1
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Aljani B, Lindner A, Weigelt M, Zhao M, Sharma V, Bonifacio E, Jones P, Eugster A. Small RNA-Seq and real time rt-qPCR reveal islet miRNA released under stress conditions. Islets 2024; 16:2392343. [PMID: 39154325 PMCID: PMC11332650 DOI: 10.1080/19382014.2024.2392343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 08/09/2024] [Accepted: 08/09/2024] [Indexed: 08/19/2024] Open
Abstract
Replacement of beta cells through transplantation is a potential therapeutic approach for individuals with pancreas removal or poorly controllable type 1 diabetes. However, stress and death of beta cells pose significant challenges. Circulating miRNA has emerged as potential biomarkers reflecting early beta cell stress and death, allowing for timely intervention. The aim of this study was to identify miRNAs as potential biomarkers for beta cell health. Literature review combined with small RNA sequencing was employed to select islet-enriched miRNA. The release of those miRNA was assessed by RT-qPCR in vivo, using a streptozotocin induced diabetes mouse model and in vitro, through mouse and human islets exposed to varying degrees of hypoxic and cytokine stressors. Utilizing the streptozotocin induced model, we identified 18 miRNAs out of 39 candidate islet-enriched miRNA to be released upon islet stress in vivo. In vitro analysis of culture supernatants from cytokine and/or hypoxia stressed islets identified the release of 45 miRNAs from mouse and 8 miRNAs from human islets. Investigation into the biological pathways targeted by the cytokine- and/or hypoxia-induced miRNA suggested the involvement of MAPK and PI3K-Akt signaling pathways in both mouse and human islets. We have identified miRNAs associated with beta cell health and stress. The findings allowed us to propose a panel of 47 islet-related human miRNA that is potentially valuable for application in clinical contexts of beta cell transplantation and presymptomatic early-stage type 1 diabetes.
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Affiliation(s)
- Bssam Aljani
- Faculty of Medicine, Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Annett Lindner
- Faculty of Medicine, Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Marc Weigelt
- Faculty of Medicine, Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Min Zhao
- German Center for Environmental Health, Institute of Diabetes Research, Helmholtz Munich, Munich, Germany
| | - Virag Sharma
- Faculty of Medicine, Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Ezio Bonifacio
- Faculty of Medicine, Center for Regenerative Therapies Dresden, Dresden, Germany
- Faculty of Medicine, German Center for Diabetes Research (DZD), Paul Langerhans Institute Dresden of Helmholtz Centre Munich at University Clinic Carl Gustav Carus of TU Dresden, Dresden, Germany
| | - Peter Jones
- Department of Diabetes, School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London, London, UK
| | - Anne Eugster
- Faculty of Medicine, Center for Regenerative Therapies Dresden, Dresden, Germany
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2
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Meng Y, Huang X, Zhang G, Fu S, Li Y, Song J, Zhu Y, Xu X, Peng X. MicroRNA-450b-5p modulated RPLP0 promotes hepatocellular carcinoma progression via activating JAK/STAT3 pathway. Transl Oncol 2024; 50:102150. [PMID: 39383650 DOI: 10.1016/j.tranon.2024.102150] [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: 06/12/2024] [Revised: 09/07/2024] [Accepted: 10/02/2024] [Indexed: 10/11/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is distinguished by its insidious onset, difficult treatment, and poor prognosis. Ribosomal Protein Lateral Stalk Subunit P0 (RPLP0) is implicated in numerous tumor progression processes. Nevertheless, the regulatory mechanism of RPLP0 in HCC progression remains unclear. Our study suggested that RPLP0 exhibits high expression levels in HCC and possesses promising diagnostic capabilities, as indicated by its area under the curve (AUC) of 0.908. Further analysis showed that RPLP0 was a significant independent prognostic factor, and elevated expression levels of RPLP0 were linked with poorer overall survival (OS) and progression-free interval (PFI) outcomes. Additionally, reducing RPLP0 levels led to a decrease in HCC cell proliferation, clonality, invasion, migration, and xenograft tumor growth, as well as an increase in apoptosis. Furthermore, our findings indicated that microRNA(miR)-450b-5p induced downregulation of RPLP0, leading to the suppression of the JAK/STAT3 pathway and consequently hindering the advancement of HCC. The study indicates that RPLP0 plays a role as a carcinogenic factor in HCC and carries important diagnostic and prognostic implications. Targeting the miR-450b-5p/RPLP0/JAK/STAT3 axis has potential clinical value in treating HCC.
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Affiliation(s)
- Yanqiu Meng
- Department of Oncology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, PR China
| | - Xianbin Huang
- Department of Oncology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, PR China
| | - Guangxin Zhang
- Department of Oncology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, PR China
| | - Sansan Fu
- Department of Oncology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, PR China
| | - Youhua Li
- Department of Oncology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, PR China
| | - Jielong Song
- Department of Oncology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, PR China
| | - Yizi Zhu
- Department of Oncology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, PR China
| | - Xinping Xu
- Jiangxi Clinical Research Center for Respiratory Diseases, Jiangxi Institute of Respiratory Diseases, The Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, PR China.
| | - Xiaodong Peng
- Department of Oncology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, PR China.
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3
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Corti G, Kim J, Enguita FJ, Guarnieri JW, Grossman LI, Costes SV, Fuentealba M, Scott RT, Magrini A, Sanders LM, Singh K, Sen CK, Juran CM, Paul AM, Furman D, Calleja-Agius J, Mason CE, Galeano D, Bottini M, Beheshti A. To boldly go where no microRNAs have gone before: spaceflight impact on risk for small-for-gestational-age infants. Commun Biol 2024; 7:1268. [PMID: 39369042 PMCID: PMC11455966 DOI: 10.1038/s42003-024-06944-6] [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: 04/03/2024] [Accepted: 09/24/2024] [Indexed: 10/07/2024] Open
Abstract
In the era of renewed space exploration, comprehending the effects of the space environment on human health, particularly for deep space missions, is crucial. While extensive research exists on the impacts of spaceflight, there is a gap regarding female reproductive risks. We hypothesize that space stressors could have enduring effects on female health, potentially increasing risks for future pregnancies upon return to Earth, particularly related to small-for-gestational-age (SGA) fetuses. To address this, we identify a shared microRNA (miRNA) signature between SGA and the space environment, conserved across humans and mice. These miRNAs target genes and pathways relevant to diseases and development. Employing a machine learning approach, we identify potential FDA-approved drugs to mitigate these risks, including estrogen and progesterone receptor antagonists, vitamin D receptor antagonists, and DNA polymerase inhibitors. This study underscores potential pregnancy-related health risks for female astronauts and proposes pharmaceutical interventions to counteract the impact of space travel on female health.
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Affiliation(s)
- Giada Corti
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - JangKeun Kim
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Joseph W Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lawrence I Grossman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | | | - Ryan T Scott
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Andrea Magrini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Lauren M Sanders
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Kanhaiya Singh
- McGowan Institute for Regenerative Medicine and Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chandan K Sen
- McGowan Institute for Regenerative Medicine and Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Cassandra M Juran
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
- Embry-Riddle Aeronautical University, Department of Human Factors and Behavioral Neurobiology, Daytona Beach, FL, USA
| | - Amber M Paul
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
- Embry-Riddle Aeronautical University, Department of Human Factors and Behavioral Neurobiology, Daytona Beach, FL, USA
| | - David Furman
- Buck Institute for Research on Aging, Novato, CA, USA
- Stanford 1000 Immunomes Project, Stanford University School of Medicine, Stanford, CA, USA
| | - Jean Calleja-Agius
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Christopher E Mason
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Diego Galeano
- Facultad de Ingeniería, Universidad Nacional de Asunción, MF9M + 958, San Lorenzo, Paraguay
| | - Massimo Bottini
- Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
- Sanford Children's Health Research Center, Sanford Burnham Prebys, La Jolla, CA, USA
| | - Afshin Beheshti
- McGowan Institute for Regenerative Medicine and Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA.
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Space Biomedicine, University of Pittsburgh, Pittsburgh, PA, USA.
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4
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Sindhu KJ, Nalini V, Suraishkumar GK, Karunagaran D. MiR-34b promotes oxidative stress and induces cellular senescence through TWIST1 in human cervical cancer. Transl Oncol 2024; 48:102063. [PMID: 39094513 PMCID: PMC11342277 DOI: 10.1016/j.tranon.2024.102063] [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: 05/16/2024] [Revised: 06/22/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
PURPOSE The aim of this research was to elucidate the role of miR-34b in cervical cancer progression and the underlying mechanism behind the miR-34b-mediated tumor suppression. The study revealed the role of miR-34b as a senescence inducer and serves as a potential therapeutic target in developing combination therapy with senotherapeutics. METHODS MiR-34b was ectopically expressed in cervical cancer cell lines using a tetracycline inducible system and its effects on cell viability, apoptosis, senescence, DNA damage and oxidative stress were studied using MTT assay, acridine orange/ ethidium bromide staining, senescence associated β-galactosidase assay, gamma H2AX foci staining assay, western blotting and specific dyes for the detection of total and individual ROS species. RESULTS Ectopic expression of miR-34b promoted cellular senescence but no significant induction of apoptosis was observed in cervical cancer cell lines. MiR-34b promoted increase in oxidative stress through increase in total and individual ROS species and contributed to increase in cellular senescence. Mechanistically, miR-34b mediates its action by targeting TWIST1 as evidenced by the similar actions of TWIST1 shRNA in cervical cancer cell lines. Furthermore, our study revealed TWIST1 is one of the most significant targets of miR-34b targetome and identified RITA as a novel senolytic agent for use in combination therapy with miR-34b. CONCLUSION MiR-34b promotes cellular senescence and oxidative stress by targeting TWIST1, a known oncogene and EMT regulator. This study delved into the mechanism of miR-34b-mediated tumor suppression and provided novel insights for development of miR-34b based therapeutics for cervical cancer.
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Affiliation(s)
- K J Sindhu
- Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Venkatesan Nalini
- Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - G K Suraishkumar
- Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India
| | - Devarajan Karunagaran
- Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu 600036, India.
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5
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Heidari N, Vosough M, Bagherifard A, Sami SH, Sarabi PA, Behmanesh A, Shams R. Exploring circulating MiRNA signature for osteosarcoma detection: Bioinformatics-based analyzing and validation. Pathol Res Pract 2024; 263:155615. [PMID: 39378797 DOI: 10.1016/j.prp.2024.155615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 09/15/2024] [Accepted: 09/25/2024] [Indexed: 10/10/2024]
Abstract
Early detection followed by efficient treatment still remain a considerable challenge for osteosarcoma (OS), indicating the importance of emerging innovative diagnostic methods. Circulating miRNAs offer a promising and non-invasive approach to assess the OS molecular landscapes. This study utilized RNAseq data from OS plasma miRNA expression profiles (PRJEB30542) and PCR Array data (GSE65071) from GEO and ENA databases. In total, 43 miRNAs demonstrated significant differential expression in OS samples of training dataset. A diagnostic model, including hsa-miR-30a-5p, hsa-miR-556-3p, hsa-miR-200a-3p, and hsa-miR-582-5p was identified through multivariate logistic regression analysis and demonstrated significant efficacy in differentiating OS patients from healthy controls in the validation group (AUC: 0.917, sensitivity: 1, specificity: 0.85). The result of target gene prediction and functional enrichment analyses revealed significant associations with terms such as epithelial morphogenesis, P53 and Wnt signaling pathways, and neoplasm metastasis. Further bioinformatics-based evaluations showed that the down-regulation of these miRNAs significantly correlates with poor prognosis and lower survival rate in OS patients and propose their tumor suppressor function in pathogenesis of OS. Furthermore, the study developed a miRNA-mRNA subnetwork that connects these miRNAs to the P53 and Wnt signaling pathways, which are critical pathways with oncogenic effects on OS progression. This comprehensive approach not only presents a promising diagnostic model but also proposes potential molecular markers for OS early diagnosis, making prognosis, and targeted therapy. The identified miRNA-mRNA functional axis holds promise as a valuable resource for further research in understanding OS pathogenesis and establishing therapeutic modalities.
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Affiliation(s)
- Negar Heidari
- Department of Cellular and Molecular Biology, Faculty of Sciences and Advanced Technology in Biology, University of Science and Culture, Tehran, Iran.
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Experimental Cancer Medicine, Institution for Laboratory Medicine, Karolinska Institute, Stockholm, Sweden.
| | - Abolfazl Bagherifard
- Bone and Joint Reconstruction Research Center, Department of Orthopedics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Sam Hajialilo Sami
- Bone and Joint Reconstruction Research Center, Department of Orthopedics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Pedram Asadi Sarabi
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
| | - Ali Behmanesh
- Bone and Joint Reconstruction Research Center, Department of Orthopedics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Roshanak Shams
- Bone and Joint Reconstruction Research Center, Department of Orthopedics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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6
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Darvish L, Bahreyni-Toossi MT, Hamid Aghaee-Bakhtiari S, Akbari Naserkiadeh A, Nezamdoust FV, Azimian H. Increasing prostate cancer radiosensitivity by miR-7-5p knockdown of anti-apoptotic genes. Gene 2024; 933:148951. [PMID: 39303820 DOI: 10.1016/j.gene.2024.148951] [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: 03/17/2024] [Revised: 09/12/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
Abstract
Despite the success of radiotherapy for prostate cancer treatment, the recent discovery of radiation resistance prevents it from reaching its full potential. This study aims to use hsa-miR-7-5p for the expression of anti-apoptotic genes. The search for anti-apoptotic genes was carried out through databases. The selected genes included XIAP, MCL1, REL, and BIRC3. Our selection was based on the best miRNA because it has a greater impact on genes. The second step involved transfecting the miRNA into a prostate cancer cell line. Subsequently, radiosensitivity was tested using real-time PCR, clonogenic assay, and annexin V flow cytometry. The highest apoptosis rate in the transfected cells was at 0 Gy in hsa-miR-7-5p (28.88 ± 0.80), plenti III (18.81 ± 0.59), and the control group (4.10 ± 1.52) (P<0.001). Also, its rate was at 4 Gy in hsa-miR-7-5p (36.11 ± 1.93), plenti III (26.42 ± 0.42), and the control group (8.79 ± 2.29) (P<0.001). This study showed a decreasing trend in survival with increasing doses. Suppression of anti-apoptotic genes, including XIAP, MCL1, Birc3, and REL, enhanced radiosensitivity by increasing the expression of hsa-miR-7-5p in the PC3 and LNCaP cell lines. Hsa-miR-7-5p is a miRNA that can suppress the expression of anti-apoptotic genes and thus plays an essential role in the process of cell apoptosis. Targeting genes that are associated with apoptosis could potentially enhance the efficacy of treatments for patients with prostate cancer.
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Affiliation(s)
- Leili Darvish
- Mother and Child Welfare Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran; Department of Radiology, Faculty of Paramedicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | | | - Seyed Hamid Aghaee-Bakhtiari
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Bioinformatics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amin Akbari Naserkiadeh
- Department of Clinical Nutrition, Faculty of Nutrition and Food Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fereshteh Vaziri Nezamdoust
- Medical Physics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hosein Azimian
- Medical Physics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical Physics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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7
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Saranya I, Preetha D, Nivruthi S, Selvamurugan N. A comprehensive bioinformatic analysis of the role of TGF-β1-stimulated activating transcription factor 3 by non-coding RNAs during breast cancer progression. Comput Biol Chem 2024; 113:108208. [PMID: 39276678 DOI: 10.1016/j.compbiolchem.2024.108208] [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: 08/07/2024] [Revised: 09/01/2024] [Accepted: 09/06/2024] [Indexed: 09/17/2024]
Abstract
A potent growth inhibitor for normal mammary epithelial cells is transforming growth factor beta 1 (TGF-β1). When breast tissues lose the anti-proliferative activity of this factor, invasion and bone metastases increase. Human breast cancer (hBC) cells express more activating transcription factor 3 (ATF3) when exposed to TGF-β1, and this transcription factor is essential for BC development and bone metastases. Non-coding RNAs (ncRNAs), including circular RNAs (circRNAs) and microRNAs (miRNAs), have emerged as key regulators controlling several cellular processes. In hBC cells, TGF-β1 stimulated the expression of hsa-miR-4653-5p that putatively targets ATF3. Bioinformatics analysis predicted that hsa-miR-4653-5p targets several key signaling components and transcription factors, including NFKB1, STAT1, STAT3, NOTCH1, JUN, TCF3, p300, NRF2, SUMO2, and NANOG, suggesting the diversified role of hsa-miR-4653-5p under physiological and pathological conditions. Despite the high abundance of hsa-miR-4653-5p in hBC cells, the ATF3 level remained elevated, indicating other ncRNAs could inhibit hsa-miR-4653-5p's activity. In silico analysis identified several circRNAs having the binding sites for hsa-miR-4653-5p, indicating the sponging activity of circRNAs towards hsa-miR-4653-5p. The study's findings suggest that TGF-β1 regulates circRNAs and hsa-miR-4653-5p, which in turn affects ATF3 expression, thus influencing BC progression and bone metastasis. Therefore, focusing on the TGF-β1/circRNAs/hsa-miR-4653-5p/ATF3 network could lead to new ways of diagnosing and treating BC.
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Affiliation(s)
- Iyyappan Saranya
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603 203, India
| | - Dilipkumar Preetha
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603 203, India
| | - Sasi Nivruthi
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603 203, India
| | - Nagarajan Selvamurugan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu 603 203, India.
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8
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Ju M, Zhang Z, Gao F, Chen G, Zhao S, Wang D, Wang H, Jia Y, Shen L, Yuan Y, Yao H. Intranasal Delivery of circATF7IP siRNA via Lipid Nanoparticles Alleviates LPS-induced Depressive-Like Behaviors. Adv Healthc Mater 2024:e2402219. [PMID: 39254274 DOI: 10.1002/adhm.202402219] [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: 06/18/2024] [Revised: 08/30/2024] [Indexed: 09/11/2024]
Abstract
Major depressive disorder (MDD) is a prevalent mental disorder that significantly impacts social and psychological function, but no effective medication is currently available. Circular RNAs (circRNAs) have been reported to participate in the pathogenesis of MDD which are envisioned as promising therapeutic targets. However, nonviral-based delivery strategies targeting circRNA against MDD are not thoroughly investigated. Here, it is identified that circATF7IP is significantly upregulated in plasma samples and positively correlated with 24-Hamilton Depression Scale (HAMD-24) scores of MDD patients. Synergistic amine lipid nanoparticles (SALNPs) are designed to deliver siRNA targeting circATF7IP (si-circATF7IP) into the hippocampus brain region by intranasal administration. Intranasal delivery of SALNP-si-circATF7IP successfully alleviated the depressive-like behaviors in the LPS-induced mouse depression model via decreasing CD11b+CD45dim microglia population and pro-inflammatory cytokine productions (TNF-α and IL-6). These results indicate that the level of circATF7IP positively correlates with MDD pathogenesis, and SALNP delivery of si-circATF7IP via intranasal administration is an effective strategy to ameliorate LPS-induced depressive-like behaviors.
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Affiliation(s)
- Minzi Ju
- Department of Pharmacology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Zhongkun Zhang
- Department of Pharmacology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Feng Gao
- Department of Pharmacology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Gang Chen
- Department of Psychosomatics and Psychiatry, ZhongDa Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
- Institute of Psychosomatics, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
- Department of Psychiatry, the Third People's Hospital of Huai'an, Huai'an, Jiangsu, 223001, China
| | - Sibo Zhao
- Department of Pharmacology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Dan Wang
- Department of Pharmacology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Huijuan Wang
- Department of Pharmacology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Yanpeng Jia
- Department of Pharmacology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Ling Shen
- Department of Pharmacology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Yonggui Yuan
- Department of Psychosomatics and Psychiatry, ZhongDa Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
- Institute of Psychosomatics, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
| | - Honghong Yao
- Department of Pharmacology, Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Medicine, Southeast University, Nanjing, Jiangsu, 210009, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu, 226019, China
- Institute of Life Sciences, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, Jiangsu, 210009, China
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9
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Davoodi Nik B, Hashemi Karoii D, Favaedi R, Ramazanali F, Jahangiri M, Movaghar B, Shahhoseini M. Differential expression of ion channel coding genes in the endometrium of women experiencing recurrent implantation failures. Sci Rep 2024; 14:19822. [PMID: 39192025 PMCID: PMC11349755 DOI: 10.1038/s41598-024-70778-9] [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: 04/14/2024] [Accepted: 08/21/2024] [Indexed: 08/29/2024] Open
Abstract
Our study probed the differences in ion channel gene expression in the endometrium of women with Recurrent Implantation Failure (RIF) compared to fertile women. We analyzed the relative expression of genes coding for T-type Ca2+, ENaC, CFTR, and KCNQ1 channels in endometrial samples from 20 RIF-affected and 10 control women, aged 22-35, via microarray analysis and quantitative real-time PCR. Additionally, we examined DNA methylation in the regulatory region of KCNQ1 using ChIP real-time PCR. The bioinformatics component of our research included Gene Ontology analysis, protein-protein interaction networks, and signaling pathway mapping to identify key biological processes and pathways implicated in RIF. This led to the discovery of significant alterations in the expression of ion channel genes in RIF women's endometrium, most notably an overexpression of CFTR and reduced expression of SCNN1A, SCNN1B, SCNN1G, CACNA1H, and KCNQ1. A higher DNA methylation level of KCNQ1's regulatory region was also observed in RIF patients. Gene-set enrichment analysis highlighted a significant presence of genes involved with ion transport and membrane potential regulation, particularly in sodium and calcium channel complexes, which are vital for cation movement across cell membranes. Genes were also enriched in broader ion channel and transmembrane transporter complexes, underscoring their potential extensive role in cellular ion homeostasis and signaling. These findings suggest a potential involvement of ion channels in the pathology of implantation failure, offering new insights into the mechanisms behind RIF and possible therapeutic targets.
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Affiliation(s)
- Bahar Davoodi Nik
- Department of Genetics, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Danial Hashemi Karoii
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Raha Favaedi
- Department of Genetics, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, ACECR, No. 12, Hafez St., Banihashem Sq, Resalat Ave., P.O. Box: 19395-4644, Tehran, Iran
| | - Fariba Ramazanali
- Department of Endocrinology and Female Infertility, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Maryam Jahangiri
- Department of Embryology, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, ACECR, No. 12, Hafez St., Banihashem Sq, Resalat Ave., P.O. Box: 19395-4644, Tehran, Iran
| | - Bahar Movaghar
- Department of Embryology, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, ACECR, No. 12, Hafez St., Banihashem Sq, Resalat Ave., P.O. Box: 19395-4644, Tehran, Iran.
| | - Maryam Shahhoseini
- Department of Genetics, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran.
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
- Department of Genetics, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, ACECR, No. 12, Hafez St., Banihashem Sq, Resalat Ave., P.O. Box: 19395-4644, Tehran, Iran.
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10
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Khanal R, Heinen N, Bogomolova A, Meister TL, Herrmann ST, Westhoven S, Nocke MK, Todt D, Jockenhövel F, Klein IM, Hartmann L, Vondran FWR, Steinmann E, Zimmer G, Ott M, Brown RJP, Sharma AD, Pfaender S. MicroRNAs modulate SARS-CoV-2 infection of primary human hepatocytes by regulating the entry factors ACE2 and TMPRSS2. Liver Int 2024. [PMID: 39175256 DOI: 10.1111/liv.16079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 08/10/2024] [Indexed: 08/24/2024]
Abstract
BACKGROUND AND AIMS Severe acute respiratory syndrome coronavirus (SARS-CoV-2) preferentially infects the respiratory tract; however, several studies have implicated a multi-organ involvement. Hepatic dysfunctions caused by SARS-CoV-2 infection have been increasingly recognized and described to correlate with disease severity. To elucidate molecular factors that could contribute towards hepatic infection, we concentrated on microRNAs (miRNAs), a class of small non-coding RNAs that modulate various cellular processes and which are reported to be differentially regulated during liver injury. We aimed to study the infection of primary human hepatocytes (PHH) with SARS-CoV-2 and to evaluate the potential of miRNAs for modulating viral infection. METHODS We analysed liver autopsies from a coronavirus disease 19 (COVID-19)-positive cohort for the presence of viral RNA using Nanopore sequencing. PHH were used for the infection with SARS-CoV-2. The candidate miRNAs targeting angiotensin converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) were identified using in silico approaches. To discover the potential regulatory mechanism, transfection experiments, qRT-PCRs, western blots and luciferase reporter assays were performed. RESULTS We could detect SARS-CoV-2 RNA in COVID-19-positive liver autopsies. We show that PHH express ACE2 and TMPRSS2 and can be readily infected with SARS-CoV-2, resulting in robust replication. Transfection of selected miRNA mimics reduced SARS-CoV-2 receptor expression and SARS-CoV-2 burden in PHH. In silico and biochemical analyses supported a potential direct binding of miR-141-3p to the SARS-CoV-2 genome. CONCLUSION We confirm that PHH are susceptible to SARS-CoV-2 infection and demonstrate selected miRNAs targeting SARS-CoV-2 entry factors and/or the viral genome reduce viral loads. These data provide novel insights into hepatic susceptibility to SARS-CoV-2 and associated dysfunctions in COVID-19.
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Affiliation(s)
- Rajendra Khanal
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
- Research Group Liver Regeneration & RNA Therapeutics, REBIRTH-Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Natalie Heinen
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Alexandra Bogomolova
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
- Research Group Liver Regeneration & RNA Therapeutics, REBIRTH-Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Toni L Meister
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
- Institute for Infection Research and Vaccine Development (IIRVD), Centre for Internal Medicine, University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
- Department for Clinical Immunology of Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Centre for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Simon T Herrmann
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
- Research Unit Emerging Viruses, Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Saskia Westhoven
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
- Research Unit Emerging Viruses, Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Maximilian K Nocke
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Daniel Todt
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
- European Virus Bioinformatics Center (EVBC), Jena, Germany
| | - Freya Jockenhövel
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Isabel M Klein
- Tissue Bank of the German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Laura Hartmann
- Tissue Bank of the German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Florian W R Vondran
- Department of General, Visceral, Pediatric and Transplant Surgery, University Hospital RWTH Aachen, Aachen, Germany
| | - Eike Steinmann
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Gert Zimmer
- Institute of Virology and Immunology, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Michael Ott
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Richard J P Brown
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Amar Deep Sharma
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
- Research Group Liver Regeneration & RNA Therapeutics, REBIRTH-Research Center for Translational Regenerative Medicine, Hannover Medical School, Hannover, Germany
| | - Stephanie Pfaender
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
- Research Unit Emerging Viruses, Leibniz Institute of Virology (LIV), Hamburg, Germany
- University of Lübeck, Lübeck, Germany
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11
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Das S, Rai SN. Predicting the Effect of miRNA on Gene Regulation to Foster Translational Multi-Omics Research-A Review on the Role of Super-Enhancers. Noncoding RNA 2024; 10:45. [PMID: 39195574 DOI: 10.3390/ncrna10040045] [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: 06/13/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 08/29/2024] Open
Abstract
Gene regulation is crucial for cellular function and homeostasis. It involves diverse mechanisms controlling the production of specific gene products and contributing to tissue-specific variations in gene expression. The dysregulation of genes leads to disease, emphasizing the need to understand these mechanisms. Computational methods have jointly studied transcription factors (TFs), microRNA (miRNA), and messenger RNA (mRNA) to investigate gene regulatory networks. However, there remains a knowledge gap in comprehending gene regulatory networks. On the other hand, super-enhancers (SEs) have been implicated in miRNA biogenesis and function in recent experimental studies, in addition to their pivotal roles in cell identity and disease progression. However, statistical/computational methodologies harnessing the potential of SEs in deciphering gene regulation networks remain notably absent. However, to understand the effect of miRNA on mRNA, existing statistical/computational methods could be updated, or novel methods could be developed by accounting for SEs in the model. In this review, we categorize existing computational methods that utilize TF and miRNA data to understand gene regulatory networks into three broad areas and explore the challenges of integrating enhancers/SEs. The three areas include unraveling indirect regulatory networks, identifying network motifs, and enriching pathway identification by dissecting gene regulators. We hypothesize that addressing these challenges will enhance our understanding of gene regulation, aiding in the identification of therapeutic targets and disease biomarkers. We believe that constructing statistical/computational models that dissect the role of SEs in predicting the effect of miRNA on gene regulation is crucial for tackling these challenges.
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Affiliation(s)
- Sarmistha Das
- Biostatistics and Informatics Shared Resource, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Cancer Data Science Center, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Division of Biostatistics and Bioinformatics, Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Shesh N Rai
- Biostatistics and Informatics Shared Resource, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Cancer Data Science Center, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Division of Biostatistics and Bioinformatics, Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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12
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Causin RL, Polezi MR, Freitas AJAD, Calfa S, Altei WF, Dias JO, Laus AC, Pessôa-Pereira D, Komoto TT, Evangelista AF, Souza CDP, Reis RM, Marques MMC. EV-miRNAs from breast cancer patients of plasma as potential prognostic biomarkers of disease recurrence. Heliyon 2024; 10:e33933. [PMID: 39104474 PMCID: PMC11298852 DOI: 10.1016/j.heliyon.2024.e33933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 08/07/2024] Open
Abstract
Background Extracellular vesicles (EVs), ubiquitously released by blood cells, facilitate intercellular communication. In cancer, tumor-derived EVs profoundly affect the microenvironment, promoting tumor progression and raising the risk of recurrence. These EVs contain miRNAs (EV-miRNAs), promising cancer biomarkers. Characterizing plasma EVs and identifying EV-miRNAs associated with breast cancer recurrence are crucial aspects of cancer research since they allow us to discover new biomarkers that are effective for understanding tumor biology and for being used for early detection, disease monitoring, or approaches to personalized medicine. This study aimed to characterize plasma EVs in breast cancer (BC) patients and identify EV-miRNAs associated with BC recurrence. Methods This retrospective observational study included 24 BC patients divided into recurrence (n= 11) and non-recurrence (n= 13) groups. Plasma EVs were isolated and characterized. Total RNA from EVs was analyzed for miRNA expression using NanoString's nCounter® miRNA Expression Assays panel. MicroRNA target prediction used mirDIP, and pathway interactions were assessed via Reactome. Results A stronger presence of circulating EVs was found to be linked with a less favorable prognosis (p = 0.0062). We discovered a distinct signature of EV-miRNAs, notably including miR-19a-3p and miR-130b-3p, which are significantly associated with breast cancer recurrence. Furthermore, miR-19a-3p and miR-130b-3p were implicated in the regulation of PTEN and MDM4, potentially contributing to breast cancer progression.A notable association emerged, indicating a high concentration of circulating EVs predicts poor prognosis (p = 0.0062). Our study found a distinct EV-miRNA signature involving miR-19a-3p and miR-130b-3p, strongly associated with disease recurrence. We also presented compelling evidence for their regulatory roles in PTEN and MDM4 genes, contributing to BC development. Conclusion This study revealed that increased plasma EV concentration is associated with BC recurrence. The prognostic significance of EVs is closely tied to the unique expression profiles of miR-19a-3p and miR-130b-3p. These findings underscore the potential of EV-associated miRNAs as valuable indicators for BC recurrence, opening new avenues for diagnosis and treatment exploration.
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Affiliation(s)
- Rhafaela Lima Causin
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
| | - Mariana Regatieri Polezi
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
| | | | - Stéphanie Calfa
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
| | - Wanessa Fernanda Altei
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
- Radiation Oncology Department, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
| | - Júlia Oliveira Dias
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
| | - Ana Carolina Laus
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
| | - Danielle Pessôa-Pereira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
| | - Tatiana Takahasi Komoto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
| | - Adriane Feijó Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
- Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Manguinhos, Rio de Janeiro, 21040-361, Brazil
| | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
- Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, 4710-057, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga, 4710-057, Portugal
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13
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Khemka N, Morris G, Kazemzadeh L, Costard LS, Neubert V, Bauer S, Rosenow F, Venø MT, Kjems J, Henshall DC, Prehn JHM, Connolly NMC. Integrative network analysis of miRNA-mRNA expression profiles during epileptogenesis in rats reveals therapeutic targets after emergence of first spontaneous seizure. Sci Rep 2024; 14:15313. [PMID: 38961125 PMCID: PMC11222454 DOI: 10.1038/s41598-024-66117-7] [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: 05/25/2023] [Accepted: 06/27/2024] [Indexed: 07/05/2024] Open
Abstract
Epileptogenesis is the process by which a normal brain becomes hyperexcitable and capable of generating spontaneous recurrent seizures. The extensive dysregulation of gene expression associated with epileptogenesis is shaped, in part, by microRNAs (miRNAs) - short, non-coding RNAs that negatively regulate protein levels. Functional miRNA-mediated regulation can, however, be difficult to elucidate due to the complexity of miRNA-mRNA interactions. Here, we integrated miRNA and mRNA expression profiles sampled over multiple time-points during and after epileptogenesis in rats, and applied bi-clustering and Bayesian modelling to construct temporal miRNA-mRNA-mRNA interaction networks. Network analysis and enrichment of network inference with sequence- and human disease-specific information identified key regulatory miRNAs with the strongest influence on the mRNA landscape, and miRNA-mRNA interactions closely associated with epileptogenesis and subsequent epilepsy. Our findings underscore the complexity of miRNA-mRNA regulation, can be used to prioritise miRNA targets in specific systems, and offer insights into key regulatory processes in epileptogenesis with therapeutic potential for further investigation.
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Affiliation(s)
- Niraj Khemka
- Centre for Systems Medicine & Dept. of Physiology & Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Gareth Morris
- FutureNeuro SFI Research Centre, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Neuroscience, Physiology and Pharmacology, University College London, London, UK
- Division of Neuroscience, University of Manchester, Manchester, UK
| | - Laleh Kazemzadeh
- Centre for Systems Medicine & Dept. of Physiology & Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Lara S Costard
- Epilepsy Center, Department of Neurology, Philipps University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhine-Main, Neurocenter, University Hospital Frankfurt and Center for Personalized Translational Epilepsy Research, Goethe-University, Frankfurt, Germany
| | - Valentin Neubert
- Epilepsy Center, Department of Neurology, Philipps University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhine-Main, Neurocenter, University Hospital Frankfurt and Center for Personalized Translational Epilepsy Research, Goethe-University, Frankfurt, Germany
| | - Sebastian Bauer
- Epilepsy Center, Department of Neurology, Philipps University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhine-Main, Neurocenter, University Hospital Frankfurt and Center for Personalized Translational Epilepsy Research, Goethe-University, Frankfurt, Germany
| | - Felix Rosenow
- Epilepsy Center, Department of Neurology, Philipps University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhine-Main, Neurocenter, University Hospital Frankfurt and Center for Personalized Translational Epilepsy Research, Goethe-University, Frankfurt, Germany
| | - Morten T Venø
- Interdisciplinary Nanoscience Center, Dept. of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Omiics ApS, Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Dept. of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - David C Henshall
- Centre for Systems Medicine & Dept. of Physiology & Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- FutureNeuro SFI Research Centre, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - Jochen H M Prehn
- Centre for Systems Medicine & Dept. of Physiology & Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
- FutureNeuro SFI Research Centre, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
| | - Niamh M C Connolly
- Centre for Systems Medicine & Dept. of Physiology & Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
- FutureNeuro SFI Research Centre, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
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14
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McDonald JT, Kim J, Farmerie L, Johnson ML, Trovao NS, Arif S, Siew K, Tsoy S, Bram Y, Park J, Overbey E, Ryon K, Haltom J, Singh U, Enguita FJ, Zaksas V, Guarnieri JW, Topper M, Wallace DC, Meydan C, Baylin S, Meller R, Muratani M, Porterfield DM, Kaufman B, Mori MA, Walsh SB, Sigaudo-Roussel D, Mebarek S, Bottini M, Marquette CA, Wurtele ES, Schwartz RE, Galeano D, Mason CE, Grabham P, Beheshti A. Space radiation damage rescued by inhibition of key spaceflight associated miRNAs. Nat Commun 2024; 15:4825. [PMID: 38862542 PMCID: PMC11166944 DOI: 10.1038/s41467-024-48920-y] [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: 12/19/2022] [Accepted: 05/17/2024] [Indexed: 06/13/2024] Open
Abstract
Our previous research revealed a key microRNA signature that is associated with spaceflight that can be used as a biomarker and to develop countermeasure treatments to mitigate the damage caused by space radiation. Here, we expand on this work to determine the biological factors rescued by the countermeasure treatment. We performed RNA-sequencing and transcriptomic analysis on 3D microvessel cell cultures exposed to simulated deep space radiation (0.5 Gy of Galactic Cosmic Radiation) with and without the antagonists to three microRNAs: miR-16-5p, miR-125b-5p, and let-7a-5p (i.e., antagomirs). Significant reduction of inflammation and DNA double strand breaks (DSBs) activity and rescue of mitochondria functions are observed after antagomir treatment. Using data from astronaut participants in the NASA Twin Study, Inspiration4, and JAXA missions, we reveal the genes and pathways implicated in the action of these antagomirs are altered in humans. Our findings indicate a countermeasure strategy that can potentially be utilized by astronauts in spaceflight missions to mitigate space radiation damage.
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Affiliation(s)
- J Tyson McDonald
- Department of Radiation Medicine, Georgetown University School of Medicine, Washington, D.C, USA
| | - JangKeun Kim
- Department of Physiology, Biophysics and Systems Biology and the WorldQuant Initiative, Weill Cornell Medicine, New York, NY, USA
| | - Lily Farmerie
- Vascular Medicine Institute at the University of Pittsburgh Department of Medicine, Pittsburgh, PA, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Meghan L Johnson
- Vascular Medicine Institute at the University of Pittsburgh Department of Medicine, Pittsburgh, PA, USA
| | - Nidia S Trovao
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Shehbeel Arif
- Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Neurosurgery, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Keith Siew
- London Tubular Centre, Department of Renal Medicine, University College London, London, UK
| | - Sergey Tsoy
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jiwoon Park
- Department of Physiology, Biophysics and Systems Biology and the WorldQuant Initiative, Weill Cornell Medicine, New York, NY, USA
| | - Eliah Overbey
- Department of Physiology, Biophysics and Systems Biology and the WorldQuant Initiative, Weill Cornell Medicine, New York, NY, USA
| | - Krista Ryon
- Department of Physiology, Biophysics and Systems Biology and the WorldQuant Initiative, Weill Cornell Medicine, New York, NY, USA
| | - Jeffrey Haltom
- The Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Urminder Singh
- Bioinformatics and Computational Biology Program, Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 90011, USA
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Victoria Zaksas
- Center for Translational Data Science, University of Chicago, Chicago, IL, 60637, USA
- Clever Research Lab, Springfield, IL, 62704, USA
| | - Joseph W Guarnieri
- The Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Michael Topper
- Departments of Oncology and Medicine and the Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Douglas C Wallace
- The Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Division of Human Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
| | - Cem Meydan
- Department of Physiology, Biophysics and Systems Biology and the WorldQuant Initiative, Weill Cornell Medicine, New York, NY, USA
| | - Stephen Baylin
- Departments of Oncology and Medicine and the Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Robert Meller
- Neuroscience Institute, Department of Neurobiology/ Department of Pharmacology and Toxicology, Morehouse School of Medicine, Atlanta, GA, 30310, USA
| | - Masafumi Muratani
- Transborder Medical Research Center, University of Tsukuba, Ibaraki, 305-8575, Japan
- Department of Genome Biology, Institute of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan
| | - D Marshall Porterfield
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Brett Kaufman
- Vascular Medicine Institute at the University of Pittsburgh Department of Medicine, Pittsburgh, PA, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Marcelo A Mori
- Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas, Campinas, SP, Brazil
- Obesity and Comorbidities Research Center (OCRC), Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Stephen B Walsh
- London Tubular Centre, Department of Renal Medicine, University College London, London, UK
| | | | - Saida Mebarek
- ICBMS, UMR5246, CNRS, INSA, CPE-Lyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Massimo Bottini
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Christophe A Marquette
- 3d.FAB, CNRS, INSA, CPE-Lyon, UMR5246, ICBMS, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 90011, USA
- Genetics Program, Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 90011, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Diego Galeano
- Facultad de Ingeniería, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Christopher E Mason
- Department of Physiology, Biophysics and Systems Biology and the WorldQuant Initiative, Weill Cornell Medicine, New York, NY, USA
| | - Peter Grabham
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University, New York, NY, USA.
| | - Afshin Beheshti
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, US.
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15
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Balasundaram A, Mitra TS, Tayubi IA, Zayed H, Doss GPC. Deciphering the miRNA-mRNA Interaction Landscape between Breast Cancer and Triple-Negative Breast Cancer: An Integrated Bioinformatics Approach. ACS OMEGA 2024; 9:24379-24395. [PMID: 38882157 PMCID: PMC11170726 DOI: 10.1021/acsomega.4c00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/13/2024] [Accepted: 04/19/2024] [Indexed: 06/18/2024]
Abstract
Breast cancer (BC) is globally recognized as the second most prevalent form of cancer. It predominantly affects women and can be categorized into distinct types based on the overexpression of specific cancer receptors.The key receptors implicated in this context are the human epidermal growth factor receptor-2 (HER2), estrogen receptor (ER), and progesterone receptor (PR), alongside a particularly intricate subclass known as triple-negative breast cancer (TNBC). This subclassification is critical for the stratification of breast cancer and informs therapeutic decision-making processes. Due to a lack of therapeutic targets, such as growth factor receptors, TNBC is the most aggressive type. Hence, identifying targetable regulators such as miRNAs could pave the way for potential therapeutic interventions. To identify common differentially expressed mRNAs (DE-mRNAs) in BC, including TNBC, we leveraged two data sets from the GEO collection and The Cancer Genome Atlas (TCGA). Significant DE-mRNAs were identified through PPI, MCODE, CytoNCA, and CytoHubba analyses. Following this, miRNAs were predicted using mirDIP. We utilized GSE42568, GSE185645, and TCGA and identified 159 common DE-mRNAs. Using Cytoscape plug-ins, we identified the 10 most significant DE-mRNAs in BC. Using mirDIP, target miRNAs for 10 DE-mRNAs were identified. We conducted an advanced analysis on the TNBC GEO data set (GSE45498) to corroborate the significance of shared DE-mRNAs and DE-miRNAs in TNBC. We identified four downregulated DE-miRNAs, including hsa-miR-802, hsa-miR-1258, hsa-miR-548a-3p, and hsa-miR-2053, significantly associated with TNBC. Our study revealed significant miRNA-mRNA interactions, specifically hsa-miR-802/MELK, hsa-miR-1258/NCAPG, miR-548a-3p/CCNA2, and hsa-miR-2053/NUSAP1, in both BC and TNBC. The observed downregulation of hsa-miR-548a-3p is associated with diminished survival rates in BC patients, emphasizing their potential utility as prognostic indicators. Furthermore, the differential expression of mRNAs, including CCNB2, UBE2C, MELK, and KIF2C, correlates with reduced survival outcomes, signifying their critical role as potential targets for therapeutic intervention in both BC and TNBC. These findings highlight specific regulatory mechanisms that are potentially crucial for understanding and treating these cancer types.
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Affiliation(s)
- Ambritha Balasundaram
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Tanisha Saurav Mitra
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - Iftikhar Aslam Tayubi
- Department of Computer Science, Faculty of Computing and Information Technology, Rabigh (FCITR), King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha 2713, Qatar
| | - George Priya C Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
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16
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Wang Y, Li S, Hu M, Yang Y, McCabe E, Zhang L, Withrow AM, Ting JPY, Liu R. Universal STING mimic boosts antitumour immunity via preferential activation of tumour control signalling pathways. NATURE NANOTECHNOLOGY 2024; 19:856-866. [PMID: 38480836 DOI: 10.1038/s41565-024-01624-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 01/29/2024] [Indexed: 03/21/2024]
Abstract
The efficacy of STING (stimulator of interferon genes) agonists is due to various factors, primarily inefficient intracellular delivery, low/lack of endogenous STING expression in many tumours, and a complex balance between tumour control and progression. Here we report a universal STING mimic (uniSTING) based on a polymeric architecture. UniSTING activates STING signalling in a range of mouse and human cell types, independent of endogenous STING expression, and selectively stimulates tumour control IRF3/IFN-I pathways, but not tumour progression NF-κB pathways. Intratumoural or systemic injection of uniSTING-mRNA via lipid nanoparticles (LNPs) results in potent antitumour efficacy across established and advanced metastatic tumour models, including triple-negative breast cancer, lung cancer, melanoma and orthotopic/metastatic liver malignancies. Furthermore, uniSTING displays an effective antitumour response superior to 2'3'-cGAMP and ADU-S100. By favouring IRF3/IFN-I activity over the proinflammatory NF-κB signalling pathway, uniSTING promotes dendritic cell maturation and antigen-specific CD8+ T-cell responses. Extracellular vesicles released from uniSTING-treated tumour cells further sensitize dendritic cells via exosome-containing miRNAs that reduced the immunosuppressive Wnt2b, and a combination of LNP-uniSTING-mRNA with α-Wnt2b antibodies synergistically inhibits tumour growth and prolongs animal survival. Collectively, these results demonstrate the LNP-mediated delivery of uniSTING-mRNA as a strategy to overcome the current STING therapeutic barriers, particularly for the treatment of multiple cancer types in which STING is downregulated or absent.
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Affiliation(s)
- Ying Wang
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sirui Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mengying Hu
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Yuchen Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Ellie McCabe
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lillian Zhang
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrew M Withrow
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jenny P-Y Ting
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Rihe Liu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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17
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Dimoff Z, Lofft Z, Liang F, Chen S, Massara P, Wu D, Paetau-Robinson I, Khoo C, Taibi A, Comelli EM. Data on microRNA expression, predicted gene targets and pathway analysis in response to different concentrations of a cranberry proanthocyanidin-rich extract and its metabolite 3-(4-hydroxyphenyl)-propionic acid in intestinal Caco-2BBe1 cells. Data Brief 2024; 54:110238. [PMID: 38516278 PMCID: PMC10951455 DOI: 10.1016/j.dib.2024.110238] [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: 12/05/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/23/2024] Open
Abstract
Cranberry-derived proanthocyanidin (PAC) is processed by the gut microbiota to produce 3-(4-hydroxyphenyl)-propionic acid (HPPA), among other metabolites. These data are in support of the article entitled, "Cranberry proanthocyanidin and its microbial metabolite 3,4-dihydroxyphenylacetic acid, but not 3-(4-hydroxyphenyl)-propionic acid, partially reverse pro-inflammatory microRNA responses in human intestinal epithelial cells," published in Molecular Nutrition and Food Research [1]. Here we describe data generated by nCounterⓇ Human v3 miRNA Expression Panel of RNA obtained from Caco-2BBe1 cells exposed to two different concentrations of cranberry extract rich in PAC (50 µg/ml or 100 µg/ml) or 3-(4-hydroxyphenyl)-propionic acid (5 µg/ml or 10 µg/ml) for 24 h, then stimulated with 1 ng/ml of IL-1ß or not (mock) for three hours. The raw data are publicly available at the NCBI GEO database GSE237078. This work also includes descriptive methodological procedures, treatment-responsive microRNA (miRNA) expression profiles in Caco-2BBe1 cells, and in silico mRNA gene target and pathway enrichment analyses of significantly differentially expressed miRNAs (q < 0.001). Cranberry and its components have recognized health benefits, particularly in relation to combatting inflammation and pathogenic bacterial adhesion. These data will be valuable as a reference to study the response of intestinal cells to other polyphenol-rich food sources, analyze gut microbial responses to cranberry and its metabolites in different cell lines and mammalian hosts to elucidate individualized effects, and to delineate the role of the gut microbiota in facilitating the benefits of cranberry. Moreover, these data will aid in expanding our knowledge on the mechanisms underlying the benefits of cranberry and its components.
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Affiliation(s)
- Zoe Dimoff
- Department of Nutritional Sciences2, University of Toronto, ON, Canada
| | - Zoe Lofft
- Department of Nutritional Sciences2, University of Toronto, ON, Canada
| | - Fred Liang
- Department of Nutritional Sciences2, University of Toronto, ON, Canada
| | - Siying Chen
- Department of Nutritional Sciences2, University of Toronto, ON, Canada
| | - Paraskevi Massara
- Department of Nutritional Sciences2, University of Toronto, ON, Canada
| | - Diana Wu
- Department of Nutritional Sciences2, University of Toronto, ON, Canada
| | | | - Christina Khoo
- Ocean Spray Cranberries, Inc., Lakeville-Middleboro, MA 02349, USA
| | - Amel Taibi
- Department of Nutritional Sciences2, University of Toronto, ON, Canada
| | - Elena M. Comelli
- Department of Nutritional Sciences2, University of Toronto, ON, Canada
- Joannah and Brian Lawson Centre for Child Nutrition, University of Toronto, ON, Canada
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18
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Bloomquist R, Mondal AK, Vashisht A, Sahajpal N, Jones K, Vashisht V, Singh H, Farmaha J, Kolhe R. Gene Regulatory Network Analysis of Post-Mortem Lungs Unveils Novel Insights into COVID-19 Pathogenesis. Viruses 2024; 16:853. [PMID: 38932146 PMCID: PMC11209433 DOI: 10.3390/v16060853] [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: 05/02/2024] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
The novel coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has emerged as one of the most significant global health crises in recent history. The clinical characteristics of COVID-19 patients have revealed the possibility of immune activity changes contributing to disease severity. Nevertheless, limited information is available regarding the immune response in human lung tissue, which is the primary site of infection. In this study, we conducted an extensive analysis of lung tissue to screen for differentially expressed miRNAs and mRNAs in five individuals who died due to COVID-19 and underwent a rapid autopsy, as well as seven control individuals who died of other causes unrelated to COVID-19. To analyze the host response gene expression, miRNA microarray and Nanostring's nCounter XT gene expression assay were performed. Our study identified 37 downregulated and 77 upregulated miRNAs in COVID-19 lung biopsy samples compared to the controls. A total of 653 mRNA transcripts were differentially expressed between the two sample types, with most transcripts (472) being downregulated in COVID-19-positive specimens. Hierarchical and PCA K-means clustering analysis showed distinct clustering between COVID-19 and control samples. Enrichment and network analyses revealed differentially expressed genes important for innate immunity and inflammatory response in COVID-19 lung biopsies. The interferon-signaling pathway was highly upregulated in COVID-19 specimens while genes involved in interleukin-17 signaling were downregulated. These findings shed light on the mechanisms of host cellular responses to COVID-19 infection in lung tissues and could help identify new targets for the prevention and treatment of COVID-19 infection.
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Affiliation(s)
- Ryan Bloomquist
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
- School of Medicine, University of South Carolina, Columbia, SC 29209, USA
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | - Ashutosh Vashisht
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | | | - Kimya Jones
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | - Vishakha Vashisht
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | - Harmanpreet Singh
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | - Jaspreet Farmaha
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30909, USA; (R.B.); (A.K.M.); (A.V.); (K.J.); (V.V.); (H.S.); (J.F.)
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19
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Zhang M, Niu Z, Huang Q, Han L, Du J, Liang J, Cheng Y, Cao R, Yawalkar N, Zhang Z, Yan K. Identification of an exosomal miRNA-mRNA regulatory network contributing to methotrexate efficacy. Int Immunopharmacol 2024; 135:112280. [PMID: 38776848 DOI: 10.1016/j.intimp.2024.112280] [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: 08/12/2023] [Revised: 05/05/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024]
Abstract
OBJECTIVE Methotrexate (MTX) is an economic and effective medicine treatment for psoriasis. Extracellular vesicle (EV) miRNA biomarkers related to its efficiency have been identified in various diseases. Whether certain miRNA profiles are associated with psoriasis treatment is unknown. In order to determine specific miRNA biomarkers for MTX effectiveness prediction and the severity of psoriasis, our study looked at the variations in circulating EV miRNA profiles before and after MTX therapy. METHODS Plasma EV isolation and next-generation sequencing were performed to identify differentially expressed EV miRNAs between GRs (n = 14) and NRs (n = 6). Univariate and multiple linear regression analyses were performed to evaluate the correlation between PASI scores and miRNA expression levels. RESULTS 15 miRNAs out of a total profile of 443 miRNAs were substantially different between GRs and NRs at baseline, 4 of them (miR-199a-5p, miR-195-5p, miR-196a-5p, and miR-1246) have the potential to distinguish between GRs and NRs [area under the curve (AUC) ≥ 0.70, all P < 0.05]. KEGG pathway analyses revealed differentially expressed miRNAs to potentially target immune-related pathways. SIRT1 was discovered to be a target of miR-199a-5p and involved in MAPK signaling pathway. MiR-191-5p and miR-21-5p expression levels have been discovered to positively correlate with PASI scores[P < 0.05]. CONCLUSION This pilot investigation found that miR-199a-5p, miR-195-5p, miR-196a-5p, and miR-1246 might be prospective biomarkers to predict the efficacy of MTX, and that miR-191-5p and miR-21-5p were correlated with psoriasis severity. Five of them previously reported to be involved in MAPK signaling pathway, indicating a potential role of MTX in delaying the progression of psoriatic inflammation.
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Affiliation(s)
- Mengmeng Zhang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhenmin Niu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Qiong Huang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Ling Han
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Juan Du
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jun Liang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yanwen Cheng
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Ruoshui Cao
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Nikhil Yawalkar
- Department of Dermatology, Inselspital, Bern University Hospital, University of Bern, Switzerland
| | - Zhenghua Zhang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China.
| | - Kexiang Yan
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China.
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20
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Zhao H, Meng L, Du P, Liao X, Mo X, Gong M, Chen J, Liao Y. IDH1 mutation produces R-2-hydroxyglutarate (R-2HG) and induces mir-182-5p expression to regulate cell cycle and tumor formation in glioma. Biol Res 2024; 57:30. [PMID: 38760850 PMCID: PMC11100189 DOI: 10.1186/s40659-024-00512-2] [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: 10/31/2023] [Accepted: 05/02/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Mutations in isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2), are present in most gliomas. IDH1 mutation is an important prognostic marker in glioma. However, its regulatory mechanism in glioma remains incompletely understood. RESULTS miR-182-5p expression was increased within IDH1-mutant glioma specimens according to TCGA, CGGA, and online dataset GSE119740, as well as collected clinical samples. (R)-2-hydroxyglutarate ((R)-2HG) treatment up-regulated the expression of miR-182-5p, enhanced glioma cell proliferation, and suppressed apoptosis; miR-182-5p inhibition partially eliminated the oncogenic effects of R-2HG upon glioma cells. By direct binding to Cyclin Dependent Kinase Inhibitor 2 C (CDKN2C) 3'UTR, miR-182-5p inhibited CDKN2C expression. Regarding cellular functions, CDKN2C knockdown promoted R-2HG-treated glioma cell viability, suppressed apoptosis, and relieved cell cycle arrest. Furthermore, CDKN2C knockdown partially attenuated the effects of miR-182-5p inhibition on cell phenotypes. Moreover, CDKN2C knockdown exerted opposite effects on cell cycle check point and apoptosis markers to those of miR-182-5p inhibition; also, CDKN2C knockdown partially attenuated the functions of miR-182-5p inhibition in cell cycle check point and apoptosis markers. The engineered CS-NPs (antagomir-182-5p) effectively encapsulated and delivered antagomir-182-5p, enhancing anti-tumor efficacy in vivo, indicating the therapeutic potential of CS-NPs(antagomir-182-5p) in targeting the miR-182-5p/CDKN2C axis against R-2HG-driven oncogenesis in mice models. CONCLUSIONS These insights highlight the potential of CS-NPs(antagomir-182-5p) to target the miR-182-5p/CDKN2C axis, offering a promising therapeutic avenue against R-2HG's oncogenic influence to glioma.
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Affiliation(s)
- Haiting Zhao
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
- Department of Neurology, Xiangya Hospital, The Central South University (CSU), Changsha, 410008, P.R. China
| | - Li Meng
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
- Department of Radiology, Xiangya Hospital, Central South University (CSU), Changsha, 410008, P.R. China
| | - Peng Du
- Department of Neurosurgery, The Second Affiliated Hospital, Xinjiang Medical University, Urumqi, 830063, PR China
| | - Xinbin Liao
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
- Department of Neurosurgery, Xiangya Hospital, Central South University (CSU), Changsha, 410008, P.R. China
| | - Xin Mo
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
- Department of Neurosurgery, Xiangya Hospital, Central South University (CSU), Changsha, 410008, P.R. China
| | - Mengqi Gong
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
- Department of Neurosurgery, Xiangya Hospital, Central South University (CSU), Changsha, 410008, P.R. China
| | - Jiaxin Chen
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
- Department of Neurology, Xiangya Hospital, The Central South University (CSU), Changsha, 410008, P.R. China
| | - Yiwei Liao
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China.
- Department of Neurosurgery, Xiangya Hospital, Central South University (CSU), Changsha, 410008, P.R. China.
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21
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Kubat Oktem E. Biomarkers of Alzheimer's Disease Associated with Programmed Cell Death Reveal Four Repurposed Drugs. J Mol Neurosci 2024; 74:51. [PMID: 38700745 DOI: 10.1007/s12031-024-02228-0] [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: 12/29/2023] [Accepted: 04/21/2024] [Indexed: 07/20/2024]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder and the most common cause of dementia. Programmed cell death (PCD) is mainly characterized by unique morphological features and energy-dependent biochemical processes. The predominant pathway leading to cell death in AD has not been thoroughly analyzed, although there is evidence of neuron loss in AD and numerous pathways of PCD have been associated with this process. A better understanding of the systems biology underlying the relationship between AD and PCD could lead to the development of new therapeutic approaches. To this end, publicly available transcriptome data were examined using bioinformatic methods such as differential gene expression and weighted gene coexpression network analysis (WGCNA) to find PCD-related AD biomarkers. The diagnostic significance of these biomarkers was evaluated using a logistic regression-based predictive model. Using these biomarkers, a multifactorial regulatory network was developed. Last, a drug repositioning study was conducted to propose new drugs for the treatment of AD targeting PCD. The development of 3PM (predictive, preventive, and personalized) drugs for the treatment of AD would be enabled by additional research on the effects of these drugs on this disease.
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Affiliation(s)
- Elif Kubat Oktem
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Istanbul Medeniyet University, North Campus, Istanbul, 34700, Turkey.
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22
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Guo Y, Huang C, Qiu L, Fu J, Xu C, Yang F. CircTHBS1 promotes trophoblast cell migration and invasion and inhibits trophoblast apoptosis by regulating miR-136-3p/IGF2R axis. FASEB J 2024; 38:e23598. [PMID: 38581244 DOI: 10.1096/fj.202302113rr] [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: 10/17/2023] [Revised: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 04/08/2024]
Abstract
The precise molecular mechanism behind fetal growth restriction (FGR) is still unclear, although there is a strong connection between placental dysfunction, inadequate trophoblast invasion, and its etiology and pathogenesis. As a new type of non-coding RNA, circRNA has been shown to play a crucial role in the development of FGR. This investigation identified the downregulation of hsa_circ_0034533 (circTHBS1) in FGR placentas through high-sequencing analysis and confirmed this finding in 25 clinical placenta samples using qRT-PCR. Subsequent in vitro functional assays demonstrated that silencing circTHBS1 inhibited trophoblast proliferation, migration, invasion, and epithelial mesenchymal transition (EMT) progression and promoted apoptosis. Furthermore, when circTHBS1 was overexpressed, cell function experiments showed the opposite result. Analysis using fluorescence in situ hybridization revealed that circTHBS1 was primarily found in the cytoplasmic region. Through bioinformatics analysis, we anticipated the involvement of miR-136-3p and IGF2R in downstream processes, which was subsequently validated through qRT-PCR and dual-luciferase assays. Moreover, the inhibition of miR-136-3p or the overexpression of IGF2R partially reinstated proliferation, migration, and invasion abilities following the silencing of circTHBS1. In summary, the circTHBS1/miR-136-3p/IGF2R axis plays a crucial role in the progression and development of FGR, offering potential avenues for the exploration of biological indicators and treatment targets.
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Affiliation(s)
- Yanyan Guo
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Chuyi Huang
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Liyan Qiu
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jiahui Fu
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Cailing Xu
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Fang Yang
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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23
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Khorsand M, Mostafavi-Pour Z, Tahmasebi A, Omidvar Kordshouli S, Mousavi P. Construction of lncRNA/Pseudogene-miRNA Network Based on In Silico Approaches for Glycolysis Pathway to Identify Prostate Adenocarcinoma-Related Potential Biomarkers. Appl Biochem Biotechnol 2024; 196:2332-2355. [PMID: 37542606 DOI: 10.1007/s12010-023-04617-4] [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] [Accepted: 07/01/2023] [Indexed: 08/07/2023]
Abstract
LncRNAs, pseudogenes, and miRNAs participate a fundamental function in tumorigenesis, metabolism, and invasion of cancer cells, although their regulation of tumor glycolysis in prostate adenocarcinoma (PRAD) is thoroughly not well studied. In this study, we applied transcriptomic, proteomic, and medical information to identify glycolysis-related key genes and modules associated with PRAD. Then, the glycolysis-related lncRNA/lncRNAs/pseudogenes-miRNA-mRNA network was constructed. Analysis of DNA methylation status and expression data determined a DNA methylation-dysregulated three-DE-mRNAs signature for predicting diagnosis, ANGPTL4, GNE, and HSPA in PRAD patients and healthy control. Several lncRNAs/pseudogenes, significantly correlated with the overall survival PVT1, CA5BP1, MIRLET7BHG, SNHG12, and ZNF37BP and disease-free survival status, MALAT1, GUSBP11, MIRLET7BHG, and SNHG1, of patients with PRAD were determined. The methylation profile of DE-lncRNA/pseudogenes was significantly proper for predicting PRAD prognostic model. The transcription level of 6 DE-mRNA ANGPTL4, QSOX1, BIK, CLDN3, DDIT4, and TFF3 was correlated with cancer-related fibroblast infiltration in PRAD. The mutated form of 7 mRNAs, COL5A1, IDH1, HK2, DDIT4, GNE, and QSOX1, was associated with PRAD. In addition to the glycolysis pathway, DE-RNAs play regulatory roles on several pathways, including DNA damage, RTK, cell cycle, RAS/MAPK, TSC/mTOR and PI3K/AKT, AR hormone, and EMT. Overall, our study improves our knowledge of the relation between lncRNAs/pseudogenes and miRNA related to glycolysis and PRAD pathogenesis.
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Affiliation(s)
- Marjan Khorsand
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Laboratory Science, Paramedical School, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zohreh Mostafavi-Pour
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | | | - Pegah Mousavi
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
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24
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Yuan YY, Wu H, Chen QY, Fan H, Shuai B. Construction of the underlying circRNA-miRNA-mRNA regulatory network and a new diagnostic model in ulcerative colitis by bioinformatics analysis. World J Clin Cases 2024; 12:1606-1621. [PMID: 38576737 PMCID: PMC10989427 DOI: 10.12998/wjcc.v12.i9.1606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/02/2024] [Accepted: 03/04/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) are involved in the pathogenesis of many diseases through competing endogenous RNA (ceRNA) regulatory mechanisms. AIM To investigate a circRNA-related ceRNA regulatory network and a new predictive model by circRNA to understand the diagnostic mechanism of circRNAs in ulcerative colitis (UC). METHODS We obtained gene expression profiles of circRNAs, miRNAs, and mRNAs in UC from the Gene Expression Omnibus dataset. The circRNA-miRNA-mRNA network was constructed based on circRNA-miRNA and miRNA-mRNA interactions. Functional enrichment analysis was performed to identify the biological mechanisms involved in circRNAs. We identified the most relevant differential circRNAs for diagnosing UC and constructed a new predictive nomogram, whose efficacy was tested with the C-index, receiver operating characteristic curve (ROC), and decision curve analysis (DCA). RESULTS A circRNA-miRNA-mRNA regulatory network was obtained, containing 12 circRNAs, three miRNAs, and 38 mRNAs. Two optimal prognostic-related differentially expressed circRNAs, hsa_circ_0085323 and hsa_circ_0036906, were included to construct a predictive nomogram. The model showed good discrimination, with a C-index of 1(> 0.9, high accuracy). ROC and DCA suggested that the nomogram had a beneficial diagnostic ability. CONCLUSION This novel predictive nomogram incorporating hsa_circ_0085323 and hsa_circ_0036906 can be conveniently used to predict the risk of UC. The circRNa-miRNA-mRNA network in UC could be more clinically significant.
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Affiliation(s)
- Yu-Yi Yuan
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Hui Wu
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Qian-Yun Chen
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Heng Fan
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Bo Shuai
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
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25
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Ahmadi M, Fathi M, Malmir A, Ghafouri-Fard S. Role of circular RNA/miRNA axes in the pathophysiology of polycystic ovary syndrome. Mol Biol Rep 2024; 51:437. [PMID: 38520572 DOI: 10.1007/s11033-024-09376-x] [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: 12/06/2023] [Accepted: 02/23/2024] [Indexed: 03/25/2024]
Abstract
Polycystic ovary syndrome (PCOS) is a disorder resulted from interactions between genetic and environmental factors. Based on the importance of epigenetic factors in the pathoetiology of PCOS, the current review focused on identification of circular RNAs (circRNAs) that are involved in PCOS through acting as molecular sponges for microRNAs (miRNAs). The literature search led to identification of circ_0043533/miR-1179, circ_0030018/miR-136, circ_FURIN/miR-423-5p, circ-FURIN/miR-195-5p, circ_0043532/miR-182, circ_RANBP9/miR-136-5p, circRHBG/miR-515-5p, circMTO1/miR-320b, circASPH/miR-375, circPSMC3/miR-296-3p, circLDLR/miR-1294, circPUM1/miR-760, and hsa_circ_0118530/miR-136 as molecular axes contributing to the pathogenesis of PCOS. To set the stage for future research on the role of the ceRNA network in PCOS, in-silico analyses were performed using miRWalk, miRNet, and miRDIP databases. miRWalk identified 80 genes regulated by 5 miRNAs, miRNet revealed 6449 circRNAs potentially controlling 11 miRNAs, and miRDIP identified 11 miRNAs associated with 35 human pathways. These targets can be used in the treatment options, design of personalized medicine and prediction of prognosis of PCOS.
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Affiliation(s)
- Mohsen Ahmadi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohadeseh Fathi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Malmir
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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26
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Yi H, Liu L, Zhang J, Guo K, Cao Y, Sun P, Wang H. GALNT2 targeted by miR-139-5p promotes proliferation of clear cell renal cell carcinoma via inhibition of LATS2 activation. Discov Oncol 2024; 15:73. [PMID: 38478152 PMCID: PMC10937861 DOI: 10.1007/s12672-024-00930-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/08/2024] [Indexed: 03/17/2024] Open
Abstract
Polypeptide N-Acetylgalactosaminyltransferase (GALNTs) are critical enzymes that initiate mucin type-O glycosylation, and are closely associated with the occurrence and development of multiple cancers. However, the significance of GALNT2 in clear cell renal cell carcinoma (ccRCC) progression remains largely undetermined. Based on public multi-omics analysis, GALNT2 was strongly elevated in ccRCC versus adjoining nontumor tissues, and it displayed a relationship with poor overall survival (OS) of ccRCC patients. In addition, GALNT2 over-expression accelerated proliferation of renal cancer cell (RCC) lines. In contrast, GALNT2 knockdown using shRNAs suppressed cell proliferation, and this was rescued by LATS2 knockdown. Similarly, GALNT2 deficiency enhanced p-LATS2/LATS2 expression. LATS2 is activated by phosphorylation (p-LATS2) and, in turn, phosphorylate the downstream substrate protein YAP. Phosphorylated YAP (p-YAP) stimulated its degradation and cytoplasmic retention, as it was unable to translocate to the nucleus. This resulted in reduced cell proliferation. Subsequently, we explored the upstream miRNAs of GALNT2. Using dual luciferase reporter assay, we revealed that miR-139-5p interacted with the 3' UTR of GALNT2. Low miR-139-5p expression was associated with worse ccRCC patient outcome. Based on our experiments, miR-139-5p overexpression inhibited RCC proliferation, and this phenotype was rescued by GALNT2 overexpression. Given these evidences, the miR-139-5p-GALNT2-LATS2 axis is critical for RCC proliferation, and it is an excellent candidate for a new therapeutic target in ccRCC.
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Affiliation(s)
- Haisheng Yi
- Department of Andrology, The First Hospital of Jilin University, Changchun, 130012, China
| | - Lingyun Liu
- Department of Andrology, The First Hospital of Jilin University, Changchun, 130012, China
| | - Jingshun Zhang
- Reproductive Medical Center, Department of Obstetrics and Gynecology, The Second Hospital of Jilin University, Changchun, 130041, China
| | - Kaimin Guo
- Department of Andrology, The First Hospital of Jilin University, Changchun, 130012, China
| | - Yin Cao
- Department of Andrology, The First Hospital of Jilin University, Changchun, 130012, China
| | - Penghao Sun
- Department of Andrology, The First Hospital of Jilin University, Changchun, 130012, China
| | - Hongliang Wang
- Department of Andrology, The First Hospital of Jilin University, Changchun, 130012, China.
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27
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Iftimovici A, He Q, Jiao C, Duchesnay E, Krebs MO, Kebir O, Chaumette B. Longitudinal MicroRNA Signature of Conversion to Psychosis. Schizophr Bull 2024; 50:363-373. [PMID: 37607340 PMCID: PMC10919777 DOI: 10.1093/schbul/sbad080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
BACKGROUND AND HYPOTHESIS The emergence of psychosis in ultra-high-risk subjects (UHR) is influenced by gene-environment interactions that rely on epigenetic mechanisms such as microRNAs. However, whether they can be relevant pathophysiological biomarkers of psychosis' onset remains unknown. STUDY DESIGN We present a longitudinal study of microRNA expression, measured in plasma by high-throughput sequencing at baseline and follow-up, in a prospective cohort of 81 UHR, 35 of whom developed psychosis at follow-up (converters). We combined supervised machine learning and differential graph analysis to assess the relative weighted contribution of each microRNA variation to the difference in outcome and identify outcome-specific networks. We then applied univariate models to the resulting microRNA variations common to both strategies, to interpret them as a function of demographic and clinical covariates. STUDY RESULTS We identified 207 microRNA variations that significantly contributed to the classification. The differential network analysis found 276 network-specific correlations of microRNA variations. The combination of both strategies identified 25 microRNAs, whose gene targets were overrepresented in cognition and schizophrenia genome-wide association studies findings. Interpretable univariate models further supported the relevance of miR-150-5p and miR-3191-5p variations in psychosis onset, independent of age, sex, cannabis use, and medication. CONCLUSIONS In this first longitudinal study of microRNA variation during conversion to psychosis, we combined 2 methodologically independent data-driven strategies to identify a dynamic epigenetic signature of the emergence of psychosis that is pathophysiologically relevant.
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Affiliation(s)
- Anton Iftimovici
- Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, GDR 3557-Institut de Psychiatrie, Université de Paris, Paris, France
- CEA Paris-Saclay, Joliot Institute, NeuroSpin, BAOBAB, Centre d'études de Saclay, Gif-sur-Yvette, France
| | - Qin He
- Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, GDR 3557-Institut de Psychiatrie, Université de Paris, Paris, France
| | - Chuan Jiao
- Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, GDR 3557-Institut de Psychiatrie, Université de Paris, Paris, France
| | - Edouard Duchesnay
- CEA Paris-Saclay, Joliot Institute, NeuroSpin, BAOBAB, Centre d'études de Saclay, Gif-sur-Yvette, France
| | - Marie-Odile Krebs
- Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, GDR 3557-Institut de Psychiatrie, Université de Paris, Paris, France
- GHU Paris Psychiatrie et Neurosciences, Pôle hospitalo-universitaire d'Evaluation, Prévention, et Innovation Thérapeutique (PEPIT), Paris, France
| | - Oussama Kebir
- Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, GDR 3557-Institut de Psychiatrie, Université de Paris, Paris, France
- GHU Paris Psychiatrie et Neurosciences, Pôle hospitalo-universitaire d'Evaluation, Prévention, et Innovation Thérapeutique (PEPIT), Paris, France
| | - Boris Chaumette
- Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, GDR 3557-Institut de Psychiatrie, Université de Paris, Paris, France
- GHU Paris Psychiatrie et Neurosciences, Pôle hospitalo-universitaire d'Evaluation, Prévention, et Innovation Thérapeutique (PEPIT), Paris, France
- Department of Psychiatry, McGill University, Montréal, Québec, Canada
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Liu XS, Zhang Y, Liu ZY, Gao Y, Yuan LL, Zeng DB, Tan F, Wan HB, Pei ZJ. METTL3 as a novel diagnosis and treatment biomarker and its association with glycolysis, cuproptosis and ceRNA in oesophageal carcinoma. J Cell Mol Med 2024; 28:e18195. [PMID: 38429907 PMCID: PMC10907846 DOI: 10.1111/jcmm.18195] [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: 09/06/2023] [Revised: 11/22/2023] [Accepted: 02/09/2024] [Indexed: 03/03/2024] Open
Abstract
METTL3 has been shown to be involved in regulating a variety of biological processes. However, the relationship between METTL3 expression and glycolysis, cuproptosis-related genes and the ceRNA network in oesophageal carcinoma (ESCA) remains unclear. ESCA expression profiles from databases were obtained, and target genes were identified using differential analysis and visualization. Immunohistochemistry (IHC) staining assessed METTL3 expression differences. Functional enrichment analysis using GO, KEGG and GSEA was conducted on the co-expression profile of METTL3. Cell experiments were performed to assess the effect of METTL3 interference on tumour cells. Correlation and differential analyses were carried out to assess the relationship between METTL3 with glycolysis and cuproptosis. qRT-PCR was used to validate the effects of METTL3 interference on glycolysis-related genes. Online tools were utilized to screen and construct ceRNA networks based on the ceRNA theory. METTL3 expression was significantly higher in ESCA compared to the controls. The IHC results were consistent with the above results. Enrichment analysis revealed that METTL3 is involved in multiple pathways associated with tumour development. Significant correlations were observed between METTL3 and glycolysis-related genes and cuproptosis-related gene. Experiments confirmed that interfered with METTL3 significantly inhibited glucose uptake and lactate production in tumour cells, and affected the expression of glycolytic-related genes. Finally, two potential ceRNA networks were successfully predicted and constructed. Our study establishes the association between METTL3 overexpression and ESCA progression. Additionally, we propose potential links between METTL3 and glycolysis, cuproptosis and ceRNA, presenting a novel targeted therapy strategy for ESCA.
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Affiliation(s)
- Xu-Sheng Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for precision Diagnosis and Treatment of liver cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, China
- Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yu Zhang
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for precision Diagnosis and Treatment of liver cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Zi-Yue Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for precision Diagnosis and Treatment of liver cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yan Gao
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for precision Diagnosis and Treatment of liver cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Ling-Ling Yuan
- Department of Pathology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Dao-Bing Zeng
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for precision Diagnosis and Treatment of liver cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Fan Tan
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for precision Diagnosis and Treatment of liver cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Hua-Bing Wan
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for precision Diagnosis and Treatment of liver cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Zhi-Jun Pei
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for precision Diagnosis and Treatment of liver cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, China
- Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, China
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Sathipati SY, Tsai MJ, Aimalla N, Moat L, Shukla S, Allaire P, Hebbring S, Beheshti A, Sharma R, Ho SY. An evolutionary learning-based method for identifying a circulating miRNA signature for breast cancer diagnosis prediction. NAR Genom Bioinform 2024; 6:lqae022. [PMID: 38406797 PMCID: PMC10894035 DOI: 10.1093/nargab/lqae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/11/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024] Open
Abstract
Breast cancer (BC) is one of the most commonly diagnosed cancers worldwide. As key regulatory molecules in several biological processes, microRNAs (miRNAs) are potential biomarkers for cancer. Understanding the miRNA markers that can detect BC may improve survival rates and develop new targeted therapeutic strategies. To identify a circulating miRNA signature for diagnostic prediction in patients with BC, we developed an evolutionary learning-based method called BSig. BSig established a compact set of miRNAs as potential markers from 1280 patients with BC and 2686 healthy controls retrieved from the serum miRNA expression profiles for the diagnostic prediction. BSig demonstrated outstanding prediction performance, with an independent test accuracy and area under the receiver operating characteristic curve were 99.90% and 0.99, respectively. We identified 12 miRNAs, including hsa-miR-3185, hsa-miR-3648, hsa-miR-4530, hsa-miR-4763-5p, hsa-miR-5100, hsa-miR-5698, hsa-miR-6124, hsa-miR-6768-5p, hsa-miR-6800-5p, hsa-miR-6807-5p, hsa-miR-642a-3p, and hsa-miR-6836-3p, which significantly contributed towards diagnostic prediction in BC. Moreover, through bioinformatics analysis, this study identified 65 miRNA-target genes specific to BC cell lines. A comprehensive gene-set enrichment analysis was also performed to understand the underlying mechanisms of these target genes. BSig, a tool capable of BC detection and facilitating therapeutic selection, is publicly available at https://github.com/mingjutsai/BSig.
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Affiliation(s)
| | - Ming-Ju Tsai
- Hinda and Arthur Marcus Institute for Aging Research at Hebrew Senior Life, Boston, MA 02131, USA
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02131, USA
| | - Nikhila Aimalla
- Department of Internal Medicine-Pediatrics, Marshfield Clinic Health System, Marshfield, WI 54449, USA
| | - Luke Moat
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | - Sanjay K Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | - Patrick Allaire
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | - Scott Hebbring
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | - Afshin Beheshti
- Blue Marble Space Institute of Science, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA94035, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Rohit Sharma
- Department of Surgical Oncology, Marshfield Clinic Health System, Marshfield, WI 54449, USA
| | - Shinn-Ying Ho
- Institute of Bioinformatics and Systems biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- College of Health Sciences, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Biomedical Engineering, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
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30
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Wang R, Chen Y, Kuang W, Jiang W, Zeng W, Chen Y, Liu Z. Valproic acid regulates the miR-155/Jarid2 axis by affecting miR-155 promoter methylation in glioma. Acta Biochim Biophys Sin (Shanghai) 2024; 56:174-183. [PMID: 38273784 PMCID: PMC10984859 DOI: 10.3724/abbs.2023259] [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: 05/08/2023] [Accepted: 09/05/2023] [Indexed: 01/27/2024] Open
Abstract
The most frequent primary brain tumor in adults is glioma, yet no effective curative treatments are currently available. Our previous study demonstrated the enhancing effects of JARID2 on glioma sensitivity to TMZ treatment. In this study, miR-155 is predicted to target JARID2. miR-155 is overexpressed in clinical glioma specimens and cell lines. miR-155 overexpression in glioma cells enhances cell viability and represses cell apoptosis. Through targeting, miR-155 inhibits JARID2 expression. miR-155 inhibition inhibits glioma cell viability and enhances cell apoptosis, whereas JARID2 knockdown enhances cell viability and inhibits cell apoptosis; JARID2 knockdown partially reverses miR-155 inhibition effects on glioma phenotypes. miR-155 inhibition reduces but knockdown of JARID2 promotes the tumor formation ability of glioma cells in vivo. Valproic acid (VPA) upregulates JARID2 expression, inhibits glioma cell viability and enhances cell apoptosis. VPA downregulates the expression level of miR-155 by increasing the methylation level of the miR-155 promoter, suggesting that the miR-155/JARID2 axis is implicated in VPA inhibition of glioma cell viability and enhancement of glioma cell apoptosis. This study demonstrates a new mechanism of VPA treatment of gliomas by affecting the miR-155/JARID2 axis, which could be regarded as a new strategy for the prevention and treatment of glioma.
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Affiliation(s)
- Ruixuan Wang
- Department of OncologyXiangya HospitalCentral South UniversityChangsha410008China
| | - Yanhong Chen
- Department of Clinical PharmacologyXiangya HospitalCentral South UniversityChangsha410008China
| | - Weilu Kuang
- Department of OncologyXiangya HospitalCentral South UniversityChangsha410008China
| | - Wuzhong Jiang
- Department of OncologyXiangya HospitalCentral South UniversityChangsha410008China
| | - Wenjing Zeng
- Department of Clinical PharmacologyXiangya HospitalCentral South UniversityChangsha410008China
| | - Yinyun Chen
- The Third Department of GastroenterologyHunan Provincial People’s HospitalChangsha410000China
| | - Zhengzheng Liu
- Department of OncologyXiangya HospitalCentral South UniversityChangsha410008China
- National Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangsha410008China
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31
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Niu X, Xu C, Cheuk YC, Xu X, Liang L, Zhang P, Rong R. Characterizing hub biomarkers for post-transplant renal fibrosis and unveiling their immunological functions through RNA sequencing and advanced machine learning techniques. J Transl Med 2024; 22:186. [PMID: 38378674 PMCID: PMC10880303 DOI: 10.1186/s12967-024-04971-9] [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: 12/11/2023] [Accepted: 02/09/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Kidney transplantation stands out as the most effective renal replacement therapy for patients grappling with end-stage renal disease. However, post-transplant renal fibrosis is a prevalent and irreversible consequence, imposing a substantial clinical burden. Unfortunately, the clinical landscape remains devoid of reliable biological markers for diagnosing post-transplant renal interstitial fibrosis. METHODS We obtained transcriptome and single-cell sequencing datasets of patients with renal fibrosis from NCBI Gene Expression Omnibus (GEO). Subsequently, we employed Weighted Gene Co-Expression Network Analysis (WGCNA) to identify potential genes by integrating core modules and differential genes. Functional enrichment analysis was conducted to unveil the involvement of potential pathways. To identify key biomarkers for renal fibrosis, we utilized logistic analysis, a LASSO-based tenfold cross-validation approach, and gene topological analysis within Cytoscape. Furthermore, histological staining, Western blotting (WB), and quantitative PCR (qPCR) experiments were performed in a murine model of renal fibrosis to verify the identified hub genes. Moreover, molecular docking and molecular dynamics simulations were conducted to explore possible effective drugs. RESULTS Through WGCNA, the intersection of core modules and differential genes yielded a compendium of 92 potential genes. Logistic analysis, LASSO-based tenfold cross-validation, and gene topological analysis within Cytoscape identified four core genes (CD3G, CORO1A, FCGR2A, and GZMH) associated with renal fibrosis. The expression of these core genes was confirmed through single-cell data analysis and validated using various machine learning methods. Wet experiments also verified the upregulation of these core genes in the murine model of renal fibrosis. A positive correlation was observed between the core genes and immune cells, suggesting their potential role in bolstering immune system activity. Moreover, four potentially effective small molecules (ZINC000003830276-Tessalon, ZINC000003944422-Norvir, ZINC000008214629-Nonoxynol-9, and ZINC000085537014-Cobicistat) were identified through molecular docking and molecular dynamics simulations. CONCLUSION Four potential hub biomarkers most associated with post-transplant renal fibrosis, as well as four potentially effective small molecules, were identified, providing valuable insights for studying the molecular mechanisms underlying post-transplant renal fibrosis and exploring new targets.
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Affiliation(s)
- Xinhao Niu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Shanghai, 200032, China
| | - Cuidi Xu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Shanghai, 200032, China
| | - Yin Celeste Cheuk
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Shanghai, 200032, China
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Xiaoqing Xu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Shanghai, 200032, China
| | - Lifei Liang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Shanghai, 200032, China
| | - Pingbao Zhang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Key Laboratory of Organ Transplantation, Shanghai, 200032, China
| | - Ruiming Rong
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Shanghai Key Laboratory of Organ Transplantation, Shanghai, 200032, China.
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Liu XS, Liu ZY, Zeng DB, Hu J, Chen XL, Gu JL, Gao Y, Pei ZJ. Functional enrichment analysis reveals the involvement of DARS2 in multiple biological pathways and its potential as a therapeutic target in esophageal carcinoma. Aging (Albany NY) 2024; 16:3934-3954. [PMID: 38382106 PMCID: PMC10929822 DOI: 10.18632/aging.205569] [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: 10/06/2023] [Accepted: 01/17/2024] [Indexed: 02/23/2024]
Abstract
OBJECTIVE The enzyme Aspartyl tRNA synthetase 2 (DARS2) is a crucial enzyme in the mitochondrial tRNA synthesis pathway, playing a critical role in maintaining normal mitochondrial function and protein synthesis. However, the role of DARS2 in ESCA is unclear. MATERIALS AND METHODS Transcriptional data of pan-cancer and ESCA were downloaded from UCSC XENA, TCGA, and GEO databases to analyze the differential expression of DARS2 between tumor samples and normal samples, and its correlation with clinicopathological features of ESCA patients. R was used for GO, KEGG, and GSEA functional enrichment analysis of DARS2 co-expression and to analyze the connection of DARS2 with glycolysis and m6A-related genes. In vitro experiments were performed to assess the effects of interfering with DARS2 expression on ESCA cells. TarBase v.8, mirDIP, miRTarBase, ENCORI, and miRNet databases were used to analyze and construct a ceRNA network containing DARS2. RESULTS DARS2 was overexpressed in various types of tumors. In vitro experiments confirmed that interfering with DARS2 expression significantly affected the proliferation, migration, apoptosis, cell cycle, and glycolysis of ESCA cells. DARS2 may be involved in multiple biological pathways related to tumor development. Furthermore, correlation and differential analysis revealed that DARS2 may regulate ESCA m6A modification through its interaction with METTL3 and YTHDF1. A ceRNA network containing DARS2, DLEU2/has-miR-30a-5p/DARS2, was successfully predicted and constructed. CONCLUSIONS Our findings reveal the upregulation of DARS2 in ESCA and its association with clinical features, glycolysis pathway, m6A modification, and ceRNA network. These discoveries provide valuable insights into the molecular mechanisms underlying ESCA.
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Affiliation(s)
- Xu-Sheng Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Zi-Yue Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Dao-Bing Zeng
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Jian Hu
- Department of Critical Care Medicine, Danjiangkou First Hospital, Danjiangkou 420381, Hubei, China
| | - Xuan-Long Chen
- Department of Medical Ultrasound, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Jiao-Long Gu
- Department of Obstetrics and Gynecology, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Yan Gao
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Zhi-Jun Pei
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
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Yu Z, Wu X, Zhu J, Yan H, Li Y, Zhang H, Zhong Y, Lin M, Ye G, Li X, Jin J, Li K, Wang J, Zhuang H, Lin T, He J, Lu C, Xu Z, Zhang X, Li H, Jin X. BCLAF1 binds SPOP to stabilize PD-L1 and promotes the development and immune escape of hepatocellular carcinoma. Cell Mol Life Sci 2024; 81:82. [PMID: 38340178 PMCID: PMC10858942 DOI: 10.1007/s00018-024-05144-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: 09/17/2023] [Revised: 12/21/2023] [Accepted: 01/23/2024] [Indexed: 02/12/2024]
Abstract
Interaction between programmed death-1 (PD-1) ligand 1 (PD-L1) on tumor cells and PD-1 on T cells allows tumor cells to evade T cell-mediated immune surveillance. Strategies targeting PD-1/PD-L1 have shown clinical benefits in a variety of cancers. However, limited response rates in hepatocellular carcinoma (HCC) have prompted us to investigate the molecular regulation of PD-L1. Here, we identify B cell lymphoma-2-associated transcription factor 1 (BCLAF1) as a key PD-L1 regulator in HCC. Specifically, BCLAF1 interacts with SPOP, an E3 ligase that mediates the ubiquitination and degradation of PD-L1, thereby competitively inhibiting SPOP-PD-L1 interaction and subsequent ubiquitination and degradation of PD-L1. Furthermore, we determined an SPOP-binding consensus (SBC) motif mediating the BCLAF1-SPOP interaction on BCLAF1 protein and mutation of BCLAF1-SBC motif disrupts the regulation of the SPOP-PD-L1 axis. In addition, BCLAF1 expression was positively correlated with PD-L1 expression and negatively correlated with biomarkers of T cell activation, including CD3 and CD8, as well as with the level of immune cell infiltration in HCC tissues. Besides, BCLAF1 depletion leads to a significant reduction of PD-L1 expression in vitro, and this reduction of PD-L1 promoted T cell-mediated cytotoxicity. Notably, overexpression of BCLAF1 sensitized tumor cells to checkpoint therapy in an in vitro HCC cells-Jurkat cells co-culture model, whereas BCLAF1-SBC mutant decreased tumor cell sensitivity to checkpoint therapy, suggesting that BCLAF1 and its SBC motif serve as a novel therapeutic target for enhancing anti-tumor immunity in HCC.
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Affiliation(s)
- Zongdong Yu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Li Huili Hospital, Ningbo University, Ningbo, 315040, China
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, China
| | - Xiang Wu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Li Huili Hospital, Ningbo University, Ningbo, 315040, China
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, China
| | - Jie Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Li Huili Hospital, Ningbo University, Ningbo, 315040, China
| | - Huan Yan
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Li Huili Hospital, Ningbo University, Ningbo, 315040, China
| | - Yuxuan Li
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Li Huili Hospital, Ningbo University, Ningbo, 315040, China
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, China
| | - Hui Zhang
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, China
| | - Yeling Zhong
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, China
| | - Man Lin
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, China
| | - Ganghui Ye
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, China
| | - Xinming Li
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, China
| | - Jiabei Jin
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, China
| | - Kailang Li
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, China
| | - Jie Wang
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, China
| | - Hui Zhuang
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, China
| | - Ting Lin
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, China
| | - Jian He
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, China
| | - Changjiang Lu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Li Huili Hospital, Ningbo University, Ningbo, 315040, China
| | - Zeping Xu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Li Huili Hospital, Ningbo University, Ningbo, 315040, China
| | - Xie Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Li Huili Hospital, Ningbo University, Ningbo, 315040, China
| | - Hong Li
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Li Huili Hospital, Ningbo University, Ningbo, 315040, China.
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, China.
| | - Xiaofeng Jin
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Li Huili Hospital, Ningbo University, Ningbo, 315040, China.
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Nngbo University, Ningbo, 315211, China.
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Huang C, Pei J, Li D, Liu T, Li Z, Zhang G, Chen R, Xu X, Li B, Lian Z, Chu XM. Analysis and Validation of Critical Signatures and Immune Cell Infiltration Characteristics in Doxorubicin-Induced Cardiotoxicity by Integrating Bioinformatics and Machine Learning. J Inflamm Res 2024; 17:669-685. [PMID: 38328563 PMCID: PMC10849057 DOI: 10.2147/jir.s444600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/23/2024] [Indexed: 02/09/2024] Open
Abstract
Purpose Doxorubicin-induced cardiotoxicity (DIC) is a severe side reaction in cancer chemotherapy that greatly impacts the well-being of cancer patients. Currently, there is still an insufficiency of effective and reliable biomarkers in the field of clinical practice for the early detection of DIC. This study aimed to determine and validate the potential diagnostic and predictive values of critical signatures in DIC. Methods We obtained high-throughput sequencing data from the GEO database and performed data analysis and visualization using R software, GO, KEGG and Cytoscape. Machine learning methods and weighted gene coexpression network (WGCNA) were used to identify key genes for diagnostic model construction. Receiver operating characteristic (ROC) analysis and a nomogram were used to assess their diagnostic values. A multiregulatory network was built to reveal the possible regulatory relationships of critical signatures. Cell-type identification by estimating relative subsets of RNA transcript (CIBERSORT) analysis was used to investigate differential immune cell infiltration. Additionally, a cell and animal model were constructed to investigate the relationship between the identified genes and DIC. Results Among the 3713 differentially expressed genes, three key genes (CSGALNACT1, ZNF296 and FANCB) were identified. A nomogram and ROC curves based on three key genes showed excellent diagnostic predictive performance. The regulatory network analysis showed that the TFs CREB1, EP300, FLI1, FOXA1, MAX, and MAZ modulated three key genes. An analysis of immune cell infiltration indicated that many immune cells (activated NK cells, M0 macrophages, activated dendritic cells and neutrophils) might be related to the progression of DIC. Furthermore, there may be various degrees of correlation between the three critical signatures and immune cells. RT‒qPCR demonstrated that the mRNA expression of CSGALNACT1 and ZNF296 was significantly upregulated, while FANCB was significantly downregulated in DOX-treated cardiomyocytes in vitro and in vivo. Conclusion Our study suggested that the differential expression of CSGALNACT1, ZNF296 and FANCB is associated with cardiotoxicity and is also involved in immune cell infiltration in DIC. They might be potential biomarkers for the early occurrence of DIC.
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Affiliation(s)
- Chao Huang
- Department of Cardiology, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266100, People’s Republic of China
| | - Jixiang Pei
- Department of Cardiology, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266100, People’s Republic of China
| | - Daisong Li
- Department of Cardiology, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266100, People’s Republic of China
| | - Tao Liu
- The Affiliated Qingdao Central Hospital of Qingdao University, The Second Affiliated Hospital of Medical College of Qingdao University, Qingdao, Shandong, 266042, People’s Republic of China
| | - Zhaoqing Li
- Department of Cardiology, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266100, People’s Republic of China
| | - Guoliang Zhang
- Department of Cardiology, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266100, People’s Republic of China
| | - Ruolan Chen
- Department of Cardiology, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266100, People’s Republic of China
| | - Xiaojian Xu
- Department of Cardiology, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266100, People’s Republic of China
| | - Bing Li
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, 266000, People’s Republic of China
- Department of Dermatology, The Affiliated Haici Hospital of Qingdao University, Qingdao, 266033, People’s Republic of China
| | - Zhexun Lian
- Department of Cardiology, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266100, People’s Republic of China
| | - Xian-Ming Chu
- Department of Cardiology, the Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266100, People’s Republic of China
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao, 266071, People’s Republic of China
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Samir H, Samir M, Radwan F, Mandour AS, El-Sherbiny HR, Ahmed AE, Al Syaad KM, Al-Saeed FA, Watanabe G. Effect of pre-treatment of melatonin on superovulation response, circulatory hormones, and miRNAs in goats during environmental heat stress conditions. Vet Res Commun 2024; 48:459-474. [PMID: 37831382 DOI: 10.1007/s11259-023-10239-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/10/2023] [Indexed: 10/14/2023]
Abstract
Environmental heat stress has a deleterious impact on farm animal reproductive performance. The purpose of this study was to see how the addition of melatonin affected the efficacy of the superovulation regimen in goats in hot climatic conditions. Sixteen Shiba goats were synchronized and divided into two equal groups (n = 8, each): the melatonin group, which received a single S/C dose of melatonin, and a control group, treated with one ml of corn oil only. Ultrasonographic assessment of ovarian structures (Graafian follicles; GFs and corpus lutea; CLs) morphometry and hemodynamics were performed during the estrous phase of the superovulation (D0) and at day7 after ovulation (D7) of the superovulation regimen. The peripheral reproductive hormones were measured, and microRNAs were characterized. The mean diameter and the total-colored area of GFs during the D0 were significantly (P˂0.05) higher in the melatonin group (5.42 ± 0.11 mm and 1592.20 ± 45.26 pixels, respectively) compared to the control group (4.62 ± 0.12 mm and 1052.55 ± 29.47 pixels, respectively). Concentrations of LH and E2 increased significantly (P˂0.05) in the melatonin group (1.06 ± 0.06 ng/ml and 46.34 ± 2.77 pg/ml, respectively) compared to the control group (0.75 ± 0.12 ng/ml and 29.33 ± 1.89 pg/ml, respectively). At D7, the melatonin-received goats attained greater values in the mean count (6.75 ± 0.33, P˂0.005), diameters (6.08 ± 0.12 mm, P˂0.01), and total-colored area (17137.30 ± 128.53 pixels, P˂0.01) of detected CLs and progesterone concentrations (4.08 ± 0.24 ng/ml) compared to control goats (4.00 ± 0.28, 4.50 ± 0.19 mm, 11156.87 ± 117.90 pixels, and 2.90 ± 0.18 ng/ml respectively). MiRNA expression analysis was identified during both stages denoting several up and downregulated miRNA candidates among the studied groups. In conclusion, incorporating melatonin enhanced the efficiency of the superovulation regimen in goats under hot climatic conditions.
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Affiliation(s)
- Haney Samir
- Department of Theriogenology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt.
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu, Tokyo, 183-8509, Japan.
| | - Mohamed Samir
- Department of Zoonoses, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
- Immunogenetics Department, Pirbright Institute, Woking, UK
| | - Faten Radwan
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu, Tokyo, 183-8509, Japan
- Veterinarian graduated from the Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Elqaliobiya, 13736, Egypt
| | - Ahmed S Mandour
- Department of Animal Medicine (Internal Medicine), Faculty of Veterinary Medicine, Suez Canal University, Ismailia, 41522, Egypt
| | - Hossam R El-Sherbiny
- Department of Theriogenology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Ahmed Ezzat Ahmed
- Biology Department, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
| | - Khalid M Al Syaad
- Biology Department, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
| | - Fatimah A Al-Saeed
- Biology Department, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
| | - Gen Watanabe
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-Cho, Fuchu, Tokyo, 183-8509, Japan
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Seyhan AA. Trials and Tribulations of MicroRNA Therapeutics. Int J Mol Sci 2024; 25:1469. [PMID: 38338746 PMCID: PMC10855871 DOI: 10.3390/ijms25031469] [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: 12/22/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024] Open
Abstract
The discovery of the link between microRNAs (miRNAs) and a myriad of human diseases, particularly various cancer types, has generated significant interest in exploring their potential as a novel class of drugs. This has led to substantial investments in interdisciplinary research fields such as biology, chemistry, and medical science for the development of miRNA-based therapies. Furthermore, the recent global success of SARS-CoV-2 mRNA vaccines against the COVID-19 pandemic has further revitalized interest in RNA-based immunotherapies, including miRNA-based approaches to cancer treatment. Consequently, RNA therapeutics have emerged as highly adaptable and modular options for cancer therapy. Moreover, advancements in RNA chemistry and delivery methods have been pivotal in shaping the landscape of RNA-based immunotherapy, including miRNA-based approaches. Consequently, the biotechnology and pharmaceutical industry has witnessed a resurgence of interest in incorporating RNA-based immunotherapies and miRNA therapeutics into their development programs. Despite substantial progress in preclinical research, the field of miRNA-based therapeutics remains in its early stages, with only a few progressing to clinical development, none reaching phase III clinical trials or being approved by the US Food and Drug Administration (FDA), and several facing termination due to toxicity issues. These setbacks highlight existing challenges that must be addressed for the broad clinical application of miRNA-based therapeutics. Key challenges include establishing miRNA sensitivity, specificity, and selectivity towards their intended targets, mitigating immunogenic reactions and off-target effects, developing enhanced methods for targeted delivery, and determining optimal dosing for therapeutic efficacy while minimizing side effects. Additionally, the limited understanding of the precise functions of miRNAs limits their clinical utilization. Moreover, for miRNAs to be viable for cancer treatment, they must be technically and economically feasible for the widespread adoption of RNA therapies. As a result, a thorough risk evaluation of miRNA therapeutics is crucial to minimize off-target effects, prevent overdosing, and address various other issues. Nevertheless, the therapeutic potential of miRNAs for various diseases is evident, and future investigations are essential to determine their applicability in clinical settings.
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Affiliation(s)
- Attila A. Seyhan
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA;
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Joint Program in Cancer Biology, Lifespan Health System and Brown University, Providence, RI 02912, USA
- Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
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Liu XS, Zhang Y, Ming X, Hu J, Chen XL, Wang YL, Zhang YH, Gao Y, Pei ZJ. SPC25 as a novel therapeutic and prognostic biomarker and its association with glycolysis, ferroptosis and ceRNA in lung adenocarcinoma. Aging (Albany NY) 2024; 16:779-798. [PMID: 38217547 PMCID: PMC10817414 DOI: 10.18632/aging.205418] [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: 09/06/2023] [Accepted: 12/04/2023] [Indexed: 01/15/2024]
Abstract
OBJECTIVE Spindle pole body component 25 (SPC25) is an important cyclin involved in chromosome segregation and spindle dynamics regulation during mitosis. However, the role of SPC25 in lung adenocarcinoma (LAUD) is unclear. MATERIALS AND METHODS The differential expression of SPC25 in tumor samples and normal samples was analyzed using TIMER, TCGA, GEO databases, and the correlation between its expression and clinicopathological features and prognosis in LUAD patients. Biological pathways that may be enriched by SPC25 were analyzed using GSEA. In vitro cell experiments were used to evaluate the effect of knocking down SPC25 expression on LUAD cells. Correlation analysis and differential analysis were used to assess the association of SPC25 expression with genes related to cell cycle, glycolysis, and ferroptosis. A ceRNA network involving SPC25 was constructed using multiple database analyses. RESULTS SPC25 was highly expressed in LUAD, and its expression level could guide staging and predict prognosis. GSEA found that high expression of SPC25 involved multiple cell cycles and glycolytic pathways. Knocking down SPC25 expression significantly affected the proliferation, migration and apoptosis of LUAD cells. Abnormal SPC25 expression levels can affect cell cycle progression, glycolytic ability and ferroptosis regulation. A ceRNA network containing SPC25, SNHG15/hsa-miR-451a/SPC25, was successfully predicted and constructed. CONCLUSIONS Our findings reveal the association of up-regulation of SPC25 in LUAD and its expression with clinical features, prognosis prediction, proliferation migration, cell cycle, glycolysis, ferroptosis, and ceRNA networks. Our results indicate that SPC25 can be used as a biomarker in LUAD therapy and a target for therapeutic intervention.
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Affiliation(s)
- Xu-Sheng Liu
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
- Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Yu Zhang
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Xing Ming
- Department of Infection Control, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Jian Hu
- Department of Critical Care Medicine, Danjiangkou First Hospital, Danjiangkou 420381, China
| | - Xuan-Long Chen
- Department of Medical Ultrasound, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Ya-Lan Wang
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Yao-Hua Zhang
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Yan Gao
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Zhi-Jun Pei
- Department of Nuclear Medicine, Hubei Provincial Clinical Research Center for Precision Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
- Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
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Linder H, Zhang Y, Wang Y, Ouyang Z. Integrative pathway analysis with gene expression, miRNA, methylation and copy number variation for breast cancer subtypes. Stat Appl Genet Mol Biol 2024; 23:sagmb-2019-0050. [PMID: 38363177 DOI: 10.1515/sagmb-2019-0050] [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: 10/06/2019] [Accepted: 01/27/2024] [Indexed: 02/17/2024]
Abstract
Developments in biotechnologies enable multi-platform data collection for functional genomic units apart from the gene. Profiling of non-coding microRNAs (miRNAs) is a valuable tool for understanding the molecular profile of the cell, both for canonical functions and malignant behavior due to complex diseases. We propose a graphical mixed-effects statistical model incorporating miRNA-gene target relationships. We implement an integrative pathway analysis that leverages measurements of miRNA activity for joint analysis with multimodal observations of gene activity including gene expression, methylation, and copy number variation. We apply our analysis to a breast cancer dataset, and consider differential activity in signaling pathways across breast tumor subtypes. We offer discussion of specific signaling pathways and the effect of miRNA integration, as well as publish an interactive data visualization to give public access to the results of our analysis.
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Affiliation(s)
- Henry Linder
- Department of Statistics, University of Connecticut, Storrs, CT, 06269, USA
| | - Yuping Zhang
- Department of Statistics, University of Connecticut, Storrs, CT, 06269, USA
| | - Yunqi Wang
- Department of Statistics, University of Connecticut, Storrs, CT, 06269, USA
| | - Zhengqing Ouyang
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, MA, 01003, USA
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Yan J, Fang Z, Shi M, Tu C, Zhang S, Jiang C, Li Q, Shao Y. Clinical Significance of Disulfidptosis-related Genes and Functional Analysis in Gastric Cancer. J Cancer 2024; 15:1053-1066. [PMID: 38230212 PMCID: PMC10788733 DOI: 10.7150/jca.91796] [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: 11/01/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024] Open
Abstract
Background: Worldwide, gastric cancer (GC) remains intractable due to its poor prognosis and high morbidity and mortality. Disulfidptosis is a novel kind of cell death mediated by abnormal accumulation of intracellular disulphides. The correlation between disulfidptosis and GC is still unknown. Therefore, it is necessary to elucidate the pathogenesis and mechanism of disulfidptosis and GC for clinical diagnosis and intervention. Methods: RNA-sequencing data from several public data portals and clinical samples were collected. We compared the expression levels of four key genes of disulfidptosis, including SLC7A11, SLC3A2, RPN1, and NCKAP1, in GC and selected prognostic genes to build a novel GC prognosis-related nomogram model. The biological functions and immune landscape of the identified prognostic genes were explored. Results: Overexpressed NCKAP1 and SLC7A11 were prognostic disulfidptosis-related genes in GC. We combined these genes and several clinicopathological factors to build a prognostic nomogram model for GC. Meanwhile, the ROC curves showed that NCKAP1 and SLC7A11 were promising biomarkers for GC screening. The biological and cellular functions were focused on actin activities, GTPase and immunoreaction. The tumour immune microenvironment and immune therapy targets were identified. Competing endogenous RNA network was built to explore the downstream regulatory mechanisms. Finally, the elevated NCKAP1 and SLC7A11 expression in GC was validated via qRT-PCR in a cell line and tissue line. Conclusion: In conclusion, NCKAP1 and SLC7A11 are promising prognostic and diagnostic biomarkers for GC that correlate with the activities of actin, energy metabolism of GTPase, immune infiltration and immunotherapy.
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Affiliation(s)
- Jianing Yan
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
| | - Ziyi Fang
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
| | - Meiqi Shi
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
| | - Can Tu
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
| | - Shengke Zhang
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Chenglu Jiang
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Qier Li
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
| | - Yongfu Shao
- Department of Gastroenterology, The First Affiliated Hospital of Ningbo University, Ningbo 315020, China
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Yan L, Lin P, Wu Z, Lu Z, Ma L, Dong X, He L, Dai Z, Zhou C, Hong P, Li C. Exosomal miRNA analysis provides new insights into exposure to nanoplastics and okadaic acid. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167010. [PMID: 37722421 DOI: 10.1016/j.scitotenv.2023.167010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/02/2023] [Accepted: 09/10/2023] [Indexed: 09/20/2023]
Abstract
As an emerging environmental pollutant, nanoplastics (NPs) have attracted wide attention in terms of their impact on the ecological environment and human health. Currently, researches on the cytotoxicity of NPs mainly focus on oxidative stress, damage to the cell membrane and organelles, induction of immune response and genotoxicity. Okadaic acid (OA) is the main component of diarrheal shellfish toxin. Based on the previous combined toxicity exploration of polystyrene (PS) NPs and (OA) to human gastric adenocarcinoma (AGS) cells, cell-derived exosomes were extracted and exosomal miRNA profiles were analyzed for the first time in this study. The results showed that the composition of miRNAs varied after the exposure of NPs and OA. Specifically, the expression of miR-1-3p in both PS-Exo and PS-OA-Exo was significantly reduced. And the expression of miR-1248 was upregulated most significantly by comparing the DE miRNAs between PS-Exo and PS-OA-Exo. MiR-1-3p and miR-1248 may be the key genes for the combined toxicity of NPs and OA. After analysis, we found that both the decreased expression of miR-1-3p and the increased expression of miR-1248 can increase the expression of FN1 and affect DNA replication, which was surprisingly consistent with the results of our previous cytotoxicity studies. Since exosomal miRNAs are selectively encapsulated by donor cell, we speculate that the changes of exosomal miRNAs may due to the synchronous changes of intracellular environment and the downregulation of intracellular FN1 may be attributed to decreased expression of miR-1-3p and increased expression of miR-1248 in donor cells. Accordingly, we come to the conclusion that the changes of miRNAs in the exosomes derived from AGS cells after environmental stimulation could reflect the biological effects of donor cells.
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Affiliation(s)
- Linhong Yan
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Zhanjiang 524088, PR China
| | - Peichun Lin
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Zijie Wu
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Zhanjiang 524088, PR China
| | - Zifan Lu
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Lihua Ma
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Zhanjiang 524088, PR China
| | - Xiaoling Dong
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Zhanjiang 524088, PR China
| | - Lei He
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Zhenqing Dai
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518108, PR China; Guangdong Provincial Key Laboratory of Intelligent Equipment for South China Sea Marine Ranching, Guangdong Ocean University, Zhanjiang 524088, PR China
| | - Chunxia Zhou
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Zhanjiang 524088, PR China
| | - Pengzhi Hong
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Zhanjiang 524088, PR China
| | - Chengyong Li
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, PR China; Shenzhen Institute of Guangdong Ocean University, Shenzhen 518108, PR China; Guangdong Provincial Key Laboratory of Intelligent Equipment for South China Sea Marine Ranching, Guangdong Ocean University, Zhanjiang 524088, PR China.
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Chen R, Coleborn E, Bhavsar C, Wang Y, Alim L, Wilkinson AN, Tran MA, Irgam G, Atluri S, Wong K, Shim JJ, Adityan S, Lee JS, Overwijk WW, Steptoe R, Yang D, Wu SY. miR-146a inhibits ovarian tumor growth in vivo via targeting immunosuppressive neutrophils and enhancing CD8 + T cell infiltration. Mol Ther Oncolytics 2023; 31:100725. [PMID: 37781339 PMCID: PMC10539880 DOI: 10.1016/j.omto.2023.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/08/2023] [Indexed: 10/03/2023] Open
Abstract
Immunotherapies have emerged as promising strategies for cancer treatment. However, existing immunotherapies have poor activity in high-grade serous ovarian cancer (HGSC) due to the immunosuppressive tumor microenvironment and the associated low tumoral CD8+ T cell (CTL) infiltration. Through multiple lines of evidence, including integrative analyses of human HGSC tumors, we have identified miR-146a as a master regulator of CTL infiltration in HGSC. Tumoral miR-146a expression is positively correlated with anti-cancer immune signatures in human HGSC tumors, and delivery of miR-146a to tumors resulted in significant reduction in tumor growth in both ID8-p53-/- and IG10 murine HGSC models. Increasing miR-146a expression in tumors improved anti-tumor immune responses by decreasing immune suppressive neutrophils and increasing CTL infiltration. Mechanistically, miR-146a targets IL-1 receptor-associated kinase 1 and tumor necrosis factor receptor-associated factor 6 adaptor molecules of the transcription factor nuclear factor κB signaling pathway in ID8-p53-/- cells and decreases production of the downstream neutrophil chemoattractant, C-X-C motif chemokine ligand 1. In addition to HGSC, tumoral miR-146a expression also correlates strongly with CTL infiltration in other cancer types including thyroid, prostate, breast, and adrenocortical cancers. Altogether, our findings highlight the ability of miR-146a to overcome immune suppression and improve CTL infiltration in tumors.
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Affiliation(s)
- Rui Chen
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Elaina Coleborn
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Chintan Bhavsar
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yue Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Louisa Alim
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Andrew N. Wilkinson
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Gowri Irgam
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sharat Atluri
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kiefer Wong
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jae-Jun Shim
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Siddharth Adityan
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Ju-Seog Lee
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Willem W. Overwijk
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Raymond Steptoe
- Frazer Institute, University of Queensland, Brisbane, QLD 4102, Australia
| | - Da Yang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Sherry Y. Wu
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
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42
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Zulian V, Fiscon G, Paci P, Garbuglia AR. Hepatitis B Virus and microRNAs: A Bioinformatics Approach. Int J Mol Sci 2023; 24:17224. [PMID: 38139051 PMCID: PMC10743825 DOI: 10.3390/ijms242417224] [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: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
In recent decades, microRNAs (miRNAs) have emerged as key regulators of gene expression, and the identification of viral miRNAs (v-miRNAs) within some viruses, including hepatitis B virus (HBV), has attracted significant attention. HBV infections often progress to chronic states (CHB) and may induce fibrosis/cirrhosis and hepatocellular carcinoma (HCC). The presence of HBV can dysregulate host miRNA expression, influencing several biological pathways, such as apoptosis, innate and immune response, viral replication, and pathogenesis. Consequently, miRNAs are considered a promising biomarker for diagnostic, prognostic, and treatment response. The dynamics of miRNAs during HBV infection are multifaceted, influenced by host variability and miRNA interactions. Given the ability of miRNAs to target multiple messenger RNA (mRNA), understanding the viral-host (human) interplay is complex but essential to develop novel clinical applications. Therefore, bioinformatics can help to analyze, identify, and interpret a vast amount of miRNA data. This review explores the bioinformatics tools available for viral and host miRNA research. Moreover, we introduce a brief overview focusing on the role of miRNAs during HBV infection. In this way, this review aims to help the selection of the most appropriate bioinformatics tools based on requirements and research goals.
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Affiliation(s)
- Verdiana Zulian
- Virology Laboratory, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy;
| | - Giulia Fiscon
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (P.P.)
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, 00185 Rome, Italy
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (P.P.)
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, 00185 Rome, Italy
| | - Anna Rosa Garbuglia
- Virology Laboratory, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy;
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43
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Howe CG, Armstrong DA, Muse ME, Gilbert-Diamond D, Gui J, Hoen AG, Palys TJ, Barnaby RL, Stanton BA, Jackson BP, Christensen BC, Karagas MR. Periconceptional and Prenatal Exposure to Metals and Extracellular Vesicle and Particle miRNAs in Human Milk: A Pilot Study. EXPOSURE AND HEALTH 2023; 15:731-743. [PMID: 38074282 PMCID: PMC10707483 DOI: 10.1007/s12403-022-00520-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 06/30/2024]
Abstract
Human milk is a rich source of microRNAs (miRNAs), which can be transported by extracellular vesicles and particles (EVPs) and are hypothesized to contribute to maternal-offspring communication and child development. Environmental contaminant impacts on EVP miRNAs in human milk are largely unknown. In a pilot study of 54 mother-child pairs from the New Hampshire Birth Cohort Study, we examined relationships between five metals (arsenic, lead, manganese, mercury, and selenium) measured in maternal toenail clippings, reflecting exposures during the periconceptional and prenatal periods, and EVP miRNA levels in human milk. 798 miRNAs were profiled using the NanoString nCounter platform; 200 miRNAs were widely detectable and retained for downstream analyses. Metal-miRNA associations were evaluated using covariate-adjusted robust linear regression models. Arsenic exposure during the periconceptional and prenatal periods was associated with lower total miRNA content in human milk EVPs (PBonferroni < 0.05). When evaluating miRNAs individually, 13 miRNAs were inversely associated with arsenic exposure, two in the periconceptional period and 11 in the prenatal period (PBonferroni < 0.05). Other metal-miRNA associations were not statistically significant after multiple testing correction (PBonferroni ≥ 0.05). Many of the arsenic-associated miRNAs are involved in lactation and have anti-inflammatory properties in the intestine and tumor suppressive functions in breast cells. Our findings raise the possibility that periconceptional and prenatal arsenic exposure may reduce levels of multiple miRNAs in human milk EVPs. However, larger confirmatory studies, which can apply environmental mixture approaches, evaluate potential effect modifiers of these relationships, and examine possible downstream consequences for maternal and child health and breastfeeding outcomes, are needed.
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Affiliation(s)
- Caitlin G. Howe
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, 1 Medical Center Dr, Lebanon, NH, USA
| | - David A. Armstrong
- Department of Dermatology, Dartmouth-Hitchcock Medical Center, 1 Medical Center Dr, Lebanon, NH, USA
- Research Service, VA Medical Center, 215 N Main St, White River Junction, VT, USA
| | - Meghan E. Muse
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, 1 Medical Center Dr, Lebanon, NH, USA
| | - Diane Gilbert-Diamond
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, 1 Medical Center Dr, Lebanon, NH, USA
| | - Jiang Gui
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, 1 Medical Center Dr, Lebanon, NH, USA
| | - Anne G. Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, 1 Medical Center Dr, Lebanon, NH, USA
| | - Thomas J. Palys
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, 1 Medical Center Dr, Lebanon, NH, USA
| | - Roxanna L. Barnaby
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, 66 College St, Hanover, NH, USA
| | - Bruce A. Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, 66 College St, Hanover, NH, USA
| | - Brian P. Jackson
- Department of Earth Sciences, Dartmouth College, 6105 Sherman Fairchild Hall, Hanover, NH, USA
| | - Brock C. Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, 1 Medical Center Dr, Lebanon, NH, USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, 1 Medical Center Dr, Lebanon, NH, USA
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Yang L, Feng H. Cross-kingdom regulation by plant-derived miRNAs in mammalian systems. Animal Model Exp Med 2023; 6:518-525. [PMID: 38064180 PMCID: PMC10757204 DOI: 10.1002/ame2.12358] [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: 08/28/2023] [Accepted: 10/15/2023] [Indexed: 12/31/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules ubiquitously distributed across diverse organisms, serving as pivotal regulators of genetic expression. Notably, plant-derived miRNAs have been demonstrated to have unique bioactivity and certain stability in mammalian systems, thereby facilitating their capacity for cross-kingdom modulation of gene expression. While there is substantial evidence supporting the regulation of mammalian cells by plant-derived miRNAs, several questions remain unanswered. Specifically, a comprehensive investigation of the mechanisms underlying the stability and transport of plant miRNAs and their cross-kingdom regulation of gene expression in mammals remains to be done. In this review, we summarized the origin, processing, and functional mechanisms of plant miRNAs in mammalian tissues and circulation, emphasizing their greater resistance to mammalian digestion and circulation systems compared to animal miRNAs. Additionally, we introduce four well-known plant miRNAs that have been extensively studied for their functions and mechanisms in mammalian systems. By delving into these aspects, we aim to offer a fundamental understanding of this intriguing field and shed light on the complex interactions between plant miRNAs and mammalian biology.
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Affiliation(s)
- Linpu Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
| | - Han Feng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
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45
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Zabihi MR, Norouzkhani N, Karkhah S, Akhoondian M. Identification of a valuable gene network for the diagnosis and treatment of non-obstructive azoospermia: in-silico analyses - experimental research. Ann Med Surg (Lond) 2023; 85:5941-5951. [PMID: 38098601 PMCID: PMC10718319 DOI: 10.1097/ms9.0000000000001358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 09/17/2023] [Indexed: 12/17/2023] Open
Abstract
Introduction Non-obstructive azoospermia (NOA) is an etiology of infertility in men. NOA may have various classifications; however, hypogonadotropic hypogonadism can be regarded as a class of NOA associated with genetic factors. Former studies have shown that noncoding RNA (ncRNA) plays an essential role in NOA incidence, but few studies have been performed on the NOA-related ncRNA interaction network. In the current study, genes, NOA-related microRNA (miRNA), and circular RNA (circRNA) were found by bioinformatics methods to offer a new perspective on NOA treatment. Methods The gonadotropin-releasing hormone receptor (GnRHR)-related protein-protein interaction (PPI) network was extracted by searching in 'string-database'. GO, KEGG, and Enrichr databases were used to identify pathways, molecular function, and biological processing. Four databases, including TargetScan, mirDIP, miRmap, and miRWalk, were used to extract miRNAs. At last, the circ2GO, circBase, and literature were used to identify circRNAs and their genes. Results The current study identified the four proteins associated with the GnRHR signaling; eight shared miRNAs that affect the expression of found proteins and 25 circRNAs and their origin genes that regulate the miRNAs' function. Conclusion The two miRNAs, hsa-miR-134-3p and hsa-miR-513C-3p, the three genes, VCAN, NFATC3, and PRDM5, and their associated circRNAs can perform as a valuable gene network in the diagnosis and treatment of NOA pathogenesis.
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Affiliation(s)
- Mohammad Reza Zabihi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran
| | - Narges Norouzkhani
- Department of Medical Informatics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad
| | - Samad Karkhah
- Department of Medical-Surgical Nursing, School of Nursing and Midwifery
- Burn and Regenerative Medicine Research Center
| | - Mohammad Akhoondian
- Department of Physiology, School of Medicine, Cellular and The Molecular Research Center, Guilan University of Medical Science, Rasht, Iran
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46
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Madè A, Bibi A, Garcia-Manteiga JM, Tascini AS, Piella SN, Tikhomirov R, Voellenkle C, Gaetano C, Leszek P, Castelvecchio S, Menicanti L, Martelli F, Greco S. circRNA-miRNA-mRNA Deregulated Network in Ischemic Heart Failure Patients. Cells 2023; 12:2578. [PMID: 37947656 PMCID: PMC10648415 DOI: 10.3390/cells12212578] [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: 09/15/2023] [Revised: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
Noncoding RNAs (ncRNAs), which include circular RNAs (circRNAs) and microRNAs (miRNAs), regulate the development of cardiovascular diseases (CVD). Notably, circRNAs can interact with miRNAs, influencing their specific mRNA targets' levels and shaping a competing endogenous RNAs (ceRNA) network. However, these interactions and their respective functions remain largely unexplored in ischemic heart failure (IHF). This study is aimed at identifying circRNA-centered ceRNA networks in non-end-stage IHF. Approximately 662 circRNA-miRNA-mRNA interactions were identified in the heart by combining state-of-the-art bioinformatics tools with experimental data. Importantly, KEGG terms of the enriched mRNA indicated CVD-related signaling pathways. A specific network centered on circBPTF was validated experimentally. The levels of let-7a-5p, miR-18a-3p, miR-146b-5p, and miR-196b-5p were enriched in circBPTF pull-down experiments, and circBPTF silencing inhibited the expression of HDAC9 and LRRC17, which are targets of miR-196b-5p. Furthermore, as suggested by the enriched pathway terms of the circBPTF ceRNA network, circBPTF inhibition elicited endothelial cell cycle arrest. circBPTF expression increased in endothelial cells exposed to hypoxia, and its upregulation was confirmed in cardiac samples of 36 end-stage IHF patients compared to healthy controls. In conclusion, circRNAs act as miRNA sponges, regulating the functions of multiple mRNA targets, thus providing a novel vision of HF pathogenesis and laying the theoretical foundation for further experimental studies.
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Affiliation(s)
- Alisia Madè
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
| | - Alessia Bibi
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
- Department of Biosciences, University of Milan, 20122 Milan, Italy
| | - Jose Manuel Garcia-Manteiga
- Center for Omics Sciences COSR, BioInformatics Laboratory, San Raffaele Scientific Institute, 20132 Milan, Italy; (J.M.G.-M.); (A.S.T.)
| | - Anna Sofia Tascini
- Center for Omics Sciences COSR, BioInformatics Laboratory, San Raffaele Scientific Institute, 20132 Milan, Italy; (J.M.G.-M.); (A.S.T.)
- Università Vita-Salute San Raffaele, 20132 Milan, Italy
| | - Santiago Nicolas Piella
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
| | - Roman Tikhomirov
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
| | - Christine Voellenkle
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
| | - Carlo Gaetano
- Laboratory of Epigenetics, Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy;
| | - Przemyslaw Leszek
- Department of Heart Failure and Transplantology, National Institute of Cardiology, 04-628 Warsaw, Poland;
| | - Serenella Castelvecchio
- Department of Adult Cardiac Surgery, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (S.C.); (L.M.)
| | - Lorenzo Menicanti
- Department of Adult Cardiac Surgery, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (S.C.); (L.M.)
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
| | - Simona Greco
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy; (A.M.); (A.B.); (S.N.P.); (R.T.); (C.V.); (S.G.)
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Gschwendtberger T, Thau-Habermann N, von der Ohe J, Luo T, Hass R, Petri S. Protective effects of EVs/exosomes derived from permanently growing human MSC on primary murine ALS motor neurons. Neurosci Lett 2023; 816:137493. [PMID: 37774774 DOI: 10.1016/j.neulet.2023.137493] [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: 06/15/2023] [Revised: 08/29/2023] [Accepted: 09/19/2023] [Indexed: 10/01/2023]
Abstract
In recent years, the neuroprotective potential of mesenchymal stroma-/stem-like cells (MSC) as well as of MSC-derived extracellular vesicles (EVs) like exosomes has been intensively explored. This included preclinical evaluation regarding treatment of neurodegenerative disorders such as the fatal motor neuron disease amyotrophic Lateral Sclerosis (ALS). Several studies have reported that MSC-derived exosomes can stimulate tissue regeneration and reduce inflammation. MSC release EVs and trophic factors and thereby modify cell-to-cell communication. These cell-free products may protect degenerating motor neurons (MNs) and represent a potential therapeutic approach for ALS. In the present study we investigated the effects of exosomes derived from a permanently growing MSC line on both, wild type and ALS (SOD1G93A transgenic) primary motor neurons. Following application in a normal and stressed environment we could demonstrate beneficial effects of MSC exosomes on neurite growth and morphology indicating the potential for further preclinical evaluation and clinical therapeutic development. Investigation of gene expression profiles detected transcripts of several antioxidant and anti-inflammatory genes in MSC exosomes. Characterization of their microRNA (miRNA) content revealed miRNAs capable of regulating antioxidant and anti-apoptotic pathways.
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Affiliation(s)
- Thomas Gschwendtberger
- Department of Neurology, Hannover Medical School, Hannover 30625, Germany; Center for Systems Neuroscience (ZSN), Hannover, Germany
| | | | - Juliane von der Ohe
- Biochemistry and Tumor Biology Lab, Department of Obstetrics and Gynecology, Hannover Medical School, Hannover 30625, Germany
| | - Tianjiao Luo
- Biochemistry and Tumor Biology Lab, Department of Obstetrics and Gynecology, Hannover Medical School, Hannover 30625, Germany
| | - Ralf Hass
- Biochemistry and Tumor Biology Lab, Department of Obstetrics and Gynecology, Hannover Medical School, Hannover 30625, Germany.
| | - Susanne Petri
- Department of Neurology, Hannover Medical School, Hannover 30625, Germany; Center for Systems Neuroscience (ZSN), Hannover, Germany.
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Piergiorge RM, da Silva Francisco Junior R, de Vasconcelos ATR, Santos-Rebouças CB. Multi-layered transcriptomic analysis reveals a pivotal role of FMR1 and other developmental genes in Alzheimer's disease-associated brain ceRNA network. Comput Biol Med 2023; 166:107494. [PMID: 37769462 DOI: 10.1016/j.compbiomed.2023.107494] [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: 05/08/2023] [Revised: 09/05/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023]
Abstract
Alzheimer's disease (AD) is an increasingly neurodegenerative disorder that causes progressive cognitive decline and memory impairment. Despite extensive research, the underlying causes of late-onset AD (LOAD) are still in progress. This study aimed to establish a network of competing regulatory interactions involving circular RNAs (circRNAs), microRNAs (miRNAs), RNA-binding proteins (RBPs), and messenger RNAs (mRNAs) connected to LOAD. A systematic analysis of publicly available expression data was conducted to identify integrated differentially expressed genes (DEGs) from the hippocampus of LOAD patients. Subsequently, gene co-expression analysis identified modules comprising highly expressed DEGs that act cooperatively. The competition between co-expressed DEGs and miRNAs/RBPs and the simultaneous interactions between circRNA and miRNA/RBP revealed a complex ceRNA network responsible for post-transcriptional regulation in LOAD. Hippocampal expression data for miRNAs, circRNAs, and RBPs were used to filter relevant relationships for AD. An integrated topological score was used to identify the highly connected hub gene, from which a brain core ceRNA subnetwork was generated. The Fragile X Messenger Ribonucleoprotein 1 (FMR1) coding for the RBP FMRP emerged as the prominent driver gene in this subnetwork. FMRP has been previously related to AD but not in a ceRNA network context. Also, the substantial number of neurodevelopmental genes in the ceRNA subnetwork and their related biological pathways strengthen that AD shares common pathological mechanisms with developmental conditions. Our results enhance the current knowledge about the convergent ceRNA regulatory pathways underlying AD and provide potential targets for identifying early biomarkers and developing novel therapeutic interventions.
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Affiliation(s)
- Rafael Mina Piergiorge
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Cíntia Barros Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil.
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Petri BJ, Piell KM, Wilt AE, Howser AD, Winkler L, Whitworth MR, Valdes BL, Lehman NL, Clem BF, Klinge CM. MicroRNA regulation of the serine synthesis pathway in endocrine-resistant breast cancer cells. Endocr Relat Cancer 2023; 30:e230148. [PMID: 37650685 PMCID: PMC10546957 DOI: 10.1530/erc-23-0148] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/25/2023] [Indexed: 09/01/2023]
Abstract
Despite the successful combination of therapies improving survival of estrogen receptor α (ER+) breast cancer patients with metastatic disease, mechanisms for acquired endocrine resistance remain to be fully elucidated. The RNA binding protein HNRNPA2B1 (A2B1), a reader of N(6)-methyladenosine (m6A) in transcribed RNA, is upregulated in endocrine-resistant, ER+ LCC9 and LY2 cells compared to parental MCF-7 endocrine-sensitive luminal A breast cancer cells. The miRNA-seq transcriptome of MCF-7 cells overexpressing A2B1 identified the serine metabolic processes pathway. Increased expression of two key enzymes in the serine synthesis pathway (SSP), phosphoserine aminotransferase 1 (PSAT1) and phosphoglycerate dehydrogenase (PHGDH), correlates with poor outcomes in ER+ breast patients who received tamoxifen (TAM). We reported that PSAT1 and PHGDH were higher in LCC9 and LY2 cells compared to MCF-7 cells and their knockdown enhanced TAM sensitivity in these-resistant cells. Here we demonstrate that stable, modest overexpression of A2B1 in MCF-7 cells increased PSAT1 and PHGDH and endocrine resistance. We identified four miRNAs downregulated in MCF-7-A2B1 cells that directly target the PSAT1 3'UTR (miR-145-5p and miR-424-5p), and the PHGDH 3'UTR (miR-34b-5p and miR-876-5p) in dual luciferase assays. Lower expression of miR-145-5p and miR-424-5p in LCC9 and ZR-75-1-4-OHT cells correlated with increased PSAT1 and lower expression of miR-34b-5p and miR-876-5p in LCC9 and ZR-75-1-4-OHT cells correlated with increased PHGDH. Transient transfection of these miRNAs restored endocrine-therapy sensitivity in LCC9 and ZR-75-1-4-OHT cells. Overall, our data suggest a role for decreased A2B1-regulated miRNAs in endocrine resistance and upregulation of the SSP to promote tumor progression in ER+ breast cancer.
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Affiliation(s)
- Belinda J. Petri
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
| | - Kellianne M. Piell
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
| | - Ali E. Wilt
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
| | - Alexa D. Howser
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
| | - Laura Winkler
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
| | - Mattie R. Whitworth
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
| | - Bailey L. Valdes
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
| | - Norman L. Lehman
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
- Pathology and Laboratory Medicine, University of Louisville, Louisville, KY, 40202, USA
- The Brown Cancer Center, University of Louisville, Louisville, KY, 40202, USA
| | - Brian F. Clem
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
- The Brown Cancer Center, University of Louisville, Louisville, KY, 40202, USA
| | - Carolyn M. Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine; Louisville, KY 40292 USA
- The Brown Cancer Center, University of Louisville, Louisville, KY, 40202, USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS)
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Tavasolian F, Lively S, Pastrello C, Tang M, Lim M, Pacheco A, Qaiyum Z, Yau E, Baskurt Z, Jurisica I, Kapoor M, Inman RD. Proteomic and genomic profiling of plasma exosomes from patients with ankylosing spondylitis. Ann Rheum Dis 2023; 82:1429-1443. [PMID: 37532285 DOI: 10.1136/ard-2022-223791] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/14/2023] [Indexed: 08/04/2023]
Abstract
INTRODUCTION Recent advances in understanding the biology of ankylosing spondylitis (AS) using innovative genomic and proteomic approaches offer the opportunity to address current challenges in AS diagnosis and management. Altered expression of genes, microRNAs (miRNAs) or proteins may contribute to immune dysregulation and may play a significant role in the onset and persistence of inflammation in AS. The ability of exosomes to transport miRNAs across cells and alter the phenotype of recipient cells has implicated exosomes in perpetuating inflammation in AS. This study reports the first proteomic and miRNA profiling of plasma-derived exosomes in AS using comprehensive computational biology analysis. METHODS Plasma samples from patients with AS and healthy controls (HC) were isolated via ultracentrifugation and subjected to extracellular vesicle flow cytometry analysis to characterise exosome surface markers by a multiplex immunocapture assay. Cytokine profiling of plasma-derived exosomes and cell culture supernatants was performed. Next-generation sequencing was used to identify miRNA populations in exosomes enriched from plasma fractions. CD4+ T cells were sorted, and the frequency and proliferation of CD4+ T-cell subsets were analysed after treatment with AS-exosomes using flow cytometry. RESULTS The expression of exosome marker proteins CD63 and CD81 was elevated in the patients with AS compared with HC (q<0.05). Cytokine profiling in plasma-derived AS-exosomes demonstrated downregulation of interleukin (IL)-8 and IL-10 (q<0.05). AS-exosomes cocultured with HC CD4+ T cells induced significant upregulation of IFNα2 and IL-33 (q<0.05). Exosomes from patients with AS inhibited the proliferation of regulatory T cells (Treg), suggesting a mechanism for chronically activated T cells in this disease. Culture of CD4+ T cells from healthy individuals in the presence of AS-exosomes reduced the proliferation of FOXP3+ Treg cells and decreased the frequency of FOXP3+IRF4+ Treg cells. miRNA sequencing identified 24 differentially expressed miRNAs found in circulating exosomes of patients with AS compared with HC; 22 of which were upregulated and 2 were downregulated. CONCLUSIONS Individuals with AS have different immunological and genetic profiles, as determined by evaluating the exosomes of these patients. The inhibitory effect of exosomes on Treg in AS suggests a mechanism contributing to chronically activated T cells in this disease.
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Affiliation(s)
- Fataneh Tavasolian
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Starlee Lively
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada
| | - Chiara Pastrello
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada
- Krembil Research Institute, - Data Science Discovery Centre for Chronic Diseases, University Health Network, Toronto, Ontario, Canada
| | - Michael Tang
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Melissa Lim
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Addison Pacheco
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Zoya Qaiyum
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Enoch Yau
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Zeynep Baskurt
- Department of Biostatistics, Princess Margaret Cancer Center, 610 University Ave, Toronto, Ontario, Canada
| | - Igor Jurisica
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada
- Krembil Research Institute, - Data Science Discovery Centre for Chronic Diseases, University Health Network, Toronto, Ontario, Canada
- Departments of Medical Biophysics and Computer Science, and Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Mohit Kapoor
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
- Osteoarthritis Research Program, Division of Orthopaedics, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada
- Department of Surgery, Division of Orthopaedic Surgery and Department of Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Robert D Inman
- Schroeder Arthritis Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Spondylitis Program, Division of Rheumatology, Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada
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