1
|
Wheeler BD, Gagnon JD, Zhu WS, Muñoz-Sandoval P, Wong SK, Simeonov DS, Li Z, DeBarge R, Spitzer MH, Marson A, Ansel KM. The lncRNA Malat1 inhibits miR-15/16 to enhance cytotoxic T cell activation and memory cell formation. eLife 2023; 12:RP87900. [PMID: 38127070 PMCID: PMC10735224 DOI: 10.7554/elife.87900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Proper activation of cytotoxic T cells via the T cell receptor and the costimulatory receptor CD28 is essential for adaptive immunity against viruses, intracellular bacteria, and cancers. Through biochemical analysis of RNA:protein interactions, we uncovered a non-coding RNA circuit regulating activation and differentiation of cytotoxic T cells composed of the long non-coding RNA Malat1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) and the microRNA family miR-15/16. miR-15/16 is a widely and highly expressed tumor suppressor miRNA family important for cell proliferation and survival. miR-15/16 play important roles in T cell responses to viral infection, including the regulation of antigen-specific T cell expansion and memory. Comparative Argonaute-2 high-throughput sequencing of crosslinking immunoprecipitation (AHC) combined with gene expression profiling in normal and miR-15/16-deficient mouse T cells revealed a large network of hundreds of direct miR-15/16 target mRNAs, many with functional relevance for T cell activation, survival and memory formation. Among these targets, Malat1 contained the largest absolute magnitude miR-15/16-dependent AHC peak. This binding site was among the strongest lncRNA:miRNA interactions detected in the T cell transcriptome. We used CRISPR targeting with homology directed repair to generate mice with a 5-nucleotide mutation in the miR-15/16-binding site in Malat1. This mutation interrupted Malat1:miR-15/16 interaction, and enhanced the repression of other miR-15/16 target genes, including CD28. Interrupting Malat1 interaction with miR-15/16 decreased cytotoxic T cell activation, including the expression of interleukin 2 (IL-2) and a broader CD28-responsive gene program. Accordingly, Malat1 mutation diminished memory cell persistence in mice following LCMV Armstrong and Listeria monocytogenes infection. This study marks a significant advance in the study of long non-coding RNAs in the immune system by ascribing cell-intrinsic, sequence-specific in vivo function to Malat1. These findings have implications for T cell-mediated autoimmune diseases, antiviral and anti-tumor immunity, as well as lung adenocarcinoma and other malignancies where Malat1 is overexpressed.
Collapse
Affiliation(s)
- Benjamin D Wheeler
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| | - John D Gagnon
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| | - Wandi S Zhu
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| | - Priscila Muñoz-Sandoval
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| | - Simon K Wong
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
| | - Dimitre S Simeonov
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
| | - Zhongmei Li
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
| | - Rachel DeBarge
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
- Department of Otolaryngology-Head and Neck Surgery, University of California San FranciscoSan FranciscoUnited States
| | - Matthew H Spitzer
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
- Department of Otolaryngology-Head and Neck Surgery, University of California San FranciscoSan FranciscoUnited States
- Parker Institute for Cancer Immunotherapy, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Alexander Marson
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
- Department of Medicine, University of California San FranciscoLexingtonUnited States
| | - K Mark Ansel
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| |
Collapse
|
2
|
Johansson K, Gagnon JD, Zhou SK, Fassett MS, Schroeder AW, Kageyama R, Bautista RA, Pham H, Woodruff PG, Ansel KM. An essential role for miR-15/16 in Treg suppression and restriction of proliferation. Cell Rep 2023; 42:113298. [PMID: 37862171 PMCID: PMC10664750 DOI: 10.1016/j.celrep.2023.113298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/07/2023] [Accepted: 10/02/2023] [Indexed: 10/22/2023] Open
Abstract
The miR-15/16 family targets a large network of genes in T cells to restrict their cell cycle, memory formation, and survival. Upon T cell activation, miR-15/16 are downregulated, allowing rapid expansion of differentiated effector T cells to mediate a sustained response. Here, we used conditional deletion of miR-15/16 in regulatory T cells (Tregs) to identify immune functions of the miR-15/16 family in T cells. miR-15/16 are indispensable to maintain peripheral tolerance by securing efficient suppression by a limited number of Tregs. miR-15/16 deficiency alters expression of critical Treg proteins and results in accumulation of functionally impaired FOXP3loCD25loCD127hi Tregs. Excessive proliferation in the absence of miR-15/16 shifts Treg fate and produces an effector Treg phenotype. These Tregs fail to control immune activation, leading to spontaneous multi-organ inflammation and increased allergic inflammation in a mouse model of asthma. Together, our results demonstrate that miR-15/16 expression in Tregs is essential to maintain immune tolerance.
Collapse
Affiliation(s)
- Kristina Johansson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530 Gothenburg, Sweden; Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, 40530 Gothenburg, Sweden
| | - John D Gagnon
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Simon K Zhou
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Marlys S Fassett
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Andrew W Schroeder
- Department of Medicine, Genomics CoLab, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robin Kageyama
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rodriel A Bautista
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hewlett Pham
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Prescott G Woodruff
- Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - K Mark Ansel
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA.
| |
Collapse
|
3
|
Wheeler BD, Gagnon JD, Zhu WS, Muñoz-Sandoval P, Wong SK, Simeonov DR, Li Z, Debarge R, Spitzer MH, Marson A, Ansel KM. The lncRNA Malat1 Inhibits miR-15/16 to Enhance Cytotoxic T Cell Activation and Memory Cell Formation. bioRxiv 2023:2023.04.14.536843. [PMID: 37547023 PMCID: PMC10401941 DOI: 10.1101/2023.04.14.536843] [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: 08/08/2023]
Abstract
Proper activation of cytotoxic T cells via the T cell receptor and the costimulatory receptor CD28 is essential for adaptive immunity against viruses, many intracellular bacteria and cancers. Through biochemical analysis of RNA:protein interactions, we uncovered a non-coding RNA circuit regulating activation and differentiation of cytotoxic T cells composed of the long non-coding RNA Malat1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) and the microRNA family miR-15/16. miR-15/16 is a widely and highly expressed tumor suppressor miRNA family important for cell proliferation and survival. miR-15/16 also play important roles in T cell responses to viral infection, including the regulation of antigen-specific T cell expansion and T cell memory. Comparative Argonaute-2 high throughput sequencing of crosslinking immunoprecipitation (Ago2 HITS-CLIP, or AHC) combined with gene expression profiling in normal and miR-15/16-deficient T cells revealed a large network of several hundred direct miR-15/16 target mRNAs, many with functional relevance for T cell activation, survival and memory formation. Among these targets, the long non-coding RNA Malat1 contained the largest absolute magnitude miR-15/16-dependent AHC peak in T cells. This binding site was also among the strongest lncRNA:miRNA interactions detected in the T cell transcriptome. We used CRISPR targeting with homology directed repair to generate mice with a 5-nucleotide mutation in the miR-15/16 binding site in Malat1. This mutation interrupted Malat1:miR-15/16 interaction, and enhanced the repression of other miR-15/16 target genes, including CD28. Interrupting Malat1 interaction with miR-15/16 decreased cytotoxic T cell activation, including the expression of IL-2 and a broader CD28-responsive gene program. Accordingly, Malat1 mutation diminished memory cell persistence following LCMV Armstrong and Listeria monocytogenes infection. This study marks a significant advance in the study of long noncoding RNAs in the immune system by ascribing cell-intrinsic, sequence-specific in vivo function to Malat1. These findings have implications for T cell-mediated autoimmune diseases, antiviral and anti-tumor immunity, as well as lung adenocarcinoma and other malignancies where Malat1 is overexpressed.
Collapse
Affiliation(s)
- Benjamin D Wheeler
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Sandler Asthma Basic Research Program, University of California, San Francisco, San Francisco, CA, USA
| | - John D Gagnon
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Sandler Asthma Basic Research Program, University of California, San Francisco, San Francisco, CA, USA
| | - Wandi S Zhu
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Sandler Asthma Basic Research Program, University of California, San Francisco, San Francisco, CA, USA
| | - Priscila Muñoz-Sandoval
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Sandler Asthma Basic Research Program, University of California, San Francisco, San Francisco, CA, USA
| | - Simon K Wong
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Dimitre R Simeonov
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Zhongmei Li
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
| | - Rachel Debarge
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew H Spitzer
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
- Department of Otolaryngology-Head and Neck Surgery, University of California San Francisco, San Francisco, CA 94143, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Alexander Marson
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - K Mark Ansel
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- Sandler Asthma Basic Research Program, University of California, San Francisco, San Francisco, CA, USA
| |
Collapse
|
4
|
Johansson K, Gagnon JD, Zhou S, Fassett MS, Schroeder AW, Kageyama R, Bautista RA, Pham H, Woodruff PG, Ansel KM. An essential role for miR-15/16 in Treg suppression and restriction of proliferation. bioRxiv 2023:2023.03.26.533356. [PMID: 36993421 PMCID: PMC10055372 DOI: 10.1101/2023.03.26.533356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The miR-15/16 family is a highly expressed group of tumor suppressor miRNAs that target a large network of genes in T cells to restrict their cell cycle, memory formation and survival. Upon T cell activation, miR-15/16 are downregulated, allowing rapid expansion of differentiated effector T cells to mediate a sustained immune response. Here, using conditional deletion of miR-15/16 in immunosuppressive regulatory T cells (Tregs) that express FOXP3, we identify new functions of the miR-15/16 family in T cell immunity. miR-15/16 are indispensable to maintain peripheral tolerance by securing efficient suppression by a limited number of Tregs. miR-15/16-deficiency alters Treg expression of critical functional proteins including FOXP3, IL2Rα/CD25, CTLA4, PD-1 and IL7Rα/CD127, and results in accumulation of functionally impaired FOXP3loCD25loCD127hi Tregs. Excessive proliferation in the absence of miR-15/16 inhibition of cell cycle programs shifts Treg diversity and produces an effector Treg phenotype characterized by low expression of TCF1, CD25 and CD62L, and high expression of CD44. These Tregs fail to control immune activation of CD4+ effector T cells, leading to spontaneous multi-organ inflammation and increased allergic airway inflammation in a mouse model of asthma. Together, our results demonstrate that miR-15/16 expression in Tregs is essential to maintain immune tolerance.
Collapse
|
5
|
Dölz M, Hasiuk M, Gagnon JD, Kornete M, Marone R, Bantug G, Kageyama R, Hess C, Ansel KM, Seyres D, Roux J, Jeker LT. Forced expression of the non-coding RNA miR-17∼92 restores activation and function in CD28-deficient CD4 + T cells. iScience 2022; 25:105372. [PMID: 36388982 PMCID: PMC9646923 DOI: 10.1016/j.isci.2022.105372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 08/12/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
CD28 provides the prototypical costimulatory signal required for productive T-cell activation. Known molecular consequences of CD28 costimulation are mostly based on studies of protein signaling molecules. The microRNA cluster miR-17∼92 is induced by T cell receptor stimulation and further enhanced by combined CD28 costimulation. We demonstrate that transgenic miR-17∼92 cell-intrinsically largely overcomes defects caused by CD28 deficiency. Combining genetics, transcriptomics, bioinformatics, and biochemical miRNA:mRNA interaction maps we empirically validate miR-17∼92 target genes that include several negative regulators of T cell activation. CD28-deficient T cells exhibit derepressed miR-17∼92 target genes during activation. CRISPR/Cas9-mediated ablation of the miR-17∼92 targets Pten and Nrbp1 in naive CD28-/- CD4+ T cells differentially increases proliferation and expression of the activation markers CD25 and CD44, respectively. Thus, we propose that miR-17∼92 constitutes a central mediator for T cell activation, integrating signals by the TCR and CD28 costimulation by dampening multiple brakes that prevent T cell activation.
Collapse
Affiliation(s)
- Marianne Dölz
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland.,Transplantation Immunology & Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland
| | - Marko Hasiuk
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland.,Transplantation Immunology & Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland
| | - John D Gagnon
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.,Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mara Kornete
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland
| | - Romina Marone
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland.,Transplantation Immunology & Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland
| | - Glenn Bantug
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland
| | - Robin Kageyama
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.,Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christoph Hess
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland.,Department of Medicine - CITIID, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - K Mark Ansel
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA.,Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Denis Seyres
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland.,Transplantation Immunology & Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland
| | - Julien Roux
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Lukas T Jeker
- Department of Biomedicine, Basel University Hospital and University of Basel, Hebelstrasse 20, CH-4031 Basel, Switzerland.,Transplantation Immunology & Nephrology, Basel University Hospital, Petersgraben 4, CH-4031 Basel, Switzerland
| |
Collapse
|
6
|
Gagnon JD, Kageyama R, Shehata HM, Fassett MS, Mar DJ, Wigton EJ, Johansson K, Litterman AJ, Odorizzi P, Simeonov D, Laidlaw BJ, Panduro M, Patel S, Jeker LT, Feeney ME, McManus MT, Marson A, Matloubian M, Sanjabi S, Ansel KM. miR-15/16 Restrain Memory T Cell Differentiation, Cell Cycle, and Survival. Cell Rep 2020; 28:2169-2181.e4. [PMID: 31433990 PMCID: PMC6715152 DOI: 10.1016/j.celrep.2019.07.064] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 05/03/2019] [Accepted: 07/18/2019] [Indexed: 12/20/2022] Open
Abstract
Coordinate control of T cell proliferation, survival, and differentiation are essential for host protection from pathogens and cancer. Long-lived memory cells, whose precursors are formed during the initial immunological insult, provide protection from future encounters, and their generation is the goal of many vaccination strategies. microRNAs (miRNAs) are key nodes in regulatory networks that shape effective T cell responses through the fine-tuning of thousands of genes. Here, using compound conditional mutant mice to eliminate miR-15/16 family miRNAs in T cells, we show that miR-15/16 restrict T cell cycle, survival, and memory T cell differentiation. High throughput sequencing of RNA isolated by cross-linking immunoprecipitation of AGO2 combined with gene expression analysis in miR-15/16-deficient T cells indicates that these effects are mediated through the direct inhibition of an extensive network of target genes within pathways critical to cell cycle, survival, and memory.
Collapse
Affiliation(s)
- John D Gagnon
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robin Kageyama
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hesham M Shehata
- Virology and Immunology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Marlys S Fassett
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Darryl J Mar
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eric J Wigton
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kristina Johansson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Adam J Litterman
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Pamela Odorizzi
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dimitre Simeonov
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brian J Laidlaw
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Marisella Panduro
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sana Patel
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lukas T Jeker
- Diabetes Center and Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Margaret E Feeney
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael T McManus
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mehrdad Matloubian
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Shomyseh Sanjabi
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Virology and Immunology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - K Mark Ansel
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA.
| |
Collapse
|
7
|
Khor B, Conway KL, Omar AS, Biton M, Haber AL, Rogel N, Baxt LA, Begun J, Kuballa P, Gagnon JD, Lassen KG, Regev A, Xavier RJ. Distinct Tissue-Specific Roles for the Disease-Associated Autophagy Genes ATG16L2 and ATG16L1. J Immunol 2019; 203:1820-1829. [PMID: 31451676 PMCID: PMC6761021 DOI: 10.4049/jimmunol.1800419] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/30/2019] [Indexed: 12/19/2022]
Abstract
The clear role of autophagy in human inflammatory diseases such as Crohn disease was first identified by genome-wide association studies and subsequently dissected in multiple mechanistic studies. ATG16L1 has been particularly well studied in knockout and hypomorph settings as well as models recapitulating the Crohn disease-associated T300A polymorphism. Interestingly, ATG16L1 has a single homolog, ATG16L2, which is independently implicated in diseases, including Crohn disease and systemic lupus erythematosus. However, the contribution of ATG16L2 to canonical autophagy pathways and other cellular functions is poorly understood. To better understand its role, we generated and analyzed the first, to our knowledge, ATG16L2 knockout mouse. Our results show that ATG16L1 and ATG16L2 contribute very distinctly to autophagy and cellular ontogeny in myeloid, lymphoid, and epithelial lineages. Dysregulation of any of these lineages could contribute to complex diseases like Crohn disease and systemic lupus erythematosus, highlighting the value of examining cell-specific effects. We also identify a novel genetic interaction between ATG16L2 and epithelial ATG16L1. These findings are discussed in the context of how these genes may contribute distinctly to human disease.
Collapse
Affiliation(s)
- Bernard Khor
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; .,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114.,The Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142; and.,Pathology Service, Massachusetts General Hospital, Boston, MA 02114
| | - Kara L Conway
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Abdifatah S Omar
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Moshe Biton
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Adam L Haber
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Noga Rogel
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Leigh A Baxt
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Jakob Begun
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Petric Kuballa
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - John D Gagnon
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Kara G Lassen
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Aviv Regev
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; .,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114.,The Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142; and
| |
Collapse
|
8
|
Abstract
MicroRNAs (miRNAs) are a class of short noncoding RNAs that play critical roles in the regulation of a broad range of biological processes. Like transcription factors, miRNAs exert their effects by modulating the expression of networks of genes that operate in common or convergent pathways. CD8+ T cells are critical agents of the adaptive immune system that provide protection from infection and cancer. Here, we review the important roles of miRNAs in the regulation of CD8+ T cell biology and provide perspectives on the broader emerging principles of miRNA function.
Collapse
Affiliation(s)
- John D Gagnon
- Sandler Asthma Basic Research Center, Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, USA
| | - K Mark Ansel
- Sandler Asthma Basic Research Center, Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, USA
| |
Collapse
|
9
|
Litterman AJ, Kageyama R, Le Tonqueze O, Zhao W, Gagnon JD, Goodarzi H, Erle DJ, Ansel KM. A massively parallel 3' UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization. Genome Res 2019; 29:896-906. [PMID: 31152051 PMCID: PMC6581050 DOI: 10.1101/gr.242552.118] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 05/02/2019] [Indexed: 01/02/2023]
Abstract
Compared to coding sequences, untranslated regions of the transcriptome are not well conserved, and functional annotation of these sequences is challenging. Global relationships between nucleotide composition of 3′ UTR sequences and their sequence conservation have been appreciated since mammalian genomes were first sequenced, but the functional relevance of these patterns remain unknown. We systematically measured the effect on gene expression of the sequences of more than 25,000 RNA-binding protein (RBP) binding sites in primary mouse T cells using a massively parallel reporter assay. GC-rich sequences were destabilizing of reporter mRNAs and come from more rapidly evolving regions of the genome. These sequences were more likely to be folded in vivo and contain a number of structural motifs that reduced accumulation of a heterologous reporter protein. Comparison of full-length 3′ UTR sequences across vertebrate phylogeny revealed that strictly conserved 3′ UTRs were GC-poor and enriched in genes associated with organismal development. In contrast, rapidly evolving 3′ UTRs tended to be GC-rich and derived from genes involved in metabolism and immune responses. Cell-essential genes had lower GC content in their 3′ UTRs, suggesting a connection between unstructured mRNA noncoding sequences and optimal protein production. By reducing gene expression, GC-rich RBP-occupied sequences act as a rapidly evolving substrate for gene regulatory interactions.
Collapse
Affiliation(s)
- Adam J Litterman
- Department of Microbiology and Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, California 94143, USA
| | - Robin Kageyama
- Department of Microbiology and Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, California 94143, USA
| | - Olivier Le Tonqueze
- Department of Medicine and Lung Biology Center, University of California San Francisco, San Francisco, California 94143, USA
| | - Wenxue Zhao
- Department of Medicine and Lung Biology Center, University of California San Francisco, San Francisco, California 94143, USA.,School of Medicine, Sun Yat-Sen University, Guangzhou, People's Republic of China, 510245
| | - John D Gagnon
- Department of Microbiology and Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, California 94143, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, Department of Urology, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94143, USA
| | - David J Erle
- Department of Medicine and Lung Biology Center, University of California San Francisco, San Francisco, California 94143, USA
| | - K Mark Ansel
- Department of Microbiology and Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, California 94143, USA
| |
Collapse
|
10
|
Camarda R, Williams J, Malkov S, Zimmerman LJ, Manning S, Aran D, Beardsley A, Mark DVD, Haren JV, Chen Y, Berdan C, Louie S, Mahieu C, Winkler J, Willey E, Gagnon JD, Shinoda K, Ansel KM, Werb Z, Nomura DC, Kajimura S, Wittmann T, Butte AJ, Sanders ME, Liebler DC, Krings G, Shepherd JA, Goga A. Abstract 2398: Tumor cell-adipocyte gap junctions activate lipolysis in breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2398] [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
During mammary tumorigenesis, a cell-cell interface exists between adipocytes and cancer cells. Several studies have demonstrated that breast tumor cells can secrete cytokines that induce lipolysis in adjacent adipocytes. However, evidence of tumor-adjacent lipolysis in clinical samples has been lacking. We therefore assayed for lipolysis in normal tissue adjacent to breast tumors (NAT) using (1) the three-component breast composition measure, a radiographic imaging method derived from dual-energy mammography that allows lipid content of a tissue to be quantified, on breast tumors and NAT from 46 patients, (2) a publically available dataset of gene expression in primary breast tumors and NAT from 9 patients, (3) laser capture microdissection and proteomics on primary breast tumors, stroma and NAT from 75 patients, and (4) immunoblot analysis of NAT from several patient-derived and transgenic mouse models of breast cancer. We found strong evidence in all cases that lipolysis is activated in breast cancer-adjacent adipose tissue. We next set out to model the breast cancer-adipocyte interface and determine the contribution of cell-cell contact to induced lipolysis. Gap junctions are cell-cell junctions formed by proteins called connexins, which are known to transport a variety of small molecules (<1kD) including cAMP, a critical pro-lipolytic signaling molecule. Using established dye transfer assays, we determined that gap junctions form between breast cancer cells, and between breast cancer cells and adipocytes. Using biochemical assays, we demonstrated that cAMP is a substrate of breast cancer cell gap junctions, that transfer of cAMP from breast cancer cells to adipocytes occurs, and that breast cancer cells activate lipolytic signaling, all in a gap junction-dependent manner. Finally, we found that gap junction communication in this context is dependent upon connexin 31 (Cx31), and we establish the importance of Cx31 for breast tumor growth and activation of lipolysis in tumor-adjacent adipose tissue in vivo.
Citation Format: Roman Camarda, Jeremy Williams, Serghei Malkov, Lisa J. Zimmerman, Suzanne Manning, Dvir Aran, Andrew Beardsley, Daniel Van de Mark, Jeffrey van Haren, Yong Chen, Charles Berdan, Sharon Louie, Celine Mahieu, Juliane Winkler, Elizabeth Willey, John D. Gagnon, Kosaku Shinoda, K. Mark Ansel, Zena Werb, Daniel C. Nomura, Shingo Kajimura, Torsten Wittmann, Atul J. Butte, Melinda E. Sanders, Daniel C. Liebler, Gregor Krings, John A. Shepherd, Andrei Goga. Tumor cell-adipocyte gap junctions activate lipolysis in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2398.
Collapse
Affiliation(s)
| | | | | | | | | | - Dvir Aran
- 1University of California San Francisco, CA
| | | | | | | | - Yong Chen
- 1University of California San Francisco, CA
| | | | | | | | | | | | | | | | | | - Zena Werb
- 1University of California San Francisco, CA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Simeonov DR, Gowen BG, Boontanrart M, Roth TL, Gagnon JD, Mumbach MR, Satpathy AT, Lee Y, Bray NL, Chan AY, Lituiev DS, Nguyen ML, Gate RE, Subramaniam M, Li Z, Woo JM, Mitros T, Ray GJ, Curie GL, Naddaf N, Chu JS, Ma H, Boyer E, Van Gool F, Huang H, Liu R, Tobin VR, Schumann K, Daly MJ, Farh KK, Ansel KM, Ye CJ, Greenleaf WJ, Anderson MS, Bluestone JA, Chang HY, Corn JE, Marson A. Author Correction: Discovery of stimulation-responsive immune enhancers with CRISPR activation. Nature 2018; 559:E13. [PMID: 29899441 DOI: 10.1038/s41586-018-0227-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this Letter, analysis of steady-state regulatory T (Treg) cell percentages from Il2ra enhancer deletion (EDEL) and wild-type (WT) mice revealed no differences between them (Extended Data Fig. 9d). This analysis included two mice whose genotypes were incorrectly assigned. Even after correction of the genotypes, no significant differences in Treg cell percentages were seen when data across experimental cohorts were averaged (as was done in Extended Data Fig. 9d). However, if we normalize the corrected data to account for variation among experimental cohorts, a subtle decrease in EDEL Treg cell percentages is revealed and, using the corrected and normalized data, we have redrawn Extended Data Fig. 9d in Supplementary Fig. 1. The Supplementary Information to this Amendment contains the corrected and reanalysed Extended Data Fig. 9d. The sentence "This enhancer deletion (EDEL) strain also had no obvious T cell phenotypes at steady state (Extended Data Fig. 9)." should read: "This enhancer deletion (EDEL) strain had a small decrease in the percentage of Treg cells (Extended Data Fig. 9).". This error does not affect any of the main figures in the Letter or the data from mice with the human autoimmune-associated single nucleotide polymorphism (SNP) knocked in or with a 12-base-pair deletion at the site (12DEL). In addition, we stated in the Methods that we observed consistent immunophenotypes of EDEL mice across three founders, but in fact, we observed consistent phenotypes in mice from two founders. This does not change any of our conclusions and the original Letter has not been corrected.
Collapse
Affiliation(s)
- Dimitre R Simeonov
- Biomedical Sciences Graduate Program, University of California, San Francisco, California, 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Benjamin G Gowen
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Mandy Boontanrart
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Theodore L Roth
- Biomedical Sciences Graduate Program, University of California, San Francisco, California, 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - John D Gagnon
- Biomedical Sciences Graduate Program, University of California, San Francisco, California, 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Sandler Asthma Basic Research Center, University of California, San Francisco, California, 94143, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, 94305, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Youjin Lee
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Nicolas L Bray
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Alice Y Chan
- Diabetes Center, University of California, San Francisco, California, 94143, USA.,Department of Pediatrics, University of California, San Francisco, California, 94143, USA
| | - Dmytro S Lituiev
- Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California, 94143, USA
| | - Michelle L Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Rachel E Gate
- Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California, 94143, USA.,Biological and Medical Informatics Graduate Program, University of California, San Francisco, California, 94158, USA
| | - Meena Subramaniam
- Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California, 94143, USA.,Biological and Medical Informatics Graduate Program, University of California, San Francisco, California, 94158, USA
| | - Zhongmei Li
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Jonathan M Woo
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Therese Mitros
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Graham J Ray
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Gemma L Curie
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Nicki Naddaf
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Julia S Chu
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Hong Ma
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Eric Boyer
- Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Frederic Van Gool
- Diabetes Center, University of California, San Francisco, California, 94143, USA
| | - Hailiang Huang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Ruize Liu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Victoria R Tobin
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Kathrin Schumann
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Mark J Daly
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Kyle K Farh
- Illumina Inc., 5200 Illumina Way, San Diego, California, 92122, USA
| | - K Mark Ansel
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Sandler Asthma Basic Research Center, University of California, San Francisco, California, 94143, USA
| | - Chun J Ye
- Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California, 94143, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA.,Department of Applied Physics, Stanford University, Stanford, California, 94025, USA.,Chan Zuckerberg Biohub, San Francisco, California, 94158, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, California, 94143, USA.,Department of Medicine, University of California, San Francisco, California, 94143, USA
| | - Jeffrey A Bluestone
- Diabetes Center, University of California, San Francisco, California, 94143, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, 94305, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA. .,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA.
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA. .,Diabetes Center, University of California, San Francisco, California, 94143, USA. .,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA. .,Chan Zuckerberg Biohub, San Francisco, California, 94158, USA. .,Department of Medicine, University of California, San Francisco, California, 94143, USA. .,UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, 94158, USA.
| |
Collapse
|
12
|
Khor B, Gagnon JD, Goel G, Roche MI, Conway KL, Tran K, Aldrich LN, Sundberg TB, Paterson AM, Mordecai S, Dombkowski D, Schirmer M, Tan PH, Bhan AK, Roychoudhuri R, Restifo NP, O'Shea JJ, Medoff BD, Shamji AF, Schreiber SL, Sharpe AH, Shaw SY, Xavier RJ. The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells. eLife 2015; 4:e05920. [PMID: 25998054 PMCID: PMC4441007 DOI: 10.7554/elife.05920] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [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: 12/05/2014] [Accepted: 04/27/2015] [Indexed: 12/12/2022] Open
Abstract
The balance between Th17 and T regulatory (Treg) cells critically modulates immune homeostasis, with an inadequate Treg response contributing to inflammatory disease. Using an unbiased chemical biology approach, we identified a novel role for the dual specificity tyrosine-phosphorylation-regulated kinase DYRK1A in regulating this balance. Inhibition of DYRK1A enhances Treg differentiation and impairs Th17 differentiation without affecting known pathways of Treg/Th17 differentiation. Thus, DYRK1A represents a novel mechanistic node at the branch point between commitment to either Treg or Th17 lineages. Importantly, both Treg cells generated using the DYRK1A inhibitor harmine and direct administration of harmine itself potently attenuate inflammation in multiple experimental models of systemic autoimmunity and mucosal inflammation. Our results identify DYRK1A as a physiologically relevant regulator of Treg cell differentiation and suggest a broader role for other DYRK family members in immune homeostasis. These results are discussed in the context of human diseases associated with dysregulated DYRK activity.
Collapse
Affiliation(s)
- Bernard Khor
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, United States
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, United States
- Broad Institute of MIT and Harvard, Cambridge, United States
- Pathology Service, Massachusetts General Hospital, Boston, United States
| | - John D Gagnon
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Gautam Goel
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Marly I Roche
- Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, United States
| | - Kara L Conway
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, United States
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, United States
- Broad Institute of MIT and Harvard, Cambridge, United States
| | - Khoa Tran
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Leslie N Aldrich
- Broad Institute of MIT and Harvard, Cambridge, United States
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | | | - Alison M Paterson
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, United States
| | - Scott Mordecai
- Pathology Service, Massachusetts General Hospital, Boston, United States
| | - David Dombkowski
- Pathology Service, Massachusetts General Hospital, Boston, United States
| | | | - Pauline H Tan
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Atul K Bhan
- Pathology Service, Massachusetts General Hospital, Boston, United States
| | - Rahul Roychoudhuri
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Nicholas P Restifo
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - John J O'Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, United States
| | - Benjamin D Medoff
- Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, United States
| | | | - Stuart L Schreiber
- Broad Institute of MIT and Harvard, Cambridge, United States
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Arlene H Sharpe
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, United States
| | - Stanley Y Shaw
- Center for Systems Biology, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, United States
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, United States
- Broad Institute of MIT and Harvard, Cambridge, United States
| |
Collapse
|
13
|
Fisher J, Scott C, Stevens R, Marconi B, Champion L, Freedman GM, Asrari F, Pilepich MV, Gagnon JD, Wong G. Randomized phase III study comparing Best Supportive Care to Biafine as a prophylactic agent for radiation-induced skin toxicity for women undergoing breast irradiation: Radiation Therapy Oncology Group (RTOG) 97-13. Int J Radiat Oncol Biol Phys 2000; 48:1307-10. [PMID: 11121627 DOI: 10.1016/s0360-3016(00)00782-3] [Citation(s) in RCA: 196] [Impact Index Per Article: 8.2] [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] [Indexed: 11/17/2022]
Abstract
PURPOSE To determine if Biafine compared to Best Supportive Care (BSC) is effective in minimizing or preventing radiation-induced dermatitis in women undergoing breast irradiation. METHODS AND MATERIALS Patients were randomized between Biafine (n = 83) vs. BSC (n = 89). The institutions identified preference for BSC at the time of randomization. A no-treatment arm was allowed (16% received no treatment). Patients were instructed to apply randomized product three times a day, but not within 4 h of their daily RT session. Application began following their first radiation treatment and continued 2 weeks postradiation. Skin dermatitis was scored weekly utilizing the RTOG and ONS (Oncology Nursing Society) skin toxicity scales, a weekly patient satisfaction and quality-of-life questionnaire. RESULTS Using the RTOG toxicity scale there was no overall difference for maximum dermatitis during RT between Biafine and BSC (p = 0.77). There was no difference in maximum toxicity by arm or breast size. There was an interaction between breast size and toxicity, with large-breasted women exhibiting more toxicity. Large-breasted women receiving Biafine were more likely to have no toxicity 6 weeks post RT. CONCLUSION There was no overall difference between BSC and Biafine in the prevention, time to, or duration of radiation-induced dermatitis.
Collapse
Affiliation(s)
- J Fisher
- Radiation Oncology Center, Oakwood Hospital and Medical Center, Dearborn, MI 48123, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Gagnon JD. Autonomy in physician-assisted suicide. Hastings Cent Rep 2000; 30:4. [PMID: 10862360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
|
15
|
Affiliation(s)
- J D Gagnon
- Cancer Care Center, St. Joseph Medical Center, Joliet, IL 60435, USA
| |
Collapse
|
16
|
Gagnon JD. Doctor bashing? Hastings Cent Rep 1989; 19:44. [PMID: 2714968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
17
|
Gagnon JD. The path to high ethics in freestanding oncology centers. Adm Radiol 1988; 7:30-2. [PMID: 10290293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
|
18
|
Russ JE, Smoron GL, Gagnon JD. Omental transposition flap in colorectal carcinoma: adjunctive use in prevention and treatment of radiation complications. Int J Radiat Oncol Biol Phys 1984; 10:55-62. [PMID: 6698825 DOI: 10.1016/0360-3016(84)90412-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The versatility of the omentum has led to its use as a surgical adjunct in the total oncological management of primary and recurrent colorectal carcinoma. The omentum is used as a transposition pedicle flap, broadly based on the left gastroepiploic vascular supply. Following abdominoperineal resection or low anterior resection of the rectum, the small bowel is elevated out of the pelvis by the omental bulk. The pelvic defect is reperitonealized and the risk of pelvic small bowel adhesions is diminished. With the increasing use of postoperative radiation to the pelvis for rectal carcinoma, the tolerance to therapy may be improved and the incidence of radiation enteritis and enteropathy should be reduced. Surgical complications such as leakage from low anterior anastomoses and pelvic abscesses, which may delay or contraindicate necessary postoperative radiation, are dramatically decreased. Reconstruction of the perineum with omental flap provides adequate soft tissue bulk and contour when a radical resection has been performed. The omentum has the potential for neovascular proliferation and can act to prevent anastomotic dehiscence of intestinal anastomoses involving previously irradiated bowel. Furthermore, covering unresectable recurrent carcinoma in the pelvis and retroperitoneum with the omentum as a palliative measure provides a thick anatomical barrier against potential ureteral, bladder, and small bowel invasion and obstruction. The omental flap has been used in 24 patients with colorectal carcinoma; one flap was lost as a result of distal omental infarction in a patient with recurrent rectal carcinoma and radionecrosis of the perineum. The safety and ease of this procedure has allowed increased surgical innovation, especially in the prevention and treatment of radiation complications.
Collapse
|
19
|
|
20
|
Abstract
Twenty-nine patients with stage II endometrial carcinoma were reviewed and the possible risk factors involved in state II disease are presented. Twenty-four patients received external irradiation as part of their treatment with or without intracavitary or intravaginal radium and/or TAH BSO. The 5-year actuarial survival in our series was 81.4%. The data showed that preoperative external irradiation can be effectively administered without undue complication. A strong argument against the traditional use of preoperative intracavitary radium is presented. Preoperative external irradiation administered with a 4-field box technique to deliver a minimum dose of 5000 rad in 5--6 weeks to all the structures at risk is the recommended treatment for stage II endometrial carcinoma.
Collapse
|
21
|
Abstract
We studied 38 patients with prostatic cancer who received breast irradiation before oral estrogen administration. Our data are combined with those from other institutions to determine the effectiveness of pre-estrogen breast irradiation in minimizing gynecomastia and/or pain. Based on our review the incidence of estrogen-induced breast changes is 70%. Irradiation given before estrogen administration can prevent or minimize these changes in 89.3% of the treated patients. Histologic changes of gynecomastia are reviewed and recommendations for optimum radiation therapy technique are included.
Collapse
|