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Sacramento CM, Saito MT, Casati MZ, Sallum EA, Casarin RCV, Silvério KG. CCKR signaling map, G-Protein bindings, hormonal regulation, and neural mechanisms may influence the osteogenic/cementogenic differentiation potential of hPDLSCs. Arch Oral Biol 2024; 168:106069. [PMID: 39208712 DOI: 10.1016/j.archoralbio.2024.106069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 08/14/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
OBJECTIVE Periodontal regeneration poses challenges due to the periodontium's complexity, relying on mesenchymal cells from the periodontal ligament (hPDLSCs) to regenerate hard tissues like bone and cementum. While some hPDLSCs have high regeneration potential (HOP-hPDLSCs), most are low potential (LOP-hPDLSCs). This study analyzed hPDLSCs from a single donor to minimize inter-individual variability and focus on key differences in differentiation potentials. DESIGN This study used RNA-seq, genomic databases, and bioinformatics tools to explore signaling pathways (SPs), biological processes (BPs), and molecular functions (MFs) guiding HOP cells to mineralized matrix production. It also investigated limitations of LOP cells and strategies for enhancing their osteo/cementogenesis. RESULTS In basal conditions, HOP exhibited a multifunctional gene network with higher expression of genes related to osteo/cementogenesis, cell differentiation, immune modulation, stress response, and hormonal regulation. In contrast, LOP focused on steroid hormone biosynthesis and nucleic acid maintenance. During osteo/cementogenic induction, HOP showed strong modulation of genes related to angiogenesis, cell division, mesenchymal differentiation, and extracellular matrix production. LOP demonstrated neural synaptic-related processes and preserved cellular cytoskeleton integrity. CCKR map signaling and G-protein receptor bindings gained significance during osteo/cementogenesis in HOP-hPDLSCs. Both HOP and LOP shared common BPs related to gastrointestinal and reproductive system development. CONCLUSION The osteo/cementogenic differentiation of HOP cells may be regulated by CCKR signaling, G-protein bindings, and specific hormonal regulation. LOP cells seem committed to neural mechanisms. This study sheds light on hPDLSCs' complex characteristics, offering a deeper understanding of their differentiation potential for future periodontal regeneration research and therapies.
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Affiliation(s)
- Catharina Marques Sacramento
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas - UNICAMP, Piracicaba 13414-903, Brazil
| | - Miki Taketomi Saito
- Faculdade de Odontologia, Universidade Federal do Pará - UFPA, Departamento de Saúde Coletiva, Belém 66075-110, Brazil.
| | - Márcio Zaffalon Casati
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas - UNICAMP, Piracicaba 13414-903, Brazil.
| | - Enilson Antonio Sallum
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas - UNICAMP, Piracicaba 13414-903, Brazil.
| | - Renato Correa Viana Casarin
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas - UNICAMP, Piracicaba 13414-903, Brazil.
| | - Karina Gonzales Silvério
- Faculdade de Odontologia de Piracicaba, Universidade Estadual de Campinas - UNICAMP, Piracicaba 13414-903, Brazil.
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Moura SR, Sousa AB, Olesen JB, Barbosa MA, Søe K, Almeida MI. Stage-specific modulation of multinucleation, fusion, and resorption by the long non-coding RNA DLEU1 and miR-16 in human primary osteoclasts. Cell Death Dis 2024; 15:741. [PMID: 39389940 PMCID: PMC11467329 DOI: 10.1038/s41419-024-06983-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 08/01/2024] [Accepted: 08/07/2024] [Indexed: 10/12/2024]
Abstract
Osteoclasts are the only cells able to resorb all the constituents of the bone matrix. While the modulation of osteoclast activity is well established for preventing bone-related diseases, there is an increasing demand for novel classes of anti-resorption agents. Herein, we investigated non-coding RNA molecules and proposed DLEU1 and miR-16 as potential candidates for modulating osteoclast functions. DLEU1 and miR-16 target cell fusion at both the early and late stages of osteoclastogenesis but operate through independent pathways. DLEU1 silencing hinders the fusion process, leading to abrogation of the phagocytic cup fusion modality and a reduction in the fusion events between mononucleated precursors and multinucleated osteoclasts, while miR-16 influences monocyte-to-osteoclast differentiation, impairing osteoclasts formation but not the number of nuclei at early stages. On the other hand, using these non-coding RNAs to engineer mature osteoclasts has implications for bone resorption. Both DLEU1 and miR-16 influence the speed of resorption in pit-forming osteoclasts, without affecting the resorbed area. However, the impact of increasing miR-16 levels extends more broadly, affecting trench-forming osteoclasts as well, leading to a reduction in their percentage, speed, and resorbed area. These findings offer potential new therapeutic targets to ameliorate bone destruction in skeletal diseases.
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Affiliation(s)
- Sara Reis Moura
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Ana Beatriz Sousa
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Jacob Bastholm Olesen
- Department of Pathology, Odense University Hospital, Odense, Denmark
- Clinical Cell Biology, Pathology Research Unit, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Mário Adolfo Barbosa
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Kent Søe
- Department of Pathology, Odense University Hospital, Odense, Denmark
- Clinical Cell Biology, Pathology Research Unit, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Maria Inês Almeida
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- INEB-Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal.
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.
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3
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Canchi Sistla H, Talluri S, Rajagopal T, Venkatabalasubramanian S, Rao Dunna N. Genomic instability in ovarian cancer: Through the lens of single nucleotide polymorphisms. Clin Chim Acta 2024:119992. [PMID: 39395774 DOI: 10.1016/j.cca.2024.119992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 10/04/2024] [Accepted: 10/04/2024] [Indexed: 10/14/2024]
Abstract
Ovarian cancer (OC) is the deadliest gynecological malignancy among all female reproductive cancers. It is characterized by high mortality rate and poor prognosis. Genomic instability caused by mutations, single nucleotide polymorphisms (SNPs), copy number variations (CNVs), microsatellite instability (MSI), and chromosomal instability (CIN) are associated with OC predisposition. SNPs, which are highly prevalent in the general population, show a greater relative risk contribution, particularly in sporadic cancers. Understanding OC etiology in terms of genetic basis can increase the use of molecular diagnostics and provide promising approaches for designing novel treatment modalities. This will help deliver personalized medicine to OC patients, which may soon be within reach. Given the pivotal impact of SNPs in cancers, the primary emphasis of this review is to shed light on their prevalence in key caretaker genes that closely monitor genomic integrity, viz., DNA damage response, repair, cell cycle checkpoints, telomerase maintenance, and apoptosis and their clinical implications in OC. We highlight the current challenges faced in different SNP-based studies. Various computational methods and bioinformatic tools employed to predict the functional impact of SNPs have also been comprehensively reviewed concerning OC research. Overall, this review identifies that variants in the DDR and HRR pathways are the most studied, implying their critical role in the disease. Conversely, variants in other pathways, such as NHEJ, MMR, cell cycle, apoptosis, telomere maintenance, and PARP genes, have been explored the least.
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Affiliation(s)
- Harshavardhani Canchi Sistla
- Cancer Genomics Laboratory, Department of Biotechnology, School of Chemical and Biotechnology, SASTRA- Deemed University, Thanjavur 613 401, India
| | - Srikanth Talluri
- Dana Farber Cancer Institute, Boston, MA 02215, USA; Veterans Administration Boston Healthcare System, West Roxbury, MA 02132, USA
| | | | - Sivaramakrishna Venkatabalasubramanian
- Department of Genetic Engineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur Campus, Chennai 603 203, India
| | - Nageswara Rao Dunna
- Cancer Genomics Laboratory, Department of Biotechnology, School of Chemical and Biotechnology, SASTRA- Deemed University, Thanjavur 613 401, India.
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Chen K, Ashtiani KC, Monfared RV, Baldi P, Alachkar A. Circadian cilia transcriptome in mouse brain across physiological and pathological states. Mol Brain 2024; 17:67. [PMID: 39304885 PMCID: PMC11414107 DOI: 10.1186/s13041-024-01143-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 09/12/2024] [Indexed: 09/22/2024] Open
Abstract
Primary cilia are dynamic sensory organelles that continuously undergo structural modifications in response to environmental and cellular signals, many of which exhibit rhythmic patterns. Building on our previous findings of rhythmic cilia-related gene expression in diurnal primates (baboon), this study extends the investigation to the nocturnal mouse brain to identify circadian patterns of cilia gene expression across brain regions. We used computational techniques and transcriptomic data from four publicly available databases, to examine the circadian expression of cilia-associated genes within six brain areas: brainstem, cerebellum, hippocampus, hypothalamus, striatum, and suprachiasmatic nucleus. Our analysis reveals that a substantial proportion of cilia transcripts exhibit circadian rhythmicity across the examined regions, with notable overrepresentation in the striatum, hippocampus, and cerebellum. We also demonstrate region-specific variations in the abundance and timing of circadian cilia genes' peaks, indicating an adaptation to the distinct physiological roles of each brain region. Additionally, we show that the rhythmic patterns of cilia transcripts are shifted under various physiological and pathological conditions, including modulation of the dopamine system, high-fat diet, and epileptic conditions, indicating the adaptable nature of cilia transcripts' oscillation. While limited to a few mouse brain regions, our study provides initial insights into the distinct circadian patterns of cilia transcripts and highlights the need for future research to expand the mapping across wider brain areas to fully understand the role of cilia's spatiotemporal dynamics in brain functions.
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Affiliation(s)
- Kiki Chen
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, 356A Med Surge II, Irvine, CA, 92697-4625, USA
| | - Kousha Changizi Ashtiani
- Departments of Computer Science, School of Information and Computer Sciences, University of California, Irvine, CA, 92697-4625, USA
| | - Roudabeh Vakil Monfared
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, 356A Med Surge II, Irvine, CA, 92697-4625, USA
| | - Pierre Baldi
- Departments of Computer Science, School of Information and Computer Sciences, University of California, Irvine, CA, 92697-4625, USA.
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA, 92697, USA.
| | - Amal Alachkar
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, 356A Med Surge II, Irvine, CA, 92697-4625, USA.
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA, 92697, USA.
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5
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Sirek T, Sirek A, Borawski P, Zmarzły N, Sułkowska J, Król-Jatręga K, Opławski M, Boroń D, Chalcarz M, Ossowski P, Dziobek K, Strojny D, Boroń K, Janiszewska-Bil D, Grabarek BO. miRNAs in Signal Transduction of SMAD Proteins in Breast Cancer. Int J Mol Sci 2024; 25:10088. [PMID: 39337574 PMCID: PMC11432703 DOI: 10.3390/ijms251810088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 09/10/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
The aim of this study was to identify miRNAs that could potentially influence the activity of SMAD proteins involved in TGFβ signal transduction in five types of breast cancer in Polish women. Patients with five breast cancer subtypes were included in the study: luminal A (n = 130), luminal B HER2- (n = 100), luminal B HER2+ (n = 96), non-luminal HER2+ (n = 36), and TNBC (n = 43). During surgery, tumor tissue was removed along with a margin of healthy tissue (control). Molecular analysis included determination of the expression of genes related to SMAD protein signal transduction using mRNA microarrays and reverse transcription quantitative polymerase chain reaction (RT-qPCR). Protein expression was determined using an enzyme-linked immunosorbent assay (ELISA). The miRNA profiling was performed using miRNA microarrays and the miRDB database. SMAD3 and SMAD5 were overexpressed in all types of breast cancer, which could be related to the reduced expression of miR-145, and the findings for SMAD4 and miR-155 were similar. Additionally, the level of SMAD7 was reduced, which may be due to the low activity of miR-15b and miR21b. This study determined the gene expression profiles involved in SMAD protein signal transduction across five different types of breast cancer and identified the miRNAs potentially regulating their activity. Overexpression of SMAD3, SMAD4, and SMAD5 suggests excessive activation of the TGFβ pathway, potentially promoting tumor growth and development. Concurrently, a significant reduction in SMAD7 expression removes inhibitory control in the TGFβ pathway, a phenomenon that is particularly evident in more aggressive breast cancer types.
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Affiliation(s)
- Tomasz Sirek
- Department of Plastic and Reconstructive Surgery, Hospital for Minimally Invasive and Reconstructive Surgery in Bielsko-Biała, 43-316 Bielsko-Biala, Poland
- Department of Medical and Health Sciences, Collegium Medicum, WSB University, 41-300 Dabrowa Górnicza, Poland
| | - Agata Sirek
- Department of Plastic and Reconstructive Surgery, Hospital for Minimally Invasive and Reconstructive Surgery in Bielsko-Biała, 43-316 Bielsko-Biala, Poland
- Department of Medical and Health Sciences, Collegium Medicum, WSB University, 41-300 Dabrowa Górnicza, Poland
| | | | - Nikola Zmarzły
- Department of Medical and Health Sciences, Collegium Medicum, WSB University, 41-300 Dabrowa Górnicza, Poland
| | - Joanna Sułkowska
- Department of Medical and Health Sciences, Collegium Medicum, WSB University, 41-300 Dabrowa Górnicza, Poland
| | - Katarzyna Król-Jatręga
- Department of Plastic and Reconstructive Surgery, Hospital for Minimally Invasive and Reconstructive Surgery in Bielsko-Biała, 43-316 Bielsko-Biala, Poland
- Department of Medical and Health Sciences, Collegium Medicum, WSB University, 41-300 Dabrowa Górnicza, Poland
| | - Marcin Opławski
- Department of Gynecology and Obstetrics with Gynecologic Oncology, Ludwik Rydygier Memorial Specialized Hospital, 31-826 Kraków, Poland
- Department of Gynecology and Obstetrics, Faculty of Medicine and Health Sciences, Andrzej Frycz Modrzewski University in Cracow, 30-705 Kraków, Poland
| | - Dariusz Boroń
- Department of Medical and Health Sciences, Collegium Medicum, WSB University, 41-300 Dabrowa Górnicza, Poland
- Department of Gynecology and Obstetrics with Gynecologic Oncology, Ludwik Rydygier Memorial Specialized Hospital, 31-826 Kraków, Poland
- Institute of Clinical Science, Skłodowska-Curie Medical University, 00-136 Warszawa, Poland
- Department of Gynecology and Obstetrics, TOMMED Specjalisci od Zdrowia, 40-662 Katowice, Poland
| | - Michał Chalcarz
- Department of Medical and Health Sciences, Collegium Medicum, WSB University, 41-300 Dabrowa Górnicza, Poland
- Chalcarz Clinic-Aesthetic Surgery, Aesthetic Medicine, 60-001 Poznan, Poland
- Bieńkowski Medical Center-Plastic Surgery, 85-020 Bydgoszcz, Poland
| | - Piotr Ossowski
- Department of Medical and Health Sciences, Collegium Medicum, WSB University, 41-300 Dabrowa Górnicza, Poland
| | - Konrad Dziobek
- Department of Medical and Health Sciences, Collegium Medicum, WSB University, 41-300 Dabrowa Górnicza, Poland
| | - Damian Strojny
- Department of Medical and Health Sciences, Collegium Medicum, WSB University, 41-300 Dabrowa Górnicza, Poland
- Institute of Health Care, National Academy of Applied Sciences in Przemyśl, 37-700 Przemyśl, Poland
- New Medical Techniques Specjalist Hospital of St. Family in Rudna Mała, 36-054 Rudna Mala, Poland
| | - Kacper Boroń
- Department of Medical and Health Sciences, Collegium Medicum, WSB University, 41-300 Dabrowa Górnicza, Poland
| | - Dominika Janiszewska-Bil
- Department of Medical and Health Sciences, Collegium Medicum, WSB University, 41-300 Dabrowa Górnicza, Poland
| | - Beniamin Oskar Grabarek
- Department of Medical and Health Sciences, Collegium Medicum, WSB University, 41-300 Dabrowa Górnicza, Poland
- Department of Molecular, Biology Gyncentrum Fertility Clinic, 40-055 Katowice, Poland
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6
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Liu X, Wang C, Gai W, Sun Z, Fang L, Hua Z. Critical role of msgA in invasive capacity and intracellular survivability of Salmonella. Appl Environ Microbiol 2024; 90:e0020124. [PMID: 39136487 PMCID: PMC11409701 DOI: 10.1128/aem.00201-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 07/04/2024] [Indexed: 09/19/2024] Open
Abstract
Salmonella enterica serovar Typhimurium, which is a common foodborne pathogen, causes both intestinal and systemic infections in hosts. Salmonella has a complex pathogenic mechanism that involves invasive capacity and intracellular survivability, which hampers research on virulence of Salmonella. The virulence of Salmonella is primarily studied through Salmonella pathogenicity islands (SPIs). However, there are also genes outside these SPIs that significantly impact virulence. Macrophage survival gene msgA is positioned at a region independent of the SPIs and conserved in Salmonella. However, there has been limited research on msgA to date. This study aims to investigate the virulent function of msgA to deepen our understanding of Salmonella virulence. Proteomic and RT-qPCR analyses reveal that MsgA influences multiple metabolic pathways and the expression of SPIs. The depletion of msgA led to the significantly reduced invasive capacity and intracellular survivability, and thus the decreased virulence of Salmonella. In conclusion, our study suggests that MsgA is an important regulator that mainly regulates virulence. Further research into the function of MsgA will enhance the understanding of Salmonella pathogenesis and promote the application of Salmonella for medical treatment. IMPORTANCE Salmonella enterica serovar Typhimurium is a common foodborne pathogen, it has a complex pathogenic mechanism that involves invasive capacity and intracellular survivability. The virulence of Salmonella is primarily studied through its pathogenicity islands. In contrast, virulence genes located outside the Salmonella pathogenicity islands (SPIs) have received less attention. Macrophage survival gene (MsgA) is positioned at a region independent of the SPIs and conserved in Salmonella. Our research indicates that MsgA is a novel global regulator influencing the metabolic pathways and SPIs. Further research into the function of MsgA will enhance the understanding of Salmonella pathogenesis and promote the application of Salmonella for medical treatment.
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Affiliation(s)
- Xinqi Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chengzhi Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing, China
| | - Wenhua Gai
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zhaotong Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Lei Fang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing, China
| | - Zichun Hua
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- Changzhou High-Tech Research Institute of Nanjing University and Jiangsu Target Pharma Laboratories Inc, Changzhou, China
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7
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Kawa AB, Hashimoto JG, Beutler MM, Guizzetti M, Wolf ME. Changes in nucleus accumbens core translatome accompanying incubation of cocaine craving. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.15.613147. [PMID: 39345421 PMCID: PMC11429699 DOI: 10.1101/2024.09.15.613147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
In the 'incubation of cocaine craving' model of relapse, rats exhibit progressive intensification (incubation) of cue-induced craving over several weeks of forced abstinence from cocaine self-administration. The expression of incubated craving depends on plasticity of excitatory synaptic transmission in nucleus accumbens core (NAcC) medium spiny neurons (MSN). Previously, we found that the maintenance of this plasticity and the expression of incubation depends on ongoing protein translation, and the regulation of translation is altered after incubation of cocaine craving. Here we used male and female rats that express Cre recombinase in either dopamine D1 receptor- or adenosine 2a (A2a) receptor-expressing MSN to express a GFP-tagged ribosomal protein in a cell-type specific manner, enabling us to use Translating Ribosome Affinity Purification (TRAP) to isolate actively translating mRNAs from both MSN subtypes for analysis by RNA-seq. We compared rats that self-administered saline or cocaine. Saline rats were assessed on abstinence day (AD) 1, while cocaine rats were assessed on AD1 or AD40-50. For both D1-MSN and A2a-MSN, there were few differentially translated genes between saline and cocaine AD1 groups. In contrast, pronounced differences in the translatome were observed between cocaine rats on AD1 and AD40-50, and this was far more robust in D1-MSN. Notably, all comparisons revealed sex differences in translating mRNAs. Sequencing results were validated by qRT-PCR for several genes of interest. This study, the first to combine TRAP-seq, transgenic rats, and a cocaine self-administration paradigm, identifies translating mRNAs linked to incubation of cocaine craving in D1-MSN and A2a-MSN of the NAcC.
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Affiliation(s)
- Alex B Kawa
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239
| | - Joel G Hashimoto
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239
- VA Portland Health Care System, Portland, OR 97239
| | - Madelyn M Beutler
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239
| | - Marina Guizzetti
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239
- VA Portland Health Care System, Portland, OR 97239
| | - Marina E Wolf
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239
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Jonas D, Tatrai K, Sandor S, Egyed B, Kubinyi E. Dog Domestication Strongly Relied on Translation Regulation According to Differential Gene Expression Analysis. Animals (Basel) 2024; 14:2655. [PMID: 39335245 PMCID: PMC11428534 DOI: 10.3390/ani14182655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/28/2024] [Accepted: 09/07/2024] [Indexed: 09/30/2024] Open
Abstract
Domestication of dogs from their shared ancestors with wolves occurred more than 15,000 years ago and affected many characteristics of the species. We analyzed the blood RNA sequence data of 12 dogs and 11 wolves from Europe and Asia to shed more light on the domestication history of dogs. We implemented a differential gene expression analysis, a weighted gene correlation network analysis, gene ontology and genetic pathway analyses. We found that both the sample origin (Europe or Asia) and the species had a significant effect on the blood gene expression profiles of the animals. We identified 1567 differentially expressed genes between wolves and dogs and found several significantly overrepresented gene ontology terms, such as RNA polymerase II transcription regulatory region sequence-specific DNA binding or translation. We identified 11 significant gene co-expression networks, hosting a total of 4402 genes, related to DNA replication, metabolism of RNA or metabolism of proteins, for example. Our findings suggest that gene expression regulation played a cardinal role in dog domestication. We recommend further diversifying the analyzed dog and wolf populations in the future by including individuals from different dog breeds and geographical origins, in order to enhance the specificity of detecting significant, true positive genes related to domestication as well as to reduce the false positive rate.
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Affiliation(s)
- David Jonas
- Department of Ethology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (K.T.); (E.K.)
- MTA-ELTE Lendület “Momentum” Companion Animal Research Group, 1117 Budapest, Hungary
| | - Kitti Tatrai
- Department of Ethology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (K.T.); (E.K.)
- Department of Genetics, ELTE Eötvös Loránd University, 1117 Budapest, Hungary;
| | - Sara Sandor
- Department of Ethology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (K.T.); (E.K.)
| | - Balazs Egyed
- Department of Genetics, ELTE Eötvös Loránd University, 1117 Budapest, Hungary;
| | - Eniko Kubinyi
- Department of Ethology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (K.T.); (E.K.)
- MTA-ELTE Lendület “Momentum” Companion Animal Research Group, 1117 Budapest, Hungary
- ELTE NAP Canine Brain Research Group, 1117 Budapest, Hungary
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9
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Cavarischia-Rega C, Sharma K, Fitzgerald JC, Macek B. Proteome Dynamics in iPSC-Derived Human Dopaminergic Neurons. Mol Cell Proteomics 2024; 23:100838. [PMID: 39251023 DOI: 10.1016/j.mcpro.2024.100838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 08/18/2024] [Accepted: 08/25/2024] [Indexed: 09/11/2024] Open
Abstract
Dopaminergic neurons participate in fundamental physiological processes and are the cell type primarily affected in Parkinson's disease. Their analysis is challenging due to the intricate nature of their function, involvement in diverse neurological processes, and heterogeneity and localization in deep brain regions. Consequently, most of the research on the protein dynamics of dopaminergic neurons has been performed in animal cells ex vivo. Here we use iPSC-derived human mid-brain-specific dopaminergic neurons to study general features of their proteome biology and provide datasets for protein turnover and dynamics, including a human axonal translatome. We cover the proteome to a depth of 9409 proteins and use dynamic SILAC to measure the half-life of more than 4300 proteins. We report uniform turnover rates of conserved cytosolic protein complexes such as the proteasome and map the variable rates of turnover of the respiratory chain complexes in these cells. We use differential dynamic SILAC labeling in combination with microfluidic devices to analyze local protein synthesis and transport between axons and soma. We report 105 potentially novel axonal markers and detect translocation of 269 proteins between axons and the soma in the time frame of our analysis (120 h). Importantly, we provide evidence for local synthesis of 154 proteins in the axon and their retrograde transport to the soma, among them several proteins involved in RNA editing such as ADAR1 and the RNA helicase DHX30, involved in the assembly of mitochondrial ribosomes. Our study provides a workflow and resource for the future applications of quantitative proteomics in iPSC-derived human neurons.
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Affiliation(s)
- Claudia Cavarischia-Rega
- Quantitative Proteomics, Department of Biology, Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - Karan Sharma
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Julia C Fitzgerald
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.
| | - Boris Macek
- Quantitative Proteomics, Department of Biology, Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany.
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10
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Cumming KT, Reitzner SM, Hanslien M, Skilnand K, Seynnes OR, Horwath O, Psilander N, Sundberg CJ, Raastad T. Muscle memory in humans: evidence for myonuclear permanence and long-term transcriptional regulation after strength training. J Physiol 2024; 602:4171-4193. [PMID: 39159314 DOI: 10.1113/jp285675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 07/17/2024] [Indexed: 08/21/2024] Open
Abstract
The objective of this work was to investigate myonuclear permanence and transcriptional regulation as mechanisms for cellular muscle memory after strength training in humans. Twelve untrained men and women performed 10 weeks of unilateral elbow-flexor strength training followed by 16 weeks of de-training. Thereafter, 10 weeks' re-training was conducted with both arms: the previously trained arm and the contralateral untrained control arm. Muscle biopsies were taken from the trained arm before and after both training periods and from the control arm before and after re-training. Muscle biopsies were analysed for fibre cross-sectional area (fCSA), myonuclei and global transcriptomics (RNA sequencing). During the first training period, myonuclei increased in type 1 (13 ± 17%) and type 2 (33 ± 23%) fibres together with a 30 ± 43% non-significant increase in mixed fibre fCSA (P = 0.069). Following de-training, fCSA decreased in both fibre types, whereas myonuclei were maintained, resulting in 33% higher myonuclear number in previously trained vs. control muscle in type 2 fibres. Furthermore, in the previously trained muscle, three differentially expressed genes (DEGs; EGR1, MYL5 and COL1A1) were observed. Following re-training, the previously trained muscle showed larger type 2 fCSA compared to the control (P = 0.035). However, delta change in type 2 fCSA was not different between muscles. Gene expression was more dramatically changed in the control arm (1338 DEGs) than in the previously trained arm (822 DEGs). The sustained higher number of myonuclei in the previously trained muscle confirms myonuclear accretion and permanence in humans. Nevertheless, because of the unclear effect on the subsequent hypertrophy with re-training, the physiological benefit remains to be determined. KEY POINTS: Muscle memory is a cellular mechanism that describes the capacity of skeletal muscle fibres to respond differently to training stimuli if the stimuli have been previously encountered. This study overcomes past methodological limitations related to the choice of muscles and analytical procedures. We show that myonuclear number is increased after strength training and maintained during de-training. Increased myonuclear number and differentially expressed genes related to muscle performance and development in the previously trained muscle did not translate into a clearly superior responses during re-training. Because of the unclear effect on the subsequent hypertrophy and muscle strength gain with re-training, the physiological benefit remains to be determined.
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Affiliation(s)
- Kristoffer Toldnes Cumming
- Department of Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
- Faculty of Health, Welfare and Organisation, Østfold University College, Fredrikstad, Norway
| | - Stefan Markus Reitzner
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Marit Hanslien
- Department of Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
| | - Kenneth Skilnand
- Department of Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
| | - Olivier R Seynnes
- Department of Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
| | - Oscar Horwath
- Department of Physiology, Nutrition and Biomechanics, Åstrand Laboratory, Swedish School of Sport and Health Sciences, Stockholm, Sweden
| | - Niklas Psilander
- Department of Physiology, Nutrition and Biomechanics, Åstrand Laboratory, Swedish School of Sport and Health Sciences, Stockholm, Sweden
| | - Carl Johan Sundberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Learning, Informatics, Management and Ethics, Karolinska Institutet, Stockholm, Sweden
| | - Truls Raastad
- Department of Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
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11
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Paul I, Roy A, Chakrabarti D, Nandi C, Ray S. Mutations in LIFR rewire the JAK/STAT signaling pathway: A study unveiling mechanistic details of Stüve-Wiedemann syndrome. Comput Biol Med 2024; 179:108797. [PMID: 38968765 DOI: 10.1016/j.compbiomed.2024.108797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/14/2024] [Accepted: 06/19/2024] [Indexed: 07/07/2024]
Abstract
Stüve-Wiedemann syndrome (SWS), a rare autosomal recessive disorder, characterized by diminutive size, curvature of the elongated bones, bent fingers, episodes of heightened body temperature, respiratory distress or periods of breath-holding, and challenges with feeding, especially causes fatality in infants. SWS is an outcome of potential missense mutations in the leukemia inhibitory factor receptor gene reflected as numerous amino acid mutations at protein level. Employing in silico tools and techniques like mutational screening with Pred_MutHTP, I-Mutant2.0, PANTHER.db, PolyPhen, to classify mutations as deleterious/destabilizing, in conjunction with experimental data analysis, P136A and S279P emerged as 'effect'-causing mutations. Pre-existing knowledge suggests, SWS progression is effectuated conformationally altered and dysfunctional LIFR, unable to bind to LIF and further form the LIF/LIFR/gp130 signalling complex. To gain functional insights into the effect of the said mutations on the wild type protein, an all-atom, explicit, solvent molecular dynamics simulation was performed following docking approaches. Consequently, referring to the RMSD, RMSF, protein dynamic network analysis, energy landscape plots and domain motion analysis, it was revealed that unbound LIFR_WT was more prone to LIF binding as usual whereas the mutants exhibited considerable domain closure to inhibit LIF binding. We conducted binding affinity analysis via MM/GBSA and dissociation constant estimation after LIFR-LIF docking and found the WT_complex to be more stable and compact as a whole when compared to the flexible mutant complexes thus being associated with SWS. Our study offers a route for understanding molecular level implications upon LIFR mutations which opens an avenue for therapeutic interventions.
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Affiliation(s)
- Ishani Paul
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Alankar Roy
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | | | - Chandreyee Nandi
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Sujay Ray
- Amity Institute of Biotechnology, Amity University, Kolkata, India.
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12
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Hamilton KR, McGill LS, Campbell CM, Lanzkron SM, Carroll CP, Latremoliere A, Haythornthwaite JA, Korczeniewska OA. Genetic contributions to pain modulation in sickle cell: A focus on single nucleotide polymorphisms. GENE REPORTS 2024; 36:101983. [PMID: 39219841 PMCID: PMC11361162 DOI: 10.1016/j.genrep.2024.101983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Background Despite recent advances in our knowledge of genetic contributions to the highly variable sickle cell disease (SCD) phenotype, our understanding of genetic factors associated with pain sensitivity in SCD remains limited. Previous studies investigated specific variants in single candidate genes and their association with SCD pain variability. The primary aim of the current study was to expand the genes and polymorphisms tested to discover new risk genes (polymorphisms) associated with central sensitization for individuals with SCD. Methods Adults with sickle cell disease (n = 59, Mage = 36.8 ± 11.5, 65.8 % female) underwent quantitative sensory testing to examine central sensitization and general pain sensitivity. Participants reported average crisis and non-crisis pain intensities weekly using a 0-100 scale, and provided salivary samples for genotyping. The Hardy-Weinberg equilibrium was verified for controls, and allele distributions were tested with chi-square and odds ratio tests. The Benjamini-Hochberg procedure was used to control for false discovery rate. Regression analyses and Wilcoxon tests were used to test associations for normally distributed and skewed data, respectively. Results Central sensitization and general pain sensitivity were not associated with hemoglobin genotype (Ps > 0.05). Of 4145 SNPs tested, following false discovery rate adjustments, 11 SNPs (rs11575839, rs12185625, rs12289836, rs1493383, rs2233976, rs3131787, rs3739693, rs4292454, rs4364, rs4678, rs6773307) were significantly associated with central sensitization, and one SNP (rs7778077) was significantly associated with average weekly non-crisis pain. No SNPs were associated with general pain sensitivity. Conclusions These findings provide insights into genetic variants association with average non-crisis pain and central sensitization for individuals with SCD, and may provide support for genetic predictors of heightened pain experience within SCD.
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Affiliation(s)
- Katrina R. Hamilton
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Lakeya S. McGill
- Department of Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Claudia M. Campbell
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Sophie M. Lanzkron
- Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - C. Patrick Carroll
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Alban Latremoliere
- Department of Neurosurgery, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Jennifer A. Haythornthwaite
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Olga A. Korczeniewska
- Center for Orofacial Pain and Temporomandibular Disorders, Department of Diagnostic Sciences, Rutgers School of Dental Medicine, Newark, NJ, USA
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13
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Kırbaş OK, Bozkurt BT, Yıldırım MR, Taşlı PN, Abdik H, Şahin F, Avşar Abdik E. A Perspective on the Characterization of Early Neural Progenitor Cell-Derived Extracellular Vesicles for Targeted Delivery to Neuroblastoma Cells. Neurochem Res 2024; 49:2364-2378. [PMID: 38837091 PMCID: PMC11310242 DOI: 10.1007/s11064-024-04165-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 04/24/2024] [Accepted: 05/22/2024] [Indexed: 06/06/2024]
Abstract
As an element of the cellular signaling systems, extracellular vesicles (EVs) exhibit many desirable traits for usage as targeted delivery vehicles. When administered, EVs cause little to no toxic or immune response, stay in circulation for longer periods compared to synthetic carriers, preferentially accumulate in tissues that are the same or similar to their cell-of-origin and can pass through the blood-brain barrier. Combined, these traits make neural EVs a particularly promising tool for delivering drugs to the brain. This study aims to combine tissue and EVs engineering to prepare neural differentiated cells derived EVs that exhibit neural properties, to develop an effective, tissue-homing drug and gene delivery platform for the brain. Early neural differentiated cell-derived EVs were produced with neural characteristics from neural differentiated human neonatal dermal fibroblasts. The EVs carried key neural proteins such as Nestin, Sox2 and Doublecortin. The cellular uptake of early neural differentiated cell-derived EVs was higher compared to non-neural EVs during in vitro uptake assays on neuroblastoma cells. Moreover, eND-EVs were significantly decreased the viability of neuroblastoma cells. In conclusion, this study revealed that early neural differentiated cell-derived EVs have potential as a promising drug carrier for the treatment of various neural disorders.
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Affiliation(s)
- Oğuz Kaan Kırbaş
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Yeditepe University, Istanbul, 34755, Turkey
| | - Batuhan Turhan Bozkurt
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Yeditepe University, Istanbul, 34755, Turkey
| | - Melis Rahime Yıldırım
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Yeditepe University, Istanbul, 34755, Turkey
| | - Pakize Neslihan Taşlı
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Yeditepe University, Istanbul, 34755, Turkey
| | - Hüseyin Abdik
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, İstanbul Sabahattin Zaim University, Istanbul, 34303, Turkey
| | - Fikrettin Şahin
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Yeditepe University, Istanbul, 34755, Turkey
| | - Ezgi Avşar Abdik
- Department of Genomics, Faculty of Aquatic Sciences, Istanbul University, Istanbul, 34134, Turkey.
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14
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Tuomivaara ST, Teo CF, Jan YN, Wiita AP, Jan LY. SLAPSHOT reveals rapid dynamics of extracellularly exposed proteome in response to calcium-activated plasma membrane phospholipid scrambling. Commun Biol 2024; 7:1060. [PMID: 39210032 PMCID: PMC11362511 DOI: 10.1038/s42003-024-06729-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
To facilitate our understanding of proteome dynamics during signaling events, robust workflows affording fast time resolution without confounding factors are essential. We present Surface-exposed protein Labeling using PeroxidaSe, H2O2, and Tyramide-derivative (SLAPSHOT) to label extracellularly exposed proteins in a rapid, specific, and sensitive manner. Simple and flexible SLAPSHOT utilizes recombinant soluble APEX2 protein applied to cells, thus circumventing the engineering of tools and cells, biological perturbations, and labeling biases. We applied SLAPSHOT and quantitative proteomics to examine the TMEM16F-dependent plasma membrane remodeling in WT and TMEM16F KO cells. Time-course data ranging from 1 to 30 min of calcium stimulation revealed co-regulation of known protein families, including the integrin and ICAM families, and identified proteins known to reside in intracellular organelles as occupants of the freshly deposited extracellularly exposed membrane. Our data provide the first accounts of the immediate consequences of calcium signaling on the extracellularly exposed proteome.
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Affiliation(s)
- Sami T Tuomivaara
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, CA, USA
| | - Chin Fen Teo
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
- Department of Physiology, University of California, San Francisco, CA, USA
| | - Yuh Nung Jan
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
- Department of Physiology, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA.
| | - Lily Y Jan
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA.
- Department of Physiology, University of California, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
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15
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Fluke KA, Fuchs RT, Tsai YL, Talbott V, Elkins L, Febvre HP, Dai N, Wolf EJ, Burkhart BW, Schiltz J, Brett Robb G, Corrêa IR, Santangelo TJ. The extensive m 5C epitranscriptome of Thermococcus kodakarensis is generated by a suite of RNA methyltransferases that support thermophily. Nat Commun 2024; 15:7272. [PMID: 39179532 PMCID: PMC11344067 DOI: 10.1038/s41467-024-51410-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 08/06/2024] [Indexed: 08/26/2024] Open
Abstract
RNAs are often modified to invoke new activities. While many modifications are limited in frequency, restricted to non-coding RNAs, or present only in select organisms, 5-methylcytidine (m5C) is abundant across diverse RNAs and fitness-relevant across Domains of life, but the synthesis and impacts of m5C have yet to be fully investigated. Here, we map m5C in the model hyperthermophile, Thermococcus kodakarensis. We demonstrate that m5C is ~25x more abundant in T. kodakarensis than human cells, and the m5C epitranscriptome includes ~10% of unique transcripts. T. kodakarensis rRNAs harbor tenfold more m5C compared to Eukarya or Bacteria. We identify at least five RNA m5C methyltransferases (R5CMTs), and strains deleted for individual R5CMTs lack site-specific m5C modifications that limit hyperthermophilic growth. We show that m5C is likely generated through partial redundancy in target sites among R5CMTs. The complexity of the m5C epitranscriptome in T. kodakarensis argues that m5C supports life in the extremes.
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Affiliation(s)
- Kristin A Fluke
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Ryan T Fuchs
- New England Biolabs Inc., Beverly, MA, 01915, USA
| | | | - Victoria Talbott
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Liam Elkins
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Hallie P Febvre
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Nan Dai
- New England Biolabs Inc., Beverly, MA, 01915, USA
| | - Eric J Wolf
- New England Biolabs Inc., Beverly, MA, 01915, USA
| | - Brett W Burkhart
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jackson Schiltz
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - G Brett Robb
- New England Biolabs Inc., Beverly, MA, 01915, USA
| | | | - Thomas J Santangelo
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA.
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA.
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16
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Saraji A, Wulf K, Stegmann-Frehse J, Kang D, Offermann A, Jonigk D, Kuehnel MP, Kirfel J, Perner S, Sailer VW. Comprehensive transcriptomic analysis of prostate cancer lung metastases. PLoS One 2024; 19:e0306525. [PMID: 39146303 PMCID: PMC11326543 DOI: 10.1371/journal.pone.0306525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/19/2024] [Indexed: 08/17/2024] Open
Abstract
Metastatic prostate cancer (mPCa) is a widespread disease with high mortality. Unraveling molecular mechanisms of disease progression is of utmost importance. The microenvironment in visceral organs and the skeletal system is of particular interest as a harbinger of metastatic spread. Therefore, we performed a comprehensive transcriptomic analysis of prostate cancer lung metastases with a special focus on differentially expressed genes attributable to the microenvironment. Digital gene expression analysis using the NanoString nCounter analysis system was performed on formalin-fixed, paraffin-embedded (FFPE) tissue from prostate cancer (PCa) lung metastases (n = 24). Data were compared to gene expression data from primary PCa and PCa bone metastases. Bioinformatic analysis was performed using several publicly available tools. In comparison to prostate cancer bone metastases, 209 genes were significantly upregulated, and 100 genes were significantly downregulated in prostate cancer lung metastases. Among the up-regulated genes, the top 10 genes with the most significant P-value were HLA-DPB1, PTPRC, ITGB7, C3, CCL21, CCL5, ITGAM, SERPINA1, MFAP4, ARAP2 and among the down-regulated genes, the top 10 genes with the most significant P-value were FOXC2, TWIST1, CDK14, CHAD, IBSP, EPN3, VIT, HAPLN1, SLC44A4, TBX1. In PCa lung metastases genes associated with immunogenic responses were upregulated while genes associated with epithelial-mesenchymal transition were down-regulated. We also showed that CXCR3/CXCL10 axis plays a significant role in prostate cancer lung metastases in comparison to bone metastases. In this study, we comprehensively explored transcriptomic alterations in PCa lung metastases in comparison to primary PCa and PCa bone metastases. In PCa lung metastases genes associated with immunogenic responses are upregulated while genes associated with epithelial-mesenchymal transition are down-regulated. This points to a more immunogenic phenotype of PCa lung metastases thus potentially making patients more susceptible to immunotherapeutic approaches.
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Affiliation(s)
- Alireza Saraji
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Katharina Wulf
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Janine Stegmann-Frehse
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Duan Kang
- Guangdong Second Provincial General Hospital, Guangzhou, P. R. China
| | - Anne Offermann
- Institute of Pathology, University of Muenster, Muenster, Germany
| | - Danny Jonigk
- Institute of Pathology, RWTH Aachen, Aachen, Germany
| | - Mark Philipp Kuehnel
- Institute of Pathology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Center for Lung Research, Hannover, Germany
| | - Jutta Kirfel
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Sven Perner
- Institute for Hematopathology, Hamburg, Germany
| | - Verena Wilbeth Sailer
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
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17
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Saied-Santiago K, Baxter M, Mathiaparanam J, Granato M. Serotonin neuromodulation directs optic nerve regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.12.607648. [PMID: 39185204 PMCID: PMC11343150 DOI: 10.1101/2024.08.12.607648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Optic nerve (ON) regeneration in mammalian systems is limited by an overshadowing dominance of inhibitory factors. This has severely hampered the identification of pro- regenerative pathways. Here, we take advantage of the regenerative capacity of larval zebrafish to identify pathways that promote ON regeneration. From a small molecule screen, we identified modulators of serotonin (5-HT) signaling that inhibit ON regeneration. We find several serotonin type-1 receptor genes are expressed in RGC neurons during regeneration and that inhibiting 5- HT1 receptors or components of the 5-HT pathway selectively impedes ON regeneration. We show that 5-HT1 receptor signaling is dispensable during ON development yet is critical for regenerating axons to emerge from the injury site. Blocking 5-HT receptors once ON axons have crossed the chiasm does not inhibit regeneration, suggesting a selective role for 5-HT receptor signaling early during ON regeneration. Finally, we show that agonist-mediated activation of 5-HT1 receptors leads to enhanced and ectopic axonal regrowth. Combined, our results provide evidence for mechanisms through which serotonin-dependent neuromodulation directs ON regeneration in vivo. Summary Statement 5-HT1 receptors selectively promote early optic nerve regrowth in zebrafish but are dispensable during development. Serotonin receptor-dependent modulation instructs regenerating optic nerve axons toward the brain in vivo.
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18
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Rybiczka-Tešulov M, Garritsen O, Venø MT, Wieg L, Dijk RV, Rahimi K, Gomes-Duarte A, Wit MD, van de Haar LL, Michels L, van Kronenburg NCH, van der Meer C, Kjems J, Vangoor VR, Pasterkamp RJ. Circular RNAs regulate neuron size and migration of midbrain dopamine neurons during development. Nat Commun 2024; 15:6773. [PMID: 39117691 PMCID: PMC11310423 DOI: 10.1038/s41467-024-51041-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
Midbrain dopamine (mDA) neurons play an essential role in cognitive and motor behaviours and are linked to different brain disorders. However, the molecular mechanisms underlying their development, and in particular the role of non-coding RNAs (ncRNAs), remain incompletely understood. Here, we establish the transcriptomic landscape and alternative splicing patterns of circular RNAs (circRNAs) at key developmental timepoints in mouse mDA neurons in vivo using fluorescence-activated cell sorting followed by short- and long-read RNA sequencing. In situ hybridisation shows expression of several circRNAs during early mDA neuron development and post-transcriptional silencing unveils roles for different circRNAs in regulating mDA neuron morphology. Finally, in utero electroporation and time-lapse imaging implicate circRmst, a circRNA with widespread morphological effects, in the migration of developing mDA neurons in vivo. Together, these data for the first time suggest a functional role for circRNAs in developing mDA neurons and characterise poorly defined aspects of mDA neuron development.
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Affiliation(s)
- Mateja Rybiczka-Tešulov
- Department of Translational Neuroscience, UMC Utrecht Brain Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Oxana Garritsen
- Department of Translational Neuroscience, UMC Utrecht Brain Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Morten T Venø
- Department of Molecular Biology and Genetics, Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus C, Denmark
- Omiics ApS, Aarhus N, Denmark
| | - Laura Wieg
- Department of Translational Neuroscience, UMC Utrecht Brain Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Roland van Dijk
- Department of Translational Neuroscience, UMC Utrecht Brain Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- VectorY Therapeutics, Matrix Innovation Center VI, Amsterdam, The Netherlands
| | - Karim Rahimi
- Department of Molecular Biology and Genetics, Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus C, Denmark
- Department of Genetics, Blavatnik Institute, Harvard Medical School, MA, Boston, USA
| | - Andreia Gomes-Duarte
- Department of Translational Neuroscience, UMC Utrecht Brain Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- VectorY Therapeutics, Matrix Innovation Center VI, Amsterdam, The Netherlands
| | - Marina de Wit
- Department of Translational Neuroscience, UMC Utrecht Brain Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Lieke L van de Haar
- Department of Translational Neuroscience, UMC Utrecht Brain Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany
| | - Lars Michels
- Department of Translational Neuroscience, UMC Utrecht Brain Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- VectorY Therapeutics, Matrix Innovation Center VI, Amsterdam, The Netherlands
| | - Nicky C H van Kronenburg
- Department of Translational Neuroscience, UMC Utrecht Brain Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Christiaan van der Meer
- Department of Translational Neuroscience, UMC Utrecht Brain Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics, Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus C, Denmark
| | - Vamshidhar R Vangoor
- Department of Translational Neuroscience, UMC Utrecht Brain Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
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19
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Chatterjee B, Thakur SS. miRNA-protein-metabolite interaction network reveals the regulatory network and players of pregnancy regulation in dairy cows. Front Cell Dev Biol 2024; 12:1377172. [PMID: 39156977 PMCID: PMC11329941 DOI: 10.3389/fcell.2024.1377172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 07/05/2024] [Indexed: 08/20/2024] Open
Abstract
Pregnancy is a complex process involving complex molecular interaction networks, such as between miRNA-protein, protein-protein, metabolite-metabolite, and protein-metabolite interactions. Advances in technology have led to the identification of many pregnancy-associated microRNA (miRNA), protein, and metabolite fingerprints in dairy cows. An array of miRNA, protein, and metabolite fingerprints produced during the early pregnancy of dairy cows were described. We have found the in silico interaction networks between miRNA-protein, protein-protein, metabolite-metabolite, and protein-metabolite. We have manually constructed miRNA-protein-metabolite interaction networks such as bta-miR-423-3p-IGFBP2-PGF2α interactomes. This interactome is obtained by manually combining the interaction network formed between bta-miR-423-3p-IGFBP2 and the interaction network between IGFBP2-PGF2α with IGFBP2 as a common interactor with bta-miR-423-3p and PGF2α with the provided sources of evidence. The interaction between bta-miR-423-3p and IGFBP2 has many sources of evidence including a high miRanda score of 169, minimum free energy (MFE) score of -25.14, binding probability (p) of 1, and energy of -25.5. The interaction between IGFBP2 and PGF2α occurs at high confidence scores (≥0.7 or 70%). Interestingly, PGF2α is also found to interact with different metabolites, such as PGF2α-PGD2, PGF2α-thromboxane B2, PGF2α-PGE2, and PGF2α-6-keto-PGF1α at high confidence scores (≥0.7 or 70%). Furthermore, the interactions between C3-PGE2, C3-PGD2, PGE2-PGD2, PGD2-thromboxane B2, PGE2-thromboxane B2, 6-keto-PGF1α-thromboxane B2, and PGE2-6-keto-PGF1α were also obtained at high confidence scores (≥0.7 or 70%). Therefore, we propose that miRNA-protein-metabolite interactomes involving miRNA, protein, and metabolite fingerprints of early pregnancy of dairy cows such as bta-miR-423-3p, IGFBP2, PGF2α, PGD2, C3, PGE2, 6-keto-PGF1 alpha, and thromboxane B2 may form the key regulatory networks and players of pregnancy regulation in dairy cows. This is the first study involving miRNA-protein-metabolite interactomes obtained in the early pregnancy stage of dairy cows.
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Hollinshead FK, Hanlon DW, Hou W, Tasma Z, Damani T, Bouma GJ, Murtazina DA, Chamley L. Use of equine embryo -derived mesenchymal stromal cells and their extracellular vesicles as a treatment for persistent breeding-induced endometritis in susceptible mares. J Equine Vet Sci 2024; 139:105079. [PMID: 38718968 DOI: 10.1016/j.jevs.2024.105079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/22/2024] [Accepted: 04/29/2024] [Indexed: 06/06/2024]
Abstract
Persistent breeding induced endometritis (PBIE) is a significant cause of infertility in mares. The development of a safe, universal, readily available therapeutic to manage PBIE and facilitate an optimal uterine environment for embryo development may improve pregnancy rates in susceptible mares. Mesenchymal stromal cells (MSCs) are being used increasingly as a therapeutic mediator for inflammatory conditions such as endometritis, and early gestational tissue provides a unique source of multipotent stem cells for creating MSCs. Extracellular vesicles (EVs) are mediators of cell communication produced by many different cell types. This study utilized embryo-derived mesenchymal stromal cells (EDMSCs) and their EVs as a potential therapeutic modality for PBIE in two groups: a) PBIE-susceptible mares challenged with pooled dead sperm (n=5); and b) client-owned mares diagnosed as susceptible to PBIE (n=37 mares and 40 estrous cycles). Mares pre-treated with intrauterine EDMSCs or their EVs resulted in a significant reduction in the accumulation of intrauterine fluid post-breeding. Nine of 19 (47 %) mares treated with EDMSCs prior to natural breeding and 13 of 20 (65 %) mares treated with EDMSC derived EVs were pregnant after the first cycle and 12 of 18 (67 %) mares treated with EDMSCs, and 15 of 19 (79 %) mares treated with EVs conceived by the end of the breeding season. These preliminary clinical studies are the first reports of the use of EDMSCs or their EVs as a potential intrauterine therapy for the management of PBIE susceptible mares.
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Affiliation(s)
- F K Hollinshead
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, 300 West Drake Road, Fort Collins CO 80521, USA.
| | - D W Hanlon
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, 300 West Drake Road, Fort Collins CO 80521, USA
| | - W Hou
- Department of Obstetrics and Gynaecology, Hub for Extracellular Vesicle Investigations, University of Auckland, 85 Park Rd, Grafton, 1010 New Zealand; Hub for Extracellular Vesicle Investigations, University of Auckland, 85 Park Rd, Grafton, 1010, New Zealand
| | - Z Tasma
- Department of Obstetrics and Gynaecology, Hub for Extracellular Vesicle Investigations, University of Auckland, 85 Park Rd, Grafton, 1010 New Zealand; Hub for Extracellular Vesicle Investigations, University of Auckland, 85 Park Rd, Grafton, 1010, New Zealand
| | - T Damani
- Department of Obstetrics and Gynaecology, Hub for Extracellular Vesicle Investigations, University of Auckland, 85 Park Rd, Grafton, 1010 New Zealand; Hub for Extracellular Vesicle Investigations, University of Auckland, 85 Park Rd, Grafton, 1010, New Zealand
| | - G J Bouma
- Department of Biomedical Sciences, Homer Stryker MD School of Medicine, Western Michigan University, 300 Portage Street, Kalamazoo, MI, 49007, USA
| | - D A Murtazina
- Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, 1350 Centre Avenue, Fort Collins, 80521, USA
| | - L Chamley
- Department of Obstetrics and Gynaecology, Hub for Extracellular Vesicle Investigations, University of Auckland, 85 Park Rd, Grafton, 1010 New Zealand; Hub for Extracellular Vesicle Investigations, University of Auckland, 85 Park Rd, Grafton, 1010, New Zealand
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21
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Liu Y, Zhang F, Hawkins JL, Elder JR, Baranzoni GM, Huang Z, Fratamico PM, Parveen S. Comparative Gene Expression Analysis of Salmonella Typhimurium DT104 in Ground Chicken Extract and Brain Heart Infusion Broth. Microorganisms 2024; 12:1461. [PMID: 39065229 PMCID: PMC11279075 DOI: 10.3390/microorganisms12071461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Salmonella enterica Typhimurium DT104 (S. Typhimurium DT104) is an important foodborne pathogen that is associated with poultry and poultry products. Currently, there is very little information on the underlying molecular mechanisms that allow DT104 to survive and propagate in poultry meat and the poultry processing environment. The current study assessed the global gene expression of DT104 in ground chicken extract (GCE) compared to brain heart infusion (BHI) medium using RNA-Seq technology. DT104 was grown to the early stationary phase (ESP), inoculated into GCE or BHI, and then re-grown to the log phase before RNA was extracted and transcripts were quantified by RNA-Seq. Gene expression for DT104 grown in GCE was then compared to that of DT104 grown in BHI for samples grown to the ESP. Growth in GCE resulted in the up-regulated expression of genes related to translation, carnitine metabolism (23-283-fold change), and cobalamin (vitamin B12) biosynthesis (14-fold change). In particular, the presence of carnitine in chicken meat, and thus, in GCE, which lacks carbohydrates, may allow Salmonella to utilize this compound as a carbon and nitrogen source. This study demonstrates that RNA-Seq data can provide a comprehensive analysis of DT104 gene expression in a food model for poultry products. This study also provides additional evidence for the importance of metabolic adaptation in the ability of S. enterica to successfully adapt to and occupy niches outside of its host and provides potential targets that could be used to develop intervention strategies to control Salmonella in poultry.
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Affiliation(s)
- Yanhong Liu
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA (G.M.B.)
| | - Fangyuan Zhang
- Department of Chemical and Biological Engineering, Villanova University, Villanova, PA 19085, USA
| | - Jabari L. Hawkins
- Food and Agricultural Sciences Graduate Program, Food and Resource Sciences, U.S. Department of Agriculture, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
| | - Jake R. Elder
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA (G.M.B.)
| | - Gian Marco Baranzoni
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA (G.M.B.)
| | - Zuyi Huang
- Department of Chemical and Biological Engineering, Villanova University, Villanova, PA 19085, USA
| | - Pina M. Fratamico
- Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA (G.M.B.)
| | - Salina Parveen
- Food and Agricultural Sciences Graduate Program, Food and Resource Sciences, U.S. Department of Agriculture, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
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22
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Horníková M, Lanier HC, Marková S, Escalante MA, Searle JB, Kotlík P. Genetic admixture drives climate adaptation in the bank vole. Commun Biol 2024; 7:863. [PMID: 39009753 PMCID: PMC11251159 DOI: 10.1038/s42003-024-06549-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
Genetic admixture introduces new variants at relatively high frequencies, potentially aiding rapid responses to environmental changes. Here, we evaluate its role in adaptive variation related to climatic conditions in bank voles (Clethrionomys glareolus) in Britain, using whole-genome data. Our results reveal loci showing excess ancestry from one of the two postglacial colonist populations inconsistent with overall admixture patterns. Notably, loci associated with climate adaptation exhibit disproportionate amounts of excess ancestry, highlighting the impact of admixture between colonist populations on local adaptation. The results suggest strong and localized selection on climate-adaptive loci, as indicated by steep clines and/or shifted cline centres, during population replacement. A subset, including a haemoglobin gene, is associated with oxidative stress responses, underscoring a role of oxidative stress in local adaptation. Our study highlights the important contribution of admixture during secondary contact between populations from distinct climatic refugia enriching adaptive diversity. Understanding these dynamics is crucial for predicting future adaptive capacity to anthropogenic climate change.
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Affiliation(s)
- Michaela Horníková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Hayley C Lanier
- Department of Biology, Program in Ecology & Evolutionary Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Museum, University of Oklahoma, Norman, OK, USA
| | - Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic.
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23
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Kravitz A, Liao M, Morota G, Tyler R, Cockrum R, Manohar BM, Ronald BSM, Collins MT, Sriranganathan N. Retrospective Single Nucleotide Polymorphism Analysis of Host Resistance and Susceptibility to Ovine Johne's Disease Using Restored FFPE DNA. Int J Mol Sci 2024; 25:7748. [PMID: 39062990 PMCID: PMC11276633 DOI: 10.3390/ijms25147748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024] Open
Abstract
Johne's disease (JD), also known as paratuberculosis, is a chronic, untreatable gastroenteritis of ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP) infection. Evidence for host genetic resistance to disease progression exists, although it is limited due to the extended incubation period (years) and diagnostic challenges. To overcome this, previously restored formalin-fixed paraffin embedded tissue (FFPE) DNA from archived FFPE tissue cassettes was utilized for a novel retrospective case-control genome-wide association study (GWAS) on ovine JD. Samples from known MAP-infected flocks with ante- and postmortem diagnostic data were used. Cases (N = 9) had evidence of tissue infection, compared to controls (N = 25) without evidence of tissue infection despite positive antemortem diagnostics. A genome-wide efficient mixed model analysis (GEMMA) to conduct a GWAS using restored FFPE DNA SNP results from the Illumina Ovine SNP50 Bead Chip, identified 10 SNPs reaching genome-wide significance of p < 1 × 10-6 on chromosomes 1, 3, 4, 24, and 26. Pathway analysis using PANTHER and the Kyoto Encyclopedia of Genes and Genomes (KEGG) was completed on 45 genes found within 1 Mb of significant SNPs. Our work provides a framework for the novel use of archived FFPE tissues for animal genetic studies in complex diseases and further evidence for a genetic association in JD.
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Affiliation(s)
- Amanda Kravitz
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Mingsi Liao
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Ron Tyler
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Rebecca Cockrum
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - B. Murali Manohar
- Department of Veterinary Pathology, Tamilnadu Veterinary and Animal Sciences University, Madhavaram Milk Colony, Chennai 600051, Tamil Nadu India, India
| | - B. Samuel Masilamoni Ronald
- Department of Veterinary Pathology, Tamilnadu Veterinary and Animal Sciences University, Madhavaram Milk Colony, Chennai 600051, Tamil Nadu India, India
| | - Michael T. Collins
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nammalwar Sriranganathan
- Center for One Health Research, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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24
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Viengkhou B, Hayashida E, McGlasson S, Emelianova K, Forbes D, Wiseman S, Wardlaw J, Verdillo R, Irani SR, Duffy D, Piehl F, Loo L, Pagenstecher A, Neely GG, Crow YJ, Campbell IL, Hunt DPJ, Hofer MJ. The brain microvasculature is a primary mediator of interferon-α neurotoxicity in human cerebral interferonopathies. Immunity 2024; 57:1696-1709.e10. [PMID: 38878770 PMCID: PMC11250091 DOI: 10.1016/j.immuni.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 01/10/2024] [Accepted: 05/17/2024] [Indexed: 07/12/2024]
Abstract
Aicardi-Goutières syndrome (AGS) is an autoinflammatory disease characterized by aberrant interferon (IFN)-α production. The major cause of morbidity in AGS is brain disease, yet the primary source and target of neurotoxic IFN-α remain unclear. Here, we demonstrated that the brain was the primary source of neurotoxic IFN-α in AGS and confirmed the neurotoxicity of intracerebral IFN-α using astrocyte-driven Ifna1 misexpression in mice. Using single-cell RNA sequencing, we demonstrated that intracerebral IFN-α-activated receptor (IFNAR) signaling within cerebral endothelial cells caused a distinctive cerebral small vessel disease similar to that observed in individuals with AGS. Magnetic resonance imaging (MRI) and single-molecule ELISA revealed that central and not peripheral IFN-α was the primary determinant of microvascular disease in humans. Ablation of endothelial Ifnar1 in mice rescued microvascular disease, stopped the development of diffuse brain disease, and prolonged lifespan. These results identify the cerebral microvasculature as a primary mediator of IFN-α neurotoxicity in AGS, representing an accessible target for therapeutic intervention.
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Affiliation(s)
- Barney Viengkhou
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Emina Hayashida
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Sarah McGlasson
- UK Dementia Research Institute at University of Edinburgh, Edinburgh EH16 4SB, UK; Centre for Clinical Brain Sciences at University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Katie Emelianova
- UK Dementia Research Institute at University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Deborah Forbes
- UK Dementia Research Institute at University of Edinburgh, Edinburgh EH16 4SB, UK; Centre for Clinical Brain Sciences at University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Stewart Wiseman
- Centre for Clinical Brain Sciences at University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Joanna Wardlaw
- UK Dementia Research Institute at University of Edinburgh, Edinburgh EH16 4SB, UK; Centre for Clinical Brain Sciences at University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Rovin Verdillo
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Sarosh R Irani
- Oxford Autoimmune Neurology Group, University of Oxford, Oxford, UK
| | - Darragh Duffy
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Fredrik Piehl
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Lipin Loo
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Axel Pagenstecher
- Department of Neuropathology, University of Marburg, Baldingerstrasse, 35043 Marburg, Germany
| | - G Greg Neely
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Yanick J Crow
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK; Laboratory of Neurogenetics and Neuroinflammation, Institut Imagine, Université de Paris, Paris, France
| | - Iain L Campbell
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - David P J Hunt
- UK Dementia Research Institute at University of Edinburgh, Edinburgh EH16 4SB, UK; Centre for Clinical Brain Sciences at University of Edinburgh, Edinburgh EH16 4SB, UK.
| | - Markus J Hofer
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia.
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25
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Irani Shemirani M. Transcriptional markers classifying Escherichia coli and Staphylococcus aureus induced sepsis in adults: A data-driven approach. PLoS One 2024; 19:e0305920. [PMID: 38968271 PMCID: PMC11226107 DOI: 10.1371/journal.pone.0305920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 06/06/2024] [Indexed: 07/07/2024] Open
Abstract
Sepsis is a life-threatening condition mainly caused by gram-negative and gram-positive bacteria. Understanding the type of causative agent in the early stages is essential for precise antibiotic therapy. This study sought to identify a host gene set capable of distinguishing between sepsis induced by gram-negative bacteria; Escherichia coli and gram-positive bacteria; Staphylococcus aureus in community-onset adult patients. In the present study, microarray expression information was used to apply the Least Absolute Shrinkage and Selection Operator (Lasso) technique to select the predictive gene set for classifying sepsis induced by E. coli or S. aureus pathogens. We identified 25 predictive genes, including LILRA5 and TNFAIP6, which had previously been associated with sepsis in other research. Using these genes, we trained a logistic regression classifier to distinguish whether a sample contains an E. coli or S. aureus infection or belongs to a healthy control group, and subsequently assessed its performance. The classifier achieved an Area Under the Curve (AUC) of 0.96 for E. coli and 0.98 for S. aureus-induced sepsis, and perfect discrimination (AUC of 1) for healthy controls from the other conditions in a 10-fold cross-validation. The genes demonstrated an AUC of 0.75 in distinguishing between sepsis patients with E. coli and S. aureus pathogens. These findings were further confirmed in two distinct independent validation datasets which gave high prediction AUC ranging from 0.72-0.87 and 0.62 in distinguishing three groups of participants and two groups of patients respectively. These genes were significantly enriched in the immune system, cytokine signaling in immune system, innate immune system, and interferon signaling. Transcriptional patterns in blood can differentiate patients with E. coli-induced sepsis from those with S. aureus-induced sepsis. These diagnostic markers, upon validation in larger trials, may serve as a foundation for a reliable differential diagnostics assay.
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Affiliation(s)
- Mahnaz Irani Shemirani
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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26
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Rappold R, Kalogeropoulos K, Auf dem Keller U, Vogel V, Slack E. Salmonella-driven intestinal edema in mice is characterized by tensed fibronectin fibers. FEBS J 2024; 291:3104-3127. [PMID: 38487972 DOI: 10.1111/febs.17120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/04/2023] [Accepted: 03/05/2024] [Indexed: 07/19/2024]
Abstract
Intestinal edema is a common manifestation of numerous gastrointestinal diseases and is characterized by the accumulation of fluid in the interstitial space of the intestinal wall. Technical advances in laser capture microdissection and low-biomass proteomics now allow us to specifically characterize the intestinal edema proteome. Using advanced proteomics, we identify peptides derived from antimicrobial factors with high signal intensity, but also highlight major contributions from the blood clotting system, extracellular matrix (ECM) and protease-protease inhibitor networks. The ECM is a complex fibrillar network of macromolecules that provides structural and mechanical support to the intestinal tissue. One abundant component of the ECM observed in Salmonella-driven intestinal edema is the glycoprotein fibronectin, recognized for its structure-function interplay regulated by mechanical forces. Using mechanosensitive staining of fibronectin fibers reveals that they are tensed in the edema, despite the high abundance of proteases able to cleave fibronectin. In contrast, fibronectin fibers increasingly relax in other cecal tissue areas as the infection progresses. Co-staining for fibrin(ogen) indicates the formation of a provisional matrix in the edema, similar to what is observed in response to skin injury, while collagen staining reveals a sparse and disrupted collagen fiber network. These observations plus the absence of low tensional fibronectin fibers and the additional finding of a high number of protease inhibitors in the edema proteome could indicate a critical role of stretched fibronectin fibers in maintaining tissue integrity in the severely inflamed cecum. Understanding these processes may also provide valuable functional diagnostic markers of intestinal disease progression in the future.
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Affiliation(s)
- Ronja Rappold
- Institute of Translational Medicine, ETH Zurich, Switzerland
- Institute of Food, Nutrition and Health, ETH Zurich, Switzerland
| | | | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Viola Vogel
- Institute of Translational Medicine, ETH Zurich, Switzerland
- Botnar Research Center for Child Health, Basel, Switzerland
| | - Emma Slack
- Institute of Food, Nutrition and Health, ETH Zurich, Switzerland
- Botnar Research Center for Child Health, Basel, Switzerland
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27
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Yang M, Shulkin N, Gonzalez E, Castillo J, Yan C, Zhang K, Arvanitis L, Borok Z, Wallace WD, Raz D, Torres ETR, Marconett CN. Cell of origin alters myeloid-mediated immunosuppression in lung adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599651. [PMID: 38948812 PMCID: PMC11213232 DOI: 10.1101/2024.06.19.599651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Solid carcinomas are often highly heterogenous cancers, arising from multiple epithelial cells of origin. Yet, how the cell of origin influences the response of the tumor microenvironment is poorly understood. Lung adenocarcinoma (LUAD) arises in the distal alveolar epithelium which is populated primarily by alveolar epithelial type I (AT1) and type II (AT2) cells. It has been previously reported that Gramd2 + AT1 cells can give rise to a histologically-defined LUAD that is distinct in pathology and transcriptomic identity from that arising from Sftpc + AT2 cells1,2. To determine how cells of origin influence the tumor immune microenvironment (TIME) landscape, we comprehensively characterized transcriptomic, molecular, and cellular states within the TIME of Gramd2 + AT1 and Sftpc + AT2-derived LUAD using KRASG12D oncogenic driver mouse models. Myeloid cells within the Gramd2 + AT1-derived LUAD TIME were increased, specifically, immunoreactive monocytes and tumor associated macrophages (TAMs). In contrast, the Sftpc + AT2 LUAD TIME was enriched for Arginase-1+ myeloid derived suppressor cells (MDSC) and TAMs expressing profiles suggestive of immunosuppressive function. Validation of immune infiltration was performed using flow cytometry, and intercellular interaction analysis between the cells of origin and major myeloid cell populations indicated that cell-type specific markers SFTPD in AT2 cells and CAV1 in AT1 cells mediated unique interactions with myeloid cells of the differential immunosuppressive states within each cell of origin mouse model. Taken together, Gramd2 + AT1-derived LUAD presents with an anti-tumor, immunoreactive TIME, while the TIME of Sftpc + AT2-derived LUAD has hallmarks of immunosuppression. This study suggests that LUAD cell of origin influences the composition and suppression status of the TIME landscape and may hold critical implications for patient response to immunotherapy.
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Affiliation(s)
- Minxiao Yang
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, CA USA 91010
- Department of Surgery, University of Southern California, Los Angeles, CA USA 90089
- Department of Translational Genomics, University of Southern California, Los Angeles, CA USA 90089
| | - Noah Shulkin
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, CA USA 91010
| | - Edgar Gonzalez
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA USA 90089
| | - Jonathan Castillo
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, CA USA 91010
| | - Chunli Yan
- Department of Surgery, University of Southern California, Los Angeles, CA USA 90089
| | - Keqiang Zhang
- Division of Thoracic Surgery, Department of Surgery, City of Hope National Medical Center, City of Hope, Duarte, CA USA 91010
| | - Leonidas Arvanitis
- Department of Pathology, City of Hope National Medical Center, City of Hope, Duarte, CA USA 91010
| | - Zea Borok
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA USA 92093
| | - W. Dean Wallace
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA USA 90089
| | - Dan Raz
- Division of Thoracic Surgery, Department of Surgery, City of Hope National Medical Center, City of Hope, Duarte, CA USA 91010
| | - Evanthia T. Roussos Torres
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA USA 90089
| | - Crystal N. Marconett
- Department of Integrative Translational Sciences, Beckman Research Institute, City of Hope, Duarte, CA USA 91010
- Department of Surgery, University of Southern California, Los Angeles, CA USA 90089
- Department of Translational Genomics, University of Southern California, Los Angeles, CA USA 90089
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Dunn-Davies H, Dudnakova T, Nogara A, Rodor J, Thomas AC, Parish E, Gautier P, Meynert A, Ulitsky I, Madeddu P, Caporali A, Baker A, Tollervey D, Mitić T. Control of endothelial cell function and arteriogenesis by MEG3:EZH2 epigenetic regulation of integrin expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102173. [PMID: 38617973 PMCID: PMC11015509 DOI: 10.1016/j.omtn.2024.102173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/14/2024] [Indexed: 04/16/2024]
Abstract
Epigenetic processes involving long non-coding RNAs regulate endothelial gene expression. However, the underlying regulatory mechanisms causing endothelial dysfunction remain to be elucidated. Enhancer of zeste homolog 2 (EZH2) is an important rheostat of histone H3K27 trimethylation (H3K27me3) that represses endothelial targets, but EZH2 RNA binding capacity and EZH2:RNA functional interactions have not been explored in post-ischemic angiogenesis. We used formaldehyde/UV-assisted crosslinking ligation and sequencing of hybrids and identified a new role for maternally expressed gene 3 (MEG3). MEG3 formed the predominant RNA:RNA hybrid structures in endothelial cells. Moreover, MEG3:EZH2 assists recruitment onto chromatin. By EZH2-chromatin immunoprecipitation, following MEG3 depletion, we demonstrated that MEG3 controls recruitment of EZH2/H3K27me3 onto integrin subunit alpha4 (ITGA4) promoter. Both MEG3 knockdown or EZH2 inhibition (A-395) promoted ITGA4 expression and improved endothelial cell migration and adhesion to fibronectin in vitro. The A-395 inhibitor re-directed MEG3-assisted chromatin remodeling, offering a direct therapeutic benefit by increasing endothelial function and resilience. This approach subsequently increased the expression of ITGA4 in arterioles following ischemic injury in mice, thus promoting arteriogenesis. Our findings show a context-specific role for MEG3 in guiding EZH2 to repress ITGA4. Novel therapeutic strategies could antagonize MEG3:EZH2 interaction for pre-clinical studies.
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Affiliation(s)
- Hywel Dunn-Davies
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building Max Born Crescent, King’s Buildings, Edinburgh EH9 3BF, UK
| | - Tatiana Dudnakova
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Antonella Nogara
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Julie Rodor
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Anita C. Thomas
- Bristol Medical School, Translational Health Sciences, University of Bristol, Research and Teaching Floor Level 7, Queens Building, Bristol Royal Infirmary, Bristol BS2 8HW, UK
| | - Elisa Parish
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Philippe Gautier
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Alison Meynert
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann-UK Building rm. 007, Weizmann Institute of Science Rehovot 76100, Israel
| | - Paolo Madeddu
- Bristol Medical School, Translational Health Sciences, University of Bristol, Research and Teaching Floor Level 7, Queens Building, Bristol Royal Infirmary, Bristol BS2 8HW, UK
| | - Andrea Caporali
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Andrew Baker
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building Max Born Crescent, King’s Buildings, Edinburgh EH9 3BF, UK
| | - Tijana Mitić
- University/British Heart Foundation Centre for Cardiovascular Science, Queen’s Medical Research Institute (QMRI), The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
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Marshall ML, Fung KY, Jans DA, Wagstaff KM. Tumour-specific phosphorylation of serine 419 drives alpha-enolase (ENO1) nuclear export in triple negative breast cancer progression. Cell Biosci 2024; 14:74. [PMID: 38849850 PMCID: PMC11157870 DOI: 10.1186/s13578-024-01249-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/24/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND The glycolytic enzyme alpha-enolase is a known biomarker of many cancers and involved in tumorigenic functions unrelated to its key role in glycolysis. Here, we show that expression of alpha-enolase correlates with subcellular localisation and tumorigenic status in the MCF10 triple negative breast cancer isogenic tumour progression model, where non-tumour cells show diffuse nucleocytoplasmic localisation of alpha-enolase, whereas tumorigenic cells show a predominantly cytoplasmic localisation. Alpha-enolase nucleocytoplasmic localisation may be regulated by tumour cell-specific phosphorylation at S419, previously reported in pancreatic cancer. RESULTS Here we show ENO1 phosphorylation can also be observed in triple negative breast cancer patient samples and MCF10 tumour progression cell models. Furthermore, prevention of alpha-enolase-S419 phosphorylation by point mutation or a casein kinase-1 specific inhibitor D4476, induced tumour-specific nuclear accumulation of alpha-enolase, implicating S419 phosphorylation and casein kinase-1 in regulating subcellular localisation in tumour cell-specific fashion. Strikingly, alpha-enolase nuclear accumulation was induced in tumour cells by treatment with the specific exportin-1-mediated nuclear export inhibitor Leptomycin B. This suggests that S419 phosphorylation in tumour cells regulates alpha-enolase subcellular localisation by inducing its exportin-1-mediated nuclear export. Finally, as a first step to analyse the functional consequences of increased cytoplasmic alpha-enolase in tumour cells, we determined the alpha-enolase interactome in the absence/presence of D4476 treatment, with results suggesting clear differences with respect to interaction with cytoskeleton regulating proteins. CONCLUSIONS The results suggest for the first time that tumour-specific S419 phosphorylation may contribute integrally to alpha-enolase cytoplasmic localisation, to facilitate alpha-enolase's role in modulating cytoskeletal organisation in triple negative breast cancer. This new information may be used for development of triple negative breast cancer specific therapeutics that target alpha-enolase.
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Affiliation(s)
- Morgan L Marshall
- Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Kim Yc Fung
- Health and Biosecurity, CSIRO, Westmead, NSW, 2145, Australia
| | - David A Jans
- Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Kylie M Wagstaff
- Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
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Xie Y, Cao J, Gan S, Xu L, Zhang D, Qian S, Xu F, Ding Q, Schoggins JW, Fan W. TRIM32 inhibits Venezuelan Equine Encephalitis Virus Infection by targeting a late step in viral entry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597282. [PMID: 38895352 PMCID: PMC11185716 DOI: 10.1101/2024.06.04.597282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Alphaviruses are mosquito borne RNA viruses that are a reemerging public health threat. Alphaviruses have a broad host range, and can cause diverse disease outcomes like arthritis, and encephalitis. The host ubiquitin proteasome system (UPS) plays critical roles in regulating cellular processes to control the infections with various viruses, including alphaviruses. Previous studies suggest alphaviruses hijack UPS for virus infection, but the molecular mechanisms remain poorly characterized. In addition, whether certain E3 ubiquitin ligases or deubiquitinases act as alphavirus restriction factors remains poorly understood. Here, we employed a cDNA expression screen to identify E3 ubiquitin ligase TRIM32 as a novel intrinsic restriction factor against alphavirus infection, including VEEV-TC83, SINV, and ONNV. Ectopic expression of TRIM32 reduces alphavirus infection, whereas depletion of TRIM32 with CRISPR-Cas9 increases infection. We demonstrate that TRIM32 inhibits alphaviruses through a mechanism that is independent of the TRIM32-STING-IFN axis. Combining reverse genetics and biochemical assays, we found that TRIM32 interferes with genome translation after membrane fusion, prior to replication of the incoming viral genome. Furthermore, our data indicate that the monoubiquitination of TRIM32 is important for its antiviral activity. Notably, we also show two TRIM32 pathogenic mutants R394H and D487N, related to Limb-girdle muscular dystrophy (LGMD), have a loss of antiviral activity against VEEV-TC83. Collectively, these results reveal that TRIM32 acts as a novel intrinsic restriction factor suppressing alphavirus infection and provides insights into the interaction between alphaviruses and the host UPS.
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Affiliation(s)
- Yifan Xie
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jie Cao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Shuyi Gan
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Lingdong Xu
- Laboratory Animal Center, Zhejiang University, Hangzhou, China
| | - Dongjie Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Suhong Qian
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Feng Xu
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Research Center for Life Science and Human Health, Binjiang Institute of Zhejiang University, Hangzhou, China
| | - Qiang Ding
- School of Medical Sciences, Tsinghua University, Beijing, China
| | - John W. Schoggins
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wenchun Fan
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
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31
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Pradhan UK, Meher PK, Naha S, Das R, Gupta A, Parsad R. ProkDBP: Toward more precise identification of prokaryotic DNA binding proteins. Protein Sci 2024; 33:e5015. [PMID: 38747369 PMCID: PMC11094783 DOI: 10.1002/pro.5015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/18/2024] [Accepted: 04/21/2024] [Indexed: 05/19/2024]
Abstract
Prokaryotic DNA binding proteins (DBPs) play pivotal roles in governing gene regulation, DNA replication, and various cellular functions. Accurate computational models for predicting prokaryotic DBPs hold immense promise in accelerating the discovery of novel proteins, fostering a deeper understanding of prokaryotic biology, and facilitating the development of therapeutics targeting for potential disease interventions. However, existing generic prediction models often exhibit lower accuracy in predicting prokaryotic DBPs. To address this gap, we introduce ProkDBP, a novel machine learning-driven computational model for prediction of prokaryotic DBPs. For prediction, a total of nine shallow learning algorithms and five deep learning models were utilized, with the shallow learning models demonstrating higher performance metrics compared to their deep learning counterparts. The light gradient boosting machine (LGBM), coupled with evolutionarily significant features selected via random forest variable importance measure (RF-VIM) yielded the highest five-fold cross-validation accuracy. The model achieved the highest auROC (0.9534) and auPRC (0.9575) among the 14 machine learning models evaluated. Additionally, ProkDBP demonstrated substantial performance with an independent dataset, exhibiting higher values of auROC (0.9332) and auPRC (0.9371). Notably, when benchmarked against several cutting-edge existing models, ProkDBP showcased superior predictive accuracy. Furthermore, to promote accessibility and usability, ProkDBP (https://iasri-sg.icar.gov.in/prokdbp/) is available as an online prediction tool, enabling free access to interested users. This tool stands as a significant contribution, enhancing the repertoire of resources for accurate and efficient prediction of prokaryotic DBPs.
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Affiliation(s)
- Upendra Kumar Pradhan
- Division of Statistical GeneticsICAR‐Indian Agricultural Statistics Research Institute, PUSANew DelhiIndia
| | - Prabina Kumar Meher
- Division of Statistical GeneticsICAR‐Indian Agricultural Statistics Research Institute, PUSANew DelhiIndia
| | - Sanchita Naha
- Division of Computer ApplicationsICAR‐Indian Agricultural Statistics Research Institute, PUSANew DelhiIndia
| | - Ritwika Das
- Division of Agricultural BioinformaticsICAR‐Indian Agricultural Statistics Research Institute, PUSANew DelhiIndia
| | - Ajit Gupta
- Division of Statistical GeneticsICAR‐Indian Agricultural Statistics Research Institute, PUSANew DelhiIndia
| | - Rajender Parsad
- ICAR‐Indian Agricultural Statistics Research Institute, PUSANew DelhiIndia
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32
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Singh MV, Wong T, Moorjani S, Mani AM, Dokun AO. Novel components in the nuclear factor-kappa B (NF-κB) signaling pathways of endothelial cells under hyperglycemic-ischemic conditions. Front Cardiovasc Med 2024; 11:1345421. [PMID: 38854657 PMCID: PMC11157070 DOI: 10.3389/fcvm.2024.1345421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/14/2024] [Indexed: 06/11/2024] Open
Abstract
Diabetes worsens the outcomes of a number of vascular disorders including peripheral arterial disease (PAD) at least in part through induction of chronic inflammation. However, in experimental PAD, recovery requires the nuclear factor-kappa B (NF-κB) activation. Previously we showed that individually, both ischemia and high glucose activate the canonical and non-canonical arms of the NF-κB pathway, but prolonged high glucose exposure specifically impairs ischemia-induced activation of the canonical NF-κB pathway through activation of protein kinase C beta (PKCβ). Although a cascade of phosphorylation events propels the NF-κB signaling, little is known about the impact of hyperglycemia on the canonical and non-canonical NF-κB pathway signaling. Moreover, signal upstream of PKCβ that lead to its activation in endothelial cells during hyperglycemia exposure have not been well defined. In this study, we used endothelial cells exposed to hyperglycemia and ischemia (HGI) and an array of approximately 250 antibodies to approximately 100 proteins and their phosphorylated forms to identify the NF-κB signaling pathway that is altered in ischemic EC that has been exposed to high glucose condition. Comparison of signals from hyperglycemic and ischemic cell lysates yielded a number of proteins whose phosphorylation was either increased or decreased under HGI conditions. Pathway analyses using bioinformatics tools implicated BLNK/BTK known for B cell antigen receptor (BCR)-coupled signaling. Inhibition of BLNK/BTK in endothelial cells by a specific pharmacological inhibitor terreic acid attenuated PKC activation and restored the IκBα degradation suggesting that these molecules play a critical role in hyperglycemic attenuation of the canonical NF-κB pathway. Thus, we have identified a potentially new component of the NF-κB pathway upstream of PKC in endothelial cells that contributes to the poor post ischemic adaptation during hyperglycemia.
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Affiliation(s)
| | | | | | | | - Ayotunde O. Dokun
- Division of Endocrinology and Metabolism, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
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33
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Hoh C, Salzberg SL. Discovering Intron Gain Events in Humans through Large-Scale Evolutionary Comparisons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592247. [PMID: 38746259 PMCID: PMC11092651 DOI: 10.1101/2024.05.02.592247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The rapid growth in the number of sequenced genomes makes it possible to search for the appearance of entirely new introns in the human lineage. In this study, we compared the genomic sequences for 19,120 human protein-coding genes to a collection of 3493 vertebrate genomes, mapping the patterns of intron alignments onto a phylogenetic tree. This mapping allowed us to trace many intron gain events to precise locations in the tree, corresponding to distinct points in evolutionary history. We discovered 584 intron gain events, all of them relatively recent, in 514 distinct human genes. Among these events, we explored the hypothesis that intronization was the mechanism responsible for intron gain. Intronization events were identified by locating instances where human introns correspond to exonic sequences in homologous vertebrate genes. Although apparently rare, we found three compelling cases of intronization, and for each of those we compared the human protein sequence and structure to homologous genes that lack the introns.
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Affiliation(s)
- Celine Hoh
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
| | - Steven L Salzberg
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21211, USA
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
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Garcia EM, Lenz JD, Schaub RE, Hackett KT, Salgado-Pabón W, Dillard JP. IL-17C is a driver of damaging inflammation during Neisseria gonorrhoeae infection of human Fallopian tube. Nat Commun 2024; 15:3756. [PMID: 38704381 PMCID: PMC11069574 DOI: 10.1038/s41467-024-48141-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/19/2024] [Indexed: 05/06/2024] Open
Abstract
The human pathogen Neisseria gonorrhoeae ascends into the upper female reproductive tract to cause damaging inflammation within the Fallopian tubes and pelvic inflammatory disease (PID), increasing the risk of infertility and ectopic pregnancy. The loss of ciliated cells from the epithelium is thought to be both a consequence of inflammation and a cause of adverse sequelae. However, the links between infection, inflammation, and ciliated cell extrusion remain unresolved. With the use of ex vivo cultures of human Fallopian tube paired with RNA sequencing we defined the tissue response to gonococcal challenge, identifying cytokine, chemokine, cell adhesion, and apoptosis related transcripts not previously recognized as potentiators of gonococcal PID. Unexpectedly, IL-17C was one of the most highly induced genes. Yet, this cytokine has no previous association with gonococcal infection nor pelvic inflammatory disease and thus it was selected for further characterization. We show that human Fallopian tubes express the IL-17C receptor on the epithelial surface and that treatment with purified IL-17C induces pro-inflammatory cytokine secretion in addition to sloughing of the epithelium and generalized tissue damage. These results demonstrate a previously unrecognized but critical role of IL-17C in the damaging inflammation induced by gonococci in a human explant model of PID.
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Affiliation(s)
- Erin M Garcia
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Jonathan D Lenz
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Ryan E Schaub
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Kathleen T Hackett
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Wilmara Salgado-Pabón
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Joseph P Dillard
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA.
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35
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Wright SN, Colton S, Schaffer LV, Pillich RT, Churas C, Pratt D, Ideker T. State of the Interactomes: an evaluation of molecular networks for generating biological insights. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.587073. [PMID: 38746239 PMCID: PMC11092493 DOI: 10.1101/2024.04.26.587073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Advancements in genomic and proteomic technologies have powered the use of gene and protein networks ("interactomes") for understanding genotype-phenotype translation. However, the proliferation of interactomes complicates the selection of networks for specific applications. Here, we present a comprehensive evaluation of 46 current human interactomes, encompassing protein-protein interactions as well as gene regulatory, signaling, colocalization, and genetic interaction networks. Our analysis shows that large composite networks such as HumanNet, STRING, and FunCoup are most effective for identifying disease genes, while smaller networks such as DIP and SIGNOR demonstrate strong interaction prediction performance. These findings provide a benchmark for interactomes across diverse network biology applications and clarify factors that influence network performance. Furthermore, our evaluation pipeline paves the way for continued assessment of emerging and updated interaction networks in the future.
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Ren X, Trotter T, Ashwath N, Stanley D, Bajagai YS, Brewer PB. Transcriptomic Insights: Phytogenic Modulation of Buffel Grass ( Cenchrus ciliaris) Seedling Emergence. PLANTS (BASEL, SWITZERLAND) 2024; 13:1174. [PMID: 38732389 PMCID: PMC11085557 DOI: 10.3390/plants13091174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/05/2024] [Accepted: 04/18/2024] [Indexed: 05/13/2024]
Abstract
This study explores the impact of a novel phytogenic product containing citric acid, carvacrol, and cinnamaldehyde on buffel grass (Cenchrus ciliaris) seedling emergence. A dilution series of the phytogenic solution revealed a concentration range that promoted seedling emergence, with an optimal concentration of 0.5%. Transcriptomic analysis using RNA-seq was performed to investigate gene expression changes in seedlings under the influence of the phytogenic product. The results revealed that the phytogenic treatment significantly altered the gene expression, with a prevalent boost in transcriptional activity compared to the control. Functional analysis indicated the positive alteration of key metabolic pathways, including the tricarboxylic acid (TCA) cycle, glycolysis, and pentose phosphate pathways. Moreover, pathways related to amino acids, nucleotide biosynthesis, heme biosynthesis, and formyltetrahydrofolate biosynthesis showed substantial modulation. The study provides valuable insights into the molecular mechanisms underlying the phytogenic product's effects on grass seedling establishment and highlights its ability to promote energy metabolism and essential biosynthetic pathways for plant growth.
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Affiliation(s)
| | | | | | | | | | - Philip B. Brewer
- Institute for Future Farming Systems, Central Queensland University, Rockhampton, QLD 4701, Australia; (X.R.); (T.T.); (Y.S.B.)
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37
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Roberts MD, Ruple BA, Godwin JS, McIntosh MC, Chen SY, Kontos NJ, Agyin-Birikorang A, Michel M, Plotkin DL, Mattingly ML, Mobley B, Ziegenfuss TN, Fruge AD, Kavazis AN. A novel deep proteomic approach in human skeletal muscle unveils distinct molecular signatures affected by aging and resistance training. Aging (Albany NY) 2024; 16:6631-6651. [PMID: 38643460 PMCID: PMC11087122 DOI: 10.18632/aging.205751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 03/18/2024] [Indexed: 04/22/2024]
Abstract
The skeletal muscle proteome alterations to aging and resistance training have been reported in prior studies. However, conventional proteomics in skeletal muscle typically yields wide protein abundance ranges that mask the detection of lowly expressed proteins. Thus, we adopted a novel deep proteomics approach whereby myofibril (MyoF) and non-MyoF fractions were separately subjected to protein corona nanoparticle complex formation prior to digestion and Liquid Chromatography Mass Spectrometry (LC-MS). Specifically, we investigated MyoF and non-MyoF proteomic profiles of the vastus lateralis muscle of younger (Y, 22±2 years old; n=5) and middle-aged participants (MA, 56±8 years old; n=6). Additionally, MA muscle was analyzed following eight weeks of resistance training (RT, 2d/week). Across all participants, the number of non-MyoF proteins detected averaged to be 5,645±266 (range: 4,888-5,987) and the number of MyoF proteins detected averaged to be 2,611±326 (range: 1,944-3,101). Differences in the non-MyoF (8.4%) and MyoF (2.5%) proteomes were evident between age cohorts, and most differentially expressed non-MyoF proteins (447/543) were more enriched in MA versus Y. Biological processes in the non-MyoF fraction were predicted to be operative in MA versus Y including increased cellular stress, mRNA splicing, translation elongation, and ubiquitin-mediated proteolysis. RT in MA participants only altered ~0.3% of MyoF and ~1.0% of non-MyoF proteomes. In summary, aging and RT predominantly affect non-contractile proteins in skeletal muscle. Additionally, marginal proteome adaptations with RT suggest more rigorous training may stimulate more robust effects or that RT, regardless of age, subtly alters basal state skeletal muscle protein abundances.
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Affiliation(s)
| | | | | | | | | | | | | | - Max Michel
- School of Kinesiology, Auburn University, Auburn, AL 36849, USA
| | | | | | - Brooks Mobley
- School of Kinesiology, Auburn University, Auburn, AL 36849, USA
| | | | - Andrew D. Fruge
- College of Nursing, Auburn University, Auburn, AL 36849, USA
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Khan SA, Anwar M, Gohar A, Roosan MR, Hoessli DC, Khatoon A, Shakeel M. Predisposing deleterious variants in the cancer-associated human kinases in the global populations. PLoS One 2024; 19:e0298747. [PMID: 38635549 PMCID: PMC11025791 DOI: 10.1371/journal.pone.0298747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/29/2024] [Indexed: 04/20/2024] Open
Abstract
Human kinases play essential and diverse roles in the cellular activities of maintaining homeostasis and growth. Genetic mutations in the genes encoding the kinases (or phosphotransferases) have been linked with various types of cancers. In this study, we cataloged mutations in 500 kinases genes in >65,000 individuals of global populations from the Human Genetic Diversity Project (HGDP) and ExAC databases, and assessed their potentially deleterious impact by using the in silico tools SIFT, Polyphen2, and CADD. The analysis highlighted 35 deleterious non-synonymous SNVs in the ExAC and 5 SNVs in the HGDP project. Notably, a higher number of deleterious mutations was observed in the Non-Finnish Europeans (26 SNVs), followed by the Africans (14 SNVs), East Asians (13 SNVs), and South Asians (12 SNVs). The gene set enrichment analysis highlighted NTRK1 and FGFR3 being most significantly enriched among the kinases. The gene expression analysis revealed over-expression of NTRK1 in liver cancer, whereas, FGFR3 was found over-expressed in lung, breast, and liver cancers compared to their expression in the respective normal tissues. Also, 13 potential drugs were identified that target the NTRK1 protein, whereas 6 potential drugs for the FGFR3 target were identified. Taken together, the study provides a framework for exploring the predisposing germline mutations in kinases to suggest the underlying pathogenic mechanisms in cancers. The potential drugs are also suggested for personalized cancer management.
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Affiliation(s)
- Salman Ahmed Khan
- Department of Molecular Medicine (DMM), Dow College of Biotechnology (DCoB), Dow University of Health Sciences (DUHS), Karachi, Pakistan
- DOW-DOGANA Advanced Molecular Genetics and Genomics Disease Research and Treatment Center (AMGGDRTC), Dow University of Health Sciences (DUHS), Karachi, Pakistan
| | - Misbah Anwar
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Atia Gohar
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Moom R. Roosan
- Department of Pharmacy Practice, Chapman University School of Pharmacy Harry and Diane Rinker Health Science Campus, Irvine, CA, United States of America
| | - Daniel C. Hoessli
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Ambrina Khatoon
- Department of Molecular Medicine, Ziauddin University, Karachi, Pakistan
| | - Muhammad Shakeel
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
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Adeyemo OM, Ashimiyu‐Abdusalam Z, Adewunmi M, Ayano TA, Sohaib M, Abdel‐Salam R. Network-based identification of key proteins and repositioning of drugs for non-small cell lung cancer. Cancer Rep (Hoboken) 2024; 7:e2031. [PMID: 38600056 PMCID: PMC11006715 DOI: 10.1002/cnr2.2031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 02/02/2024] [Accepted: 02/21/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND NSCLC is a lethal cancer that is highly prevalent and accounts for 85% of cases of lung cancer. Conventional cancer treatments, such as chemotherapy and radiation, frequently exhibit limited efficacy and notable adverse reactions. Therefore, a drug repurposing method is proposed for effective NSCLC treatment. AIMS This study aims to evaluate candidate drugs that are effective for NSCLC at the clinical level using a systems biology and network analysis approach. METHODS Differentially expressed genes in transcriptomics data were identified using the systems biology and network analysis approaches. A network of gene co-expression was developed with the aim of detecting two modules of gene co-expression. Following that, the Drug-Gene Interaction Database was used to find possible drugs that target important genes within two gene co-expression modules linked to non-small cell lung cancer (NSCLC). The use of Cytoscape facilitated the creation of a drug-gene interaction network. Finally, gene set enrichment analysis was done to validate candidate drugs. RESULTS Unlike previous research on repositioning drugs for NSCLC, which uses a gene co-expression network, this project is the first to research both gene co-expression and co-occurrence networks. And the co-occurrence network also accounts for differentially expressed genes in cancer cells and their adjacent normal cells. For effective management of non-small cell lung cancer (NSCLC), drugs that show higher gene regulation and gene affinity within the drug-gene interaction network are thought to be important. According to the discourse, NSCLC genes have a lot of control over medicines like vincristine, fluorouracil, methotrexate, clotrimazole, etoposide, tamoxifen, sorafenib, doxorubicin, and pazopanib. CONCLUSION Hence, there is a possibility of repurposing these drugs for the treatment of non-small-cell lung cancer.
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Affiliation(s)
- Oluwatosin Maryam Adeyemo
- Department of BiochemistryFederal University of TechnologyAkureNigeria
- Cancer Research with AI (CaresAI)HobartAustralia
| | - Zainab Ashimiyu‐Abdusalam
- Cancer Research with AI (CaresAI)HobartAustralia
- Department of Biochemistry and NutritionNigeria Institute of Medical ResearchLagosNigeria
| | - Mary Adewunmi
- Cancer Research with AI (CaresAI)HobartAustralia
- College of Health and MedicineUniversity of TasmaniaHobartTasmaniaAustralia
| | - Temitope Ayanfunke Ayano
- Cancer Research with AI (CaresAI)HobartAustralia
- Department of MicrobiologyObafemi Awolowo UniversityIle‐IfeNigeria
| | | | - Reem Abdel‐Salam
- Cancer Research with AI (CaresAI)HobartAustralia
- Department of Computer Engineering, Faculty of EngineeringCairo UniversityCairoEgypt
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Meng W, Fenton CG, Johnsen KM, Taman H, Florholmen J, Paulssen RH. DNA methylation fine-tunes pro-and anti-inflammatory signalling pathways in inactive ulcerative colitis tissue biopsies. Sci Rep 2024; 14:6789. [PMID: 38514698 PMCID: PMC10957912 DOI: 10.1038/s41598-024-57440-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/18/2024] [Indexed: 03/23/2024] Open
Abstract
DNA methylation has been implied to play a role in the immune dysfunction associated with inflammatory bowel disease (IBD) and the disease development of ulcerative colitis (UC). Changes of the DNA methylation and correlated gene expression in patient samples with inactive UC might reveal possible regulatory features important for further treatment options for UC. Targeted bisulfite sequencing and whole transcriptome sequencing were performed on mucosal biopsies from patients with active UC (UC, n = 14), inactive UC (RM, n = 20), and non-IBD patients which served as controls (NN, n = 11). The differentially methylated regions (DMRs) were identified by DMRseq. Correlation analysis was performed between DMRs and their nearest differentially expressed genes (DEGs). Principal component analysis (PCA) was performed based on correlated DMR regulated genes. DMR regulated genes then were functional annotated. Cell-type deconvolutions were performed based on methylation levels. The comparisons revealed a total of 38 methylation-regulated genes in inactive UC that are potentially regulated by DMRs (correlation p value < 0.1). Several methylation-regulated genes could be identified in inactive UC participating in IL-10 and cytokine signalling pathways such as IL1B and STAT3. DNA methylation events in inactive UC seem to be fine-tuned by the balancing pro- and anti- inflammatory pathways to maintain a prevailed healing process to restore dynamic epithelium homeostasis.
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Affiliation(s)
- Wei Meng
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Christopher G Fenton
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
- Genomics Support Centre Tromsø, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Sykehusveien 44, 9037, Tromsø, Norway
| | - Kay-Martin Johnsen
- Gastroenterology and Nutrition Research Group, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
- Department of Medical Gastroenterology, University Hospital of North Norway, Tromsø, Norway
| | - Hagar Taman
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
- Genomics Support Centre Tromsø, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Sykehusveien 44, 9037, Tromsø, Norway
| | - Jon Florholmen
- Gastroenterology and Nutrition Research Group, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
- Department of Medical Gastroenterology, University Hospital of North Norway, Tromsø, Norway
| | - Ruth H Paulssen
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway.
- Genomics Support Centre Tromsø, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Sykehusveien 44, 9037, Tromsø, Norway.
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Do AN, Ali M, Timsina J, Wang L, Western D, Liu M, Sanford J, Rosende-Roca M, Boada M, Puerta R, Wilson T, Ruiz A, Pastor P, Wyss-Coray T, Cruchaga C, Sung YJ. CSF proteomic profiling with amyloid/tau positivity identifies distinctive sex-different alteration of multiple proteins involved in Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.15.24304164. [PMID: 38559166 PMCID: PMC10980123 DOI: 10.1101/2024.03.15.24304164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
In Alzheimer's disease (AD), the most common cause of dementia, females have higher prevalence and faster progression, but sex-specific molecular findings in AD are limited. Here, we comprehensively examined and validated 7,006 aptamers targeting 6,162 proteins in cerebral spinal fluid (CSF) from 2,077 amyloid/tau positive cases and controls to identify sex-specific proteomic signatures of AD. In discovery (N=1,766), we identified 330 male-specific and 121 female-specific proteomic alternations in CSF (FDR <0.05). These sex-specific proteins strongly predicted amyloid/tau positivity (AUC=0.98 in males; 0.99 in females), significantly higher than those with age, sex, and APOE-ε4 (AUC=0.85). The identified sex-specific proteins were well validated (r≥0.5) in the Stanford study (N=108) and Emory study (N=148). Biological follow-up of these proteins led to sex differences in cell-type specificity, pathways, interaction networks, and drug targets. Male-specific proteins, enriched in astrocytes and oligodendrocytes, were involved in postsynaptic and axon-genesis. The male network exhibited direct connections among 152 proteins and highlighted PTEN, NOTCH1, FYN, and MAPK8 as hubs. Drug target suggested melatonin (used for sleep-wake cycle regulation), nabumetone (used for pain), daunorubicin, and verteporfin for treating AD males. In contrast, female-specific proteins, enriched in neurons, were involved in phosphoserine residue binding including cytokine activities. The female network exhibits strong connections among 51 proteins and highlighted JUN and 14-3-3 proteins (YWHAG and YWHAZ) as hubs. Drug target suggested biperiden (for muscle control of Parkinson's disease), nimodipine (for cerebral vasospasm), quinostatin and ethaverine for treating AD females. Together, our findings provide mechanistic understanding of sex differences for AD risk and insights into clinically translatable interventions.
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Affiliation(s)
- Anh N Do
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Muhammad Ali
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Jigyasha Timsina
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Lihua Wang
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel Western
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Menghan Liu
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Jessie Sanford
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Matitee Rosende-Roca
- Research Center and Memory clinic Fundació ACE. Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Merce Boada
- Research Center and Memory clinic Fundació ACE. Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Raquel Puerta
- Research Center and Memory clinic Fundació ACE. Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Ted Wilson
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Agustin Ruiz
- Research Center and Memory clinic Fundació ACE. Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Pau Pastor
- Memory Disorders Unit, Department of Neurology, University Hospital Mutua Terrassa, Terrassa, Spain
| | - Tony Wyss-Coray
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Carlos Cruchaga
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurologic Diseases, Washington University in St. Louis, St. Louis, MO, USA
| | - Yun Ju Sung
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
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Cruz SP, Zhang Q, Devarajan R, Paia C, Luo B, Zhang K, Koivusalo S, Qin L, Xia J, Ahtikoski A, Vaarala M, Wenta T, Wei G, Manninen A. Dampened Regulatory Circuitry of TEAD1/ITGA1/ITGA2 Promotes TGFβ1 Signaling to Orchestrate Prostate Cancer Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305547. [PMID: 38169150 PMCID: PMC10953553 DOI: 10.1002/advs.202305547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/18/2023] [Indexed: 01/05/2024]
Abstract
The extracellular matrix (ECM) undergoes substantial changes during prostate cancer (PCa) progression, thereby regulating PCa growth and invasion. Herein, a meta-analysis of multiple PCa cohorts is performed which revealed that downregulation or genomic loss of ITGA1 and ITGA2 integrin genes is associated with tumor progression and worse prognosis. Genomic deletion of both ITGA1 and ITGA2 activated epithelial-to-mesenchymal transition (EMT) in benign prostate epithelial cells, thereby enhancing their invasive potential in vitro and converting them into tumorigenic cells in vivo. Mechanistically, EMT is induced by enhanced secretion and autocrine activation of TGFβ1 and nuclear targeting of YAP1. An unbiased genome-wide co-expression analysis of large PCa cohort datasets identified the transcription factor TEAD1 as a key regulator of ITGA1 and ITGA2 expression in PCa cells while TEAD1 loss phenocopied the dual loss of α1- and α2-integrins in vitro and in vivo. Remarkably, clinical data analysis revealed that TEAD1 downregulation or genomic loss is associated with aggressive PCa and together with low ITGA1 and ITGA2 expression synergistically impacted PCa prognosis and progression. This study thus demonstrated that loss of α1- and α2-integrins, either via deletion/inactivation of the ITGA1/ITGA2 locus or via loss of TEAD1, contributes to PCa progression by inducing TGFβ1-driven EMT.
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Affiliation(s)
- Sara P. Cruz
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine, Biocenter OuluUniversity of OuluAapistie 5aOulu90220Finland
| | - Qin Zhang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine, Biocenter OuluUniversity of OuluAapistie 5aOulu90220Finland
| | - Raman Devarajan
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine, Biocenter OuluUniversity of OuluAapistie 5aOulu90220Finland
| | - Christos Paia
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine, Biocenter OuluUniversity of OuluAapistie 5aOulu90220Finland
| | - Binjie Luo
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine, Biocenter OuluUniversity of OuluAapistie 5aOulu90220Finland
| | - Kai Zhang
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine, Biocenter OuluUniversity of OuluAapistie 5aOulu90220Finland
| | - Saara Koivusalo
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine, Biocenter OuluUniversity of OuluAapistie 5aOulu90220Finland
| | - Longguang Qin
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine, Biocenter OuluUniversity of OuluAapistie 5aOulu90220Finland
| | - Jihan Xia
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine, Biocenter OuluUniversity of OuluAapistie 5aOulu90220Finland
| | - Anne Ahtikoski
- Departments of Urology, Pathology and Radiology, and Medical Research Center OuluOulu University Hospital and University of OuluAapistie 5aOulu90220Finland
| | - Markku Vaarala
- Departments of Urology, Pathology and Radiology, and Medical Research Center OuluOulu University Hospital and University of OuluAapistie 5aOulu90220Finland
| | - Tomasz Wenta
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine, Biocenter OuluUniversity of OuluAapistie 5aOulu90220Finland
- Department of General and Medical Biochemistry, Faculty of BiologyUniversity of GdanskJana Bażyńskiego 8Gdańsk80–309Poland
| | - Gong‐Hong Wei
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine, Biocenter OuluUniversity of OuluAapistie 5aOulu90220Finland
- Fudan University Shanghai Cancer Center & MOE Key Laboratory of Metabolism and Molecular Medicine and Department of Biochemistry and Molecular Biology of School of Basic Medical SciencesShanghai Medical College of Fudan University138 Yi Xue Yuan RoadShanghai200032China
| | - Aki Manninen
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine, Biocenter OuluUniversity of OuluAapistie 5aOulu90220Finland
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Vahab N, Bonu T, Kuhlmann L, Ramialison M, Tyagi S. Uncovering co-regulatory modules and gene regulatory networks in the heart through machine learning-based analysis of large-scale epigenomic data. Comput Biol Med 2024; 171:108068. [PMID: 38354497 DOI: 10.1016/j.compbiomed.2024.108068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/30/2023] [Accepted: 01/27/2024] [Indexed: 02/16/2024]
Abstract
The availability of large-scale epigenomic data from various cell types and conditions has yielded valuable insights for evaluating and learning features predicting the co-binding of transcription factors (TF). However, prior attempts to develop models predicting motif co-occurrence lacked scalability for globally analyzing any motif combination or making cross-species predictions. Moreover, mapping co-regulatory modules (CRM) to gene regulatory networks (GRN) is crucial for understanding underlying function. Currently, no comprehensive pipeline exists for large-scale, rapid, and accurate CRM and GRN identification. In this study, we analyzed and evaluated different TF binding characteristics facilitating biologically significant co-binding to identify all potential clusters of co-binding TFs. We curated the UniBind database, containing ChIP-Seq data from over 1983 samples and 232 TFs, and implemented two machine learning models to predict CRMs and the potential regulatory networks they operate on. Two machine learning models, Convolution Neural Networks (CNN) and Random Forest Classifier(RFC), used to predict co-binding between TFs, were compared using precision-recall Receiver Operating Characteristic (ROC) curves. CNN outperformed RFC (AUC 0.94 vs. 0.88) and achieved higher F1 scores (0.938 vs. 0.872). The CRMs generated by the clustering algorithm were validated against ChipAtlas and MCOT, revealing additional motifs forming CRMs. We predicted 200k CRMs for 50k+ human genes, validated against recent CRM prediction methods with 100% overlap. Further, we narrowed our focus to study heart-related regulatory motifs, filtering the generated CRMs to report 1784 Cardiac CRMs containing at least four cardiac TFs. Identified cardiac CRMs revealed potential novel regulators like ARID3A and RXRB for SCAD, including known TFs like PPARG for F11R. Our findings highlight the importance of the NKX family of transcription factors in cardiac development and provide potential targets for further investigation in cardiac disease.
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Affiliation(s)
- Naima Vahab
- School of Computational Technologies, RMIT University, Melbourne VIC 3000, Australia; Department of Infectious Diseases, Alfred Hospital, Prahran VIC 3008, Australia
| | - Tarun Bonu
- Faculty of Information Technology, Monash University, Clayton VIC 3800, Australia
| | - Levin Kuhlmann
- Faculty of Information Technology, Monash University, Clayton VIC 3800, Australia
| | | | - Sonika Tyagi
- School of Computational Technologies, RMIT University, Melbourne VIC 3000, Australia; Department of Infectious Diseases, Alfred Hospital, Prahran VIC 3008, Australia.
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Srivastava S, Mondal S, Rathor R, Srivastava S, Suryakumar G. Increased Expression of MiRNA-1 Contributes to Hypobaric Hypoxia-Induced Skeletal Muscle Loss. Adv Biol (Weinh) 2024; 8:e2300573. [PMID: 38149527 DOI: 10.1002/adbi.202300573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/08/2023] [Indexed: 12/28/2023]
Abstract
The present study aims to analyze the role of microRNA-1 in the regulation of skeletal muscle loss under hypobaric hypoxia (HH). Male Sprague Dawley rats (n = 10) weighing 230-250 g are divided into two groups, control and HH exposure for 7 days at 25 000 ft. After the hypoxia exposure, the animals are sacrificed and hindlimb skeletal muscles are excised for further analysis. Studies found the potential role of miR-1 (myomiR) as a biomarker under different atrophic conditions. Prolonged exposure to HH leads to enhanced expression of miR-1 in skeletal muscle as compared to unexposed controls. The Bioinformatics approach is used to identify the validated targets and the biological processes of miR-1. The target prediction tools identify PAX3 and HSP70 as major targets for miR-1. Exposure to HH significantly reduces PAX3 and HSP70 expression during 7 days of HH exposure, which further enhances the activity of FOXO3, MSTN, and ATROGIN known for the progression of skeletal muscle atrophy in relation to control rats. This study indicates the increased expressions of miR-1 and reduced expression of PAX3 and HSP70 lead to impaired myogenesis in skeletal muscle under HH. Further, enhanced expression of muscle degradation genes such as FOXO3, MSTN, and ATROGIN under HH exposure causes skeletal muscle protein loss.
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Affiliation(s)
- Sukanya Srivastava
- Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, Delhi, 110054, India
| | - Samrita Mondal
- Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, Delhi, 110054, India
| | - Richa Rathor
- Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, Delhi, 110054, India
| | - Swati Srivastava
- Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, Delhi, 110054, India
| | - Geetha Suryakumar
- Defence Institute of Physiology and Allied Sciences, Lucknow Road, Timarpur, Delhi, 110054, India
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Bowman J, Lynch VJ. Rapid evolution of genes with anti-cancer functions during the origins of large bodies and cancer resistance in elephants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582135. [PMID: 38463968 PMCID: PMC10925141 DOI: 10.1101/2024.02.27.582135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Elephants have emerged as a model system to study the evolution of body size and cancer resistance because, despite their immense size, they have a very low prevalence of cancer. Previous studies have found that duplication of tumor suppressors at least partly contributes to the evolution of anti-cancer cellular phenotypes in elephants. Still, many other mechanisms must have contributed to their augmented cancer resistance. Here, we use a suite of codon-based maximum-likelihood methods and a dataset of 13,310 protein-coding gene alignments from 261 Eutherian mammals to identify positively selected and rapidly evolving elephant genes. We found 496 genes (3.73% of alignments tested) with statistically significant evidence for positive selection and 660 genes (4.96% of alignments tested) that likely evolved rapidly in elephants. Positively selected and rapidly evolving genes are statistically enriched in gene ontology terms and biological pathways related to regulated cell death mechanisms, DNA damage repair, cell cycle regulation, epidermal growth factor receptor (EGFR) signaling, and immune functions, particularly neutrophil granules and degranulation. All of these biological factors are plausibly related to the evolution of cancer resistance. Thus, these positively selected and rapidly evolving genes are promising candidates for genes contributing to elephant-specific traits, including the evolution of molecular and cellular characteristics that enhance cancer resistance.
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Affiliation(s)
- Jacob Bowman
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, 14260, USA
| | - Vincent J. Lynch
- Department of Biological Sciences, University at Buffalo, SUNY, 551 Cooke Hall, Buffalo, NY, 14260, USA
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Bandopadhyay L, Basu D, Ranjan Sikdar S. De novo transcriptome assembly and global analysis of differential gene expression of aphid tolerant wild mustard Rorippa indica (L.) Hiern infested by mustard aphid Lipaphis Erysimi (L.) Kaltenbach. Funct Integr Genomics 2024; 24:43. [PMID: 38418630 DOI: 10.1007/s10142-024-01323-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
Rapeseed-mustard, the oleiferous Brassica species are important oilseed crops cultivated all over the globe. Mustard aphid Lipaphis erysimi (L.) Kaltenbach is a major threat to the cultivation of rapeseed-mustard. Wild mustard Rorippa indica (L.) Hiern shows tolerance to mustard aphids as a nonhost and hence is an important source for the bioprospecting of potential resistance genes and defense measures to manage mustard aphids sustainably. We performed mRNA sequencing of the R. indica plant uninfested and infested by the mustard aphids, harvested at 24 hours post-infestation. Following quality control, the high-quality reads were subjected to de novo assembly of the transcriptome. As there is no genomic information available for this potential wild plant, the raw reads will be useful for further bioinformatics analysis and the sequence information of the assembled transcripts will be helpful to design primers for the characterization of specific gene sequences. In this study, we also used the generated resource to comprehensively analyse the global profile of differential gene expression in R. indica in response to infestation by mustard aphids. The functional enrichment analysis of the differentially expressed genes reveals a significant immune response and suggests the possibility of chitin-induced defense signaling.
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Affiliation(s)
- Lekha Bandopadhyay
- Division of Plant Biology, Bose Institute, P 1/12, C. I. T. Road, Scheme VIIM, Kolkata, 700054, India.
| | - Debabrata Basu
- Division of Plant Biology, Bose Institute, P 1/12, C. I. T. Road, Scheme VIIM, Kolkata, 700054, India
| | - Samir Ranjan Sikdar
- Division of Plant Biology, Bose Institute, P 1/12, C. I. T. Road, Scheme VIIM, Kolkata, 700054, India.
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Sharma S, Koshy R, Kumar R, Mohammad G, Thinlas T, Graham BB, Pasha Q. Hypobaric hypoxia drives selection of altitude-associated adaptative alleles in the Himalayan population. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169605. [PMID: 38159773 PMCID: PMC11285711 DOI: 10.1016/j.scitotenv.2023.169605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Genetic variants play a crucial role in shaping the adaptive phenotypes associated with high-altitude populations. Nevertheless, a comprehensive understanding of the specific impacts of different environments associated with increasing altitudes on the natural selection of these genetic variants remains undetermined. Hence, this study aimed to identify genetic markers responsible for high-altitude adaptation with specific reference to different altitudes, majorly focussing on an altitude elevation range of ∼1500 m and a corresponding decrease of ≥5 % in ambient oxygen availability. We conducted a comprehensive genome-wide investigation (n = 192) followed by a validation study (n = 514) in low-altitude and three high-altitude populations (>2400 m) of Nubra village (NU) (3048 m), Sakti village (SKT) (3812 m), and Tso Moriri village (TK) (4522 m). Extensive genetic analysis identified 86 SNPs that showed significant associations with high-altitude adaptation. Frequency mapping of these SNPs revealed 38 adaptive alleles and specific haplotypes that exhibited a strong linear correlation with increasing altitude. Notably, these SNPs spanned crucial genes, such as ADH6 and NAPG along with the vastly studied genes like EGLN1 and EPAS1, involved in oxygen sensing, metabolism, and vascular homeostasis. Correlation analyses between these adaptive alleles and relevant clinical and biochemical markers provided evidence of their functional relevance in physiological adaptation to hypobaric hypoxia. High-altitude population showed a significant increase in plasma 8-isoPGF2α levels as compared to low-altitude population. Similar observation showcased increased blood pressure in NU as compared to TK (P < 0.0001). In silico analyses further confirmed that these alleles regulate gene expression of EGLN1, EPAS1, COQ7, NAPG, ADH6, DUOXA1 etc. This study provides genetic insights into the effects of hypobaric-hypoxia on the clinico-physiological characteristics of natives living in increasing high-altitude regions. Overall, our findings highlight the synergistic relationship between environment and evolutionary processes, showcasing physiological implications of genetic variants in oxygen sensing and metabolic pathway genes in increasing high-altitude environments.
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Affiliation(s)
- Samantha Sharma
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Department of Medical and Molecular Genetics, Indiana University, Indianapolis 46202, IN, USA
| | - Remya Koshy
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Rahul Kumar
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Lung Biology Center, Zuckerberg San Francisco General Hospital, San Francisco, CA, USA
| | - Ghulam Mohammad
- Department of Medicine, Sonam Norboo Memorial Hospital, Leh, Ladakh 194101, India
| | - Tashi Thinlas
- Department of Medicine, Sonam Norboo Memorial Hospital, Leh, Ladakh 194101, India
| | - Brian B Graham
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Lung Biology Center, Zuckerberg San Francisco General Hospital, San Francisco, CA, USA
| | - Qadar Pasha
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India; Institute of Hypoxia Research, New Delhi 110067, India.
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Montazerinezhad S, Solouki M, Emamjomeh A, Kavousi K, Taheri A, Shiri Y. Transcriptomic analysis of alternative splicing events for different stages of growth and development in Sistan Yaghooti grape clusters. Gene 2024; 896:148030. [PMID: 38008270 DOI: 10.1016/j.gene.2023.148030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/31/2023] [Accepted: 11/22/2023] [Indexed: 11/28/2023]
Abstract
Sistan Yaghooti grape variety, despite characteristics such as early ripening, is vulnerable to cluster rot due to small berries and dense clusters. In this regard, AS may serve as a regulatory mechanism during developmental processes and in response to environmental signals. RNA-Seq analysis was performed to measure gene expression and the extent of AS events in the cluster growth and development stages of Sistan Yaghooti grape. The number of AS events increased during stages, suggesting that it contributes to the grapevine's adaptability to various stresses. In addition, DEG and DAS genes showed little overlap in cluster growth stages. Functional analysis of 19,194 DAS -gene sets showed that VIT_06s0004g06670 gene is involved in the activation of calcium channels (Ca2+) through the activation of 5 PLC biosynthetic pathways. Among the 27,229 DEG -sets, VIT_07s0005g05320 gene showed higher expression. Interestingly, this gene is involved in the synthesis of an EF -hand domain-containing protein capable of binding to Ca2+ by activating 4 biochemical pathways. These genes increase cytosolic Ca2+ concentration, enhancing plant stress tolerance and resistance to cracking. These results show that AS can respond independently to different types of stress. Among the other DAS genes, the GA2ox gene (VvGA2ox) showed an increase in AS events during cluster development. This gene is critical for initiating the degradation process of GA and plays a crucial role in different stages of seed development. Therefore, it is very likely that this gene is one of the main factors responsible for the density and seedlessness of Sistan Yaghooti grape.
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Affiliation(s)
- Somayeh Montazerinezhad
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Mahmood Solouki
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Abbasali Emamjomeh
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran; Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Bioinformatics, Faculty of Basic Sciences, University of Zabol, Zabol, Iran.
| | - Kaveh Kavousi
- Institute of Biochemistry and Biophysics (IBB), Department of Bioinformatics, Laboratory of Complex Biological Systems and Bioinformatics (CBB), University of Tehran, Tehran, Iran
| | - Ali Taheri
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, Tenn, United States
| | - Yasoub Shiri
- Agronomy and Plant Breeding Department, Agriculture Research Center, Zabol Research Institute, Zabol, Iran; Department of Horticulture, Faculty of Agriculture and Natural Resources, Mohaghegh Ardabili University, Ardabil, Iran
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49
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Rani P, George B, V S, Biswas S, V M, Pal A, Rajmani RS, Das S. MicroRNA-22-3p displaces critical host factors from the 5' UTR and inhibits the translation of Coxsackievirus B3 RNA. J Virol 2024; 98:e0150423. [PMID: 38289119 PMCID: PMC10883805 DOI: 10.1128/jvi.01504-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024] Open
Abstract
Coxsackievirus B3 (CVB3) is known to cause acute myocarditis and pancreatitis in humans. We investigated the microRNAs (miRNAs) that can potentially govern the viral life cycle by binding to the untranslated regions (UTRs) of CVB3 RNA. MicroRNA-22-3p was short-listed, as its potential binding site overlapped with the region crucial for recruiting internal ribosome entry site trans-acting factors (ITAFs) and ribosomes. We demonstrate that miR-22-3p binds CVB3 5' UTR, hinders recruitment of key ITAFs on viral mRNA, disrupts the spatial structure required for ribosome recruitment, and ultimately blocks translation. Likewise, cells lacking miR-22-3p exhibited heightened CVB3 infection compared to wild type, confirming its role in controlling infection. Interestingly, miR-22-3p level was found to be increased at 4 hours post-infection, potentially due to the accumulation of viral 2A protease in the early phase of infection. 2Apro enhances the miR-22-3p level to dislodge the ITAFs from the SD-like sequence, rendering the viral RNA accessible for binding of replication factors to switch to replication. Furthermore, one of the cellular targets of miR-22-3p, protocadherin-1 (PCDH1), was significantly downregulated during CVB3 infection. Partial silencing of PCDH1 reduced viral replication, demonstrating its proviral role. Interestingly, upon CVB3 infection in mice, miR-22-3p level was found to be downregulated only in the small intestine, the primary target organ, indicating its possible role in influencing tissue tropism. It appears miR-22-3p plays a dual role during infection by binding viral RNA to aid its life cycle as a viral strategy and by targeting a proviral protein to restrict viral replication as a host response.IMPORTANCECVB3 infection is associated with the development of end-stage heart diseases. Lack of effective anti-viral treatments and vaccines for CVB3 necessitates comprehensive understanding of the molecular players during CVB3 infection. miRNAs have emerged as promising targets for anti-viral strategies. Here, we demonstrate that miR-22-3p binds to 5' UTR and inhibits viral RNA translation at the later stage of infection to promote viral RNA replication. Conversely, as host response, it targets PCDH1, a proviral factor, to discourage viral propagation. miR-22-3p also influences CVB3 tissue tropism. Deciphering the multifaced role of miR-22-3p during CVB3 infection unravels the necessary molecular insights, which can be exploited for novel intervening strategies to curb infection and restrict viral pathogenesis.
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Affiliation(s)
- Priya Rani
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Biju George
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Sabarishree V
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Somarghya Biswas
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Madhurya V
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Apala Pal
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Raju S. Rajmani
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- National Institute of Biomedical Genomics, Kalyani, India
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50
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Schindler H, Jawinski P, Arnatkevičiūtė A, Markett S. Molecular signatures of attention networks. Hum Brain Mapp 2024; 45:e26588. [PMID: 38401136 PMCID: PMC10893969 DOI: 10.1002/hbm.26588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/10/2023] [Accepted: 12/22/2023] [Indexed: 02/26/2024] Open
Abstract
Attention network theory proposes three distinct types of attention-alerting, orienting, and control-that are supported by separate brain networks and modulated by different neurotransmitters, that is, norepinephrine, acetylcholine, and dopamine. Here, we explore the extent of cortical, genetic, and molecular dissociation of these three attention systems using multimodal neuroimaging. We evaluated the spatial overlap between fMRI activation maps from the attention network test (ANT) and cortex-wide gene expression data from the Allen Human Brain Atlas. The goal was to identify genes associated with each of the attention networks in order to determine whether specific groups of genes were co-expressed with the corresponding attention networks. Furthermore, we analyzed publicly available PET-maps of neurotransmitter receptors and transporters to investigate their spatial overlap with the attention networks. Our analyses revealed a substantial number of genes (3871 for alerting, 6905 for orienting, 2556 for control) whose cortex-wide expression co-varied with the activation maps, prioritizing several molecular functions such as the regulation of protein biosynthesis, phosphorylation, and receptor binding. Contrary to the hypothesized associations, the ANT activation maps neither aligned with the distribution of norepinephrine, acetylcholine, and dopamine receptor and transporter molecules, nor with transcriptomic profiles that would suggest clearly separable networks. Independence of the attention networks appeared additionally constrained by a high level of spatial dependency between the network maps. Future work may need to reconceptualize the attention networks in terms of their segregation and reevaluate the presumed independence at the neural and neurochemical level.
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Affiliation(s)
| | | | - Aurina Arnatkevičiūtė
- Turner Institute for Brain and Mental Health, School of Psychological SciencesMonash UniversityMelbourneAustralia
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