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Begg LR, Orriols AM, Zannikou M, Yeh C, Vadlamani P, Kanojia D, Bolin R, Dunne SF, Balakrishnan S, Camarda R, Roth D, Zielinski-Mozny NA, Yau C, Vassilopoulos A, Huang TH, Kim KYA, Horiuchi D. S100A8/A9 predicts response to PIM kinase and PD-1/PD-L1 inhibition in triple-negative breast cancer mouse models. Commun Med (Lond) 2024; 4:22. [PMID: 38378783 PMCID: PMC10879183 DOI: 10.1038/s43856-024-00444-8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Understanding why some triple-negative breast cancer (TNBC) patients respond poorly to existing therapies while others respond well remains a challenge. This study aims to understand the potential underlying mechanisms distinguishing early-stage TNBC tumors that respond to clinical intervention from non-responders, as well as to identify clinically viable therapeutic strategies, specifically for TNBC patients who may not benefit from existing therapies. METHODS We conducted retrospective bioinformatics analysis of historical gene expression datasets to identify a group of genes whose expression levels in early-stage tumors predict poor clinical outcomes in TNBC. In vitro small-molecule screening, genetic manipulation, and drug treatment in syngeneic mouse models of TNBC were utilized to investigate potential therapeutic strategies and elucidate mechanisms of drug action. RESULTS Our bioinformatics analysis reveals a robust association between increased expression of immunosuppressive cytokine S100A8/A9 in early-stage tumors and subsequent disease progression in TNBC. A targeted small-molecule screen identifies PIM kinase inhibitors as capable of decreasing S100A8/A9 expression in multiple cell types, including TNBC and immunosuppressive myeloid cells. Combining PIM inhibition and immune checkpoint blockade induces significant antitumor responses, especially in otherwise resistant S100A8/A9-high PD-1/PD-L1-positive tumors. Notably, serum S100A8/A9 levels mirror those of tumor S100A8/A9 in a syngeneic mouse model of TNBC. CONCLUSIONS Our data propose S100A8/A9 as a potential predictive and pharmacodynamic biomarker in clinical trials evaluating combination therapy targeting PIM and immune checkpoints in TNBC. This work encourages the development of S100A8/A9-based liquid biopsy tests for treatment guidance.
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Affiliation(s)
- Lauren R Begg
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Adrienne M Orriols
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- University of Florida College of Medicine, Gainesville, FL, USA
| | - Markella Zannikou
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chen Yeh
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Biostatistics Collaboration Center, Northwestern University, Chicago, IL, USA
- Rush University Medical Center, Chicago, IL, USA
| | | | - Deepak Kanojia
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Mythic Therapeutics, Waltham, MA, USA
| | - Rosemary Bolin
- Center for Comparative Medicine, Northwestern University, Chicago, IL, USA
- Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Sara F Dunne
- High Throughput Analysis Laboratory, Northwestern University, Evanston, IL, USA
| | - Sanjeev Balakrishnan
- University of California, San Francisco, San Francisco, CA, USA
- Pulze.ai, San Francisco, CA, USA
| | - Roman Camarda
- University of California, San Francisco, San Francisco, CA, USA
- Novo Ventures US, Inc., San Francisco, CA, USA
| | - Diane Roth
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Nicolette A Zielinski-Mozny
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Comparative Medicine, Northwestern University, Chicago, IL, USA
| | - Christina Yau
- University of California, San Francisco, San Francisco, CA, USA
| | - Athanassios Vassilopoulos
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
- AbbVie, Inc., North Chicago, IL, USA
| | - Tzu-Hsuan Huang
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Kwang-Youn A Kim
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Biostatistics Collaboration Center, Northwestern University, Chicago, IL, USA
| | - Dai Horiuchi
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
- Center for Human Immunobiology, Northwestern University, Chicago, IL, USA.
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Begg LR, Orriols AM, Zannikou M, Yeh C, Vadlamani P, Kanojia D, Bolin R, Dunne SF, Balakrishnan S, Camarda R, Roth D, Zielinski-Mozny NA, Yau C, Vassilopoulos A, Huang TH, Kim KYA, Horiuchi D. S100A8/A9 predicts triple-negative breast cancer response to PIM kinase and PD-1/PD-L1 inhibition. bioRxiv 2023:2023.09.21.558870. [PMID: 37790346 PMCID: PMC10542194 DOI: 10.1101/2023.09.21.558870] [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: 10/05/2023]
Abstract
It remains elusive why some triple-negative breast cancer (TNBC) patients respond poorly to existing therapies while others respond well. Our retrospective analysis of historical gene expression datasets reveals that increased expression of immunosuppressive cytokine S100A8/A9 in early-stage tumors is robustly associated with subsequent disease progression in TNBC. Although it has recently gained recognition as a potential anticancer target, S100A8/A9 has not been integrated into clinical study designs evaluating molecularly targeted therapies. Our small molecule screen has identified PIM kinase inhibitors as capable of decreasing S100A8/A9 expression in multiple cell types, including TNBC and immunosuppressive myeloid cells. Furthermore, combining PIM inhibition and immune checkpoint blockade induces significant antitumor responses, especially in otherwise resistant S100A8/A9-high PD-1/PD-L1-positive tumors. Importantly, serum S100A8/A9 levels mirror those of tumor S100A8/A9 in a syngeneic mouse model of TNBC. Thus, our data suggest that S100A8/A9 could be a predictive and pharmacodynamic biomarker in clinical trials evaluating combination therapy targeting PIM and immune checkpoints in TNBC and encourage the development of S100A8/A9-based liquid biopsy tests.
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3
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Mahapatra A, Dhakal A, Noguchi A, Vadlamani P, Hundley HA. ADAR-mediated regulation of PQM-1 expression in neurons impacts gene expression throughout C. elegans and regulates survival from hypoxia. PLoS Biol 2023; 21:e3002150. [PMID: 37747897 PMCID: PMC10553819 DOI: 10.1371/journal.pbio.3002150] [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: 04/27/2023] [Revised: 10/05/2023] [Accepted: 08/23/2023] [Indexed: 09/27/2023] Open
Abstract
The ability to alter gene expression programs in response to changes in environmental conditions is central to the ability of an organism to thrive. For most organisms, the nervous system serves as the master regulator in communicating information about the animal's surroundings to other tissues. The information relay centers on signaling pathways that cue transcription factors in a given cell type to execute a specific gene expression program, but also provide a means to signal between tissues. The transcription factor PQM-1 is an important mediator of the insulin signaling pathway contributing to longevity and the stress response as well as impacting survival from hypoxia. Herein, we reveal a novel mechanism for regulating PQM-1 expression specifically in neural cells of larval animals. Our studies reveal that the RNA-binding protein (RBP), ADR-1, binds to pqm-1 mRNA in neural cells. This binding is regulated by the presence of a second RBP, ADR-2, which when absent leads to reduced expression of both pqm-1 and downstream PQM-1 activated genes. Interestingly, we find that neural pqm-1 expression is sufficient to impact gene expression throughout the animal and affect survival from hypoxia, phenotypes that we also observe in adr mutant animals. Together, these studies reveal an important posttranscriptional gene regulatory mechanism in Caenorhabditis elegans that allows the nervous system to sense and respond to environmental conditions to promote organismal survival from hypoxia.
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Affiliation(s)
- Ananya Mahapatra
- Genome, Cell and Developmental Biology Graduate Program, Indiana University, Bloomington, Indiana, United States of America
| | - Alfa Dhakal
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine–Bloomington, Bloomington, Indiana, United States of America
| | - Aika Noguchi
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Pranathi Vadlamani
- Medical Sciences Program, Indiana University School of Medicine–Bloomington, Bloomington, Indiana, United States of America
| | - Heather A. Hundley
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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4
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Mahapatra A, Dhakal A, Noguchi A, Vadlamani P, Hundley HA. ADARs employ a neural-specific mechanism to regulate PQM-1 expression and survival from hypoxia. bioRxiv 2023:2023.05.05.539519. [PMID: 37205482 PMCID: PMC10187282 DOI: 10.1101/2023.05.05.539519] [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: 05/21/2023]
Abstract
The ability to alter gene expression programs in response to changes in environmental conditions is central to the ability of an organism to thrive. For most organisms, the nervous system serves as the master regulator in communicating information about the animal's surroundings to other tissues. The information relay centers on signaling pathways that cue transcription factors in a given cell type to execute a specific gene expression program, but also provide a means to signal between tissues. The transcription factor PQM-1 is an important mediator of the insulin signaling pathway contributing to longevity and the stress response as well as impacting survival from hypoxia. Herein, we reveal a novel mechanism for regulating PQM-1 expression specifically in neural cells of larval animals. Our studies reveal that the RNA binding protein, ADR-1, binds to pqm-1 mRNA in neural cells. This binding is regulated by the presence of a second RNA binding protein, ADR-2, which when absent leads to reduced expression of both pqm-1 and downstream PQM-1 activated genes. Interestingly, we find that neural pqm-1 expression is sufficient to impact gene expression throughout the animal and affect survival from hypoxia; phenotypes that we also observe in adr mutant animals. Together, these studies reveal an important post-transcriptional gene regulatory mechanism that allows the nervous system to sense and respond to environmental conditions to promote organismal survival from hypoxia.
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Affiliation(s)
- Ananya Mahapatra
- Genome, Cell and Developmental Biology Graduate Program, Indiana University, Bloomington IN, 47405 USA
| | - Alfa Dhakal
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine – Bloomington, Bloomington IN, 47405 USA
| | - Aika Noguchi
- Department of Biology, Indiana University, Bloomington IN 47405 USA
| | - Pranathi Vadlamani
- Medical Sciences Program, Indiana University School of Medicine – Bloomington, Bloomington IN, 47405 USA
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5
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Shrestha RL, Balachandra V, Kim JH, Rossi A, Vadlamani P, Sethi SC, Ozbun L, Lin S, Cheng KCC, Chari R, Karpova TS, Pegoraro G, Foltz DR, Caplen NJ, Basrai MA. Histone H3/H4 chaperone CHAF1B prevents the mislocalization of CENP-A for chromosomal stability. J Cell Sci 2023; 136:307402. [PMID: 37129573 DOI: 10.1242/jcs.260944] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/06/2023] [Indexed: 05/03/2023] Open
Abstract
Restricting the localization of the evolutionarily conserved centromeric histone H3 variant CENP-A to centromeres prevents chromosomal instability (CIN). The mislocalization of CENP-A to non-centromeric regions contributes to CIN in yeasts, flies, and human cells. Even though overexpression and mislocalization of CENP-A have been reported in cancers the mechanisms responsible for its mislocalization remain poorly understood. Here, we used an imaging-based high-throughput RNAi screen to identify factors that prevent mislocalization of overexpressed YFP-tagged CENP-A (YFP-CENP-A) in HeLa cells. Amongst the top five lead candidates of the screen that showed increased nuclear YFP-CENP-A fluorescence were depletions of histone chaperones (CHAF1B/p60 and CHAF1A/p150). Follow-up validation and characterization experiments showed that CHAF1B-depleted cells exhibit CENP-A mislocalization, CIN phenotypes, and increased enrichment of CENP-A in the chromatin fraction. The depletion of DAXX, a histone H3.3 chaperone, suppressed CENP-A mislocalization and CIN in CHAF1B-depleted cells. We propose that in CHAF1B-depleted cells, DAXX promotes mislocalization of the overexpressed CENP-A to non-centromeric regions, resulting in CIN. In summary, we have identified regulators of CENP-A localization and defined a role for CHAF1B in preventing DAXX-dependent CENP-A mislocalization and CIN.
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Affiliation(s)
| | | | - Jee Hun Kim
- Yeast Genome Stability Section, Genetics Branch, CCR, NCI, NIH, USA
| | - Austin Rossi
- Yeast Genome Stability Section, Genetics Branch, CCR, NCI, NIH, USA
| | - Pranathi Vadlamani
- Department of Biochemistry and Molecular Genetics, Northwestern University, USA
| | | | - Laurent Ozbun
- High-Throughput Imaging Facility (HiTIF), Laboratory of Receptor Biology and Gene Expression, CCR, NCI, NIH, USA
| | - Shinjen Lin
- Functional Genomics Facility, National Center for Advancing Translational Sciences, NIH, USA
| | - Ken Chin-Chien Cheng
- Functional Genomics Facility, National Center for Advancing Translational Sciences, NIH, USA
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program at the Frederick National Laboratory for Cancer Research, USA
| | - Tatiana S Karpova
- Optical Microscopy Core, Laboratory of Receptor Biology and Gene Expression, CCR, NCI, NIH, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility (HiTIF), Laboratory of Receptor Biology and Gene Expression, CCR, NCI, NIH, USA
| | - Daniel R Foltz
- Department of Biochemistry and Molecular Genetics, Northwestern University, USA
| | - Natasha J Caplen
- Functional Genetics Section, Genetics Branch, CCR, NCI, NIH, USA
| | - Munira A Basrai
- Yeast Genome Stability Section, Genetics Branch, CCR, NCI, NIH, USA
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6
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Raghava Kurup R, Oakes EK, Manning AC, Mukherjee P, Vadlamani P, Hundley HA. RNA binding by ADAR3 inhibits adenosine-to-inosine editing and promotes expression of immune response protein MAVS. J Biol Chem 2022; 298:102267. [PMID: 35850307 PMCID: PMC9418441 DOI: 10.1016/j.jbc.2022.102267] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [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: 03/30/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 12/13/2022] Open
Abstract
Members of the ADAR family of double-stranded RNA–binding proteins regulate one of the most abundant RNA modifications in humans, the deamination of adenosine to inosine. Several transcriptome-wide studies have been carried out to identify RNA targets of the active deaminases ADAR1 and ADAR2. However, our understanding of ADAR3, the brain-specific deaminase-deficient ADAR family member, is limited to a few transcripts. In this study, we identified over 3300 transcripts bound by ADAR3 and observed that binding of ADAR3 correlated with reduced editing of over 400 sites in the glioblastoma transcriptome. We further investigated the impact of ADAR3 on gene regulation of the transcript that encodes MAVS, an essential protein in the innate immune response pathway. We observed reduced editing in the MAVS 3′ UTR in cells expressing increased ADAR3 or reduced ADAR1 suggesting ADAR3 acts as a negative regulator of ADAR1-mediated editing. While neither ADAR1 knockdown or ADAR3 overexpression affected MAVS mRNA expression, we demonstrate increased ADAR3 expression resulted in upregulation of MAVS protein expression. In addition, we created a novel genetic mutant of ADAR3 that exhibited enhanced RNA binding and MAVS upregulation compared with wildtype ADAR3. Interestingly, this ADAR3 mutant no longer repressed RNA editing, suggesting ADAR3 has a unique regulatory role beyond altering editing levels. Altogether, this study provides the first global view of ADAR3-bound RNAs in glioblastoma cells and identifies both a role for ADAR3 in repressing ADAR1-mediated editing and an RNA-binding dependent function of ADAR3 in regulating MAVS expression.
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Affiliation(s)
| | - Eimile K Oakes
- Department of Biology, Indiana University, Bloomington IN 47405, USA
| | - Aidan C Manning
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington IN 47405, USA
| | - Priyanka Mukherjee
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington IN 47405, USA
| | - Pranathi Vadlamani
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington IN 47405, USA
| | - Heather A Hundley
- Department of Biology, Indiana University, Bloomington IN 47405, USA.
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7
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Kunder R, Velyunskiy M, Dunne SF, Cho BK, Kanojia D, Begg L, Orriols AM, Fleming-Trujillo E, Vadlamani P, Vialichka A, Bolin R, Perrino JN, Roth D, Clutter MR, Zielinski-Mozny NA, Goo YA, Cristofanilli M, Mendillo ML, Vassilopoulos A, Horiuchi D. Synergistic PIM kinase and proteasome inhibition as a therapeutic strategy for MYC-overexpressing triple-negative breast cancer. Cell Chem Biol 2022; 29:358-372.e5. [PMID: 34525344 PMCID: PMC8901784 DOI: 10.1016/j.chembiol.2021.08.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 06/24/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022]
Abstract
Triple-negative breast cancer (TNBC) is the breast cancer subtype with the poorest clinical outcome. The PIM family of kinases has emerged as a factor that is both overexpressed in TNBC and associated with poor outcomes. Preclinical data suggest that TNBC with an elevated MYC expression is sensitive to PIM inhibition. However, clinical observations indicate that the efficacy of PIM inhibitors as single agents may be limited, suggesting the need for combination therapies. Our screening effort identifies PIM and the 20S proteasome inhibition as the most synergistic combination. PIM inhibitors, when combined with proteasome inhibitors, induce significant antitumor effects, including abnormal accumulation of poly-ubiquitinated proteins, increased proteotoxic stress, and the inability of NRF1 to counter loss in proteasome activity. Thus, the identified combination could represent a rational combination therapy against MYC-overexpressing TNBC that is readily translatable to clinical investigations.
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Affiliation(s)
- Ratika Kunder
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Michelle Velyunskiy
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Adlai E. Stevenson High School, Lincolnshire, IL 60069, USA
| | - Sara F Dunne
- High-Throughput Analysis Laboratory, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Byoung-Kyu Cho
- Proteomics Center for Excellence, Northwestern University, Chicago, IL 60611, USA
| | - Deepak Kanojia
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lauren Begg
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Adrienne M Orriols
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Erica Fleming-Trujillo
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Pranathi Vadlamani
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Alesia Vialichka
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Rosemary Bolin
- Center for Comparative Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jessica N Perrino
- Center for Comparative Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Diane Roth
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Matthew R Clutter
- High-Throughput Analysis Laboratory, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Nicolette A Zielinski-Mozny
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Comparative Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Young Ah Goo
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Proteomics Center for Excellence, Northwestern University, Chicago, IL 60611, USA
| | - Massimo Cristofanilli
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Institute for Epigenetics, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Athanassios Vassilopoulos
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Dai Horiuchi
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA.
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8
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Rajendren S, Dhakal A, Vadlamani P, Townsend J, Deffit SN, Hundley HA. Profiling neural editomes reveals a molecular mechanism to regulate RNA editing during development. Genome Res 2020; 31:27-39. [PMID: 33355311 PMCID: PMC7849389 DOI: 10.1101/gr.267575.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/18/2020] [Indexed: 12/18/2022]
Abstract
Adenosine (A) to inosine (I) RNA editing contributes to transcript diversity and modulates gene expression in a dynamic, cell type–specific manner. During mammalian brain development, editing of specific adenosines increases, whereas the expression of A-to-I editing enzymes remains unchanged, suggesting molecular mechanisms that mediate spatiotemporal regulation of RNA editing exist. Herein, by using a combination of biochemical and genomic approaches, we uncover a molecular mechanism that regulates RNA editing in a neural- and development-specific manner. Comparing editomes during development led to the identification of neural transcripts that were edited only in one life stage. The stage-specific editing is largely regulated by differential gene expression during neural development. Proper expression of nearly one-third of the neurodevelopmentally regulated genes is dependent on adr-2, the sole A-to-I editing enzyme in C. elegans. However, we also identified a subset of neural transcripts that are edited and expressed throughout development. Despite a neural-specific down-regulation of adr-2 during development, the majority of these sites show increased editing in adult neural cells. Biochemical data suggest that ADR-1, a deaminase-deficient member of the adenosine deaminase acting on RNA (ADAR) family, is competing with ADR-2 for binding to specific transcripts early in development. Our data suggest a model in which during neural development, ADR-2 levels overcome ADR-1 repression, resulting in increased ADR-2 binding and editing of specific transcripts. Together, our findings reveal tissue- and development-specific regulation of RNA editing and identify a molecular mechanism that regulates ADAR substrate recognition and editing efficiency.
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Affiliation(s)
- Suba Rajendren
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Alfa Dhakal
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, Indiana 47405, USA
| | - Pranathi Vadlamani
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, Indiana 47405, USA
| | - Jack Townsend
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, Indiana 47405, USA
| | - Sarah N Deffit
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, Indiana 47405, USA
| | - Heather A Hundley
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Bloomington, Indiana 47405, USA
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9
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Deffit SN, Yee BA, Manning AC, Rajendren S, Vadlamani P, Wheeler EC, Domissy A, Washburn MC, Yeo GW, Hundley HA. The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis. eLife 2017; 6:28625. [PMID: 28925356 PMCID: PMC5644944 DOI: 10.7554/elife.28625] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 09/18/2017] [Indexed: 12/26/2022] Open
Abstract
ADAR proteins alter gene expression both by catalyzing adenosine (A) to inosine (I) RNA editing and binding to regulatory elements in target RNAs. Loss of ADARs affects neuronal function in all animals studied to date. Caenorhabditis elegans lacking ADARs exhibit reduced chemotaxis, but the targets responsible for this phenotype remain unknown. To identify critical neural ADAR targets in C. elegans, we performed an unbiased assessment of the effects of ADR-2, the only A-to-I editing enzyme in C. elegans, on the neural transcriptome. Development and implementation of publicly available software, SAILOR, identified 7361 A-to-I editing events across the neural transcriptome. Intersecting the neural editome with adr-2 associated gene expression changes, revealed an edited mRNA, clec-41, whose neural expression is dependent on deamination. Restoring clec-41 expression in adr-2 deficient neural cells rescued the chemotaxis defect, providing the first evidence that neuronal phenotypes of ADAR mutants can be caused by altered gene expression. DNA is the blueprint that tells each cell in an organism how it should operate. It encodes the instructions to make proteins and other molecules. To make a protein, a section of DNA known as a gene is used as a template to make molecules known as messenger ribonucleic acids (or mRNAs for short). The message in RNA consists of a series of individual letters, known as nucleotides, that tell the cell how much of a protein should be produced (referred to as gene expression) as well as the specific activities of each protein. The letters in mRNAs can be changed in specific cells and at certain points in development through a process known as RNA editing. This process is essential for animals to grow and develop normally and for the brain to work properly. Errors in RNA editing are found in patients suffering from a variety of neuropathological diseases, including Alzheimer’s disease, depression and brain tumors. Humans have millions of editing sites that are predicted to affect gene expression. However, many studies of RNA editing have only focused on the changes that alter protein activity. The ADAR proteins carry out a specific type of RNA editing in animals. In a microscopic worm known as Caenorhabditis elegans the loss of an ADAR protein called ADR-2 reduces the ability of the worm to move in response to chemicals, a process known as chemotaxis. Deffit et al. found that loss of ADR-2 affected the expression of over 150 genes in the nervous system of the worm. To identify which letters in the mRNAs were edited in the nervous system, Deffit et al. developed a new publically available software program called SAILOR (software for accurately identifying locations of RNA editing). This program can be used to detect RNA editing in any cell, tissue or organism. By combining the experimental and computational approaches, Deffit et al. were able to identify a gene that was edited in normal worms and expressed at lower levels in the mutant worms. Increasing the expression of just this one of gene in the mutant worms restored the worms’ ability to move towards a chemical “scent”. Together, these findings suggest that when studying human neuropathological diseases we should consider the effect of RNA editing on the amount of gene expression as well as protein activity. Future work should investigate the importance of RNA editing in controlling gene expression in other diseases including cancers.
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Affiliation(s)
- Sarah N Deffit
- Medical Sciences Program, Indiana University, Bloomington, Indiana
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, San Diego, United States
| | - Aidan C Manning
- Medical Sciences Program, Indiana University, Bloomington, Indiana
| | - Suba Rajendren
- Department of Biology, Indiana University, Bloomington, Indiana
| | | | - Emily C Wheeler
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, San Diego, United States
| | - Alain Domissy
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, San Diego, United States
| | | | - Gene W Yeo
- Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, San Diego, United States.,Molecular Engineering Laboratory, Agency for Science, Technology and Research, Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Abstract
Totally implanted venous access ports are excellent devices for delivering chemotherapeutic agents and prolonged intravenous infusions in patients with cancer. Catheter fracture and embolization are rare and potentially serious complications of these widely used devices. Retrieval of the embolized fragment is generally indicated but may not be possible. The authors report three cases of catheter embolization in their center over a period of 9 years. Catheter "pinch-off," fracture, embolization, and retrieval are discussed.
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Affiliation(s)
- P Vadlamani
- Division of Hematology/Medical Oncology, University of Missouri/Ellis Fischel Cancer Center, Columbia 65203, USA
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