor responses to combined PARP inhibition and PD-1 blockade in patients with ovarian cancer. Controlling LPA production or sensing in tumors may therefore be useful to improve cancer immunotherapies that rely on robust induction of type I IFN. SIGNIFICANCE This study uncovers that ATX-LPA is a central immunosuppressive pathway in the ovarian tumor microenvironment. Ablating this axis sensitizes ovarian cancer hosts to various immunotherapies by unleashing protective type I IFN responses. Understanding the immunoregulatory programs induced by LPA could lead to new biomarkers predicting resistance to immunotherapy in patients with cancer. See related commentary by Conejo-Garcia and Curiel, p. 1841. This article is highlighted in the In This Issue feature, p. 1825.
Collapse
Affiliation(s)
- Chang-Suk Chae
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
| | - Tito A. Sandoval
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
| | - Sung-Min Hwang
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
| | - Eun Sil Park
- Department of Ophthalmology, Columbia University, New York, NY 10032, USA
| | - Paolo Giovanelli
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065. USA.,Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Deepika Awasthi
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
| | - Camilla Salvagno
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
| | - Alexander Emmanuelli
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065. USA
| | - Chen Tan
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
| | - Vidyanath Chaudhary
- HSS Research Institute and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021, USA
| | - Julia Casado
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland.,Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Andrew V. Kossenkov
- Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Minkyung Song
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, and Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, Gyeonggi-do, Korea
| | - Franck J. Barrat
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065. USA.,HSS Research Institute and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021, USA
| | - Kevin Holcomb
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA
| | - E. Alfonso Romero-Sandoval
- Department of Anesthesiology, Pain Mechanisms Laboratory, Wake Forest University School of Medicine, Winston-Salem, NC, 27157, USA
| | - Dmitriy Zamarin
- Department of Medicine, Gynecologic Medical Oncology Service, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - David Pépin
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital; Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Alan D. D’Andrea
- Susan F. Smith Center for Women’s Cancers, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Anniina Färkkilä
- Research Program in Systems Oncology, University of Helsinki, Helsinki, Finland.,Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Juan R. Cubillos-Ruiz
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065. USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA,Correspondence: Juan R. Cubillos-Ruiz, Ph.D., Associate Professor of Immunology, Weill Cornell Medicine, New York, NY, , Phone: 212-743-1323
| |
Collapse
|
8
|
Mancebo C, Fernández JJ, Herrero-Sánchez C, Alvarez Y, Alonso S, Sandoval TA, Cubillos-Ruiz JR, Montero O, Fernández N, Crespo MS. Fungal Patterns Induce Cytokine Expression through Fluxes of Metabolic Intermediates That Support Glycolysis and Oxidative Phosphorylation. J Immunol 2022; 208:2779-2794. [PMID: 35688467 DOI: 10.4049/jimmunol.2100666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 04/12/2022] [Indexed: 12/25/2022]
Abstract
Cytokine expression is fine-tuned by metabolic intermediates, which makes research on immunometabolism suitable to yield drugs with a wider prospect of application than the biological therapies that block proinflammatory cytokines. Switch from oxidative phosphorylation (OXPHOS) to glycolysis has been considered a characteristic feature of activated immune cells. However, some stimuli might enhance both routes concomitantly. The connection between the tricarboxylic acid cycle and cytokine expression was scrutinized in human monocyte-derived dendritic cells stimulated with the fungal surrogate zymosan. Results showed that nucleocytosolic citrate and ATP-citrate lyase activity drove IL1B, IL10, and IL23A expression by yielding acetyl-CoA and oxaloacetate, with the latter one supporting glycolysis and OXPHOS by maintaining cytosolic NAD+ and mitochondrial NADH levels through mitochondrial shuttles. Succinate dehydrogenase showed a subunit-specific ability to modulate IL23A and IL10 expression. Succinate dehydrogenase A subunit activity supported cytokine expression through the control of the 2-oxoglutarate/succinate ratio, whereas C and D subunits underpinned cytokine expression by conveying electron flux from complex II to complex III of the electron transport chain. Fatty acids may also fuel the tricarboxylic acid cycle and influence cytokine expression. Overall, these results show that fungal patterns support cytokine expression through a strong boost of glycolysis and OXPHOS supported by the use of pyruvate, citrate, and succinate, along with the compartmentalized NAD(H) redox state maintained by mitochondrial shuttles.
Collapse
Affiliation(s)
- Cristina Mancebo
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valladolid, Valladolid, Spain.,Unidad de Excelencia Instituto de Biología y Genética Molecular, CSIC-Universidad de Valladolid, Valladolid, Spain
| | - José Javier Fernández
- Unidad de Excelencia Instituto de Biología y Genética Molecular, CSIC-Universidad de Valladolid, Valladolid, Spain
| | - Carmen Herrero-Sánchez
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valladolid, Valladolid, Spain.,Unidad de Excelencia Instituto de Biología y Genética Molecular, CSIC-Universidad de Valladolid, Valladolid, Spain
| | - Yolanda Alvarez
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valladolid, Valladolid, Spain
| | - Sara Alonso
- Unidad de Excelencia Instituto de Biología y Genética Molecular, CSIC-Universidad de Valladolid, Valladolid, Spain
| | - Tito A Sandoval
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY.,Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY; and
| | - Juan R Cubillos-Ruiz
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY.,Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY; and
| | - Olimpio Montero
- Centro para el Desarrollo de la Biotecnología, CSIC, Parque Tecnológico de Boecillo, Valladolid, Spain
| | - Nieves Fernández
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valladolid, Valladolid, Spain.,Unidad de Excelencia Instituto de Biología y Genética Molecular, CSIC-Universidad de Valladolid, Valladolid, Spain
| | - Mariano Sánchez Crespo
- Unidad de Excelencia Instituto de Biología y Genética Molecular, CSIC-Universidad de Valladolid, Valladolid, Spain;
| |
Collapse
|
9
|
Urueña C, Sandoval TA, Lasso P, Tawil M, Barreto A, Torregrosa L, Fiorentino S. Evaluation of chemotherapy and P2Et extract combination in ex-vivo derived tumor mammospheres from breast cancer patients. Sci Rep 2020; 10:19639. [PMID: 33184339 PMCID: PMC7665196 DOI: 10.1038/s41598-020-76619-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 05/05/2020] [Accepted: 10/12/2020] [Indexed: 12/13/2022] Open
Abstract
The main cause of death by cancer is metastasis rather than local complications of primary tumors. Recent studies suggest that breast cancer stem cells (BCSCs), retains the ability to self-renew and differentiate to repopulate the entire tumor, also, they have been associated with resistance to chemotherapy and tumor recurrence, even after tumor resection. Chemotherapy has been implicated in the induction of resistant phenotypes with highly metastatic potential. Naturally occurring compounds, especially phytochemicals such as P2Et, can target different populations of cancer cells as well as BCSC, favoring the activation of immune response via immunogenic tumor death. Here, we evaluated the presence of BCSC as well as markers related to drug resistance in tumors obtained from 78 patients who had received (or not) chemotherapy before surgery. We evaluated the ex vivo response of patient tumor-derived organoids (or mammospheres) to chemotherapy alone or in combination with P2Et. A xenotransplant model engrafted with MDA-MB-468 was used to evaluate in vivo the activity of P2Et, in this model P2Et delay tumor growth. We show that patients with luminal and TNBC, and those who received neoadjuvant therapy before surgery have a higher frequency of BCSC. Further, the treatment with P2Et in mammospheres and human breast cancer cell lines improve the in vitro tumor death and decrease its viability and proliferation together with the release of immunogenic signals. P2Et could be a good co-adjuvant in antitumor therapy in patients, retarding the tumor growth by enabling the activation of the immune response.
Collapse
Affiliation(s)
- Claudia Urueña
- Grupo de Inmunobiología y Biología Celular, Unidad de Investigación en Ciencias Biomédicas, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7a. No. 43-82, Ed. 50, Lab. 101, 110211, Bogotá, Colombia.
| | - Tito A Sandoval
- Grupo de Inmunobiología y Biología Celular, Unidad de Investigación en Ciencias Biomédicas, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7a. No. 43-82, Ed. 50, Lab. 101, 110211, Bogotá, Colombia
| | - Paola Lasso
- Grupo de Inmunobiología y Biología Celular, Unidad de Investigación en Ciencias Biomédicas, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7a. No. 43-82, Ed. 50, Lab. 101, 110211, Bogotá, Colombia
| | - Mauricio Tawil
- Hospital Universitario San Ignacio, Centro Javeriano de Oncología, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Alfonso Barreto
- Grupo de Inmunobiología y Biología Celular, Unidad de Investigación en Ciencias Biomédicas, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7a. No. 43-82, Ed. 50, Lab. 101, 110211, Bogotá, Colombia
| | - Lilian Torregrosa
- Hospital Universitario San Ignacio, Centro Javeriano de Oncología, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Susana Fiorentino
- Grupo de Inmunobiología y Biología Celular, Unidad de Investigación en Ciencias Biomédicas, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7a. No. 43-82, Ed. 50, Lab. 101, 110211, Bogotá, Colombia.
| |
Collapse
|
10
|
Sierra MA, Li Q, Pushalkar S, Paul B, Sandoval TA, Kamer AR, Corby P, Guo Y, Ruff RR, Alekseyenko AV, Li X, Saxena D. The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community. Genes (Basel) 2020; 11:genes11080878. [PMID: 32756341 PMCID: PMC7465726 DOI: 10.3390/genes11080878] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 06/06/2020] [Revised: 07/11/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022] Open
Abstract
There is currently no criterion to select appropriate bioinformatics tools and reference databases for analysis of 16S rRNA amplicon data in the human oral microbiome. Our study aims to determine the influence of multiple tools and reference databases on α-diversity measurements and β-diversity comparisons analyzing the human oral microbiome. We compared the results of taxonomical classification by Greengenes, the Human Oral Microbiome Database (HOMD), National Center for Biotechnology Information (NCBI) 16S, SILVA, and the Ribosomal Database Project (RDP) using Quantitative Insights Into Microbial Ecology (QIIME) and the Divisive Amplicon Denoising Algorithm (DADA2). There were 15 phyla present in all of the analyses, four phyla exclusive to certain databases, and different numbers of genera were identified in each database. Common genera found in the oral microbiome, such as Veillonella, Rothia, and Prevotella, are annotated by all databases; however, less common genera, such as Bulleidia and Paludibacter, are only annotated by large databases, such as Greengenes. Our results indicate that using different reference databases in 16S rRNA amplicon data analysis could lead to different taxonomic compositions, especially at genus level. There are a variety of databases available, but there are no defined criteria for data curation and validation of annotations, which can affect the accuracy and reproducibility of results, making it difficult to compare data across studies.
Collapse
Affiliation(s)
- Maria A. Sierra
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
| | - Qianhao Li
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
| | - Smruti Pushalkar
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
| | - Bidisha Paul
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
| | - Tito A. Sandoval
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY 10065, USA;
| | - Angela R. Kamer
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
| | - Patricia Corby
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
| | - Yuqi Guo
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
| | - Ryan Richard Ruff
- Department of Epidemiology & Health Promotion, New York University College of Dentistry, New York, NY 10010, USA;
| | - Alexander V. Alekseyenko
- The Biomedical Informatics Center, Program for Human Microbiome Research, Department of Public Health Sciences, Department of Oral Health Sciences, Department of Healthcare Leadership and Management, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Xin Li
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
| | - Deepak Saxena
- Department of Basic Science, New York University College of Dentistry, New York, NY 10010, USA; (M.A.S.); (Q.L.); (S.P.); (B.P.); (A.R.K.); (P.C.); (Y.G.); (X.L.)
- S. Arthur Localio Laboratory, Departments of Surgery New York University School of Medicine, New York, NY 10016, USA
- Correspondence: ; Tel.: +1-212-9989256
| |
Collapse
|
11
|
Sierra MA, Danko DC, Sandoval TA, Pishchany G, Moncada B, Kolter R, Mason CE, Zambrano MM. The Microbiomes of Seven Lichen Genera Reveal Host Specificity, a Reduced Core Community and Potential as Source of Antimicrobials. Front Microbiol 2020; 11:398. [PMID: 32265864 PMCID: PMC7105886 DOI: 10.3389/fmicb.2020.00398] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 02/26/2020] [Indexed: 12/11/2022] Open
Abstract
The High Andean Paramo ecosystem is a unique neotropical mountain biome considered a diversity and evolutionary hotspot. Lichens, which are complex symbiotic structures that contain diverse commensal microbial communities, are prevalent in Paramos. There they play vital roles in soil formation and mineral fixation. In this study we analyzed the microbiomes of seven lichen genera in Colombian Paramos using 16S rRNA gene amplicon sequencing and provide the first description of the bacterial communities associated with Cora and Hypotrachyna lichens. Paramo lichen microbiomes varied in diversity indexes and number of OTUs, but were composed predominantly by the phyla Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria, and Verrucomicrobia. In the case of Cora and Cladonia, the microbiomes were distinguished based on the identity of the lichen host. While the majority of the lichen-associated microorganisms were not present in all lichens sampled, sixteen taxa shared among this diverse group of lichens suggest a core lichen microbiome that broadens our concept of these symbiotic structures. Additionally, we identified strains producing compounds active against clinically relevant microbial strains. These results indicate that lichen microbiomes from the Paramo ecosystem are diverse and host-specific but share a taxonomic core and can be a source of new bacterial taxa and antimicrobials.
Collapse
Affiliation(s)
- Maria A. Sierra
- Molecular Genetics, Corporación CorpoGen – Research Center, Bogotá, Colombia
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - David C. Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - Tito A. Sandoval
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, United States
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Gleb Pishchany
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Bibiana Moncada
- Licenciatura en Biología, Universidad Distrital Francisco José de Caldas, Bogotá, Colombia
| | - Roberto Kolter
- Department of Microbiology, Harvard Medical School, Boston, MA, United States
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | | |
Collapse
|
12
|
Chopra S, Giovanelli P, Alvarado-Vazquez PA, Alonso S, Song M, Sandoval TA, Chae CS, Tan C, Fonseca MM, Gutierrez S, Jimenez L, Subbaramaiah K, Iwawaki T, Kingsley PJ, Marnett LJ, Kossenkov AV, Crespo MS, Dannenberg AJ, Glimcher LH, Romero-Sandoval EA, Cubillos-Ruiz JR. IRE1α-XBP1 signaling in leukocytes controls prostaglandin biosynthesis and pain. Science 2020; 365:365/6450/eaau6499. [PMID: 31320508 DOI: 10.1126/science.aau6499] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 03/27/2019] [Accepted: 06/10/2019] [Indexed: 12/28/2022]
Abstract
Inositol-requiring enzyme 1[α] (IRE1[α])-X-box binding protein spliced (XBP1) signaling maintains endoplasmic reticulum (ER) homeostasis while controlling immunometabolic processes. Yet, the physiological consequences of IRE1α-XBP1 activation in leukocytes remain unexplored. We found that induction of prostaglandin-endoperoxide synthase 2 (Ptgs2/Cox-2) and prostaglandin E synthase (Ptges/mPGES-1) was compromised in IRE1α-deficient myeloid cells undergoing ER stress or stimulated through pattern recognition receptors. Inducible biosynthesis of prostaglandins, including the pro-algesic mediator prostaglandin E2 (PGE2), was decreased in myeloid cells that lack IRE1α or XBP1 but not other ER stress sensors. Functional XBP1 transactivated the human PTGS2 and PTGES genes to enable optimal PGE2 production. Mice that lack IRE1α-XBP1 in leukocytes, or that were treated with IRE1α inhibitors, demonstrated reduced pain behaviors in PGE2-dependent models of pain. Thus, IRE1α-XBP1 is a mediator of prostaglandin biosynthesis and a potential target to control pain.
Collapse
Affiliation(s)
- Sahil Chopra
- Weill Cornell Graduate School of Medical Sciences, Cornell University. New York, NY 10065, USA.,Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Paolo Giovanelli
- Weill Cornell Graduate School of Medical Sciences, Cornell University. New York, NY 10065, USA.,Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Perla Abigail Alvarado-Vazquez
- Department of Anesthesiology, Pain Mechanisms Laboratory, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Sara Alonso
- Instituto de Biología y Genética Molecular, CSIC-Universidad de Valladolid, Valladolid, Spain
| | - Minkyung Song
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Tito A Sandoval
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chang-Suk Chae
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Chen Tan
- Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| | - Miriam M Fonseca
- Department of Anesthesiology, Pain Mechanisms Laboratory, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Silvia Gutierrez
- Department of Anesthesiology, Pain Mechanisms Laboratory, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Leandro Jimenez
- Instituto Ludwig de Pesquisa Sobre o Câncer, São Paulo, Brazil.,Hospital Sírio-Libanês, São Paulo, Brazil
| | | | - Takao Iwawaki
- Division of Cell Medicine, Medical Research Institute, Kazanawa Medical University, Ishikawa, Japan
| | - Philip J Kingsley
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Lawrence J Marnett
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA.,A. B. Hancock Jr. Memorial Laboratory for Cancer Research, Departments of Biochemistry, Chemistry and Pharmacology, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Andrew V Kossenkov
- Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Mariano Sanchez Crespo
- Instituto de Biología y Genética Molecular, CSIC-Universidad de Valladolid, Valladolid, Spain
| | | | - Laurie H Glimcher
- Department of Medicine, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA. .,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - E Alfonso Romero-Sandoval
- Department of Anesthesiology, Pain Mechanisms Laboratory, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA.
| | - Juan R Cubillos-Ruiz
- Weill Cornell Graduate School of Medical Sciences, Cornell University. New York, NY 10065, USA. .,Department of Obstetrics and Gynecology, Weill Cornell Medicine. New York, NY 10065, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
| |
Collapse
|
13
|
Sandoval TA, Urueña CP, Llano M, Gómez-Cadena A, Hernández JF, Sequeda LG, Loaiza AE, Barreto A, Li S, Fiorentino S. Standardized Extract from Caesalpinia spinosa is Cytotoxic Over Cancer Stem Cells and Enhance Anticancer Activity of Doxorubicin. Am J Chin Med 2016. [DOI: 10.1142/s0192415x16500956 pmid: 27852125] [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] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cancer stem cells (CSC) are the primary cell type responsible for metastasis and relapse. ABC-transporters are integral membrane proteins involved in the translocation of substrates across membranes protecting CSC from chemotherapeutic agents. A plant extract derived from C. spinosa (P2Et) previously investigated for its antitumor activity has been shown to reduce lung and spleen metastasis in mice that have been transplanted with breast cancer cells, suggesting that P2Et has a significant activity against cancer stem cells (CSC). P2Et extract was thoroughly characterized by HPLC/MS. The cytotoxicity of P2Et extract was evaluated using a MTT assay in human and murine cell lines with different profiles of resistance, by Pgp overexpression or by enrichment in cancer stem cells. The synergistic effect of P2Et with doxorubicin was evaluated in vitro in several cell lines and in vivo in mice transplanted with TS/A cells, a highly resistant cell line and enriched in CD44[Formula: see text]CD24[Formula: see text]CSC. The chromatographic fingerprint of P2Et extract revealed 13 gallotannins. We also found that P2Et extract was cytotoxic to cells regardless of their resistant phenotype. Similarly, complementary activities were observed as drug efflux reversion and antioxidant activity. Short-treatment with P2Et extract, revealed a synergistic effect with doxorubicin in resistant cell lines. In vivo the P2Et increases mice survival in a TS/A breast cancer model associated with augmentation of calreticulin expression. Our results suggest that P2Et treatment could be used as adjuvant along with conventional chemotherapy to treat tumors with a MDR phenotype or with high frequency of CSC.
Collapse
Affiliation(s)
- Tito A. Sandoval
- Department of Microbiology, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| | - Claudia P. Urueña
- Department of Microbiology, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| | - Mónica Llano
- Department of Microbiology, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| | - Alejandra Gómez-Cadena
- Department of Microbiology, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| | - John F. Hernández
- Department of Microbiology, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| | - Luis Gonzalo Sequeda
- Departament of Chemistry, Pontificia Universidad Javeriana, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| | - Alix E. Loaiza
- Departament of Chemistry, Pontificia Universidad Javeriana, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| | - Alfonso Barreto
- Department of Microbiology, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| | - Shaoping Li
- Institute of Chinese Medical Sciences, University of Macau, Macau, P.R. China
| | - Susana Fiorentino
- Department of Microbiology, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| |
Collapse
|
14
|
Sandoval TA, Urueña CP, Llano M, Gómez-Cadena A, Hernández JF, Sequeda LG, Loaiza AE, Barreto A, Li S, Fiorentino S. Standardized Extract from Caesalpinia spinosa is Cytotoxic Over Cancer Stem Cells and Enhance Anticancer Activity of Doxorubicin. Am J Chin Med 2016; 44:1693-1717. [DOI: 10.1142/s0192415x16500956] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cancer stem cells (CSC) are the primary cell type responsible for metastasis and relapse. ABC-transporters are integral membrane proteins involved in the translocation of substrates across membranes protecting CSC from chemotherapeutic agents. A plant extract derived from C. spinosa (P2Et) previously investigated for its antitumor activity has been shown to reduce lung and spleen metastasis in mice that have been transplanted with breast cancer cells, suggesting that P2Et has a significant activity against cancer stem cells (CSC). P2Et extract was thoroughly characterized by HPLC/MS. The cytotoxicity of P2Et extract was evaluated using a MTT assay in human and murine cell lines with different profiles of resistance, by Pgp overexpression or by enrichment in cancer stem cells. The synergistic effect of P2Et with doxorubicin was evaluated in vitro in several cell lines and in vivo in mice transplanted with TS/A cells, a highly resistant cell line and enriched in CD44[Formula: see text]CD24[Formula: see text]CSC. The chromatographic fingerprint of P2Et extract revealed 13 gallotannins. We also found that P2Et extract was cytotoxic to cells regardless of their resistant phenotype. Similarly, complementary activities were observed as drug efflux reversion and antioxidant activity. Short-treatment with P2Et extract, revealed a synergistic effect with doxorubicin in resistant cell lines. In vivo the P2Et increases mice survival in a TS/A breast cancer model associated with augmentation of calreticulin expression. Our results suggest that P2Et treatment could be used as adjuvant along with conventional chemotherapy to treat tumors with a MDR phenotype or with high frequency of CSC.
Collapse
Affiliation(s)
- Tito A. Sandoval
- Department of Microbiology, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| | - Claudia P. Urueña
- Department of Microbiology, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| | - Mónica Llano
- Department of Microbiology, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| | - Alejandra Gómez-Cadena
- Department of Microbiology, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| | - John F. Hernández
- Department of Microbiology, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| | - Luis Gonzalo Sequeda
- Departament of Chemistry, Pontificia Universidad Javeriana, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| | - Alix E. Loaiza
- Departament of Chemistry, Pontificia Universidad Javeriana, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| | - Alfonso Barreto
- Department of Microbiology, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| | - Shaoping Li
- Institute of Chinese Medical Sciences, University of Macau, Macau, P.R. China
| | - Susana Fiorentino
- Department of Microbiology, Grupo de Investigación Fitoquímica Universidad Javeriana (GIFUJ), Bogotá, Colombia
| |
Collapse
|