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Sforzini L, Marizzoni M, Bottanelli C, Kunšteková V, Zonca V, Saleri S, Kose M, Lombardo G, Mariani N, Nettis MA, Nikkheslat N, Worrell C, Zajkowska Z, Pointon L, Cowen PJ, Cavanagh J, Harrison NA, Riva MA, Mondelli V, Bullmore ET, Cattaneo A, Pariante CM. Transcriptomic profiles in major depressive disorder: the role of immunometabolic and cell-cycle-related pathways in depression with different levels of inflammation. Mol Psychiatry 2024:10.1038/s41380-024-02736-w. [PMID: 39271754 DOI: 10.1038/s41380-024-02736-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 08/22/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024]
Abstract
Transcriptomic profiles are important indicators for molecular mechanisms and pathways involved in major depressive disorder (MDD) and its different phenotypes, such as immunometabolic depression. We performed whole-transcriptome and pathway analyses on 139 individuals from the observational, case-control, BIOmarkers in DEPression (BIODEP) study, 105 with MDD and 34 controls. We divided MDD participants based on levels of inflammation, as measured by serum high-sensitivity C-reactive protein (CRP), in n = 39 'not inflamed' (CRP < 1 mg/L), n = 31 with 'elevated CRP' (1-3 mg/L), and n = 35 with 'low-grade inflammation' (>3 mg/L). We performed whole-blood RNA sequencing using Illumina NextSeq 550 and statistical analyses with the Deseq2 package for R statistics (RUV-corrected) and subsequent pathway analyses with Ingenuity Pathway Analysis. Immunometabolic pathways were activated in individuals with CRP > 1 mg/L, although surprisingly the CRP 1-3 group showed stronger immune activation than the CRP > 3 group. The main pathways identified in the comparison between CRP < 1 group and controls were cell-cycle-related, which may be protective against immunometabolic abnormalities in this 'non-inflamed' depressed group. We further divided MDD participants based on exposure and response to antidepressants (n = 47 non-responders, n = 37 responders, and n = 22 unmedicated), and identified specific immunomodulatory and neuroprotective pathways in responders (especially vs. non-responders), which could be relevant to treatment response. In further subgroup analyses, we found that the specific transcriptional profile of responders is independent of CRP levels, and that the inhibition of cell-cycle-related pathways in MDD with CRP < 1 mg/L is present only in those who are currently depressed, and not in the responders. The present study demonstrates immunometabolic and cell-cycle-related transcriptomic pathways associated with MDD and different (CRP-based and treatment-based) MDD phenotypes, while shedding light on potential molecular mechanisms that could prevent or facilitate an individual's trajectory toward immunometabolic depression and/or treatment-non-responsive depression. The recognition and integration of these mechanisms will facilitate a precision-medicine approach in MDD.
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Affiliation(s)
- Luca Sforzini
- Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RT, UK.
- National Institute for Health Research (NIHR) Maudsley Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King's College London, London, UK.
| | - Moira Marizzoni
- Biological Psychiatric Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125, Brescia, Italy
| | - Chiara Bottanelli
- Biological Psychiatric Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125, Brescia, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, 20133, Italy
| | - Veronika Kunšteková
- Institute of Biology, Faculty of Medicine, Slovak Medical University, Limbova 14, 833 03, Bratislava, Slovakia
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08, Bratislava, Slovakia
| | - Valentina Zonca
- Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RT, UK
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, 20133, Italy
| | - Samantha Saleri
- Biological Psychiatric Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125, Brescia, Italy
| | - Melisa Kose
- Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RT, UK
| | - Giulia Lombardo
- Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RT, UK
| | - Nicole Mariani
- Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RT, UK
| | - Maria A Nettis
- Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RT, UK
| | - Naghmeh Nikkheslat
- Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RT, UK
| | - Courtney Worrell
- Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RT, UK
| | - Zuzanna Zajkowska
- Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RT, UK
| | - Linda Pointon
- Department of Psychiatry, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SZ, UK
| | - Philip J Cowen
- University of Oxford Department of Psychiatry, Warneford Hospital, Oxford, OX3 7JX, UK
| | - Jonathan Cavanagh
- Centre for Immunobiology, School of Infection & Immunity, University of Glasgow, Glasgow, G12 8TF, UK
| | - Neil A Harrison
- School of Medicine, School of Psychology, Cardiff University Brain Research Imaging Centre, Maindy Road, Cardiff, CF24 4HQ, UK
| | - Marco A Riva
- Biological Psychiatric Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125, Brescia, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, 20133, Italy
| | - Valeria Mondelli
- Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RT, UK
- National Institute for Health Research (NIHR) Maudsley Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King's College London, London, UK
| | - Edward T Bullmore
- Department of Psychiatry, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SZ, UK
| | - Annamaria Cattaneo
- Biological Psychiatric Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125, Brescia, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, 20133, Italy
| | - Carmine M Pariante
- Institute of Psychiatry, Psychology and Neuroscience, Department of Psychological Medicine, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 9RT, UK
- National Institute for Health Research (NIHR) Maudsley Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King's College London, London, UK
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Bao L, Sun Z, Dang L, Zhang Q, Zheng L, Yang F, Zhang J. LncRNA RP11-818O24.3 promotes hair-follicle recovery via FGF2-PI3K/Akt signal pathway. Cytotechnology 2024; 76:425-439. [PMID: 38933868 PMCID: PMC11196536 DOI: 10.1007/s10616-024-00624-3] [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: 06/28/2023] [Accepted: 02/16/2024] [Indexed: 06/28/2024] Open
Abstract
A previous study indicated that patients with androgenic alopecia (AGA) have significantly reduced levels of LncRNA RP11-818O24.3. This study investigates whether LncRNA RP11-818O24.3 promotes hair-follicle recovery and its possible mechanism. Hair alteration and cutaneous histopathological changes induced by testosterone propionate were observed by H&E and bromodeoxyuridinc (BrdU) stain to evaluate the therapeutic effect of LncRNA RP11-818O24.3 in C57BL/6 J mice. The cellular viability was analyzed in LncRNA RP11-818O24.3-transfected human hair-follicle stem cells (HFSCs) in vitro. The signaling pathways and pro-proliferative factors were investigated by transcriptomic gene sequencing and qRT-PCR. LncRNA RP11-818O24.3 transfection successfully recovered hair growth and hair-follicle cells in AGA mice. In a series of HFSC studies in vitro, LncRNA RP11-818O24.3 transfection greatly promoted cellular proliferation and decreased cellular apoptosis. Transcriptome gene sequencing suggested that the phosphatidylinositol 3-kinase (PI3K)-Akt pathway was upregulated by LncRNA RP11-818O24.3. The qRT-PCR results showed that fibroblast growth factor (FGF)-2 was 14-times upregulated after LncRNA RP11-818O24.3 transfection. Hair-follicle recovery activity of LncRNA RP11-818O24.3 may involve the upregulation of FGF2 and PI3K-Akt to promote follicle stem cell survival. These data not only provide a theoretical basis for AGA development but also reveal a novel therapeutic method for AGA patients. Supplementary Information The online version contains supplementary material available at 10.1007/s10616-024-00624-3.
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Affiliation(s)
- Linlin Bao
- Department of Dermatology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), No. 1017, Dongmen North Road, Luohu District, Shenzhen, 518020 Guangdong China
- Candidate Branch of National Clinical Research Center for Skin Diseases, Shenzhen, 518020 Guangdong China
| | - Zhaojun Sun
- Department of Dermatology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), No. 1017, Dongmen North Road, Luohu District, Shenzhen, 518020 Guangdong China
- Candidate Branch of National Clinical Research Center for Skin Diseases, Shenzhen, 518020 Guangdong China
| | - Lin Dang
- Department of Dermatology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), No. 1017, Dongmen North Road, Luohu District, Shenzhen, 518020 Guangdong China
- Candidate Branch of National Clinical Research Center for Skin Diseases, Shenzhen, 518020 Guangdong China
| | - Qianqian Zhang
- Department of Dermatology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), No. 1017, Dongmen North Road, Luohu District, Shenzhen, 518020 Guangdong China
- Candidate Branch of National Clinical Research Center for Skin Diseases, Shenzhen, 518020 Guangdong China
| | - Lixiong Zheng
- Department of Dermatology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), No. 1017, Dongmen North Road, Luohu District, Shenzhen, 518020 Guangdong China
- Candidate Branch of National Clinical Research Center for Skin Diseases, Shenzhen, 518020 Guangdong China
| | - Fang Yang
- Department of Dermatology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), No. 1017, Dongmen North Road, Luohu District, Shenzhen, 518020 Guangdong China
- Candidate Branch of National Clinical Research Center for Skin Diseases, Shenzhen, 518020 Guangdong China
| | - Jianglin Zhang
- Department of Dermatology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), No. 1017, Dongmen North Road, Luohu District, Shenzhen, 518020 Guangdong China
- Candidate Branch of National Clinical Research Center for Skin Diseases, Shenzhen, 518020 Guangdong China
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Akiyoshi R, Hase T, Sathiyananthavel M, Ghosh S, Kitano H, Yachie A. Noninvasive, label-free image approaches to predict multimodal molecular markers in pluripotency assessment. Sci Rep 2024; 14:15760. [PMID: 38977828 PMCID: PMC11231322 DOI: 10.1038/s41598-024-66591-z] [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: 04/05/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024] Open
Abstract
Manufacturing regenerative medicine requires continuous monitoring of pluripotent cell culture and quality assessment while eliminating cell destruction and contaminants. In this study, we employed a novel method to monitor the pluripotency of stem cells through image analysis, avoiding the traditionally used invasive procedures. This approach employs machine learning algorithms to analyze stem cell images to predict the expression of pluripotency markers, such as OCT4 and NANOG, without physically interacting with or harming cells. We cultured induced pluripotent stem cells under various conditions to induce different pluripotent states and imaged the cells using bright-field microscopy. Pluripotency states of induced pluripotent stem cells were assessed using invasive methods, including qPCR, immunostaining, flow cytometry, and RNA sequencing. Unsupervised and semi-supervised learning models were applied to evaluate the results and accurately predict the pluripotency of the cells using only image analysis. Our approach directly links images to invasive assessment results, making the analysis of cell labeling and annotation of cells in images by experts dispensable. This core achievement not only contributes for safer and more reliable stem cell research but also opens new avenues for real-time monitoring and quality control in regenerative medicine manufacturing. Our research fills an important gap in the field by providing a viable, noninvasive alternative to traditional invasive methods for assessing pluripotency. This innovation is expected to make a significant contribution to improving regenerative medicine manufacturing because it will enable a more detailed and feasible understanding of cellular status during the manufacturing process.
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Affiliation(s)
- Ryutaro Akiyoshi
- Yokogawa Electric Corporation, 2-9-32 Nakacho, Musashino-shi, Tokyo, 180-8750, Japan
| | - Takeshi Hase
- The Systems Biology Institute, Saisei Ikedayama Bldg., 5-10-25, Higashi Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan
- SBX BioSciences, Inc, 1111 West Georgia Street, 20th Floor, Vancouver, BC, V6E 4G2, Canada
| | - Mayuri Sathiyananthavel
- The Systems Biology Institute, Saisei Ikedayama Bldg., 5-10-25, Higashi Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan
- SBX BioSciences, Inc, 1111 West Georgia Street, 20th Floor, Vancouver, BC, V6E 4G2, Canada
| | - Samik Ghosh
- The Systems Biology Institute, Saisei Ikedayama Bldg., 5-10-25, Higashi Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan
| | - Hiroaki Kitano
- The Systems Biology Institute, Saisei Ikedayama Bldg., 5-10-25, Higashi Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan
| | - Ayako Yachie
- The Systems Biology Institute, Saisei Ikedayama Bldg., 5-10-25, Higashi Gotanda, Shinagawa-ku, Tokyo, 141-0022, Japan.
- SBX BioSciences, Inc, 1111 West Georgia Street, 20th Floor, Vancouver, BC, V6E 4G2, Canada.
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Khramov DE, Nedelyaeva OI, Konoshenkova AO, Volkov VS, Balnokin YV. Identification and selection of reference genes for analysis of gene expression by quantitative real-time PCR in the euhalophyte Suaeda altissima (L.) Pall. Commun Integr Biol 2024; 17:2372313. [PMID: 38988501 PMCID: PMC11236294 DOI: 10.1080/19420889.2024.2372313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/20/2024] [Indexed: 07/12/2024] Open
Abstract
Сoding sequences of seven housekeeping genes: actin SaACT7, ubiquitin-conjugating protein SaUBC10, glyceraldehyde-3-phosphate dehydrogenase SaGAPDH, protein of the large subunit of ribosomes SaL2, α-tubulin SaTUA, translation elongation factor SaeEF1α, and protein phosphatase SaPP2A were identified as candidate reference genes for expression analysis of target genes in the extremely salt tolerant plant Suaeda altissima (L.) Pall. The expression profiles of the genes differed. SaACT7 and SaeEF1α demonstrated the highest expression levels, while the lowest expression levels were found for SaPP2A and SaTUA. SaPP2A and SaeEF1α genes were the most stably expressed at different steady-state salinity levels and different nitrate concentrations in nutrient solutions (NSs). SaL2, SaPP2A, and SaeEF1α genes showed the greatest stability of expression when nitrate was added to nutrient solution of plants grown under conditions of nitrate deficiency. Less constant expression was demonstrated in this experiment by SaACT7 and SaTUA. SaL2, SaACT7, SaeEF1α, and SaUBC10 genes showed the smallest expression changes under salt shock. To validate the use of the most stably expressed genes for normalization of gene expression, we checked them as reference genes to study the expression of the nitrate transporter gene SaNPF6.3 in S. altissima roots under conditions of different salinity and different nitrate supply.
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Affiliation(s)
- Dmitrii E. Khramov
- Laboratory of Ion Transport and Salinity Tolerance, K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
| | - Olga I. Nedelyaeva
- Laboratory of Ion Transport and Salinity Tolerance, K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
| | - Alena O. Konoshenkova
- Laboratory of Ion Transport and Salinity Tolerance, K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
| | - Vadim S. Volkov
- Laboratory of Ion Transport and Salinity Tolerance, K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
- Department of Plant Sciences, College of Agricultural and Environmental Sciences, University of California, Davis, CA, USA
| | - Yurii V. Balnokin
- Laboratory of Ion Transport and Salinity Tolerance, K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Moscow, Russia
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Lopes TSB, Nankemann J, Breedlove C, Pietruska A, Espejo R, Cuadrado C, Hauck R. Changes in the Transcriptome Profile in Young Chickens after Infection with LaSota Newcastle Disease Virus. Vaccines (Basel) 2024; 12:592. [PMID: 38932321 PMCID: PMC11209074 DOI: 10.3390/vaccines12060592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/16/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Understanding gene expression changes in chicks after vaccination against Newcastle Disease (ND) can reveal vaccine biomarkers. There are limited data on chicks' early immune response after ND vaccination. Two trials focused on this knowledge gap. In experiment one, 42 13-day-old specific-pathogen-free (SPF) chicks were used. Harderian glands (Hgs) and tracheas (Tcs) from five birds per group were sampled at 12, 24, and 48 h post-vaccination (hpv) to evaluate the gene transcription levels by RNA sequencing (RNA-seq) and RT-qPCR. The results of RNA-seq were compared by glmFTest, while results of RT-qPCR were compared by t-test. With RNA-seq, a significant up-regulation of interferon-related genes along with JAK-STAT signaling pathway regulation was observed in the Hgs at 24 hpv. None of the differentially expressed genes (DEGs) identified by RNA-seq were positive for RT-qPCR. Experiment 2 used 112 SPF and commercial chickens that were 1 day old and 14 days old. Only the commercial birds had maternal antibodies for Newcastle Disease virus (NDV). By RNA-seq, 20 core DEGs associated with innate immunity and viral genome replication inhibition were identified. Genes previously unlinked to NDV response, such as USP41, were identified. This research present genes with potential as immunity biomarkers for vaccines, yet further investigation is needed to correlate the core gene expression with viral shedding post-vaccination.
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Affiliation(s)
- Taina S. B. Lopes
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (T.S.B.L.)
| | - Jannis Nankemann
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (T.S.B.L.)
| | - Cassandra Breedlove
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (T.S.B.L.)
| | - Andrea Pietruska
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (T.S.B.L.)
| | - Raimundo Espejo
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (T.S.B.L.)
| | - Camila Cuadrado
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (T.S.B.L.)
| | - Ruediger Hauck
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA; (T.S.B.L.)
- Department of Poultry Science, College of Agriculture, Auburn University, Auburn, AL 36849, USA
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Nevado JB, Cutiongco-de la Paz EMC, Paz-Pacheco ET, Jasul GV, Aman AYCL, Deguit CDT, San Pedro JVB, Francisco MDG. Transcriptional profiles associated with coronary artery disease in type 2 diabetes mellitus. Front Endocrinol (Lausanne) 2024; 15:1323168. [PMID: 38706700 PMCID: PMC11066158 DOI: 10.3389/fendo.2024.1323168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/25/2024] [Indexed: 05/07/2024] Open
Abstract
Background Coronary artery disease (CAD) is a common complication of Type 2 diabetes mellitus (T2DM). Understanding the pathogenesis of this complication is essential in both diagnosis and management. Thus, this study aimed to characterize the presence of CAD in T2DM using molecular markers and pathway analyses. Methods The study is a sex- and age-frequency matched case-control design comparing 23 unrelated adult Filipinos with T2DM-CAD to 23 controls (DM with CAD). Healthy controls served as a reference. Total RNA from peripheral blood mononuclear cells (PBMCs) underwent whole transcriptomic profiling using the Illumina HumanHT-12 v4.0 expression beadchip. Differential gene expression with gene ontogeny analyses was performed, with supporting correlational analyses using weighted correlation network analysis (WGCNA). Results The study observed that 458 genes were differentially expressed between T2DM with and without CAD (FDR<0.05). The 5 top genes the transcription factor 3 (TCF3), allograft inflammatory factor 1 (AIF1), nuclear factor, interleukin 3 regulated (NFIL3), paired immunoglobulin-like type 2 receptor alpha (PILRA), and cytoskeleton-associated protein 4 (CKAP4) with AUCs >89%. Pathway analyses show differences in innate immunity activity, which centers on the myelocytic (neutrophilic/monocytic) theme. SNP-module analyses point to a possible causal dysfunction in innate immunity that triggers the CAD injury in T2DM. Conclusion The study findings indicate the involvement of innate immunity in the development of T2DM-CAD, and potential immunity markers can reflect the occurrence of this injury. Further studies can verify the mechanistic hypothesis and use of the markers.
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Affiliation(s)
- Jose B. Nevado
- Institute of Human Genetics, National Institutes of Health-University of the Philippines Manila, Manila, Philippines
| | - Eva Maria C. Cutiongco-de la Paz
- Institute of Human Genetics, National Institutes of Health-University of the Philippines Manila, Manila, Philippines
- Philippine Genome Center, University of the Philippines System, Diliman, Quezon City, Philippines
| | - Elizabeth T. Paz-Pacheco
- Division of Endocrinology, Department of Medicine, University of the Philippines-Philippine General Hospital Medical Center, Manila, Philippines
| | - Gabriel V. Jasul
- Division of Endocrinology, Department of Medicine, University of the Philippines-Philippine General Hospital Medical Center, Manila, Philippines
| | - Aimee Yvonne Criselle L. Aman
- Institute of Human Genetics, National Institutes of Health-University of the Philippines Manila, Manila, Philippines
| | - Christian Deo T. Deguit
- Institute of Human Genetics, National Institutes of Health-University of the Philippines Manila, Manila, Philippines
| | - Jana Victoria B. San Pedro
- Institute of Human Genetics, National Institutes of Health-University of the Philippines Manila, Manila, Philippines
| | - Mark David G. Francisco
- Division of Endocrinology, Department of Medicine, University of the Philippines-Philippine General Hospital Medical Center, Manila, Philippines
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Xue R, Wang Y, Geng L, Xiao H, Kumar V, Lan X, Malhotra A, Singhal PC, Chen J. Comprehensive analysis of the gene expression profile of the male and female BTBR mice with diabetic nephropathy. Int J Biol Macromol 2024; 257:128720. [PMID: 38101684 DOI: 10.1016/j.ijbiomac.2023.128720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/26/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
Comprehensive insight into the gender-based gene expression-related omics data in a rodent model of diabetic nephropathy (DN) is scarce. In the present study, the gender-based genes regulating different pathways involved in the progression of DN were explored through an unbiased RNA sequence of kidneys from BTBR mice with DN. We identified 17,739 and 17,981 genes in male and female DN mice; 1121 and 655 genes were expressed differentially (DEGs, differentially expressed genes) in male and female DN mice; both genders displayed only 195 DEGs. In the male DN mice, the number of upregulated genes was nearly the same as that of the down-regulated genes. In contrast, the number of upregulated genes was lesser than that of the down-regulated genes in the female DN mice, manifesting a remarkable gender disparity during the progression of DN in this animal model. Gene Ontology (GO) and KEGG-enriched results showed that most of these DEGs were related to the critical biological processes, including metabolic pathways, natural oxidation, bile secretion, and PPAR signaling; all are highly associated with DN. Notably, the DEGs significantly enriched for steroid hormone biosynthesis pathway were identified in both genders; the number of DEGs increased was 22 in male DN mice and 14 in female DN mice. Specifically, the Ugt1a10, Akr1c12, and Akr1c14 were upregulated in both genders. Interestingly, the Hsd11b1 gene was upregulated in female DN mice but downregulated in male DN mice. These results suggest that a significant gender-based variance in the gene expression occurs during the progression of DN and may be playing a role in the advancement of DN in the BTBR mouse model.
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Affiliation(s)
- Rui Xue
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Ying Wang
- Department of Pathogenic Biology, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Lei Geng
- Department of Nephrology, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Haiting Xiao
- Key Laboratory of Luzhou City for Aging Medicine, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Vinod Kumar
- Department of Dermatology, Postgraduate Institute for Medical Education and Research, Chandigarh 160012, India
| | - Xiqian Lan
- Key Laboratory of Luzhou City for Aging Medicine, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Ashwani Malhotra
- Feinstein Institute for Medical Research and Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY 11030, United States
| | - Pravin C Singhal
- Feinstein Institute for Medical Research and Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY 11030, United States.
| | - Jianning Chen
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China.
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Ren S, Bai F, Schnell V, Stanko C, Ritsch M, Schenk T, Barth E, Marz M, Wang B, Pei XH, Bierhoff H. PAPAS promotes differentiation of mammary epithelial cells and suppresses breast carcinogenesis. Cell Rep 2024; 43:113644. [PMID: 38180837 DOI: 10.1016/j.celrep.2023.113644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/18/2023] [Accepted: 12/19/2023] [Indexed: 01/07/2024] Open
Abstract
Extensive remodeling of the female mammary epithelium during development and pregnancy has been linked to cancer susceptibility. The faithful response of mammary epithelial cells (MECs) to hormone signaling is key to avoiding breast cancer development. Here, we show that lactogenic differentiation of murine MECs requires silencing of genes encoding ribosomal RNA (rRNA) by the antisense transcript PAPAS. Accordingly, knockdown of PAPAS derepresses rRNA genes, attenuates the response to lactogenic hormones, and induces malignant transformation. Restoring PAPAS levels in breast cancer cells reduces tumorigenicity and lung invasion and activates many interferon-regulated genes previously linked to metastasis suppression. Mechanistically, PAPAS transcription depends on R-loop formation at the 3' end of rRNA genes, which is repressed by RNase H1 and replication protein A (RPA) overexpression in breast cancer cells. Depletion of PAPAS and upregulation of RNase H1 and RPA in human breast cancer underpin the clinical relevance of our findings.
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Affiliation(s)
- Sijia Ren
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany; Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Anatomy and Histology, Shenzhen University Medical School, Shenzhen 518060, China; Leibniz-Institute on Aging-Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745 Jena, Germany
| | - Feng Bai
- Department of Pathology, Shenzhen University Medical School, Shenzhen 518060, China
| | - Viviane Schnell
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany; Leibniz-Institute on Aging-Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745 Jena, Germany
| | - Clara Stanko
- Department of Hematology and Medical Oncology, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany; Institute of Molecular Cell Biology, Center for Molecular Biomedicine (CMB), Jena University Hospital, Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany
| | - Muriel Ritsch
- Bioinformatics Core Facility Jena, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Leutragraben 1, 07743 Jena, Germany
| | - Tino Schenk
- Department of Hematology and Medical Oncology, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany; Institute of Molecular Cell Biology, Center for Molecular Biomedicine (CMB), Jena University Hospital, Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany
| | - Emanuel Barth
- Bioinformatics Core Facility Jena, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Leutragraben 1, 07743 Jena, Germany
| | - Manja Marz
- Bioinformatics Core Facility Jena, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Leutragraben 1, 07743 Jena, Germany
| | - Bin Wang
- Department of General Surgery, Shenzhen Children's Hospital, Shenzhen 518060, China
| | - Xin-Hai Pei
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Department of Anatomy and Histology, Shenzhen University Medical School, Shenzhen 518060, China.
| | - Holger Bierhoff
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine (CMB), Friedrich Schiller University Jena, Hans-Knöll-Str. 2, 07745 Jena, Germany; Leibniz-Institute on Aging-Fritz Lipmann Institute (FLI), Beutenbergstr. 11, 07745 Jena, Germany.
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9
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Diallo LH, Mariette J, Laugero N, Touriol C, Morfoisse F, Prats AC, Garmy-Susini B, Lacazette E. Specific Circular RNA Signature of Endothelial Cells: Potential Implications in Vascular Pathophysiology. Int J Mol Sci 2024; 25:680. [PMID: 38203852 PMCID: PMC10779679 DOI: 10.3390/ijms25010680] [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: 11/21/2023] [Revised: 12/23/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Circular RNAs (circRNAs) are a recently characterized family of gene transcripts forming a covalently closed loop of single-stranded RNA. The extent of their potential for fine-tuning gene expression is still being discovered. Several studies have implicated certain circular RNAs in pathophysiological processes within vascular endothelial cells and cancer cells independently. However, to date, no comparative study of circular RNA expression in different types of endothelial cells has been performed and analysed through the lens of their central role in vascular physiology and pathology. In this work, we analysed publicly available and original RNA sequencing datasets from arterial, veinous, and lymphatic endothelial cells to identify common and distinct circRNA expression profiles. We identified 4713 distinct circRNAs in the compared endothelial cell types, 95% of which originated from exons. Interestingly, the results show that the expression profile of circular RNAs is much more specific to each cell type than linear RNAs, and therefore appears to be more suitable for distinguishing between them. As a result, we have discovered a specific circRNA signature for each given endothelial cell type. Furthermore, we identified a specific endothelial cell circRNA signature that is composed four circRNAs: circCARD6, circPLXNA2, circCASC15 and circEPHB4. These circular RNAs are produced by genes that are related to endothelial cell migration pathways and cancer progression. More detailed studies of their functions could lead to a better understanding of the mechanisms involved in physiological and pathological (lymph)angiogenesis and might open new ways to tackle tumour spread through the vascular system.
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Affiliation(s)
- Leïla Halidou Diallo
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Jérôme Mariette
- MIAT, University of Toulouse, INRAE, 31326 Castanet-Tolosan, France;
| | - Nathalie Laugero
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Christian Touriol
- UMR1037 INSERM, University of Toulouse, 2 Avenue Hubert Curien, 31100 Toulouse, France;
| | - Florent Morfoisse
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Anne-Catherine Prats
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Barbara Garmy-Susini
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Eric Lacazette
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
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10
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Richter M, Loth Y, Wigger AK, Nordhoff D, Rachinger N, Weisenstein C, Bosserhoff AK, Bolívar PH. High specificity THz metamaterial-based biosensor for label-free transcription factor detection in melanoma diagnostics. Sci Rep 2023; 13:20708. [PMID: 38001098 PMCID: PMC10673904 DOI: 10.1038/s41598-023-46876-5] [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: 04/25/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
In this work, we present a promising diagnostic tool for melanoma diagnosis. With the proposed terahertz biosensor, it was possible to selectively and sensitively detect the early growth response protein 2, a transcription factor with an increased activity in melanoma cells, from a complex sample of cellular proteins. Fundamentally, the sensor belongs to the frequency selective surface type metamaterials and consists of a two-dimensional array of asymmetrically, doubly split ring resonator unit cells. The single elements are slits in a metallic layer and are complemented by an undercut etch. This allows a selective functionalization of the active area of the sensor and increases the sensitivity towards the target analyte. Hereby, specific detection of a defined transcription factor is feasible.
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Affiliation(s)
- Merle Richter
- High Frequency and Quantum Electronics, University of Siegen, 57076, Siegen, Germany.
| | - Yannik Loth
- High Frequency and Quantum Electronics, University of Siegen, 57076, Siegen, Germany
| | - Anna Katharina Wigger
- High Frequency and Quantum Electronics, University of Siegen, 57076, Siegen, Germany
| | - Daniela Nordhoff
- High Frequency and Quantum Electronics, University of Siegen, 57076, Siegen, Germany
| | - Nicole Rachinger
- Biochemistry and Molecular Medicine, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Christian Weisenstein
- High Frequency and Quantum Electronics, University of Siegen, 57076, Siegen, Germany
| | - Anja Katrin Bosserhoff
- Biochemistry and Molecular Medicine, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Peter Haring Bolívar
- High Frequency and Quantum Electronics, University of Siegen, 57076, Siegen, Germany
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11
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Badai SS, Rasid OA, Masani MYA, Chan KL, Chan PL, Shaharuddin NA, Abdullah MP, Parveez GKA, Ho CL. Functional characterization of the MSP-C6 promoter as a potential tool for mesocarp-preferential expression of transgenes. JOURNAL OF PLANT PHYSIOLOGY 2023; 289:154080. [PMID: 37699261 DOI: 10.1016/j.jplph.2023.154080] [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: 03/09/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/14/2023]
Abstract
Modification of lipid composition in the mesocarp tissue of oil palm involves genetic manipulation of multiple genes. More than one mesocarp-preferential promoter is necessary for the expression of individual transgenes in the same plant to obviate transcriptional gene silencing. This study aimed to identify genes that are preferentially expressed in the mesocarp tissue and characterize selected candidate mesocarp-preferential promoters. Ten transcripts that were preferentially expressed in the mesocarp tissue were identified from the analysis of 82 transcriptome datasets of 12 different oil palm tissues. The expression of two candidate genes, MSP-C1 and MSP-C6, was verified to be preferentially expressed in the mesocarp tissues and shown to have a low expression level in non-mesocarp tissues by reverse transcription quantitative real-time PCR (RT-qPCR). MSP-C6 promoter fragments of different lengths were transformed into tomato plants for further characterization. Both unripe and ripe fruits of transgenic tomato plants transformed with a construct harboring the MSP-C6-F1 (2014 bp) promoter were shown to have high beta-glucuronidase (GUS) activities. The findings of this study suggest the potential applications of the MSP-C6 promoter as a molecular tool for genetic engineering of novel traits in fruit crops.
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Affiliation(s)
- Siti Suriawati Badai
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
| | - Omar Abd Rasid
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia
| | - Mat Yunus Abdul Masani
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia
| | - Kuang Lim Chan
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia
| | - Pek Lan Chan
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Mohd Puad Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Ghulam Kadir Ahmad Parveez
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia
| | - Chai Ling Ho
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
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12
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Hasenstein KH, John SP, Vandenbrink JP. Assessing Radish Health during Space Cultivation by Gene Transcription. PLANTS (BASEL, SWITZERLAND) 2023; 12:3458. [PMID: 37836197 PMCID: PMC10574649 DOI: 10.3390/plants12193458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023]
Abstract
During the Advanced Plant Habitat experiment 2, radish plants were grown in two successive grow-outs on the International Space Station (ISS) for 27 days each. On days 10, 18, and 24, leaf punch (LP) samples were collected and frozen. At harvest, bulb tissue was sampled with oligo-dT functionalized Solid Phase Gene Extraction (SPGE) probes. The space samples were compared with samples from ground controls (GC) grown at the Kennedy Space Center (KSC) under the same conditions as on the ISS, with notably elevated CO2 (about 2500 ppm), and from lab plants grown under atmospheric CO2 but with light and temperature conditions similar to the KSC control. Genes corresponding to peroxidase (RPP), glucosinolate biosynthesis (GIS), protein binding (CBP), myrosinase (RMA), napin (RSN), and ubiquitin (UBQ) were measured by qPCR. LP from day 24 and bulb samples collected at harvest were compared with RNA-seq data from material that was harvested, frozen, and analyzed after return to Earth. The results showed stable transcription in LP samples in GC but decreasing values in ISS samples during both grow-outs, possibly indicative of stress. SPGE results were similar between GC and ISS samples. However, the RNA-seq analyses showed different transcription profiles than SPGE or LP results, possibly related to localized sampling. RNA-seq of leaf samples showed greater variety than LP data, possibly because of different sampling times. RSN and RPP showed the lowest transcription regardless of method. Temporal analyses showed relatively small changes during plant development in space and in ground controls. This is the first study that compares developmental changes in space-grown plants with ground controls based on a comparison between RNA-seq and qPCR analyses.
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Affiliation(s)
- Karl H. Hasenstein
- Biology Department, University of Louisiana Lafayette, Lafayette, LA 70504, USA;
| | - Susan P. John
- Biology Department, University of Louisiana Lafayette, Lafayette, LA 70504, USA;
| | - Joshua P. Vandenbrink
- Department of Biological Sciences, Louisiana Tech University, Ruston, LA 71272, USA;
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13
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Ahmed SBM, Radwan N, Amer S, Saheb Sharif-Askari N, Mahdami A, Samara KA, Halwani R, Jelinek HF. Assessing the Link between Diabetic Metabolic Dysregulation and Breast Cancer Progression. Int J Mol Sci 2023; 24:11816. [PMID: 37511575 PMCID: PMC10380477 DOI: 10.3390/ijms241411816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Diabetes mellitus is a burdensome disease that affects various cellular functions through altered glucose metabolism. Several reports have linked diabetes to cancer development; however, the exact molecular mechanism of how diabetes-related traits contribute to cancer progression is not fully understood. The current study aimed to explore the molecular mechanism underlying the potential effect of hyperglycemia combined with hyperinsulinemia on the progression of breast cancer cells. To this end, gene dysregulation induced by the exposure of MCF7 breast cancer cells to hyperglycemia (HG), or a combination of hyperglycemia and hyperinsulinemia (HGI), was analyzed using a microarray gene expression assay. Hyperglycemia combined with hyperinsulinemia induced differential expression of 45 genes (greater than or equal to two-fold), which were not shared by other treatments. On the other hand, in silico analysis performed using a publicly available dataset (GEO: GSE150586) revealed differential upregulation of 15 genes in the breast tumor tissues of diabetic patients with breast cancer when compared with breast cancer patients with no diabetes. SLC26A11, ALDH1A3, MED20, PABPC4 and SCP2 were among the top upregulated genes in both microarray data and the in silico analysis. In conclusion, hyperglycemia combined with hyperinsulinemia caused a likely unique signature that contributes to acquiring more carcinogenic traits. Indeed, these findings might potentially add emphasis on how monitoring diabetes-related metabolic alteration as an adjunct to diabetes therapy is important in improving breast cancer outcomes. However, further detailed studies are required to decipher the role of the highlighted genes, in this study, in the pathogenesis of breast cancer in patients with a different glycemic index.
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Affiliation(s)
- Samrein B M Ahmed
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Health, Wellbeing and Life Sciences, Department of Biosciences and Chemistry, Sheffield Hallam University, Sheffield S1 1WB, UK
| | - Nada Radwan
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Sara Amer
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Narjes Saheb Sharif-Askari
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Amena Mahdami
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Kamel A Samara
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Rabih Halwani
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Herbert F Jelinek
- Department of Biomedical Engineering and Health Engineering Innovation Center, Khalifa University, Abu Dhabi 127788, United Arab Emirates
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14
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Xu X, Ma J, Li W, You Y, Jiang Q, Long P, Liu K, Mo T, Jiang J, Wang W, Lei Y, Diao T, Ruan S, Wang X, Guo H, Chen W, Wu T. Polycyclic aromatic hydrocarbons exposure and plasma lncRNA signature: A profile and functional analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 877:162932. [PMID: 36934921 DOI: 10.1016/j.scitotenv.2023.162932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 05/06/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants that pose detrimental effects on human health, and the exploration of the associations of PAHs exposure with long non-coding RNA (lncRNA) may provide novel clues to the underlying mechanisms. In the present study, we detected 10 urinary PAHs metabolites by GC-MS and plasma lncRNAs levels by Human LncRNA Array v4 among 230 participants from two panels (160 in the Shiyan panel and 70 in the Wuhan-Zhuhai panel). We applied linear regression models to assess the associations between PAHs metabolites and lncRNAs separately in each panel and combined the results using fixed-effect meta-analysis. To explore the potential origin of PAHs-related lncRNAs in plasma, we estimated their tissue-specificity and associations between lncRNAs levels in plasma and leukocytes. Leukocytes mRNA sequencing data and RNA binding proteins were utilized to explore implicated pathways of identified lncRNAs. We found that urinary 1-hydroxyphenanthrene (1-OH-Phe) was inversely associated with 8 lncRNAs and positively associated with 1 lncRNA, as well as 9-hydroxyphenanthrene (9-OH-Phe) was inversely associated with 11 lncRNAs (FDR < 0.1). Tissue specificity analysis using Genome Tissue Expression database suggested that several identified lncRNAs might specifically express in organs targeted by PAHs exposure (lung, liver, heart, kidney, and brain). Besides, plasma levels of 1-OH-Phe related ENSG00000260616 and 9-OH-Phe related STARD4-AS1 were inversely associated with their intra-leukocytes levels (P value < 0.05). Notably, STARD4-AS1 was positively associated with the expression levels of its neighboring protein-coding gene (CAMK4 and STARD4) in leukocytes and were involved in pathways related to cellular response to DNA damage, which we further confirmed using DNA damage biomarker, 8-hydroxydeoxyguanosine. Functional analysis also revealed vital pathways related to cytokine-mediated signaling and glucose homeostasis. Our findings provided novel insights into plausible biological mechanisms underlying the adverse effects of PAHs exposure.
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Affiliation(s)
- Xuedan Xu
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jixuan Ma
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wending Li
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yutong You
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qin Jiang
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Pinpin Long
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kang Liu
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; School of Public Health, Guangzhou Medical University, Guangzhou 511436, China
| | - Tingting Mo
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jing Jiang
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei Wang
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yanshou Lei
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tingyue Diao
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shuping Ruan
- Health Management Center, Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan 442008, China
| | - Xiaozheng Wang
- Health Management Center, Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan 442008, China
| | - Huan Guo
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Weihong Chen
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tangchun Wu
- Department of Occupational and Environmental Health, Key Laboratory of Environment and Health, Ministry of Education and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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15
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Wang Z, Spitz R, Vezina C, Hou J, Bjorling DE. Lack of expression of miR-29a/b1 impairs bladder function in male mice. Dis Model Mech 2023; 16:dmm050054. [PMID: 37283037 PMCID: PMC10259841 DOI: 10.1242/dmm.050054] [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: 12/23/2022] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
Lower urinary tract symptoms (LUTS) refer to various urological diseases, and incomplete bladder emptying is common among affected patients. The etiology of LUTS is largely unknown, and investigations of LUTS suggest that bladder fibrosis contributes to pathogenesis of LUTS. MicroRNAs (miRNAs) are short (∼22 nucleotides), non-coding RNAs that repress target gene expression by a combination of mRNA degradation and translation inhibition. The miR-29 family is best known for its anti-fibrotic role in various organs. miR-29 was decreased in bladders of patients with outlet obstruction and a rat model of bladder outlet obstruction, suggesting that miR-29 may contribute to impaired bladder function subsequent to tissue fibrosis. We characterized bladder function in male mice lacking expression of Mir29a and Mir29b-1 (miR-29a/b1). Lack of miR-29a/b1 resulted in severe urinary retention, increased voiding duration and reduced flow rate, and these mice failed to void or voided irregularly during anesthetized cytometry. Collagens and elastin were increased in bladders of mice lacking miR-29a/b1. These findings reveal an important role for miR-29 in bladder homeostasis and suggest the therapeutic potential of miR-29 to improve symptoms in patients with LUTS.
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Affiliation(s)
- Zunyi Wang
- Department of Surgical Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Robert Spitz
- Department of Surgical Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Chad Vezina
- The O'Brien Center for Urologic Research, University of Wisconsin-Madison, Madison, WI 53706, USA
- Comparative Biosciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jianghui Hou
- Division of Nephrology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Dale E. Bjorling
- Department of Surgical Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
- The O'Brien Center for Urologic Research, University of Wisconsin-Madison, Madison, WI 53706, USA
- Urology, University of Wisconsin-Madison, Madison, WI 53706, USA
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16
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Noël A, Yilmaz S, Farrow T, Schexnayder M, Eickelberg O, Jelesijevic T. Sex-Specific Alterations of the Lung Transcriptome at Birth in Mouse Offspring Prenatally Exposed to Vanilla-Flavored E-Cigarette Aerosols and Enhanced Susceptibility to Asthma. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:3710. [PMID: 36834405 PMCID: PMC9967225 DOI: 10.3390/ijerph20043710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/07/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Currently, approximately 8 million adult Americans use electronic cigarettes (e-cigs) daily, including women of childbearing age. It is known that more than 10% of women smoke during their pregnancy, and recent surveys show that rates of maternal vaping are similar to rates of maternal cigarette smoking. However, the effects of inhaling e-cig aerosol on the health of fetuses remain unknown. The objective of the present study was to increase our understanding of the molecular effects caused by in utero exposures to e-cig aerosols on developing mouse lungs and, later in life, on the offspring's susceptibility to developing asthma. METHODS Pregnant mice were exposed throughout gestation to either filtered air or vanilla-flavored e-cig aerosols containing 18 mg/mL of nicotine. Male and female exposed mouse offspring were sacrificed at birth, and then the lung transcriptome was evaluated. Additionally, once sub-groups of male offspring mice reached 4 weeks of age, they were challenged with house dust mites (HDMs) for 3 weeks to assess asthmatic responses. RESULTS The lung transcriptomic responses of the mouse offspring at birth showed that in utero vanilla-flavored e-cig aerosol exposure significantly regulated 88 genes in males (62 genes were up-regulated and 26 genes were down-regulated), and 65 genes were significantly regulated in females (17 genes were up-regulated and 48 genes were down-regulated). Gene network analyses revealed that in utero e-cig aerosol exposure affected canonical pathways associated with CD28 signaling in T helper cells, the role of NFAT in the regulation of immune responses, and phospholipase C signaling in males, whereas the dysregulated genes in the female offspring were associated with NRF2-mediated oxidative stress responses. Moreover, we found that in utero exposures to vanilla-flavored e-cig aerosol exacerbated HDM-induced asthma in 7-week-old male mouse offspring compared to respective in utero air + HDM controls. CONCLUSIONS Overall, these data demonstrate that in utero e-cig aerosol exposure alters the developing mouse lung transcriptome at birth in a sex-specific manner and provide evidence that the inhalation of e-cig aerosols is detrimental to the respiratory health of offspring by increasing the offspring' susceptibility to developing lung diseases later in life.
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Affiliation(s)
- Alexandra Noël
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Sultan Yilmaz
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Tori Farrow
- Department of Environmental Toxicology, Southern University and A & M College, Baton Rouge, LA 70813, USA
| | | | - Oliver Eickelberg
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Tomislav Jelesijevic
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
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17
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Moradi M, Zhandi M, Sharafi M, Akbari A, Atrabi MJ, Totonchi M. Gene expression profile of placentomes and clinical parameters in the cows with retained placenta. BMC Genomics 2022; 23:760. [PMID: 36411408 PMCID: PMC9677913 DOI: 10.1186/s12864-022-08989-5] [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: 09/06/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Retained placenta (RP) is a prevalent disorder in cattle with many health-related and economic costs for the farm owners. Its etiology has not been clarified yet and there is no definite therapy for this disorder. In this study we conducted RNA-seq, hematologic and histologic experiments to survey the causes of RP development. METHODS Blood samples were collected from 4 RP and 3 healthy cows during periparturtion period for hematological assessments followed by placentome sampling within 30 min after parturition. Cows were grouped as RP and control in case the placenta was retained or otherwise expelled, respectively. Total RNA was extracted from placentome samples followed by RNA-sequencing. RESULTS We showed 240 differentially expressed genes (DEGs) between the RP and control groups. Enrichment analyzes indicated immune system and lipid metabolism as prominent over- and under-represented pathways in RP cows, respectively. Hormonal assessments showed that estradiol-17β (E2) was lower and cortisol tended to be higher in RP cows compared to controls at the day of parturition. Furthermore, histologic experiment showed that villi-crypt junctions remain tighter in RP cows compared to controls and the crypts layer seemed thicker in the placentome of RP cows. Complete blood cell (CBC) parameters were not significantly different between the two groups. CONCLUSION Overall, DEGs derived from expression profiling and these genes contributed to enrichment of immune and lipid metabolism pathways. We suggested that E2 could be involved in development of RP and the concentrations of P4 and CBC counts periparturition might not be a determining factor.
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Affiliation(s)
- Mehdi Moradi
- grid.46072.370000 0004 0612 7950Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Mahdi Zhandi
- grid.46072.370000 0004 0612 7950Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Mohsen Sharafi
- grid.412266.50000 0001 1781 3962Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran ,grid.419336.a0000 0004 0612 4397Department of Embryology, Reproduction Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACER, Tehran, Iran
| | - Arvand Akbari
- grid.417689.5Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Mohammad Jafari Atrabi
- grid.411984.10000 0001 0482 5331Institute of Pharmacology and Toxicology, University Medical Center, Georg August University, Göttingen, Germany
| | - Mehdi Totonchi
- grid.417689.5Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
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18
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Urbański A, Johnston P, Bittermann E, Keshavarz M, Paris V, Walkowiak-Nowicka K, Konopińska N, Marciniak P, Rolff J. Tachykinin-related peptides modulate immune-gene expression in the mealworm beetle Tenebrio molitor L. Sci Rep 2022; 12:17277. [PMID: 36241888 PMCID: PMC9568666 DOI: 10.1038/s41598-022-21605-6] [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: 01/26/2022] [Accepted: 09/29/2022] [Indexed: 01/06/2023] Open
Abstract
Tachykinins (TKs) are a group of conserved neuropeptides. In insects, tachykinin-related peptides (TRPs) are important modulators of several functions such as nociception and lipid metabolism. Recently, it has become clear that TRPs also play a role in regulating the insect immune system. Here, we report a transcriptomic analysis of changes in the expression levels of immune-related genes in the storage pest Tenebrio molitor after treatment with Tenmo-TRP-7. We tested two concentrations (10-8 and 10-6 M) at two time points, 6 and 24 h post-injection. We found significant changes in the transcript levels of a wide spectrum of immune-related genes. Some changes were observed 6 h after the injection of Tenmo-TRP-7, especially in relation to its putative anti-apoptotic action. Interestingly, 24 h after the injection of 10-8 M Tenmo-TRP-7, most changes were related to the regulation of the cellular response. Applying 10-6 M Tenmo-TRP-7 resulted in the downregulation of genes associated with humoral responses. Injecting Tenmo-TRP-7 did not affect beetle survival but led to a reduction in haemolymph lysozyme-like antibacterial activity, consistent with the transcriptomic data. The results confirmed the immunomodulatory role of TRP and shed new light on the functional homology between TRPs and TKs.
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Affiliation(s)
- Arkadiusz Urbański
- grid.5633.30000 0001 2097 3545Department of Animal Physiology and Developmental Biology, Adam Mickiewicz University, Poznań, Poland ,grid.14095.390000 0000 9116 4836Evolutionary Biology, Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Paul Johnston
- Berlin Centre for Genomics in Biodiversity Research, Berlin, Germany ,grid.419247.d0000 0001 2108 8097Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Elisa Bittermann
- grid.14095.390000 0000 9116 4836Evolutionary Biology, Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Maryam Keshavarz
- grid.14095.390000 0000 9116 4836Evolutionary Biology, Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Véronique Paris
- grid.14095.390000 0000 9116 4836Evolutionary Biology, Institute for Biology, Freie Universität Berlin, Berlin, Germany ,grid.1008.90000 0001 2179 088XBio 21 Institute, University of Melbourne, Parkville, VIC 3052 Australia
| | - Karolina Walkowiak-Nowicka
- grid.5633.30000 0001 2097 3545Department of Animal Physiology and Developmental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Natalia Konopińska
- grid.5633.30000 0001 2097 3545Department of Animal Physiology and Developmental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Paweł Marciniak
- grid.5633.30000 0001 2097 3545Department of Animal Physiology and Developmental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Jens Rolff
- grid.14095.390000 0000 9116 4836Evolutionary Biology, Institute for Biology, Freie Universität Berlin, Berlin, Germany ,grid.452299.1Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
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19
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Bernard C, Locard-Paulet M, Noël C, Duchateau M, Giai Gianetto Q, Moumen B, Rattei T, Hechard Y, Jensen LJ, Matondo M, Samba-Louaka A. A time-resolved multi-omics atlas of Acanthamoeba castellanii encystment. Nat Commun 2022; 13:4104. [PMID: 35835784 PMCID: PMC9283445 DOI: 10.1038/s41467-022-31832-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/30/2022] [Indexed: 12/14/2022] Open
Abstract
Encystment is a common stress response of most protists, including free-living amoebae. Cyst formation protects the amoebae from eradication and can increase virulence of the bacteria they harbor. Here, we mapped the global molecular changes that occur in the facultatively pathogenic amoeba Acanthamoeba castellanii during the early steps of the poorly understood process of encystment. By performing transcriptomic, proteomic, and phosphoproteomic experiments during encystment, we identified more than 150,000 previously undescribed transcripts and thousands of protein sequences absent from the reference genome. These results provide molecular details to the regulation of expected biological processes, such as cell proliferation shutdown, and reveal new insights such as a rapid phospho-regulation of sites involved in cytoskeleton remodeling and translation regulation. This work constitutes the first time-resolved molecular atlas of an encysting organism and a useful resource for further investigation of amoebae encystment to allow for a better control of pathogenic amoebae.
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Affiliation(s)
- Clément Bernard
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS, 7267, Poitiers, France
| | - Marie Locard-Paulet
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Cyril Noël
- IFREMER-IRSI-Service de Bioinformatique (SeBiMER), Centre Bretagne, Plouzane, France
| | - Magalie Duchateau
- Institut Pasteur, Université de Paris, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR2024, CNRS 2000, Paris, France
| | - Quentin Giai Gianetto
- Institut Pasteur, Université de Paris, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR2024, CNRS 2000, Paris, France
- Institut Pasteur, Université de Paris, Department of Computation Biology, Bioinformatics and Biostatistics Hub, Paris, France
| | - Bouziane Moumen
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS, 7267, Poitiers, France
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science; Doctoral School Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Yann Hechard
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS, 7267, Poitiers, France
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Mariette Matondo
- Institut Pasteur, Université de Paris, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR2024, CNRS 2000, Paris, France
| | - Ascel Samba-Louaka
- Laboratoire Ecologie et Biologie des Interactions, Université de Poitiers, UMR CNRS, 7267, Poitiers, France.
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20
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Gleeson JP, Chaudhary N, Fein KC, Doerfler R, Hredzak-Showalter P, Whitehead KA. Profiling of mature-stage human breast milk cells identifies six unique lactocyte subpopulations. SCIENCE ADVANCES 2022; 8:eabm6865. [PMID: 35767604 PMCID: PMC9242445 DOI: 10.1126/sciadv.abm6865] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Breast milk is chock-full of nutrients, immunological factors, and cells that aid infant development. Maternal cells are the least studied breast milk component, and their unique properties are difficult to identify using traditional techniques. Here, we characterized the cells in mature-stage breast milk from healthy donors at the protein, gene, and transcriptome levels. Holistic analysis of flow cytometry, quantitative polymerase chain reaction, and single-cell RNA sequencing data identified the predominant cell population as epithelial with smaller populations of macrophages and T cells. Two percent of epithelial cells expressed four stem cell markers: SOX2, TRA-1-60, NANOG, and SSEA4. Furthermore, milk contained six distinct epithelial lactocyte subpopulations, including three previously unidentified subpopulations programmed toward mucosal defense and intestinal development. Pseudotime analysis delineated the differentiation pathways of epithelial progenitors. Together, these data define healthy human maternal breast milk cells and provide a basis for their application in maternal and infant medicine.
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Affiliation(s)
- John P. Gleeson
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Namit Chaudhary
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Katherine C. Fein
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Rose Doerfler
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | | | - Kathryn A. Whitehead
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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21
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Overview of Transcriptomic Research on Type 2 Diabetes: Challenges and Perspectives. Genes (Basel) 2022; 13:genes13071176. [PMID: 35885959 PMCID: PMC9319211 DOI: 10.3390/genes13071176] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 02/04/2023] Open
Abstract
Type 2 diabetes (T2D) is a common chronic disease whose etiology is known to have a strong genetic component. Standard genetic approaches, although allowing for the detection of a number of gene variants associated with the disease as well as differentially expressed genes, cannot fully explain the hereditary factor in T2D. The explosive growth in the genomic sequencing technologies over the last decades provided an exceptional impetus for transcriptomic studies and new approaches to gene expression measurement, such as RNA-sequencing (RNA-seq) and single-cell technologies. The transcriptomic analysis has the potential to find new biomarkers to identify risk groups for developing T2D and its microvascular and macrovascular complications, which will significantly affect the strategies for early diagnosis, treatment, and preventing the development of complications. In this article, we focused on transcriptomic studies conducted using expression arrays, RNA-seq, and single-cell sequencing to highlight recent findings related to T2D and challenges associated with transcriptome experiments.
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22
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Rachinger N, Mittag N, Böhme-Schäfer I, Xiang W, Kuphal S, Bosserhoff AK. Alpha-Synuclein and Its Role in Melanocytes. Cells 2022; 11:cells11132087. [PMID: 35805172 PMCID: PMC9265281 DOI: 10.3390/cells11132087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/10/2022] [Accepted: 06/29/2022] [Indexed: 12/04/2022] Open
Abstract
Pigmentation is an important process in skin physiology and skin diseases and presumably also plays a role in Parkinson’s disease (PD). In PD, alpha-Synuclein (aSyn) has been shown to be involved in the pigmentation of neurons. The presynaptic protein is intensively investigated for its pathological role in PD, but its physiological function remains unknown. We hypothesized that aSyn is both involved in melanocytic differentiation and melanosome trafficking processes. We detected a strong expression of aSyn in human epidermal melanocytes (NHEMs) and observed its regulation in melanocytic differentiation via the microphthalmia-associated transcription factor (MITF), a central regulator of differentiation. Moreover, we investigated its role in pigmentation by performing siRNA experiments but found no effect on the total melanin content. We discovered a localization of aSyn to melanosomes, and further analysis of aSyn knockdown revealed an important role in melanocytic morphology and a reduction in melanosome release. Additionally, we found a reduction of transferred melanosomes in co-culture experiments of melanocytes and keratinocytes but no complete inhibition of melanosome transmission. In summary, this study highlights a novel physiological role of aSyn in melanocytic morphology and its so far unknown function in the pigment secretion in melanocytes.
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Affiliation(s)
- Nicole Rachinger
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (N.R.); (I.B.-S.); (S.K.)
| | - Nora Mittag
- Department of Dermatology and Allergy, University Hospital, LMU Munich, 80539 Munich, Germany;
| | - Ines Böhme-Schäfer
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (N.R.); (I.B.-S.); (S.K.)
| | - Wei Xiang
- Department of Molecular Neurology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany;
| | - Silke Kuphal
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (N.R.); (I.B.-S.); (S.K.)
| | - Anja K. Bosserhoff
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (N.R.); (I.B.-S.); (S.K.)
- Correspondence:
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23
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Wu H, Wang B, Wang L, Xue Y. circular RNAs 0000515 and 0011385 as potential biomarkers for disease monitoring and determining prognosis in pancreatic ductal adenocarcinoma. Oncol Lett 2022; 23:56. [PMID: 34992688 PMCID: PMC8721853 DOI: 10.3892/ol.2021.13174] [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: 11/19/2020] [Accepted: 09/13/2021] [Indexed: 11/20/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is extremely fatal and potential biomarkers for precision medicine of patients with PDAC are yet to be elucidated. Moreover, the clinical values of circular RNAs (circRNAs) in PDAC management are yet to be investigated. The aim of the present study was to perform a secondary analysis of two PDAC public datasets (GSE69362 and GSE79634), to identify the candidate circRNAs, to validate the expression of these circRNAs, and to determine their association with the clinicopathological characteristics and survival of patients with PDAC. A total of 60 patients with PDAC were retrospectively reviewed in the present study. The expression levels of these candidate circRNAs were detected in PDAC tissues and paired adjacent normal tissues via reverse transcription-quantitative PCR analysis. In addition, the clinicopathological characteristics and overall survival (OS) of patients with PDAC were recorded. Bioinformatics analysis identified 22 overlapping differentially expressed (DE) circRNAs between the GSE69362 and GSE79634 datasets, among which nine DEcircRNAs with accordant expression trends (the DEcircRNAs that were upregulated or downregulated in tumor tissues compared with paired adjacent normal tissues in both datasets) were selected as candidate circRNAs, including circ_0000515, circ_0000517, circ_0000520, circ_0000514, circ_0011385, circ_0055033, circ_0072088, circ_0003528 and circ_0008514. In the 60 patients with PDAC, the expression levels of circ_0000515, circ_0000517, circ_0000520, circ_0000514, circ_0011385, circ_0055033, circ_0072088 and circ_0003528 were notably upregulated in PDAC tissues compared with paired adjacent normal tissues. Furthermore, circ_0000515, circ_0000520, circ_0000514, circ_0011385 and circ_0072088 were positively associated with T stage, N stage and/or TNM stage in patients with PDAC. Notably, circ_0000515 and circ_0011385 were negatively associated with OS in patients with PDAC. Taken together, the results of the present study suggest that circ_0000515 and circ_0011385 may serve as prognostic biomarkers for patients with PDAC.
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Affiliation(s)
- Hanqing Wu
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Bo Wang
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Li Wang
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Yinkai Xue
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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