1
|
Pogačar K, Grundner M, Žigon P, Coll A, Panevska A, Lukan T, Petek M, Razinger J, Gruden K, Sepčić K. Protein complexes from edible mushrooms as a sustainable potato protection against coleopteran pests. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2518-2529. [PMID: 38733093 PMCID: PMC11331795 DOI: 10.1111/pbi.14365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/08/2024] [Accepted: 04/14/2024] [Indexed: 05/13/2024]
Abstract
Protein complexes from edible oyster mushrooms (Pleurotus sp.) composed of pleurotolysin A2 (PlyA2) and pleurotolysin B (PlyB) exert toxicity in feeding tests against Colorado potato beetle (CPB) larvae, acting through the interaction with insect-specific membrane sphingolipid. Here we present a new strategy for crop protection, based on in planta production of PlyA2/PlyB protein complexes, and we exemplify this strategy in construction of transgenic potato plants of cv Désirée. The transgenics in which PlyA2 was directed to the vacuole and PlyB to the endoplasmic reticulum are effectively protected from infestation by CPB larvae without impacting plant performance. These transgenic plants showed a pronounced effect on larval feeding rate, the larvae feeding on transgenic plants being on average five to six folds lighter than larvae feeding on controls. Further, only a fraction (11%-37%) of the larvae that fed on transgenic potato plants completed their life cycle and developed into adult beetles. Moreover, gene expression analysis of CPB larvae exposed to PlyA2/PlyB complexes revealed the response indicative of a general stress status of larvae and no evidence of possibility of developing resistance due to the functional inactivation of PlyA2/PlyB sphingolipid receptors.
Collapse
Affiliation(s)
- Karmen Pogačar
- Department of Biotechnology and Systems BiologyNational Institute of BiologyLjubljanaSlovenia
- Jožef Stefan International Postgraduate SchoolLjubljanaSlovenia
| | - Maja Grundner
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Primož Žigon
- Plant Protection DepartmentAgricultural Institute of SloveniaLjubljanaSlovenia
| | - Anna Coll
- Department of Biotechnology and Systems BiologyNational Institute of BiologyLjubljanaSlovenia
| | - Anastasija Panevska
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Tjaša Lukan
- Department of Biotechnology and Systems BiologyNational Institute of BiologyLjubljanaSlovenia
| | - Marko Petek
- Department of Biotechnology and Systems BiologyNational Institute of BiologyLjubljanaSlovenia
| | - Jaka Razinger
- Plant Protection DepartmentAgricultural Institute of SloveniaLjubljanaSlovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems BiologyNational Institute of BiologyLjubljanaSlovenia
| | - Kristina Sepčić
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| |
Collapse
|
2
|
Francia M, Bot M, Boltz T, De la Hoz JF, Boks M, Kahn RS, Ophoff RA. Fibroblasts as an in vitro model of circadian genetic and genomic studies. Mamm Genome 2024; 35:432-444. [PMID: 38960898 PMCID: PMC11329553 DOI: 10.1007/s00335-024-10050-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
Bipolar disorder (BD) is a heritable disorder characterized by shifts in mood that manifest in manic or depressive episodes. Clinical studies have identified abnormalities of the circadian system in BD patients as a hallmark of underlying pathophysiology. Fibroblasts are a well-established in vitro model for measuring circadian patterns. We set out to examine the underlying genetic architecture of circadian rhythm in fibroblasts, with the goal to assess its contribution to the polygenic nature of BD disease risk. We collected, from primary cell lines of 6 healthy individuals, temporal genomic features over a 48 h period from transcriptomic data (RNA-seq) and open chromatin data (ATAC-seq). The RNA-seq data showed that only a limited number of genes, primarily the known core clock genes such as ARNTL, CRY1, PER3, NR1D2 and TEF display circadian patterns of expression consistently across cell cultures. The ATAC-seq data identified that distinct transcription factor families, like those with the basic helix-loop-helix motif, were associated with regions that were increasing in accessibility over time. Whereas known glucocorticoid receptor target motifs were identified in those regions that were decreasing in accessibility. Further evaluation of these regions using stratified linkage disequilibrium score regression analysis failed to identify a significant presence of them in the known genetic architecture of BD, and other psychiatric disorders or neurobehavioral traits in which the circadian rhythm is affected. In this study, we characterize the biological pathways that are activated in this in vitro circadian model, evaluating the relevance of these processes in the context of the genetic architecture of BD and other disorders, highlighting its limitations and future applications for circadian genomic studies.
Collapse
Affiliation(s)
- Marcelo Francia
- Interdepartmental Program for Neuroscience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
| | - Merel Bot
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Toni Boltz
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Juan F De la Hoz
- Bioinformatics Interdepartamental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Marco Boks
- Department Psychiatry, Brain Center University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - René S Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roel A Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| |
Collapse
|
3
|
Tang F, Hummitzsch K, Rodgers RJ. Unique features of KGN granulosa-like tumour cells in the regulation of steroidogenic and antioxidant genes. PLoS One 2024; 19:e0308168. [PMID: 39110703 PMCID: PMC11305538 DOI: 10.1371/journal.pone.0308168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
The ovarian KGN granulosa-like tumour cell line is commonly used as a model for human granulosa cells, especially since it produces steroid hormones. To explore this further, we identified genes that were differentially expressed by KGN cells compared to primary human granulosa cells using three public RNA sequence datasets. Of significance, we identified that the expression of the antioxidant gene TXNRD1 (thioredoxin reductase 1) was extremely high in KGN cells. This is ominous since cytochrome P450 enzymes leak electrons and produce reactive oxygen species during the biosynthesis of steroid hormones. Gene Ontology (GO) analysis identified steroid biosynthetic and cholesterol metabolic processes were more active in primary granulosa cells, whilst in KGN cells, DNA processing, chromosome segregation and kinetochore pathways were more prominent. Expression of cytochrome P450 cholesterol side-chain cleavage (CYP11A1) and cytochrome P450 aromatase (CYP19A1), which are important for the biosynthesis of the steroid hormones progesterone and oestrogen, plus their electron transport chain members (FDXR, FDX1, POR) were measured in cultured KGN cells. KGN cells were treated with 1 mM dibutyryl cAMP (dbcAMP) or 10 μM forskolin, with or without siRNA knockdown of TXNRD1. We also examined expression of antioxidant genes, H2O2 production by Amplex Red assay and DNA damage by γH2Ax staining. Significant increases in CYP11A1 and CYP19A1 were observed by either dbcAMP or forskolin treatments. However, no significant changes in H2O2 levels or DNA damage were found. Knockdown of expression of TXNRD1 by siRNA blocked the stimulation of expression of CYP11A1 and CYP19A1 by dbcAMP. Thus, with TXNRD1 playing such a pivotal role in steroidogenesis in the KGN cells and it being so highly overexpressed, we conclude that KGN cells might not be the most appropriate model of primary granulosa cells for studying the interplay between ovarian steroidogenesis, reactive oxygen species and antioxidants.
Collapse
Affiliation(s)
- Feng Tang
- School of Biomedicine, Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Katja Hummitzsch
- School of Biomedicine, Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Raymond J. Rodgers
- School of Biomedicine, Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| |
Collapse
|
4
|
Pujasatria GC, Miura C, Yamaguchi K, Shigenobu S, Kaminaka H. Colonization by orchid mycorrhizal fungi primes induced systemic resistance against necrotrophic pathogen. FRONTIERS IN PLANT SCIENCE 2024; 15:1447050. [PMID: 39145195 PMCID: PMC11322130 DOI: 10.3389/fpls.2024.1447050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 07/16/2024] [Indexed: 08/16/2024]
Abstract
Orchids and arbuscular mycorrhiza (AM) plants evolved independently and have different structures and fungal partners, but they both facilitate nutrient uptake. Orchid mycorrhiza (OM) supports orchid seed germination, but unlike AM, its role in disease resistance of mature plants is largely unknown. Here, we examined whether OM induces systemic disease resistance against a necrotrophic pathogen in a similar fashion to AM. We investigated the priming effect of mycorrhizal fungi inoculation on resistance of a terrestrial orchid, Bletilla striata, to soft rot caused by Dickeya fangzhongdai. We found that root colonization by a compatible OM fungus primed B. striata seedlings and induced systemic resistance against the infection. Transcriptome analysis showed that priming was mediated by the downregulation of jasmonate and ethylene pathways and that these pathways are upregulated once infection occurs. Comparison with the reported transcriptome of AM fungus-colonized rice leaves revealed similar mechanisms in B. striata and in rice. These findings highlight a novel aspect of commonality between OM and AM plants in terms of induced systemic resistance.
Collapse
Affiliation(s)
| | - Chihiro Miura
- Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology Core Research Facilities, Okazaki, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology Core Research Facilities, Okazaki, Japan
| | - Hironori Kaminaka
- Faculty of Agriculture, Tottori University, Tottori, Japan
- Unused Bioresource Utilization Center, Tottori University, Tottori, Japan
| |
Collapse
|
5
|
Fotopoulos I, Nguyen OTD, Nøst TH, Markaki M, Lagani V, Mjelle R, Sandanger TM, Sætrom P, Tsamardinos I, Røe OD. Promising microRNAs in pre-diagnostic serum associated with lung cancer up to eight years before diagnosis: a HUNT study. J Cancer Res Clin Oncol 2024; 150:355. [PMID: 39031255 PMCID: PMC11271336 DOI: 10.1007/s00432-024-05882-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Accepted: 07/04/2024] [Indexed: 07/22/2024]
Abstract
INTRODUCTION Blood biomarkers for early detection of lung cancer (LC) are in demand. There are few studies of the full microRNome in serum of asymptomatic subjects that later develop LC. Here we searched for novel microRNA biomarkers in blood from non-cancer, ever-smokers populations up to eight years before diagnosis. METHODS Serum samples from 98,737 subjects from two prospective population studies, HUNT2 and HUNT3, were considered initially. Inclusion criteria for cases were: ever-smokers; no known cancer at study entrance; 0-8 years from blood sampling to LC diagnosis. Each future LC case had one control matched to sex, age at study entrance, pack-years, smoking cessation time, and similar HUNT Lung Cancer Model risk score. A total of 240 and 72 serum samples were included in the discovery (HUNT2) and validation (HUNT3) datasets, respectively, and analysed by next-generation sequencing. The validated serum microRNAs were also tested in two pre-diagnostic plasma datasets from the prospective population studies NOWAC (n = 266) and NSHDS (n = 258). A new model adding clinical variables was also developed and validated. RESULTS Fifteen unique microRNAs were discovered and validated in the pre-diagnostic serum datasets when all cases were contrasted against all controls, all with AUC > 0.60. In combination as a 15-microRNAs signature, the AUC reached 0.708 (discovery) and 0.703 (validation). A non-small cell lung cancer signature of six microRNAs showed AUC 0.777 (discovery) and 0.806 (validation). Combined with clinical variables of the HUNT Lung Cancer Model (age, gender, pack-years, daily cough parts of the year, hours of indoor smoke exposure, quit time in years, number of cigarettes daily, body mass index (BMI)) the AUC reached 0.790 (discovery) and 0.833 (validation). These results could not be validated in the plasma samples. CONCLUSION There were a few significantly differential expressed microRNAs in serum up to eight years before diagnosis. These promising microRNAs alone, in concert, or combined with clinical variables have the potential to serve as early diagnostic LC biomarkers. Plasma is not suitable for this analysis. Further validation in larger prospective serum datasets is needed.
Collapse
Affiliation(s)
- Ioannis Fotopoulos
- Department of Computer Science, University of Crete, 700 13, Heraklion, Crete, Greece
| | - Olav Toai Duc Nguyen
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Prinsesse Kristinas Gate 1, 7030, Trondheim, Norway
- Cancer Clinic, Levanger Hospital, Nord-Trøndelag Health Trust, Kirkegata 2, 7600, Levanger, Norway
| | - Therese Haugdahl Nøst
- Department of Community Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, 9037, Tromsø, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU-Norwegian University of Science and Technology, Postboks 8905, 7491, Trondheim, Norway
| | - Maria Markaki
- Institute of Applied and Computational Mathematics, FORTH, 700 13, Heraklion, Crete, Greece
| | - Vincenzo Lagani
- Institute of Chemical Biology, Ilia State University, 3/5, Kakuca Cholokashvili Ave, Tbilisi, Georgia
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
- SDAIA-KAUST Center of Excellence in Data Science and Artificial Intelligence, 23952, Thuwal, Saudi Arabia
| | - Robin Mjelle
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Prinsesse Kristinas Gate 1, 7030, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU-Norwegian University of Science and Technology, Postboks 8905, 7491, Trondheim, Norway
- Bioinformatics Core Facility, NTNU-Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Torkjel Manning Sandanger
- Department of Community Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, P.O. Box 6050 Langnes, 9037, Tromsø, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Prinsesse Kristinas Gate 1, 7030, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU-Norwegian University of Science and Technology, Postboks 8905, 7491, Trondheim, Norway
- Bioinformatics Core Facility, NTNU-Norwegian University of Science and Technology, 7491, Trondheim, Norway
- Department of Computer Science, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Ioannis Tsamardinos
- Department of Computer Science, University of Crete, 700 13, Heraklion, Crete, Greece
- Institute of Applied and Computational Mathematics, FORTH, 700 13, Heraklion, Crete, Greece
- JADBio Gnosis DA S.A., STEP-C, N. Plastira 100, 700-13, Heraklion, Greece
| | - Oluf Dimitri Røe
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, Prinsesse Kristinas Gate 1, 7030, Trondheim, Norway.
- Cancer Clinic, Levanger Hospital, Nord-Trøndelag Health Trust, Kirkegata 2, 7600, Levanger, Norway.
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, 9000, Aalborg, Denmark.
- Department of Clinical Medicine, Aalborg University Hospital, 9000, Aalborg, Denmark.
| |
Collapse
|
6
|
Banerjee R, Meyer TJ, Cam MC, Kaur S, Roberts DD. Differential regulation by CD47 and thrombospondin-1 of extramedullary erythropoiesis in mouse spleen. eLife 2024; 12:RP92679. [PMID: 38979889 PMCID: PMC11233134 DOI: 10.7554/elife.92679] [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] [Indexed: 07/10/2024] Open
Abstract
Extramedullary erythropoiesis is not expected in healthy adult mice, but erythropoietic gene expression was elevated in lineage-depleted spleen cells from Cd47-/- mice. Expression of several genes associated with early stages of erythropoiesis was elevated in mice lacking CD47 or its signaling ligand thrombospondin-1, consistent with previous evidence that this signaling pathway inhibits expression of multipotent stem cell transcription factors in spleen. In contrast, cells expressing markers of committed erythroid progenitors were more abundant in Cd47-/- spleens but significantly depleted in Thbs1-/- spleens. Single-cell transcriptome and flow cytometry analyses indicated that loss of CD47 is associated with accumulation and increased proliferation in spleen of Ter119-CD34+ progenitors and Ter119+CD34- committed erythroid progenitors with elevated mRNA expression of Kit, Ermap, and Tfrc. Induction of committed erythroid precursors is consistent with the known function of CD47 to limit the phagocytic removal of aged erythrocytes. Conversely, loss of thrombospondin-1 delays the turnover of aged red blood cells, which may account for the suppression of committed erythroid precursors in Thbs1-/- spleens relative to basal levels in wild-type mice. In addition to defining a role for CD47 to limit extramedullary erythropoiesis, these studies reveal a thrombospondin-1-dependent basal level of extramedullary erythropoiesis in adult mouse spleen.
Collapse
Affiliation(s)
- Rajdeep Banerjee
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaUnited States
| | - Thomas J Meyer
- CCR Collaborative Bioinformatics Resource, Office of Science and Technology Resources, National Cancer Institute, National Institutes of HealthBethesdaUnited States
| | - Margaret C Cam
- CCR Collaborative Bioinformatics Resource, Office of Science and Technology Resources, National Cancer Institute, National Institutes of HealthBethesdaUnited States
| | - Sukhbir Kaur
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaUnited States
| | - David D Roberts
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of HealthBethesdaUnited States
| |
Collapse
|
7
|
Kamathewatta KI, Condello AK, Kulappu Arachchige SN, Young ND, Shil PK, Noormohammadi AH, Tivendale KA, Wawegama NK, Browning GF. Characterisation of the tracheal transcriptional response of chickens to chronic infection with Mycoplasma synoviae. Vet Microbiol 2024; 294:110119. [PMID: 38772075 DOI: 10.1016/j.vetmic.2024.110119] [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: 03/05/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/23/2024]
Abstract
Mycoplasma synoviae causes infectious synovitis and respiratory tract infections in chickens and is responsible for significant economic losses in the poultry industry. Effective attachment and colonisation of the trachea is critical for the persistence of the organism and progression of the disease it causes. The respiratory tract infection is usually sub-clinical, but concurrent infection with infectious bronchitis virus (IBV) is known to enhance the pathogenicity of M. synoviae. This study aimed to explore differentially expressed genes in the tracheal mucosa, and their functional categories, during chronic infection with M. synoviae, using a M. synoviae-IBV infection model. The transcriptional profiles of the trachea were assessed 2 weeks after infection using RNA sequencing. In chickens infected with M. synoviae or IBV, only 1 or 8 genes were differentially expressed compared to uninfected chickens, respectively. In contrast, the M. synoviae-IBV infected chickens had 621 upregulated and 206 downregulated genes compared to uninfected chickens. Upregulated genes and their functional categories were suggestive of uncontrolled lymphoid cell proliferation and an ongoing pro-inflammatory response. Genes associated with anti-inflammatory effects, pathogen removal, apoptosis, regulation of the immune response, airway homoeostasis, cell adhesion and tissue regeneration were downregulated. Overall, transcriptional changes in the trachea, 2 weeks after infection with M. synoviae and IBV, indicate immune dysregulation, robust inflammation and a lack of cytotoxic damage during chronic infection. This model provides insights into the pathogenesis of chronic infection with M. synoviae.
Collapse
Affiliation(s)
- Kanishka I Kamathewatta
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Anna Kanci Condello
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Sathya N Kulappu Arachchige
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, VIC, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Pollob K Shil
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, VIC, Australia
| | - Amir H Noormohammadi
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Werribee, VIC, Australia
| | - Kelly A Tivendale
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Nadeeka K Wawegama
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia.
| |
Collapse
|
8
|
Hutchison WJ, Keyes TJ, Crowell HL, Serizay J, Soneson C, Davis ES, Sato N, Moses L, Tarlinton B, Nahid AA, Kosmac M, Clayssen Q, Yuan V, Mu W, Park JE, Mamede I, Ryu MH, Axisa PP, Paiz P, Poon CL, Tang M, Gottardo R, Morgan M, Lee S, Lawrence M, Hicks SC, Nolan GP, Davis KL, Papenfuss AT, Love MI, Mangiola S. The tidyomics ecosystem: enhancing omic data analyses. Nat Methods 2024; 21:1166-1170. [PMID: 38877315 DOI: 10.1038/s41592-024-02299-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 05/05/2024] [Indexed: 06/16/2024]
Abstract
The growth of omic data presents evolving challenges in data manipulation, analysis and integration. Addressing these challenges, Bioconductor provides an extensive community-driven biological data analysis platform. Meanwhile, tidy R programming offers a revolutionary data organization and manipulation standard. Here we present the tidyomics software ecosystem, bridging Bioconductor to the tidy R paradigm. This ecosystem aims to streamline omic analysis, ease learning and encourage cross-disciplinary collaborations. We demonstrate the effectiveness of tidyomics by analyzing 7.5 million peripheral blood mononuclear cells from the Human Cell Atlas, spanning six data frameworks and ten analysis tools.
Collapse
Affiliation(s)
- William J Hutchison
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Timothy J Keyes
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Helena L Crowell
- University of Zurich, Zurich, Switzerland
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | - Jacques Serizay
- Unité Régulation Spatiale des Génomes, Institut Pasteur, CNRS UMR3525, Paris, France
| | - Charlotte Soneson
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Eric S Davis
- Bioinformatics and Computational Biology Program, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Noriaki Sato
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Lambda Moses
- California Institute of Technology, Pasadena, CA, USA
| | - Boyd Tarlinton
- Queensland Department of Agriculture and Fisheries, Brisbane, Queensland, Australia
| | - Abdullah A Nahid
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | | | | | - Victor Yuan
- Department of Statistics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Wancen Mu
- Biostatistics Department, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Ji-Eun Park
- Biostatistics Department, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Izabela Mamede
- Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Min Hyung Ryu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pierre-Paul Axisa
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Paulina Paiz
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Chi-Lam Poon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ming Tang
- Immunitas Therapeutics, Waltham, MA, USA
| | - Raphael Gottardo
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
- University of Lausanne, Lausanne, Switzerland
- Lausanne University Hospital, Lausanne, Switzerland
| | - Martin Morgan
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Stuart Lee
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA
| | - Michael Lawrence
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA
| | - Stephanie C Hicks
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kara L Davis
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Anthony T Papenfuss
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
| | - Michael I Love
- Biostatistics Department, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.
- Genetics Department, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.
| | - Stefano Mangiola
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
- South Australian immunoGENomics Cancer Institute, The University of Adelaide, Adelaide, South Australia, Australia.
| |
Collapse
|
9
|
Jackson DJ, Cerveau N, Posnien N. De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms - a brief guide. Front Zool 2024; 21:17. [PMID: 38902827 PMCID: PMC11188175 DOI: 10.1186/s12983-024-00538-y] [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: 03/05/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the democratization of diverse model systems. They allow for the economical sequencing of an entire genome or transcriptome of interest, and with technical variations can even provide insight into genome organization and the expression and regulation of genes. The analysis and biological interpretation of such large datasets can present significant challenges that depend on the 'scientific status' of the model system. While high-quality genome and transcriptome references are readily available for well-established model systems, the establishment of such references for an emerging model system often requires extensive resources such as finances, expertise and computation capabilities. The de novo assembly of a transcriptome represents an excellent entry point for genetic and molecular studies in emerging model systems as it can efficiently assess gene content while also serving as a reference for differential gene expression studies. However, the process of de novo transcriptome assembly is non-trivial, and as a rule must be empirically optimized for every dataset. For the researcher working with an emerging model system, and with little to no experience with assembling and quantifying short-read data from the Illumina platform, these processes can be daunting. In this guide we outline the major challenges faced when establishing a reference transcriptome de novo and we provide advice on how to approach such an endeavor. We describe the major experimental and bioinformatic steps, provide some broad recommendations and cautions for the newcomer to de novo transcriptome assembly and differential gene expression analyses. Moreover, we provide an initial selection of tools that can assist in the journey from raw short-read data to assembled transcriptome and lists of differentially expressed genes.
Collapse
Affiliation(s)
- Daniel J Jackson
- University of Göttingen, Department of Geobiology, Goldschmidtstr.3, Göttingen, 37077, Germany.
| | - Nicolas Cerveau
- University of Göttingen, Department of Geobiology, Goldschmidtstr.3, Göttingen, 37077, Germany
| | - Nico Posnien
- University of Göttingen, Department of Developmental Biology, GZMB, Justus-Von-Liebig-Weg 11, Göttingen, 37077, Germany.
| |
Collapse
|
10
|
Chen B, Wang Y, Zhang J, Han Y, Benhammouda H, Bian J, Kang R, Shang X. Specific feature recognition on group specific networks (SFR-GSN): a biomarker identification model for cancer stages. Front Genet 2024; 15:1407072. [PMID: 38846963 PMCID: PMC11153737 DOI: 10.3389/fgene.2024.1407072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/01/2024] [Indexed: 06/09/2024] Open
Abstract
Background and Objective Accurate identification of cancer stages is challenging due to the complexity and heterogeneity of the disease. Current clinical diagnosis methods primarily rely on phenotypic observations, which may not capture early molecular-level changes accurately. Methods In this study, a novel biomarker recognition method was proposed tailored for cancer stages by considering the change of gene expression relationships. Utilizing the sample-specific information and protein-protein interaction networks, the group specific networks were constructed to address the limited specificity of potential biomarkers. Then, a specific feature recognition method was proposed based on these group specific networks, which employed the random forest algorithm for initial screening followed by a recursive feature elimination process to identify the optimal biomarker subset. During exploring optimal results, a strategy termed the Cost-Benefit Ratio, was devised to facilitate the identification of stage-specific biomarkers. Results Comparative experiments were conducted on lung adenocarcinoma and breast cancer datasets to validate the method's efficacy and generalizability. The results showed that the identified biomarkers were highly stage-specific, and the F1 scores for predicting cancer stages were significantly improved. For the lung adenocarcinoma dataset, the F1 score reached 97.68%, and for the breast cancer dataset, it achieved 96.87%. These results significantly surpassed those of three conventional methods in terms of F1 scores. Moreover, from the perspective of biological functions, the biomarkers were proved playing an important role in cancer stage-evolution. Conclusion The proposed method demonstrated its effectiveness in identifying stage-related biomarkers. By using these biomarkers as features, accurate prediction of cancer stages was achieved. Furthermore, the method exhibited potential for biomarker identification in subtype analyses, offering novel perspectives for cancer prognosis.
Collapse
Affiliation(s)
- Bolin Chen
- School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi, China
- Key Laboratory of Big Data Storage and Management, Northwestern Polytechnical University, Ministry of Industry and Information Technology, Xi’an, Shaanxi, China
| | - Yuxin Wang
- School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Jinlei Zhang
- School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Yourui Han
- School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Hamza Benhammouda
- School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi, China
| | - Jun Bian
- Department of General Surgery, Xi’an Children’s Hosptial, Xi’an Jiaotong University Affiliated Children’s Hosptial, Xi’an, China
| | - Ruiming Kang
- Rewise (Hangzhou) Information Technology Co., Ltd, Hangzhou, China
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi, China
- Key Laboratory of Big Data Storage and Management, Northwestern Polytechnical University, Ministry of Industry and Information Technology, Xi’an, Shaanxi, China
| |
Collapse
|
11
|
Gulyas L, Glaunsinger BA. The general transcription factor TFIIB is a target for transcriptome control during cellular stress and viral infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575933. [PMID: 38746429 PMCID: PMC11092454 DOI: 10.1101/2024.01.16.575933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Many stressors, including viral infection, induce a widespread suppression of cellular RNA polymerase II (RNAPII) transcription, yet the mechanisms underlying transcriptional repression are not well understood. Here we find that a crucial component of the RNA polymerase II holoenzyme, general transcription factor IIB (TFIIB), is targeted for post-translational turnover by two pathways, each of which contribute to its depletion during stress. Upon DNA damage, translational stress, apoptosis, or replication of the oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV), TFIIB is cleaved by activated caspase-3, leading to preferential downregulation of pro-survival genes. TFIIB is further targeted for rapid proteasome-mediated turnover by the E3 ubiquitin ligase TRIM28. KSHV counteracts proteasome-mediated turnover of TFIIB, thereby preserving a sufficient pool of TFIIB for transcription of viral genes. Thus, TFIIB may be a lynchpin for transcriptional outcomes during stress and a key target for nuclear replicating DNA viruses that rely on host transcriptional machinery. Significance Statement Transcription by RNA polymerase II (RNAPII) synthesizes all cellular protein-coding mRNA. Many cellular stressors and viral infections dampen RNAPII activity, though the processes underlying this are not fully understood. Here we describe a two-pronged degradation strategy by which cells respond to stress by depleting the abundance of the key RNAPII general transcription factor, TFIIB. We further demonstrate that an oncogenic human gammaherpesvirus antagonizes this process, retaining enough TFIIB to support its own robust viral transcription. Thus, modulation of RNAPII machinery plays a crucial role in dictating the outcome of cellular perturbation.
Collapse
|
12
|
Many GM, Sanford JA, Sagendorf TJ, Hou Z, Nigro P, Whytock KL, Amar D, Caputo T, Gay NR, Gaul DA, Hirshman MF, Jimenez-Morales D, Lindholm ME, Muehlbauer MJ, Vamvini M, Bergman BC, Fernández FM, Goodyear LJ, Hevener AL, Ortlund EA, Sparks LM, Xia A, Adkins JN, Bodine SC, Newgard CB, Schenk S. Sexual dimorphism and the multi-omic response to exercise training in rat subcutaneous white adipose tissue. Nat Metab 2024; 6:963-979. [PMID: 38693320 PMCID: PMC11132991 DOI: 10.1038/s42255-023-00959-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 12/01/2023] [Indexed: 05/03/2024]
Abstract
Subcutaneous white adipose tissue (scWAT) is a dynamic storage and secretory organ that regulates systemic homeostasis, yet the impact of endurance exercise training (ExT) and sex on its molecular landscape is not fully established. Utilizing an integrative multi-omics approach, and leveraging data generated by the Molecular Transducers of Physical Activity Consortium (MoTrPAC), we show profound sexual dimorphism in the scWAT of sedentary rats and in the dynamic response of this tissue to ExT. Specifically, the scWAT of sedentary females displays -omic signatures related to insulin signaling and adipogenesis, whereas the scWAT of sedentary males is enriched in terms related to aerobic metabolism. These sex-specific -omic signatures are preserved or amplified with ExT. Integration of multi-omic analyses with phenotypic measures identifies molecular hubs predicted to drive sexually distinct responses to training. Overall, this study underscores the powerful impact of sex on adipose tissue biology and provides a rich resource to investigate the scWAT response to ExT.
Collapse
Affiliation(s)
- Gina M Many
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - James A Sanford
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tyler J Sagendorf
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Zhenxin Hou
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Pasquale Nigro
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Katie L Whytock
- Translational Research Institute, AdventHealth, Orlando, FL, USA
| | - David Amar
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Tiziana Caputo
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Nicole R Gay
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - David A Gaul
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Michael F Hirshman
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - David Jimenez-Morales
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Malene E Lindholm
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Michael J Muehlbauer
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA
| | - Maria Vamvini
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Bryan C Bergman
- Division of Endocrinology, Diabetes, and Metabolism, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Facundo M Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Laurie J Goodyear
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Andrea L Hevener
- Division of Endocrinology, Diabetes, and Hypertension, Department of Medicine, University of California, Los Angeles, CA, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Lauren M Sparks
- Translational Research Institute, AdventHealth, Orlando, FL, USA
| | - Ashley Xia
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Sue C Bodine
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA.
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
| | - Christopher B Newgard
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, NC, USA.
| | - Simon Schenk
- Department of Orthopaedic Surgery, School of Medicine, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
13
|
Simbolo M, Centonze G, Gkountakos A, Monti V, Maisonneuve P, Golovco S, Sabella G, Del Gobbo A, Gobbo S, Ferrero S, Fabbri A, Pardo C, Garzone G, Prinzi N, Pusceddu S, Testi A, Rolli L, Mangogna A, Bercich L, Benvenuti MR, Bria E, Pilotto S, Berruti A, Pastorino U, Capella C, Infante M, Milella M, Scarpa A, Milione M. Characterization of two transcriptomic subtypes of marker-null large cell carcinoma of the lung suggests different origin and potential new therapeutic perspectives. Virchows Arch 2024; 484:777-788. [PMID: 38168015 PMCID: PMC11106141 DOI: 10.1007/s00428-023-03721-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/13/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024]
Abstract
Pulmonary large cell carcinoma (LCC) is an undifferentiated neoplasm lacking morphological, histochemical, and immunohistochemical features of small cell lung cancer, adenocarcinoma (ADC), or squamous cell carcinoma (SCC). The available molecular information on this rare disease is limited. This study aimed to provide an integrated molecular overview of 16 cases evaluating the mutational asset of 409 genes and the transcriptomic profiles of 20,815 genes. Our data showed that TP53 was the most frequently inactivated gene (15/16; 93.7%) followed by RB1 (5/16; 31.3%) and KEAP1 (4/16; 25%), while CRKL and MYB genes were each amplified in 4/16 (25%) cases and MYC in 3/16 (18.8%) cases; transcriptomic analysis identified two molecular subtypes including a Pure-LCC and an adenocarcinoma like-LCC (ADLike-LCC) characterized by different activated pathways and cell of origin. In the Pure-LCC group, POU2F3 and FOXI1 were distinctive overexpressed markers. A tuft cell-like profile and the enrichment of a replication stress signature, particularly involving ATR, was related to this profile. Differently, the ADLike-LCC were characterized by an alveolar-cell transcriptomic profile and association with AIM2 inflammasome complex signature. In conclusion, our study split the histological marker-null LCC into two different transcriptomic entities, with POU2F3, FOXI1, and AIM2 genes as differential expression markers that might be probed by immunohistochemistry for the differential diagnosis between Pure-LCC and ADLike-LCC. Finally, the identification of several signatures linked to replication stress in Pure-LCC and inflammasome complex in ADLike-LCC could be useful for designing new potential therapeutic approaches for these subtypes.
Collapse
Affiliation(s)
- Michele Simbolo
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Giovanni Centonze
- 1st Pathology Division, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Anastasios Gkountakos
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Valentina Monti
- 1st Pathology Division, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Patrick Maisonneuve
- Division of Epidemiology and Biostatistics, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Stela Golovco
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Giovanna Sabella
- 1st Pathology Division, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Alessandro Del Gobbo
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Gobbo
- Department of Traslational Medicine, University of Ferrara, Ferrara, Italy
| | - Stefano Ferrero
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessandra Fabbri
- 2nd Pathology Division, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Carlotta Pardo
- 1st Pathology Division, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Giovanna Garzone
- 1st Pathology Division, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Natalie Prinzi
- Division of Pathology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Sara Pusceddu
- Medical Oncology Department, Fondazione IRCCS, Istituto Nazionale Dei Tumori, Milan, Italy
| | - Adele Testi
- 2nd Pathology Division, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Luigi Rolli
- Thoracic Surgery Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Alessandro Mangogna
- Institute for Maternal and Child Health, IRCCS Burlo Garofalo, Trieste, Italy
| | - Luisa Bercich
- Department of Pathology, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Mauro Roberto Benvenuti
- Thoracic Surgery Unit, Department of Medical and Surgical Specialties Radiological Sciences and Public Health, Medical Oncology, University of Brescia, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Emilio Bria
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Sara Pilotto
- Section of Oncology, Department of Medicine, University of Verona, Verona, Italy
| | - Alfredo Berruti
- Medical Oncology Unit, ASST Spedali Civili of Brescia, Department of Medical and Surgical Specialties, Radiological Science and Public Health, University of Brescia, Brescia, Italy
| | - Ugo Pastorino
- Thoracic Surgery Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Carlo Capella
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | | | - Michele Milella
- Section of Oncology, Department of Medicine, University of Verona, Verona, Italy
| | - Aldo Scarpa
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy.
- ARC-NET Research Centre for Applied Research On Cancer, University and Hospital Trust of Verona, Piazzale Scuro, 10, 37134, Verona (VR), Italy.
| | - Massimo Milione
- 1st Pathology Division, Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| |
Collapse
|
14
|
Sæther LS, Szabo A, Akkouh IA, Haatveit B, Mohn C, Vaskinn A, Aukrust P, Ormerod MBEG, Eiel Steen N, Melle I, Djurovic S, Andreassen OA, Ueland T, Ueland T. Cognitive and inflammatory heterogeneity in severe mental illness: Translating findings from blood to brain. Brain Behav Immun 2024; 118:287-299. [PMID: 38461955 DOI: 10.1016/j.bbi.2024.03.014] [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: 11/02/2023] [Revised: 01/25/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024] Open
Abstract
Recent findings link cognitive impairment and inflammatory-immune dysregulation in schizophrenia (SZ) and bipolar (BD) spectrum disorders. However, heterogeneity and translation between the periphery and central (blood-to-brain) mechanisms remains a challenge. Starting with a large SZ, BD and healthy control cohort (n = 1235), we aimed to i) identify candidate peripheral markers (n = 25) associated with cognitive domains (n = 9) and elucidate heterogenous immune-cognitive patterns, ii) evaluate the regulation of candidate markers using human induced pluripotent stem cell (iPSC)-derived astrocytes and neural progenitor cells (n = 10), and iii) evaluate candidate marker messenger RNA expression in leukocytes using microarray in available data from a subsample of the main cohort (n = 776), and in available RNA-sequencing deconvolution analysis of postmortem brain samples (n = 474) from the CommonMind Consortium (CMC). We identified transdiagnostic subgroups based on covariance between cognitive domains (measures of speed and verbal learning) and peripheral markers reflecting inflammatory response (CRP, sTNFR1, YKL-40), innate immune activation (MIF) and extracellular matrix remodelling (YKL-40, CatS). Of the candidate markers there was considerable variance in secretion of YKL-40 in iPSC-derived astrocytes and neural progenitor cells in SZ compared to HC. Further, we provide evidence of dysregulated RNA expression of genes encoding YKL-40 and related signalling pathways in a high neuroinflammatory subgroup in the postmortem brain samples. Our findings suggest a relationship between peripheral inflammatory-immune activity and cognitive impairment, and highlight YKL-40 as a potential marker of cognitive functioning in a subgroup of individuals with severe mental illness.
Collapse
Affiliation(s)
- Linn Sofie Sæther
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Department of Psychology, University of Oslo, Oslo, Norway.
| | - Attila Szabo
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; K.G. Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
| | - Ibrahim A Akkouh
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital/University of Oslo, Oslo, Norway
| | - Beathe Haatveit
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Christine Mohn
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; National Centre for Suicide Research and Prevention, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anja Vaskinn
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Centre for Research and Education in Forensic Psychiatry, Oslo University Hospital, Oslo, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway; Faculty of Medicine, University of Oslo, Norway
| | - Monica B E G Ormerod
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo Norway
| | - Nils Eiel Steen
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
| | - Ingrid Melle
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Srdjan Djurovic
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; K.G. Jebsen Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital/University of Oslo, Oslo, Norway
| | - Ole A Andreassen
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Torill Ueland
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway; Department of Psychology, University of Oslo, Oslo, Norway
| | - Thor Ueland
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway; Faculty of Medicine, University of Oslo, Norway; K.G. Jebsen Thrombosis Research and Expertise Centre, University of Tromsø, Tromsø, Norway
| |
Collapse
|
15
|
Ernst TR, Blischak JD, Nordlund P, Dalen J, Moore J, Bhamidipati A, Dwivedi P, LoGrasso J, Curado MR, Engelmann BW. OmicNavigator: open-source software for the exploration, visualization, and archival of omic studies. BMC Bioinformatics 2024; 25:162. [PMID: 38658834 PMCID: PMC11040775 DOI: 10.1186/s12859-024-05743-4] [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: 04/28/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND The results of high-throughput biology ('omic') experiments provide insight into biological mechanisms but can be challenging to explore, archive and share. The scale of these challenges continues to grow as omic research volume expands and multiple analytical technologies, bioinformatic pipelines, and visualization preferences have emerged. Multiple software applications exist that support omic study exploration and/or archival. However, an opportunity remains for open-source software that can archive and present the results of omic analyses with broad accommodation of study-specific analytical approaches and visualizations with useful exploration features. RESULTS We present OmicNavigator, an R package for the archival, visualization and interactive exploration of omic studies. OmicNavigator enables bioinformaticians to create web applications that interactively display their custom visualizations and analysis results linked with app-derived analytical tools, graphics, and tables. Studies created with OmicNavigator can be viewed within an interactive R session or hosted on a server for shared access. CONCLUSIONS OmicNavigator can be found at https://github.com/abbvie-external/OmicNavigator.
Collapse
Affiliation(s)
| | - John D Blischak
- AbbVie Inc., 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Paul Nordlund
- AbbVie Inc., 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Joe Dalen
- AbbVie Inc., 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | - Justin Moore
- AbbVie Inc., 1 North Waukegan Rd, North Chicago, IL, 60064, USA
- Current Address: Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
| | | | - Pankaj Dwivedi
- AbbVie Inc., 1 North Waukegan Rd, North Chicago, IL, 60064, USA
- Proteovant Therapeutics, 2500 Renaissance Blvd, King of Prussia, PA, USA
| | - Joe LoGrasso
- AbbVie Inc., 1 North Waukegan Rd, North Chicago, IL, 60064, USA
| | | | | |
Collapse
|
16
|
Juteršek M, Gerasymenko IM, Petek M, Haumann E, Vacas S, Kallam K, Gianoglio S, Navarro-Llopis V, Heethoff M, Fuertes IN, Patron N, Orzáez D, Gruden K, Warzecha H, Baebler Š. Transcriptome-informed identification and characterization of Planococcus citri cis- and trans-isoprenyl diphosphate synthase genes. iScience 2024; 27:109441. [PMID: 38523795 PMCID: PMC10960109 DOI: 10.1016/j.isci.2024.109441] [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: 06/20/2023] [Revised: 10/13/2023] [Accepted: 03/04/2024] [Indexed: 03/26/2024] Open
Abstract
Insect physiology and reproduction depend on several terpenoid compounds, whose biosynthesis is mainly unknown. One enigmatic group of insect monoterpenoids are mealybug sex pheromones, presumably resulting from the irregular coupling activity of unidentified isoprenyl diphosphate synthases (IDSs). Here, we performed a comprehensive search for IDS coding sequences of the pest mealybug Planococcus citri. We queried the available genomic and newly generated short- and long-read P. citri transcriptomic data and identified 18 putative IDS genes, whose phylogenetic analysis indicates several gene family expansion events. In vitro testing confirmed regular short-chain coupling activity with five gene products. With the candidate with highest IDS activity, we also detected low amounts of irregular coupling products, and determined amino acid residues important for chain-length preference and irregular coupling activity. This work therefore provides an important foundation for deciphering terpenoid biosynthesis in mealybugs, including the sex pheromone biosynthesis in P. citri.
Collapse
Affiliation(s)
- Mojca Juteršek
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia
| | - Iryna M. Gerasymenko
- Plant Biotechnology and Metabolic Engineering, Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
| | - Marko Petek
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Elisabeth Haumann
- Plant Biotechnology and Metabolic Engineering, Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
| | - Sandra Vacas
- Instituto Agroforestal del Mediterráneo-CEQA, Universitat Politècnica de València, Camino de Vera s/n, Valencia, Spain
| | - Kalyani Kallam
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk NR4 7UZ, UK
| | - Silvia Gianoglio
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat Politècnica de València (UPV), Valencia, Spain
| | - Vicente Navarro-Llopis
- Instituto Agroforestal del Mediterráneo-CEQA, Universitat Politècnica de València, Camino de Vera s/n, Valencia, Spain
| | - Michael Heethoff
- Animal Evolutionary Ecology, Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
| | | | - Nicola Patron
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich, Norfolk NR4 7UZ, UK
| | - Diego Orzáez
- Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat Politècnica de València (UPV), Valencia, Spain
| | - Kristina Gruden
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Heribert Warzecha
- Plant Biotechnology and Metabolic Engineering, Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, Schnittspahnstrasse 4, 64287 Darmstadt, Germany
| | - Špela Baebler
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| |
Collapse
|
17
|
Potolitsyna E, Pickering SH, Bellanger A, Germier T, Collas P, Briand N. Cytoskeletal rearrangement precedes nucleolar remodeling during adipogenesis. Commun Biol 2024; 7:458. [PMID: 38622242 PMCID: PMC11018602 DOI: 10.1038/s42003-024-06153-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 04/07/2024] [Indexed: 04/17/2024] Open
Abstract
Differentiation of adipose progenitor cells into mature adipocytes entails a dramatic reorganization of the cellular architecture to accommodate lipid storage into cytoplasmic lipid droplets. Lipid droplets occupy most of the adipocyte volume, compressing the nucleus beneath the plasma membrane. How this cellular remodeling affects sub-nuclear structure, including size and number of nucleoli, remains unclear. We describe the morphological remodeling of the nucleus and the nucleolus during in vitro adipogenic differentiation of primary human adipose stem cells. We find that cell cycle arrest elicits a remodeling of nucleolar structure which correlates with a decrease in protein synthesis. Strikingly, triggering cytoskeletal rearrangements mimics the nucleolar remodeling observed during adipogenesis. Our results point to nucleolar remodeling as an active, mechano-regulated mechanism during adipogenic differentiation and demonstrate a key role of the actin cytoskeleton in defining nuclear and nucleolar architecture in differentiating human adipose stem cells.
Collapse
Affiliation(s)
- Evdokiia Potolitsyna
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Blindern, PO Box 1112, 0317, Oslo, Norway
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sarah Hazell Pickering
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Blindern, PO Box 1112, 0317, Oslo, Norway
| | - Aurélie Bellanger
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Blindern, PO Box 1112, 0317, Oslo, Norway
| | - Thomas Germier
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Blindern, PO Box 1112, 0317, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Blindern, PO Box 1112, 0317, Oslo, Norway
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424, Oslo, Norway
| | - Nolwenn Briand
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Blindern, PO Box 1112, 0317, Oslo, Norway.
| |
Collapse
|
18
|
Kamathewatta KI, Kulappu Arachchige SN, Young ND, Condello AK, Wawegama NK, Browning GF. Transcriptomic analysis of the effects of tylosin on the protective immunity provided by the Mycoplasma gallisepticum vaccine Vaxsafe MG ts-304. Vet Microbiol 2024; 291:110029. [PMID: 38364466 DOI: 10.1016/j.vetmic.2024.110029] [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: 11/20/2023] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]
Abstract
The antimicrobial tylosin is commonly used to control mycoplasma infections, sometimes in combination with vaccination. However, the efficacy of a live mycoplasma vaccine, when combined with subsequent antimicrobial treatment, against the effects of subsequent infection with a virulent strain is unknown. This study employed differential gene expression analysis to evaluate the effects of tylosin on the protection provided by the live attenuated Vaxsafe MG ts-304 vaccine, which has been shown to be safe and to provide long-term protective immunity against infection with Mycoplasma gallisepticum. The transcriptional profiles of the tracheal mucosa revealed significantly enhanced inflammation, immune cell proliferation and adaptive immune responses in unvaccinated, untreated birds and in unvaccinated birds treated with tylosin 2 weeks after infection with virulent M. gallisepticum. These responses, indicative of the typical immune dysregulation caused by infection with M. gallisepticum, were less severe in the unvaccinated, tylosin-treated birds than in the unvaccinated, untreated birds. This was attributable to the effect of residual levels of tylosin in the tracheal mucosa on replication of virulent M. gallisepticum. These responses were not detected in vaccinated, tylosin-treated birds or in vaccinated, untreated birds after infection. The tracheal mucosal transcriptional profiles of these birds resembled those of unvaccinated, untreated, uninfected birds, suggesting a rapid and protective secondary immune response and effective vaccination. Overall, these results show that, although tylosin treatment reduced the duration of immunity, the initial protective immunity induced by Vaxsafe MG ts-304 lasted for at least 22 weeks after vaccination, even after the administration of tylosin for 16 weeks following vaccination.
Collapse
Affiliation(s)
- Kanishka I Kamathewatta
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Sathya N Kulappu Arachchige
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Anna Kanci Condello
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Nadeeka K Wawegama
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia.
| |
Collapse
|
19
|
Svensson M, Lovric A, Åkerfeldt T, Hellsten D, Haas T, Gustafsson T, Rullman E. Discordant gene expression in subcutaneous adipose and skeletal muscle tissues in response to exercise training. Physiol Rep 2024; 12:e15995. [PMID: 38561245 PMCID: PMC10984804 DOI: 10.14814/phy2.15995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
Exercise has different effects on different tissues in the body, the sum of which may determine the response to exercise and the health benefits. In the present study, we aimed to investigate whether physical training regulates transcriptional network communites common to both skeletal muscle (SM) and subcutaneous adipose tissue (SAT). Eight such shared transcriptional communities were found in both tissues. Eighteen young overweight adults voluntarily participated in 7 weeks of combined strength and endurance training (five training sessions per week). Biopsies were taken from SM and SAT before and after training. Five of the network communities were regulated by training in SM but showed no change in SAT. One community involved in insulin- AMPK signaling and glucose utilization was upregulated in SM but downregulated in SAT. This diverging exercise regulation was confirmed in two independent studies and was also associated with BMI and diabetes in an independent cohort. Thus, the current finding is consistent with the differential responses of different tissues and suggests that body composition may influence the observed individual whole-body metabolic response to exercise training and help explain the observed attenuated whole-body insulin sensitivity after exercise training, even if it has significant effects on the exercising muscle.
Collapse
Affiliation(s)
- Michael Svensson
- Department of Community Medicine and Rehabilitation, Section of Sports MedicineUmeå UniversityUmeåSweden
| | - Alen Lovric
- Department of Laboratory Medicine, Division of Clinical PhysiologyKarolinska Institutet, and Unit of Clinical Physiology, Karolinska University HospitalStockholmSweden
| | - Torbjörn Åkerfeldt
- Department of Medical Sciences, Clinical ChemistryUppsala UniversityUppsalaSweden
| | - David Hellsten
- Department of Surgical and Perioperative SciencesUmeå UniversityUmeåSweden
| | - Tara Haas
- Faculty of Health, School of Kinesiology and Health ScienceYork UniversityTorontoCanada
| | - Thomas Gustafsson
- Department of Laboratory Medicine, Division of Clinical PhysiologyKarolinska Institutet, and Unit of Clinical Physiology, Karolinska University HospitalStockholmSweden
| | - Eric Rullman
- Department of Laboratory Medicine, Division of Clinical PhysiologyKarolinska Institutet, and Unit of Clinical Physiology, Karolinska University HospitalStockholmSweden
| |
Collapse
|
20
|
Hassani M, Mahdevar M, Peymani M. Exploring the role of interleukin 11 in cancer progression, patient survival, and therapeutic insights. Mol Biol Rep 2024; 51:461. [PMID: 38551695 DOI: 10.1007/s11033-024-09358-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: 12/22/2023] [Accepted: 02/15/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND The Interleukin (IL)-11 gene, which is one of the members of the cytokine family, has an oncogenic role in some cancers. The main goal of this study is to analyze IL-11 expression level in 14 prevalent cancers and highlights its role in patients' survival, drug resistance, and sensitivities. Also, an association of this gene with metastasis and inflammation pathways has been investigated. METHODS AND RESULTS Using the cancer genome atlas (TCGA) data, the level of IL-11 expression and its role in prognosis and survival rate were evaluated in 13 common cancers. Then, confirming the obtained in-silico outcomes, the relative expression level of this gene in colorectal cancer (CRC) samples and their adjusted tissues were assayed by the RT-qPCR method. Furthermore, to examine the association between IL-11 expression and drug resistance and sensitivity, PharmacoGX data was applied. The co-expression network was used to recognize the pathways in which IL-11 was involved. The results from the TCGA dataset indicated that the expression level of IL-11 increased significantly in 13 prevalence cancers compared to the control groups. Interestingly, this enhanced expression level is associated with a high rate of mortality in patients with bladder, stomach, colorectal, and endometrial cancers. Also, the co-expression network analysis showed a strong correlation between IL-11 and the genes of metastasis pathway and the genes related to the inflammation process. Finally, regarding drug sensitivity, IL-11 expression level can be introduced as a remarkable biomarker for cancer detection due to area under curve (AUC). CONCLUSION Altered expression of the IL-11 gene is observed in 13 common cancers and is associated with prognosis and mortality rate in patients. Moreover, this gene can be considered a prognostic biomarker in different types of cancer, such as CRC.
Collapse
Affiliation(s)
- Mahsa Hassani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Mohammad Mahdevar
- Genius Gene, Genetics and Biotechnology Company, Isfahan, Iran
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| |
Collapse
|
21
|
Zhou Z, Kanchana-Udomkan C, Ford R, Bar I. Identification and Validation of Key Genes Related to Preferred Flavour Profiles in Australian Commercial Papaya ( Carica papaya L.). Int J Mol Sci 2024; 25:3046. [PMID: 38474290 DOI: 10.3390/ijms25053046] [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: 01/16/2024] [Revised: 02/22/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Commercial papaya varieties grown in Australia vary greatly in taste and aroma. Previous profiling has identified undesirable 'off tastes' in existing varieties, discouraging a portion of the population from consuming papayas. Our focus on enhancing preferred flavours led to an exploration of the genetic mechanisms and biosynthesis pathways that underlie these desired taste profiles. To identify genes associated with consumer-preferred flavours, we conducted whole RNA sequencing and de novo genome assembly on papaya varieties RB1 (known for its sweet flavour and floral aroma) and 1B (less favoured due to its bitter taste and musty aroma) at both ripe and unripe stages. In total, 180,368 transcripts were generated, and 118 transcripts related to flavours were differentially expressed between the two varieties at the ripe stage. Five genes (cpBGH3B, cpPFP, cpSUS, cpGES and cpLIS) were validated through qPCR and significantly differentially expressed. These genes are suggested to play key roles in sucrose metabolism and aromatic compound production pathways, holding promise for future selective breeding strategies. Further exploration will involve assessing their potential across broader germplasm and various growth environments.
Collapse
Affiliation(s)
- Ziwei Zhou
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | - Chutchamas Kanchana-Udomkan
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
- Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Rebecca Ford
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | - Ido Bar
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| |
Collapse
|
22
|
Oshima T, Kater MSJ, Huffels CFM, Wesseling EM, Middeldorp J, Hol EM, Verheijen MHG, Smit AB, Boddeke EWGM, Eggen BJL. Early amyloid-induced changes in microglia gene expression in male APP/PS1 mice. J Neurosci Res 2024; 102:e25295. [PMID: 38515329 DOI: 10.1002/jnr.25295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/04/2023] [Accepted: 01/12/2024] [Indexed: 03/23/2024]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease and the most common cause of dementia, characterized by deposition of extracellular amyloid-beta (Aβ) aggregates and intraneuronal hyperphosphorylated Tau. Many AD risk genes, identified in genome-wide association studies (GWAS), are expressed in microglia, the innate immune cells of the central nervous system. Specific subtypes of microglia emerged in relation to AD pathology, such as disease-associated microglia (DAMs), which increased in number with age in amyloid mouse models and in human AD cases. However, the initial transcriptional changes in these microglia in response to amyloid are still unknown. Here, to determine early changes in microglia gene expression, hippocampal microglia from male APPswe/PS1dE9 (APP/PS1) mice and wild-type littermates were isolated and analyzed by RNA sequencing (RNA-seq). By bulk RNA-seq, transcriptomic changes were detected in hippocampal microglia from 6-months-old APP/PS1 mice. By performing single-cell RNA-seq of CD11c-positive and negative microglia from 6-months-old APP/PS1 mice and analysis of the transcriptional trajectory from homeostatic to CD11c-positive microglia, we identified a set of genes that potentially reflect the initial response of microglia to Aβ.
Collapse
Affiliation(s)
- Takuya Oshima
- Department of Biomedical Sciences, Section Molecular Neurobiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mandy S J Kater
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Christiaan F M Huffels
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Evelyn M Wesseling
- Department of Biomedical Sciences, Section Molecular Neurobiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jinte Middeldorp
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
- Department of Neurobiology & Aging, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Elly M Hol
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Mark H G Verheijen
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Erik W G M Boddeke
- Department of Biomedical Sciences, Section Molecular Neurobiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
| | - Bart J L Eggen
- Department of Biomedical Sciences, Section Molecular Neurobiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| |
Collapse
|
23
|
Soylu I, Lakshman DK, Tatineni S, Galvez LC, Mitra A. Differential regulation of miRNAs involved in the susceptible and resistance responses of wheat cultivars to wheat streak mosaic virus and Triticum mosaic virus. BMC Genomics 2024; 25:221. [PMID: 38418960 PMCID: PMC10900693 DOI: 10.1186/s12864-024-10128-1] [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: 09/15/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) are components of the wheat streak mosaic virus disease complex in the Great Plains region of the U.S.A. and elsewhere. Co-infection of wheat with WSMV and TriMV causes synergistic interaction with more severe disease symptoms compared to single infections. Plants are equipped with multiple antiviral mechanisms, of which regulation of microRNAs (miRNAs) is a potentially effective constituent. In this investigation, we have analyzed the total and relative expression of miRNA transcriptome in two wheat cultivars, Arapahoe (susceptible) and Mace (temperature-sensitive-resistant), that were mock-inoculated or inoculated with WSMV, TriMV, or both at 18 °C and 27 °C. RESULTS Our results showed that the most abundant miRNA family among all the treatments was miRNA166, followed by 159a and 168a, although the order of the latter two changed depending on the infections. When comparing infected and control groups, twenty miRNAs showed significant upregulation, while eight miRNAs were significantly downregulated. Among them, miRNAs 9670-3p, 397-5p, and 5384-3p exhibited the most significant upregulation, whereas miRNAs 319, 9773, and 9774 were the most downregulated. The comparison of infection versus the control group for the cultivar Mace showed temperature-dependent regulation of these miRNAs. The principal component analysis confirmed that less abundant miRNAs among differentially expressed miRNAs were strongly correlated with the inoculated symptomatic wheat cultivars. Notably, miRNAs 397-5p, 398, and 9670-3p were upregulated in response to WSMV and TriMV infections, an observation not yet reported in this context. The significant upregulation of these three miRNAs was further confirmed with RT-qPCR analysis; in general, the RT-qPCR results were in agreement with our computational analysis. Target prediction analysis showed that the miRNAs standing out in our analysis targeted genes involved in defense response and regulation of transcription. CONCLUSION Investigation into the roles of these miRNAs and their corresponding targets holds promise for advancing our understanding of the mechanisms of virus infection and possible manipulation of these factors for developing durable virus resistance in crop plants.
Collapse
Affiliation(s)
- Inanc Soylu
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA
| | - Dilip K Lakshman
- USDA-ARS Sustainable Agricultural Systems Laboratory, Beltsville, MD, USA
| | - Satyanarayana Tatineni
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA
- USDA-ARS Wheat, Sorghum, and Forage Research Unit, University of Nebraska, Lincoln, NE, USA
| | - Leny C Galvez
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA
| | - Amitava Mitra
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA.
| |
Collapse
|
24
|
Voshart DC, Oshima T, Jiang Y, van der Linden GP, Ainslie AP, Reali Nazario L, van Buuren-Broek F, Scholma AC, van Weering HRJ, Brouwer N, Sewdihal J, Brouwer U, Coppes RP, Holtman IR, Eggen BJL, Kooistra SM, Barazzuol L. Radiotherapy induces persistent innate immune reprogramming of microglia into a primed state. Cell Rep 2024; 43:113764. [PMID: 38358885 DOI: 10.1016/j.celrep.2024.113764] [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: 05/16/2023] [Revised: 12/06/2023] [Accepted: 01/25/2024] [Indexed: 02/17/2024] Open
Abstract
Over half of patients with brain tumors experience debilitating and often progressive cognitive decline after radiotherapy treatment. Microglia, the resident macrophages in the brain, have been implicated in this decline. In response to various insults, microglia can develop innate immune memory (IIM), which can either enhance (priming or training) or repress (tolerance) the response to subsequent inflammatory challenges. Here, we investigate whether radiation affects the IIM of microglia by irradiating the brains of rats and later exposing them to a secondary inflammatory stimulus. Comparative transcriptomic profiling and protein validation of microglia isolated from irradiated rats show a stronger immune response to a secondary inflammatory insult, demonstrating that radiation can lead to long-lasting molecular reprogramming of microglia. Transcriptomic analysis of postmortem normal-appearing non-tumor brain tissue of patients with glioblastoma indicates that radiation-induced microglial priming is likely conserved in humans. Targeting microglial priming or avoiding further inflammatory insults could decrease radiotherapy-induced neurotoxicity.
Collapse
Affiliation(s)
- Daniëlle C Voshart
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Takuya Oshima
- Department of Biomedical Sciences, Section of Molecular Neurobiology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Yuting Jiang
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Gideon P van der Linden
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Anna P Ainslie
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands; European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Luiza Reali Nazario
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Fleur van Buuren-Broek
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Ayla C Scholma
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Hilmar R J van Weering
- Department of Biomedical Sciences, Section of Molecular Neurobiology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Nieske Brouwer
- Department of Biomedical Sciences, Section of Molecular Neurobiology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Jeffrey Sewdihal
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Uilke Brouwer
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Rob P Coppes
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Inge R Holtman
- Department of Biomedical Sciences, Section of Molecular Neurobiology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Bart J L Eggen
- Department of Biomedical Sciences, Section of Molecular Neurobiology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Susanne M Kooistra
- Department of Biomedical Sciences, Section of Molecular Neurobiology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Lara Barazzuol
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands.
| |
Collapse
|
25
|
Cracco RC, Alexandre PA, Polizel GHG, Fernandes AC, de Almeida Santana MH. Evaluation of Muscle Long Non-Coding RNA Profile during Rearing and Finishing Phase of Bulls Subjected to Different Prenatal Nutritional Strategies. Animals (Basel) 2024; 14:652. [PMID: 38396620 PMCID: PMC10886332 DOI: 10.3390/ani14040652] [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: 12/29/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
Maternal nutrition has the ability of influence critical processes in fetal life, including muscle development. Also, in this period, epigenetic sensitivity to external stimuli is higher and produces long-lasting effects. Thus, the aim of this study was to investigate epigenetic mechanisms, including the identification and characterization of long non-coding RNA (lncRNA) from animals that had undergone different strategies of prenatal supplementation. A group of Nellore cows (n = 126) were separated into three nutritional plans: NP (control)-Not Programmed, without protein-energy supplementation; PP-Partially Programmed, protein-energy supplementation in the final third of pregnancy; and CP-Complete Programming, protein-energy supplementation during the full period of gestation. A total of 63 male offspring were used in this study, of which 15 (5 per treatment) had Longissimus thoracis muscle at 15 (biopsy) and 22 months (slaughter). Biopsy samples were subjected to RNA extraction and sequencing. Differential expression (DE) of remodeling factors and chromatin-modifying enzyme genes were performed. For the identification and characterization of lncRNA, a series of size filters and protein coding potential tests were performed. The lncRNAs identified had their differential expression and regulatory potential tested. Regarding DE of epigenetic mechanisms, no differentially expressed gene was found (p > 0.1). Identification of potential lncRNA was successful, identifying 1823 transcripts at 15 months and 1533 at 22 months. Among these, four were considered differentially expressed between treatments at 15 months and 6 were differentially expressed at 22 months. Yet, when testing regulatory potential, 13 lncRNAs were considered key regulators in the PP group, and 17 in the CP group. PP group lncRNAs possibly regulate fat-cell differentiation, in utero embryonic development, and transforming growth factor beta receptor, whereas lncRNA in the CP group regulates in utero embryonic development, fat-cell differentiation and vasculogenesis. Maternal nutrition had no effect on differential expression of epigenetic mechanisms; however, it seems to impair lncRNA regulation of epigenetics.
Collapse
Affiliation(s)
- Roberta Cavalcante Cracco
- Department of Animal Science, College of Animal Science and Food Engineering—USP, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (R.C.C.); (G.H.G.P.)
| | - Pamela Almeida Alexandre
- Microbiomes for One Systems Health (MOSH), CSIRO Agriculture & Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia;
| | - Guilherme Henrique Gebim Polizel
- Department of Animal Science, College of Animal Science and Food Engineering—USP, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (R.C.C.); (G.H.G.P.)
| | - Arícia Christofaro Fernandes
- Department of Animal Science, College of Animal Science and Food Engineering—USP, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (R.C.C.); (G.H.G.P.)
| | - Miguel Henrique de Almeida Santana
- Department of Animal Science, College of Animal Science and Food Engineering—USP, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (R.C.C.); (G.H.G.P.)
| |
Collapse
|
26
|
Moldenhauer LM, Foyle KL, Wilson JJ, Wong YY, Sharkey DJ, Green ES, Barry SC, Hull ML, Robertson SA. A disrupted FOXP3 transcriptional signature underpins systemic regulatory T cell insufficiency in early pregnancy failure. iScience 2024; 27:108994. [PMID: 38327801 PMCID: PMC10847744 DOI: 10.1016/j.isci.2024.108994] [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: 07/12/2023] [Revised: 12/22/2023] [Accepted: 01/18/2024] [Indexed: 02/09/2024] Open
Abstract
Regulatory T (Treg) cell defects are implicated in disorders of embryo implantation and placental development, but the origins of Treg cell dysfunction are unknown. Here, we comprehensively analyzed the phenotypes and transcriptional profile of peripheral blood Treg cells in individuals with early pregnancy failure (EPF). Compared to fertile subjects, EPF subjects had 32% fewer total Treg cells and 54% fewer CD45RA+CCR7+ naive Treg cells among CD4+ T cells, an altered Treg cell phenotype with reduced transcription factor FOXP3 and suppressive marker CTLA4 expression, and lower Treg:Th1 and Treg:Th17 ratios. RNA sequencing demonstrated an aberrant gene expression profile, with upregulation of pro-inflammatory genes including CSF2, IL4, IL17A, IL21, and IFNG in EPF Treg cells. In silico analysis revealed 25% of the Treg cell dysregulated genes are targets of FOXP3. We conclude that EPF is associated with systemic Treg cell defects arising due to disrupted FOXP3 transcriptional control and loss of lineage fidelity.
Collapse
Affiliation(s)
- Lachlan M. Moldenhauer
- Robinson Research Institute and School of Biomedicine, The University of Adelaide, Adelaide, SA, Australia
| | - Kerrie L. Foyle
- Robinson Research Institute and School of Biomedicine, The University of Adelaide, Adelaide, SA, Australia
| | - Jasmine J. Wilson
- Robinson Research Institute and School of Biomedicine, The University of Adelaide, Adelaide, SA, Australia
| | - Ying Y. Wong
- Robinson Research Institute and School of Biomedicine, The University of Adelaide, Adelaide, SA, Australia
| | - David J. Sharkey
- Robinson Research Institute and School of Biomedicine, The University of Adelaide, Adelaide, SA, Australia
| | - Ella S. Green
- Robinson Research Institute and School of Biomedicine, The University of Adelaide, Adelaide, SA, Australia
| | - Simon C. Barry
- Robinson Research Institute and School of Biomedicine, The University of Adelaide, Adelaide, SA, Australia
| | - M. Louise Hull
- Robinson Research Institute and Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Sarah A. Robertson
- Robinson Research Institute and School of Biomedicine, The University of Adelaide, Adelaide, SA, Australia
| |
Collapse
|
27
|
Scoyni F, Giudice L, Väänänen M, Downes N, Korhonen P, Choo XY, Välimäki N, Mäkinen P, Korvenlaita N, Rozemuller AJ, de Vries HE, Polo J, Turunen TA, Ylä‐Herttuala S, Hansen TB, Grubman A, Kaikkonen MU, Malm T. Alzheimer's disease-induced phagocytic microglia express a specific profile of coding and non-coding RNAs. Alzheimers Dement 2024; 20:954-974. [PMID: 37828821 PMCID: PMC10916983 DOI: 10.1002/alz.13502] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/10/2023] [Accepted: 09/19/2023] [Indexed: 10/14/2023]
Abstract
INTRODUCTION Alzheimer's disease (AD) is a neurodegenerative disease and the main cause of dementia in the elderly. AD pathology is characterized by accumulation of microglia around the beta-amyloid (Aβ) plaques which assumes disease-specific transcriptional signatures, as for the disease-associated microglia (DAM). However, the regulators of microglial phagocytosis are still unknown. METHODS We isolated Aβ-laden microglia from the brain of 5xFAD mice for RNA sequencing to characterize the transcriptional signature in phagocytic microglia and to identify the key non-coding RNAs capable of regulating microglial phagocytosis. Through spatial sequencing, we show the transcriptional changes of microglia in the AD mouse brain in relation to Aβ proximity. RESULTS Finally, we show that phagocytic messenger RNAs are regulated by miR-7a-5p, miR-29a-3p and miR-146a-5p microRNAs and segregate the DAM population into phagocytic and non-phagocytic states. DISCUSSION Our study pinpoints key regulators of microglial Aβ clearing capacity suggesting new targets for future therapeutic approaches.
Collapse
Affiliation(s)
- Flavia Scoyni
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Luca Giudice
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Mari‐Anna Väänänen
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Nicholas Downes
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Paula Korhonen
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Xin Yi Choo
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonAustralia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoriaAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoriaAustralia
| | - Nelli‐Noora Välimäki
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Petri Mäkinen
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Nea Korvenlaita
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Annemieke J Rozemuller
- Department of Pathology, Amsterdam UMC, Vrije Universiteit AmsterdamVU University Medical CenterAmsterdamMBthe Netherlands
| | - Helga E de Vries
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit AmsterdamVU University Medical CenterAmsterdamMBthe Netherlands
| | - Jose Polo
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonAustralia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoriaAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoriaAustralia
| | - Tiia A Turunen
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Seppo Ylä‐Herttuala
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Thomas B Hansen
- Interdisciplinary Nanoscience CenterDepartment of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
- Present address:
Targovax ASALysaker1366Norway
| | - Alexandra Grubman
- Department of Anatomy and Developmental BiologyMonash UniversityClaytonAustralia
- Development and Stem Cells ProgramMonash Biomedicine Discovery InstituteClaytonVictoriaAustralia
- Australian Regenerative Medicine InstituteMonash UniversityClaytonVictoriaAustralia
| | - Minna U Kaikkonen
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Tarja Malm
- A.I.Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| |
Collapse
|
28
|
Fagbémi MNA, Nivelle R, Muller M, Mélard C, Lalèyè P, Rougeot C. Effect of high temperatures on sex ratio and differential expression analysis (RNA-seq) of sex-determining genes in Oreochromis niloticus from different river basins in Benin. ENVIRONMENTAL EPIGENETICS 2024; 9:dvad009. [PMID: 38487307 PMCID: PMC10939319 DOI: 10.1093/eep/dvad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/09/2023] [Accepted: 01/10/2024] [Indexed: 03/17/2024]
Abstract
The high temperature sex reversal process leading to functional phenotypic masculinization during development has been widely described in Nile tilapia (Oreochromis n iloticus) under laboratory or aquaculture conditions and in the wild. In this study, we selected five wild populations of O. niloticus from different river basins in Benin and produced twenty full-sib families of mixed-sex (XY and XX) by natural reproduction. Progenies were exposed to room temperature or high (36.5°C) temperatures between 10 and 30 days post-fertilization (dpf). In control groups, we observed sex ratios from 40% to 60% males as expected, except for 3 families from the Gobé region which showed a bias towards males. High temperature treatment significantly increased male rates in each family up to 88%. Transcriptome analysis was performed by RNA-sequencing (RNA-seq) on brains and gonads from control and treated batches of six families at 15 dpf and 40 dpf. Analysis of differentially expressed genes, differentially spliced genes, and correlations with sex reversal was performed. In 40 dpf gonads, genes involved in sex determination such as dmrt1, cyp11c1, amh, cyp19a1b, ara, and dax1 were upregulated. In 15 dpf brains, a negative correlation was found between the expression of cyp19a1b and the reversal rate, while at 40 dpf a negative correlation was found between the expression of foxl2, cyp11c1, and sf1 and positive correlation was found between dmrt1 expression and reversal rate. Ontology analysis of the genes affected by high temperatures revealed that male sex differentiation processes, primary male sexual characteristics, autophagy, and cilium organization were affected. Based on these results, we conclude that sex reversal by high temperature treatment leads to similar modifications of the transcriptomes in the gonads and brains in offspring of different natural populations of Nile tilapia, which thus may activate a common cascade of reactions inducing sex reversal in progenies.
Collapse
Affiliation(s)
- Mohammed Nambyl A Fagbémi
- Aquaculture Research and Education Centre (CEFRA), Liège University, query author on which is prefered, 10 Chemin de la Justice B-4500, Tihange, Belgium
- Laboratory of Hydrobiology and Aquaculture (LHA), Faculty of Agricultural Sciences, University of Abomey-Calavi, 01 BP: 526, Cotonou, Benin
| | - Renaud Nivelle
- Aquaculture Research and Education Centre (CEFRA), Liège University, query author on which is prefered, 10 Chemin de la Justice B-4500, Tihange, Belgium
- Laboratory for Organogenesis and Regeneration (LOR), Interdisciplinary Research Institute in Biomedical Sciences (GIGA-I3), Liège University, Sart Tilman, Liège, Belgium
| | - Marc Muller
- Laboratory for Organogenesis and Regeneration (LOR), Interdisciplinary Research Institute in Biomedical Sciences (GIGA-I3), Liège University, Sart Tilman, Liège, Belgium
| | - Charles Mélard
- Aquaculture Research and Education Centre (CEFRA), Liège University, query author on which is prefered, 10 Chemin de la Justice B-4500, Tihange, Belgium
| | - Philippe Lalèyè
- Laboratory of Hydrobiology and Aquaculture (LHA), Faculty of Agricultural Sciences, University of Abomey-Calavi, 01 BP: 526, Cotonou, Benin
| | - Carole Rougeot
- Aquaculture Research and Education Centre (CEFRA), Liège University, query author on which is prefered, 10 Chemin de la Justice B-4500, Tihange, Belgium
| |
Collapse
|
29
|
Kumari R, Ponte ME, Franczak E, Prom JC, O'Neil MF, Sardiu ME, Lutkewitte AJ, Shankar K, Morris EM, Thyfault JP. VCD-induced menopause mouse model reveals reprogramming of hepatic metabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571644. [PMID: 38168213 PMCID: PMC10760158 DOI: 10.1101/2023.12.14.571644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Menopause adversely impacts systemic energy metabolism and increases the risk of metabolic disease(s) including hepatic steatosis, but the mechanisms are largely unknown. Dosing female mice with vinyl cyclohexene dioxide (VCD) selectively causes follicular atresia in ovaries, leading to a murine menopause-like phenotype. In this study, we treated female C57BL6/J mice with VCD (160mg/kg i.p. for 20 consecutive days followed by verification of the lack of estrous cycling) to investigate changes in body composition, energy expenditure (EE), hepatic mitochondrial function, and hepatic steatosis across different dietary conditions. VCD treatment induced ovarian follicular loss and increased follicle-stimulating hormone (FSH) levels in female mice, mimicking a menopause-like phenotype. VCD treatment did not affect body composition, or EE in mice on a low-fat diet or in response to a short-term (1-week) high-fat, high sucrose diet (HFHS). However, the transition to a HFHS lowered cage activity in VCD mice. A chronic HFHS diet (16 weeks) significantly increased weight gain, fat mass, and hepatic steatosis in VCD-treated mice compared to HFHS-fed controls. In the liver, VCD mice showed suppressed hepatic mitochondrial respiration on LFD, while chronic HFHS diet resulted in compensatory increases in hepatic mitochondrial respiration. Also, liver RNA sequencing revealed that VCD promoted global upregulation of hepatic lipid/cholesterol synthesis pathways. Our findings suggest that the VCD- induced menopause model compromises hepatic mitochondrial function and lipid/cholesterol homeostasis that sets the stage for HFHS diet-induced steatosis while also increasing susceptibility to obesity.
Collapse
|
30
|
Ohtonen S, Giudice L, Jäntti H, Fazaludeen MF, Shakirzyanova A, Gómez-Budia M, Välimäki NN, Niskanen J, Korvenlaita N, Fagerlund I, Koistinaho J, Amiry-Moghaddam M, Savchenko E, Roybon L, Lehtonen Š, Korhonen P, Malm T. Human iPSC-derived microglia carrying the LRRK2-G2019S mutation show a Parkinson's disease related transcriptional profile and function. Sci Rep 2023; 13:22118. [PMID: 38092815 PMCID: PMC10719377 DOI: 10.1038/s41598-023-49294-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023] Open
Abstract
LRRK2-G2019S is one of the most common Parkinson's disease (PD)-associated mutations and has been shown to alter microglial functionality. However, the impact of LRRK2-G2019S on transcriptional profile of human induced pluripotent stem cell-derived microglia-like cells (iMGLs) and how it corresponds to microglia in idiopathic PD brain is not known. Here we demonstrate that LRRK2-G2019S carrying iMGL recapitulate aspects of the transcriptional signature of human idiopathic PD midbrain microglia. LRRK2-G2019S induced subtle and donor-dependent alterations in iMGL mitochondrial respiration, phagocytosis and cytokine secretion. Investigation of microglial transcriptional state in the midbrains of PD patients revealed a subset of microglia with a transcriptional overlap between the in vitro PD-iMGL and human midbrain PD microglia. We conclude that LRRK2-G2019S iMGL serve as a model to study PD-related effects in human microglia.
Collapse
Affiliation(s)
- Sohvi Ohtonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
| | - Luca Giudice
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Henna Jäntti
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Anastasia Shakirzyanova
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mireia Gómez-Budia
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Nelli-Noora Välimäki
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jonna Niskanen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Nea Korvenlaita
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Ilkka Fagerlund
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jari Koistinaho
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Mahmood Amiry-Moghaddam
- Division of Anatomy, Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Ekaterina Savchenko
- Stem Cell Laboratory for CNS Disease Modeling, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Laurent Roybon
- Stem Cell Laboratory for CNS Disease Modeling, Department of Experimental Medical Science, Lund University, Lund, Sweden
- Department of Neurodegenerative Science, The MiND Program, Van Andel Institute, Grand Rapids, MI, USA
| | - Šárka Lehtonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Paula Korhonen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Tarja Malm
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| |
Collapse
|
31
|
Ruera CN, Perez F, Iribarren ML, Guzman L, Menendez L, Garbi L, Chirdo FG. Coexistence of apoptosis, pyroptosis, and necroptosis pathways in celiac disease. Clin Exp Immunol 2023; 214:328-340. [PMID: 37455655 PMCID: PMC10719221 DOI: 10.1093/cei/uxad082] [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: 04/13/2023] [Revised: 06/12/2023] [Accepted: 07/14/2023] [Indexed: 07/18/2023] Open
Abstract
Usually, the massive elimination of cells under steady-state conditions occurs by apoptosis, which is also acknowledged to explain the loss of enterocytes in the small intestine of celiac disease (CD) patients. However, little is known about the role of proinflammatory cell death pathways in CD. Here, we have used confocal microscopy, western blot, and RT-qPCR analysis to assess the presence of regulated cell death pathways in the duodenum of CD patients. We found an increased number of dead (TUNEL+) cells in the lamina propria of small intestine of CD patients, most of them are plasma cells (CD138+). Many dying cells expressed FAS and were in close contact with CD3+ T cells. Caspase-8 and caspase-3 expression was increased in CD, confirming the activation of apoptosis. In parallel, caspase-1, IL-1β, and GSDMD were increased in CD samples indicating the presence of inflammasome-dependent pyroptosis. Necroptosis was also present, as shown by the increase of RIPK3 and phosphorylate MLKL. Analysis of published databases confirmed that CD has an increased expression of regulated cell death -related genes. Together, these results reveal that CD is characterized by cell death of different kinds. In particular, the presence of proinflammatory cell death pathways may contribute to mucosal damage.
Collapse
Affiliation(s)
- Carolina N Ruera
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), (UNLP-CONICET-CIC) Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Federico Perez
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), (UNLP-CONICET-CIC) Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Luz Iribarren
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), (UNLP-CONICET-CIC) Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Luciana Guzman
- Servicio de Gastroenterología Hospital de Niños “Sor María Ludovica”, La Plata, Argentina
| | - Lorena Menendez
- Servicio de Gastroenterología Hospital de Niños “Sor María Ludovica”, La Plata, Argentina
| | - Laura Garbi
- Servicio de Gastroenterología, HospitalSan Martin, La Plata, Argentina
| | - Fernando G Chirdo
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), (UNLP-CONICET-CIC) Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| |
Collapse
|
32
|
Silver KI, Patkar S, Mazcko C, Berger EP, Beck JA, LeBlanc AK. Patterns of metastatic progression and association with clinical outcomes in canine osteosarcoma: A necropsy study of 83 dogs. Vet Comp Oncol 2023; 21:646-655. [PMID: 37592810 PMCID: PMC10842475 DOI: 10.1111/vco.12927] [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: 03/13/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/19/2023]
Abstract
Osteosarcoma is a highly metastatic primary bone tumour that occurs spontaneously in both pet dogs and humans. Patterns of metastasis to organs beyond the most common site (lung) are poorly characterised and it is unknown whether specific associations between patterns of metastatic progression and patient features exist. This retrospective study characterised the necropsy findings of 83 dogs receiving standardised therapy and clinical monitoring in a prospective clinical trial setting to document patterns of metastasis and correlate outcomes with these patterns and other patient and tumour-specific factors. A total of 20 different sites of metastasis were documented, with lung as the most common site, followed by bone, kidney, liver, and heart. Two distinct clusters of dogs were identified based on patterns of metastasis. There was no significant association between site of enrollment, trial arm, sex, serum alkaline phosphatase (ALP) activity, or tumour location and clinical outcomes. A second cancer type was identified at necropsy in 10 dogs (10/83; 12%). These data showcase the extensive nature of osteosarcoma metastasis beyond the lung and provide a benchmark for clinical monitoring of the disease. Further, this study provides insight into transcriptional features of primary tumours that may relate to a propensity for osteosarcoma metastasis to specific organs and tissues.
Collapse
Affiliation(s)
- K I Silver
- Comparative Oncology Program, Molecular Imaging Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - S Patkar
- Artificial Intelligence Resource, Molecular Imaging Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - C Mazcko
- Comparative Oncology Program, Molecular Imaging Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - E P Berger
- Frederick National Laboratory for Cancer Research in the Comparative Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - J A Beck
- Comparative Oncology Program, Molecular Imaging Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - A K LeBlanc
- Comparative Oncology Program, Molecular Imaging Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| |
Collapse
|
33
|
Colbert LE, El Alam MB, Wang R, Karpinets T, Lo D, Lynn EJ, Harris TA, Elnaggar JH, Yoshida-Court K, Tomasic K, Bronk JK, Sammouri J, Yanamandra AV, Olvera AV, Carlin LG, Sims T, Delgado Medrano AY, Napravnik TC, O'Hara M, Lin D, Abana CO, Li HX, Eifel PJ, Jhingran A, Joyner M, Lin L, Ramondetta LM, Futreal AM, Schmeler KM, Mathew G, Dorta-Estremera S, Zhang J, Wu X, Ajami NJ, Wong M, Taniguchi C, Petrosino JF, Sastry KJ, Okhuysen PC, Martinez SA, Tan L, Mahmud I, Lorenzi PL, Wargo JA, Klopp AH. Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring. Cancer Cell 2023; 41:1945-1962.e11. [PMID: 37863066 PMCID: PMC10841640 DOI: 10.1016/j.ccell.2023.09.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 07/01/2023] [Accepted: 09/25/2023] [Indexed: 10/22/2023]
Abstract
Tumor microbiota can produce active metabolites that affect cancer and immune cell signaling, metabolism, and proliferation. Here, we explore tumor and gut microbiome features that affect chemoradiation response in patients with cervical cancer using a combined approach of deep microbiome sequencing, targeted bacterial culture, and in vitro assays. We identify that an obligate L-lactate-producing lactic acid bacterium found in tumors, Lactobacillus iners, is associated with decreased survival in patients, induces chemotherapy and radiation resistance in cervical cancer cells, and leads to metabolic rewiring, or alterations in multiple metabolic pathways, in tumors. Genomically similar L-lactate-producing lactic acid bacteria commensal to other body sites are also significantly associated with survival in colorectal, lung, head and neck, and skin cancers. Our findings demonstrate that lactic acid bacteria in the tumor microenvironment can alter tumor metabolism and lactate signaling pathways, causing therapeutic resistance. Lactic acid bacteria could be promising therapeutic targets across cancer types.
Collapse
Affiliation(s)
- Lauren E Colbert
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Molly B El Alam
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rui Wang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tatiana Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David Lo
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erica J Lynn
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Timothy A Harris
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jacob H Elnaggar
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; LSU School of Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Kyoko Yoshida-Court
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Katarina Tomasic
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Julianna K Bronk
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Julie Sammouri
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ananta V Yanamandra
- Department of Translational and Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Adilene V Olvera
- Departments of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lily G Carlin
- Departments of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Travis Sims
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrea Y Delgado Medrano
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tatiana Cisneros Napravnik
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Madison O'Hara
- Department of Thoracic Head and Neck Medical Oncology at The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Daniel Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chike O Abana
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hannah X Li
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patricia J Eifel
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anuja Jhingran
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Melissa Joyner
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lilie Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lois M Ramondetta
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew M Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kathleen M Schmeler
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Geena Mathew
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaogang Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nadim J Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Platform for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew Wong
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Platform for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cullen Taniguchi
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, The Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA
| | - K Jagannadha Sastry
- Department of Thoracic Head and Neck Medical Oncology at The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pablo C Okhuysen
- Departments of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sara A Martinez
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lin Tan
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Iqbal Mahmud
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Philip L Lorenzi
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer A Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; LSU School of Medicine, Louisiana State University, Baton Rouge, LA 70803, USA; Platform for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ann H Klopp
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
34
|
Niemira M, Erol A, Bielska A, Zeller A, Skwarska A, Chwialkowska K, Kuzmicki M, Szamatowicz J, Reszec J, Knapp P, Moniuszko M, Kretowski A. Identification of serum miR-1246 and miR-150-5p as novel diagnostic biomarkers for high-grade serous ovarian cancer. Sci Rep 2023; 13:19287. [PMID: 37935712 PMCID: PMC10630404 DOI: 10.1038/s41598-023-45317-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/18/2023] [Indexed: 11/09/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is one of the leading cancers in women, with high-grade serous ovarian cancer (HGSOC) being the most common and lethal subtype of this disease. A vast majority of HGSOC are diagnosed at the late stage of the disease when the treatment and total recovery chances are low. Thus, there is an urgent need for novel, more sensitive and specific methods for early and routine HGSOC clinical diagnosis. In this study, we performed miRNA expression profiling using the NanoString miRNA assay in 34 serum samples from patients with HGSOC and 36 healthy women. We identified 13 miRNAs that were differentially expressed (DE). For additional exploration of expression patterns correlated with HGSOC, we performed weighted gene co-expression network analysis (WGCNA). As a result, we showed that the module most correlated with tumour size, nodule and metastasis contained 8 DE miRNAs. The panel including miR-1246 and miR-150-5p was identified as a signature that could discriminate HGSOC patients with AUCs of 0.98 and 1 for the training and test sets, respectively. Furthermore, the above two-miRNA panel had an AUC = 0.946 in the verification cohorts of RT-qPCR data and an AUC = 0.895 using external data from the GEO public database. Thus, the model we developed has the potential to markedly improve the diagnosis of ovarian cancer.
Collapse
Affiliation(s)
- Magdalena Niemira
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland.
| | - Anna Erol
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Agnieszka Bielska
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Anna Zeller
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Anna Skwarska
- Cancer Center, Department of Oncology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Karolina Chwialkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Mariusz Kuzmicki
- Department of Gynecology and Gynecological Oncology, Medical University of Bialystok, Bialystok, Poland
| | - Jacek Szamatowicz
- Department of Gynecology and Gynecological Oncology, Medical University of Bialystok, Bialystok, Poland
| | - Joanna Reszec
- Department of Medical Pathomorphology, Medical University of Bialystok, Bialystok, Poland
| | - Pawel Knapp
- University Oncology Centre, University Clinical Hospital in Bialystok, Bialystok, Poland
| | - Marcin Moniuszko
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Bialystok, Poland
| | - Adam Kretowski
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| |
Collapse
|
35
|
Ewald J, Zhou G, Lu Y, Xia J. Using ExpressAnalyst for Comprehensive Gene Expression Analysis in Model and Non-Model Organisms. Curr Protoc 2023; 3:e922. [PMID: 37929753 DOI: 10.1002/cpz1.922] [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] [Indexed: 11/07/2023]
Abstract
ExpressAnalyst is a web-based platform that enables intuitive, end-to-end transcriptomics and proteomics data analysis. Users can start from FASTQ files, gene/protein abundance tables, or gene/protein lists. ExpressAnalyst will perform read quantification, gene expression table processing and normalization, differential expression analysis, or meta-analysis with complex study designs. The results are presented via various interactive visualizations such as volcano plots, heatmaps, networks, and ridgeline charts, with built-in functional enrichment analysis to allow flexible data exploration and understanding. ExpressAnalyst currently contains built-in support for 29 common organisms. For non-model organisms without good reference genomes, it can perform comprehensive transcriptome profiling directly from RNA-seq reads. These common tasks are covered in 11 Basic Protocols. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: RNA-seq count table uploading, processing, and normalization Basic Protocol 2: Differential expression analysis with linear models Basic Protocol 3: Functional analysis with volcano plot, enrichment network, and ridgeline visualization Basic Protocol 4: Hierarchical clustering analysis of transcriptomics data using interactive heatmaps Basic Protocol 5: Cross-species gene expression analysis based on ortholog mapping results Basic Protocol 6: Proteomics and microarray data processing and normalization Basic Protocol 7: Preparing multiple gene expression tables for meta-analysis Basic Protocol 8: Statistical and functional meta-analysis of gene expression data Basic Protocol 9: Functional analysis of transcriptomics signatures Basic Protocol 10: Dose-response and time-series data analysis Basic Protocol 11: RNA-seq reads processing and quantification with and without reference transcriptomes.
Collapse
Affiliation(s)
- Jessica Ewald
- Institute of Parasitology, McGill University, Montreal, Canada
| | - Guangyan Zhou
- Institute of Parasitology, McGill University, Montreal, Canada
| | - Yao Lu
- Department of Microbiology and Immunology, McGill University, Montreal, Canada
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Canada
| |
Collapse
|
36
|
Dong X, Du MRM, Gouil Q, Tian L, Jabbari JS, Bowden R, Baldoni PL, Chen Y, Smyth GK, Amarasinghe SL, Law CW, Ritchie ME. Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures. Nat Methods 2023; 20:1810-1821. [PMID: 37783886 DOI: 10.1038/s41592-023-02026-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/25/2023] [Indexed: 10/04/2023]
Abstract
The lack of benchmark data sets with inbuilt ground-truth makes it challenging to compare the performance of existing long-read isoform detection and differential expression analysis workflows. Here, we present a benchmark experiment using two human lung adenocarcinoma cell lines that were each profiled in triplicate together with synthetic, spliced, spike-in RNAs (sequins). Samples were deeply sequenced on both Illumina short-read and Oxford Nanopore Technologies long-read platforms. Alongside the ground-truth available via the sequins, we created in silico mixture samples to allow performance assessment in the absence of true positives or true negatives. Our results show that StringTie2 and bambu outperformed other tools from the six isoform detection tools tested, DESeq2, edgeR and limma-voom were best among the five differential transcript expression tools tested and there was no clear front-runner for performing differential transcript usage analysis between the five tools compared, which suggests further methods development is needed for this application.
Collapse
Affiliation(s)
- Xueyi Dong
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.
| | - Mei R M Du
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Quentin Gouil
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Luyi Tian
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Guangzhou National Laboratory, Guangzhou, China
| | - Jafar S Jabbari
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Rory Bowden
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Pedro L Baldoni
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Yunshun Chen
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Shanika L Amarasinghe
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- The Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Charity W Law
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.
| |
Collapse
|
37
|
Ephraim R, Fraser S, Devereaux J, Stavely R, Feehan J, Eri R, Nurgali K, Apostolopoulos V. Differential Gene Expression of Checkpoint Markers and Cancer Markers in Mouse Models of Spontaneous Chronic Colitis. Cancers (Basel) 2023; 15:4793. [PMID: 37835487 PMCID: PMC10571700 DOI: 10.3390/cancers15194793] [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: 09/04/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The presence of checkpoint markers in cancer cells aids in immune escape. The identification of checkpoint markers and early cancer markers is of utmost importance to gain clarity regarding the relationship between colitis and progressive inflammation leading to cancer. Herein, the gene expression levels of checkpoint makers, cancer-related pathways, and cancer genes in colon tissues of mouse models of chronic colitis (Winnie and Winnie-Prolapse mice) using next-generation sequencing are determined. Winnie mice are a result of a Muc2 missense mutation. The identification of such genes and their subsequent expression and role at the protein level would enable novel markers for the early diagnosis of cancer in IBD patients. The differentially expressed genes in the colonic transcriptome were analysed based on the Kyoto Encyclopedia of Genes and Genomes pathway. The expression of several oncogenes is associated with the severity of IBD, with Winnie-Prolapse mice expressing a large number of key genes associated with development of cancer. This research presents a number of new targets to evaluate for the development of biomarkers and therapeutics.
Collapse
Affiliation(s)
- Ramya Ephraim
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
| | - Sarah Fraser
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
| | - Jeannie Devereaux
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
| | - Rhian Stavely
- Pediatric Surgery Research Laboratories, Department of Pediatric Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA;
| | - Jack Feehan
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
- Immunology Program, Australian Institute of Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
| | - Rajaraman Eri
- STEM/School of Science, RMIT University, Melbourne, VIC 3001, Australia;
| | - Kulmira Nurgali
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
- Department of Medicine Western Health, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
- Regenerative Medicine and Stem Cells Program, Australian Institute of Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (R.E.); (S.F.); (J.D.); (J.F.); (K.N.)
- Immunology Program, Australian Institute of Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia
| |
Collapse
|
38
|
Nile M, Folwaczny M, Wichelhaus A, Baumert U, Janjic Rankovic M. Fluid flow shear stress and tissue remodeling-an orthodontic perspective: evidence synthesis and differential gene expression network analysis. Front Bioeng Biotechnol 2023; 11:1256825. [PMID: 37795174 PMCID: PMC10545883 DOI: 10.3389/fbioe.2023.1256825] [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: 07/17/2023] [Accepted: 08/28/2023] [Indexed: 10/06/2023] Open
Abstract
Introduction: This study aimed to identify and analyze in vitro studies investigating the biological effect of fluid-flow shear stress (FSS) on cells found in the periodontal ligament and bone tissue. Method: We followed the PRISMA guideline for systematic reviews. A PubMed search strategy was developed, studies were selected according to predefined eligibility criteria, and the risk of bias was assessed. Relevant data related to cell source, applied FSS, and locus-specific expression were extracted. Based on this evidence synthesis and, as an original part of this work, analysis of differential gene expression using over-representation and network-analysis was performed. Five relevant publicly available gene expression datasets were analyzed using gene set enrichment analysis (GSEA). Result: A total of 6,974 articles were identified. Titles and abstracts were screened, and 218 articles were selected for full-text assessment. Finally, 120 articles were included in this study. Sample size determination and statistical analysis related to methodological quality and the ethical statement item in reporting quality were most frequently identified as high risk of bias. The analyzed studies mostly used custom-made fluid-flow apparatuses (61.7%). FSS was most frequently applied for 0.5 h, 1 h, or 2 h, whereas FSS magnitudes ranged from 6 to 20 dyn/cm2 depending on cell type and flow profile. Fluid-flow frequencies of 1 Hz in human cells and 1 and 5 Hz in mouse cells were mostly applied. FSS upregulated genes/metabolites responsible for tissue formation (AKT1, alkaline phosphatase, BGLAP, BMP2, Ca2+, COL1A1, CTNNB1, GJA1, MAPK1/MAPK3, PDPN, RUNX2, SPP1, TNFRSF11B, VEGFA, WNT3A) and inflammation (nitric oxide, PGE-2, PGI-2, PTGS1, PTGS2). Protein-protein interaction networks were constructed and analyzed using over-representation analysis and GSEA to identify shared signaling pathways. Conclusion: To our knowledge, this is the first review giving a comprehensive overview and discussion of methodological technical details regarding fluid flow application in 2D cell culture in vitro experimental conditions. Therefore, it is not only providing valuable information about cellular molecular events and their quantitative and qualitative analysis, but also confirming the reproducibility of previously published results.
Collapse
Affiliation(s)
- Mustafa Nile
- Department of Orthodontics and Dentofacial Orthopedics, LMU University Hospital, LMU Munich, Munich, Germany
| | - Matthias Folwaczny
- Department of Conservative Dentistry and Periodontology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Andrea Wichelhaus
- Department of Orthodontics and Dentofacial Orthopedics, LMU University Hospital, LMU Munich, Munich, Germany
| | - Uwe Baumert
- Department of Orthodontics and Dentofacial Orthopedics, LMU University Hospital, LMU Munich, Munich, Germany
| | - Mila Janjic Rankovic
- Department of Orthodontics and Dentofacial Orthopedics, LMU University Hospital, LMU Munich, Munich, Germany
| |
Collapse
|
39
|
De la Cruz G, Blas R, Pérez W, Neyra E, Ortiz R. Foliar transcriptomes reveal candidate genes for late blight resistance in cultivars of diploid potato Solanum tuberosum L. Andigenum Group. FRONTIERS IN PLANT SCIENCE 2023; 14:1210046. [PMID: 37780511 PMCID: PMC10535101 DOI: 10.3389/fpls.2023.1210046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/10/2023] [Indexed: 10/03/2023]
Abstract
Characterization of major resistance (R) genes to late blight (LB) -caused by the oomycete Phytophthora infestans- is very important for potato breeding. The objective of this study was to identify novel genes for resistance to LB from diploid Solanum tuberosum L. Andigenum Group (StAG) cultivar accessions. Using comparative analysis with a edgeR bioconductor package for differential expression analysis of transcriptomes, two of these accessions with contrasting levels of resistance to LB were analyzed using digital gene expression data. As a result, various differentially expressed genes (P ≤ 0.0001, Log2FC ≥ 2, FDR < 0.001) were noted. The combination of transcriptomic analysis provided 303 candidate genes that are overexpressed and underexpressed, thereby giving high resistance to LB. The functional analysis showed differential expression of R genes and their corresponding proteins related to disease resistance, NBS-LRR domain proteins, and specific disease resistance proteins. Comparative analysis of specific tissue transcriptomes in resistant and susceptible genotypes can be used for rapidly identifying candidate R genes, thus adding novel genes from diploid StAG cultivar accessions for host plant resistance to P. infestans in potato.
Collapse
Affiliation(s)
- Germán De la Cruz
- Laboratorio de Genética y Biotecnología Vegetal, Facultad de Ciencias Agrarias, Universidad Nacional de San Cristóbal de Huamanga (UNSCH), Ayacucho, Peru
| | - Raúl Blas
- Instituto de Biotecnologia (IBT), Facultad de Agronomia, Universidad Nacional Agraria La Molina (UNALM), Lima, Peru
| | - Willmer Pérez
- Plant Pathology Laboratory, Crop and Systems Sciences Division, International Potato Center, Lima, Peru
| | - Edgar Neyra
- Unidad de Genómica, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento Académico de Tecnología Médica, Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| |
Collapse
|
40
|
Felipez W, Villavicencio J, Nizolli VO, Pegoraro C, da Maia L, Costa de Oliveira A. Genome-Wide Identification of Bilberry WRKY Transcription Factors: Go Wild and Duplicate. PLANTS (BASEL, SWITZERLAND) 2023; 12:3176. [PMID: 37765340 PMCID: PMC10535657 DOI: 10.3390/plants12183176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/11/2023] [Accepted: 07/20/2023] [Indexed: 09/29/2023]
Abstract
WRKY transcription factor genes compose an important family of transcriptional regulators that are present in several plant species. According to previous studies, these genes can also perform important roles in bilberry (Vaccinium myrtillus L.) metabolism, making it essential to deepen our understanding of fruit ripening regulation and anthocyanin biosynthesis. In this context, the detailed characterization of these proteins will provide a comprehensive view of the functional features of VmWRKY genes in different plant organs and in response to different intensities of light. In this study, the investigation of the complete genome of the bilberry identified 76 VmWRKY genes that were evaluated and distributed in all twelve chromosomes. The proteins encoded by these genes were classified into four groups (I, II, III, and IV) based on their conserved domains and zinc finger domain types. Fifteen pairs of VmWRKY genes in segmental duplication and four pairs in tandem duplication were detected. A cis element analysis showed that all promoters of the VmWRKY genes contain at least one potential cis stress-response element. Differential expression analysis of RNA-seq data revealed that VmWRKY genes from bilberry show preferential or specific expression in samples. These findings provide an overview of the functional characterization of these proteins in bilberry.
Collapse
Affiliation(s)
- Winder Felipez
- Instituto de Agroecología y Seguridad Alimentaria, Facultad de Ciências Agrárias, Universidad San Francisco Xavier de Chuquisaca—USFX, Casilla, Correo Central, Sucre 1046, Bolivia;
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
| | - Jennifer Villavicencio
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
- Carrera de Ingeniería Agroforestal, Facultad de Ciencias Ambientales, Universidad Cientifica del Sur—UCSUR, Antigua Panamericana Sur km 19 Villa el Salvador, Lima CP 150142, Peru
| | - Valeria Oliveira Nizolli
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
| | - Camila Pegoraro
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
| | - Luciano da Maia
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
| |
Collapse
|
41
|
Schmidt C, Cohen S, Gudenas BL, Husain S, Carlson A, Westelman S, Wang L, Phillips JJ, Northcott PA, Weiss WA, Schwer B. PRDM6 promotes medulloblastoma by repressing chromatin accessibility and altering gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555389. [PMID: 37693484 PMCID: PMC10491178 DOI: 10.1101/2023.08.29.555389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
SNCAIP duplication may promote Group 4 medulloblastoma via induction of PRDM6, a poorly characterized member of the PRDF1 and RIZ1 homology domain-containing (PRDM) family of transcription factors. Here, we investigated the function of PRDM6 in human hindbrain neuroepithelial stem cells and tested PRDM6 as a driver of Group 4 medulloblastoma. We report that human PRDM6 localizes predominantly to the nucleus, where it causes widespread repression of chromatin accessibility and complex alterations of gene expression patterns. Genome-wide mapping of PRDM6 binding reveals that PRDM6 binds to chromatin regions marked by histone H3 lysine 27 trimethylation that are located within, or proximal to, genes. Moreover, we show that PRDM6 expression in neuroepithelial stem cells promotes medulloblastoma. Surprisingly, medulloblastomas derived from PRDM6-expressing neuroepithelial stem cells match human Group 3, but not Group 4, medulloblastoma. We conclude that PRDM6 expression has oncogenic potential but is insufficient to drive Group 4 medulloblastoma from neuroepithelial stem cells. We propose that both PRDM6 and additional factors, such as specific cell-of-origin features, are required for Group 4 medulloblastoma. Given the lack of PRDM6 expression in normal tissues and its oncogenic potential shown here, we suggest that PRDM6 inhibition may have therapeutic value in PRDM6-expressing medulloblastomas.
Collapse
|
42
|
Vogel A, Ueberbach T, Wilken-Schmitz A, Hahnefeld L, Franck L, Weyer MP, Jungenitz T, Schmid T, Buchmann G, Freudenberg F, Brandes RP, Gurke R, Schwarzacher SW, Geisslinger G, Mittmann T, Tegeder I. Repetitive and compulsive behavior after Early-Life-Pain associated with reduced long-chain sphingolipid species. Cell Biosci 2023; 13:155. [PMID: 37635256 PMCID: PMC10463951 DOI: 10.1186/s13578-023-01106-3] [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: 04/04/2023] [Accepted: 08/13/2023] [Indexed: 08/29/2023] Open
Abstract
BACKGROUND Pain in early life may impact on development and risk of chronic pain. We developed an optogenetic Cre/loxP mouse model of "early-life-pain" (ELP) using mice with transgenic expression of channelrhodopsin-2 (ChR2) under control of the Advillin (Avil) promoter, which drives expression of transgenes predominantly in isolectin B4 positive non-peptidergic nociceptors in postnatal mice. Avil-ChR2 (Cre +) and ChR2-flfl control mice were exposed to blue light in a chamber once daily from P1-P5 together with their Cre-negative mother. RESULTS ELP caused cortical hyperexcitability at P8-9 as assessed via multi-electrode array recordings that coincided with reduced expression of synaptic genes (RNAseq) including Grin2b, neurexins, piccolo and voltage gated calcium and sodium channels. Young adult (8-16 wks) Avil-ChR2 mice presented with nociceptive hypersensitivity upon heat or mechanical stimulation, which did not resolve up until one year of age. The persistent hypersensitivy to nociceptive stimuli was reflected by increased calcium fluxes in primary sensory neurons of aged mice (1 year) upon capsaicin stimulation. Avil-ChR2 mice behaved like controls in maze tests of anxiety, social interaction, and spatial memory but IntelliCage behavioral studies revealed repetitive nosepokes and corner visits and compulsive lickings. Compulsiveness at the behavioral level was associated with a reduction of sphingomyelin species in brain and plasma lipidomic studies. Behavioral studies were done with female mice. CONCLUSION The results suggest that ELP may predispose to chronic "pain" and compulsive psychopathology in part mediated by alterations of sphingolipid metabolism, which have been previously described in the context of addiction and psychiatric diseases.
Collapse
Affiliation(s)
- Alexandra Vogel
- Institute of Clinical Pharmacology, Faculty of Medicine, Goethe-University, Frankfurt, Germany
| | - Timo Ueberbach
- Institute of Physiology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Annett Wilken-Schmitz
- Institute of Clinical Pharmacology, Faculty of Medicine, Goethe-University, Frankfurt, Germany
| | - Lisa Hahnefeld
- Institute of Clinical Pharmacology, Faculty of Medicine, Goethe-University, Frankfurt, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 60596, Frankfurt, Germany
- Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), 60596, Frankfurt, Germany
| | - Luisa Franck
- Institute of Clinical Pharmacology, Faculty of Medicine, Goethe-University, Frankfurt, Germany
| | - Marc-Philipp Weyer
- Institute of Clinical Pharmacology, Faculty of Medicine, Goethe-University, Frankfurt, Germany
| | - Tassilo Jungenitz
- Institute of Clinical Neuroanatomy, Neuroscience Center, Goethe University, Frankfurt, Germany
| | - Tobias Schmid
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University, Frankfurt, Germany
- Partner Site Frankfurt, German Cancer Consortium (DKTK), Frankfurt, Germany
| | - Giulia Buchmann
- Institute of Cardiovascular Physiology, Faculty of Medicine, Goethe-University, Frankfurt, Germany
| | - Florian Freudenberg
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, Goethe-University Hospital, Frankfurt, Germany
| | - Ralf P Brandes
- Institute of Cardiovascular Physiology, Faculty of Medicine, Goethe-University, Frankfurt, Germany
| | - Robert Gurke
- Institute of Clinical Pharmacology, Faculty of Medicine, Goethe-University, Frankfurt, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 60596, Frankfurt, Germany
- Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), 60596, Frankfurt, Germany
| | - Stephan W Schwarzacher
- Institute of Clinical Neuroanatomy, Neuroscience Center, Goethe University, Frankfurt, Germany
| | - Gerd Geisslinger
- Institute of Clinical Pharmacology, Faculty of Medicine, Goethe-University, Frankfurt, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 60596, Frankfurt, Germany
- Fraunhofer Cluster of Excellence for Immune Mediated Diseases (CIMD), 60596, Frankfurt, Germany
| | - Thomas Mittmann
- Institute of Physiology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Irmgard Tegeder
- Institute of Clinical Pharmacology, Faculty of Medicine, Goethe-University, Frankfurt, Germany.
| |
Collapse
|
43
|
Sachs S, Götz A, Finan B, Feuchtinger A, DiMarchi RD, Döring Y, Weber C, Tschöp MH, Müller TD, Hofmann SM. GIP receptor agonism improves dyslipidemia and atherosclerosis independently of body weight loss in preclinical mouse model for cardio-metabolic disease. Cardiovasc Diabetol 2023; 22:217. [PMID: 37592302 PMCID: PMC10436634 DOI: 10.1186/s12933-023-01940-2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Agonism at the receptor for the glucose-dependent insulinotropic polypeptide (GIPR) is a key component of the novel unimolecular GIPR:GLP-1R co-agonists, which are among the most promising drugs in clinical development for the treatment of obesity and type 2 diabetes. The therapeutic effect of chronic GIPR agonism to treat dyslipidemia and thus to reduce the cardiovascular disease risk independently of body weight loss has not been explored yet. METHODS After 8 weeks on western diet, LDL receptor knockout (LDLR-/-) male mice were treated with daily subcutaneous injections of long-acting acylated GIP analog (acyl-GIP; 10nmol/kg body weight) for 28 days. Body weight, food intake, whole-body composition were monitored throughout the study. Fasting blood glucose and intraperitoneal glucose tolerance test (ipGTT) were determined on day 21 of the study. Circulating lipid levels, lipoprotein profiles and atherosclerotic lesion size was assessed at the end of the study. Acyl-GIP effects on fat depots were determined by histology and transcriptomics. RESULTS Herein we found that treatment with acyl-GIP reduced dyslipidemia and atherogenesis in male LDLR-/- mice. Acyl-GIP administration resulted in smaller adipocytes within the inguinal fat depot and RNAseq analysis of the latter revealed that acyl-GIP may improve dyslipidemia by directly modulating lipid metabolism in this fat depot. CONCLUSIONS This study identified an unanticipated efficacy of chronic GIPR agonism to improve dyslipidemia and cardiovascular disease independently of body weight loss, indicating that treatment with acyl-GIP may be a novel approach to alleviate cardiometabolic disease.
Collapse
Affiliation(s)
- Stephan Sachs
- Institute for Diabetes and Regeneration, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764, Neuherberg, Germany
- Institute for Diabetes and Obesity, Division of Metabolic Diseases, Helmholtz Diabetes Center at Helmholtz Centre Munich, Munich, Germany
- Technische Universität München, 80333, Munich, Germany
| | - Anna Götz
- Institute for Diabetes and Regeneration, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764, Neuherberg, Germany
- Institute for Diabetes and Obesity, Division of Metabolic Diseases, Helmholtz Diabetes Center at Helmholtz Centre Munich, Munich, Germany
| | - Brian Finan
- Novo Nordisk Research Center Indianapolis, Indianapolis, IN, USA
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Center Munich, 85764, Neuherberg, Germany
| | | | - Yvonne Döring
- Department of Angiology, Swiss Cardiovascular Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University Munich, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-University Munich, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Matthias H Tschöp
- Institute for Diabetes and Obesity, Division of Metabolic Diseases, Helmholtz Diabetes Center at Helmholtz Centre Munich, Munich, Germany
- Technische Universität München, 80333, Munich, Germany
- German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Timo D Müller
- Institute for Diabetes and Obesity, Division of Metabolic Diseases, Helmholtz Diabetes Center at Helmholtz Centre Munich, Munich, Germany.
- German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany.
| | - Susanna M Hofmann
- Institute for Diabetes and Regeneration, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), 85764, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany.
- Department of Medicine IV, University Hospital, LMU Munich, Munich, Germany.
| |
Collapse
|
44
|
Carvalho D, Diaz-Amarilla P, Dapueto R, Santi MD, Duarte P, Savio E, Engler H, Abin-Carriquiry JA, Arredondo F. Transcriptomic Analyses of Neurotoxic Astrocytes Derived from Adult Triple Transgenic Alzheimer's Disease Mice. J Mol Neurosci 2023; 73:487-515. [PMID: 37318736 DOI: 10.1007/s12031-023-02105-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/03/2023] [Indexed: 06/16/2023]
Abstract
Neurodegenerative diseases such as Alzheimer's disease have been classically studied from a purely neuronocentric point of view. More recent evidences support the notion that other cell populations are involved in disease progression. In this sense, the possible pathogenic role of glial cells like astrocytes is increasingly being recognized. Once faced with tissue damage signals and other stimuli present in disease environments, astrocytes suffer many morphological and functional changes, a process referred as reactive astrogliosis. Studies from murine models and humans suggest that these complex and heterogeneous responses could manifest as disease-specific astrocyte phenotypes. Clear understanding of disease-associated astrocytes is a necessary step to fully disclose neurodegenerative processes, aiding in the design of new therapeutic and diagnostic strategies. In this work, we present the transcriptomics characterization of neurotoxic astrocytic cultures isolated from adult symptomatic animals of the triple transgenic mouse model of Alzheimer's disease (3xTg-AD). According to the observed profile, 3xTg-AD neurotoxic astrocytes show various reactivity features including alteration of the extracellular matrix and release of pro-inflammatory and proliferative factors that could result in harmful effects to neurons. Moreover, these alterations could be a consequence of stress responses at the endoplasmic reticulum and mitochondria as well as of concomitant metabolic adaptations. Present results support the hypothesis that adaptive changes of astrocytic function induced by a stressed microenvironment could later promote harmful astrocyte phenotypes and further accelerate or induce neurodegenerative processes.
Collapse
Affiliation(s)
- Diego Carvalho
- Departamento de Neuroquímica, Instituto de Investigaciones Biológicas Clemente Estable, 11600, Montevideo, Uruguay
| | - Pablo Diaz-Amarilla
- Área I+D Biomédica, Centro Uruguayo de Imagenología Molecular, 11600, Montevideo, Uruguay
| | - Rosina Dapueto
- Área I+D Biomédica, Centro Uruguayo de Imagenología Molecular, 11600, Montevideo, Uruguay
| | - María Daniela Santi
- Área I+D Biomédica, Centro Uruguayo de Imagenología Molecular, 11600, Montevideo, Uruguay
- College of Dentistry, Bluestone Center for Clinical Research, New York University, New York, 10010, USA
| | - Pablo Duarte
- Área I+D Biomédica, Centro Uruguayo de Imagenología Molecular, 11600, Montevideo, Uruguay
| | - Eduardo Savio
- Área I+D Biomédica, Centro Uruguayo de Imagenología Molecular, 11600, Montevideo, Uruguay
| | - Henry Engler
- Área I+D Biomédica, Centro Uruguayo de Imagenología Molecular, 11600, Montevideo, Uruguay
- Facultad de Medicina, Universidad de la República, 1800, Montevideo, Uruguay
| | - Juan A Abin-Carriquiry
- Departamento de Neuroquímica, Instituto de Investigaciones Biológicas Clemente Estable, 11600, Montevideo, Uruguay.
- Laboratorio de Biofármacos, Institut Pasteur de Montevideo, 11600, Montevideo, Uruguay.
| | - Florencia Arredondo
- Departamento de Neuroquímica, Instituto de Investigaciones Biológicas Clemente Estable, 11600, Montevideo, Uruguay.
- Área I+D Biomédica, Centro Uruguayo de Imagenología Molecular, 11600, Montevideo, Uruguay.
| |
Collapse
|
45
|
Mattiolo P, Gkountakos A, Centonze G, Bevere M, Piccoli P, Ammendola S, Pedrazzani C, Landoni L, Cingarlini S, Milella M, Milione M, Luchini C, Scarpa A, Simbolo M. Transcriptome analysis of primary sporadic neuroendocrine tumours of the intestine identified three different molecular subgroups. Pathol Res Pract 2023; 248:154674. [PMID: 37454491 DOI: 10.1016/j.prp.2023.154674] [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: 06/23/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Intestinal neuroendocrine tumours (I-NETs) represent a non-negligible entity among intestinal neoplasms, with metastatic spreading usually present at the time of diagnosis. In this context, effective molecular actionable targets are still lacking. Through transcriptome analysis, we aim at refining the molecular taxonomy of I-NETs, also providing insights towards the identification of new therapeutic vulnerabilities. MATERIALS AND METHODS A retrospective series of 38 primary sporadic, surgically-resected I-NETs were assessed for transcriptome profiling of 20,815 genes. RESULTS Transcriptome analysis detected 643 highly expressed genes. Unsupervised hierarchical clustering, differential expression analysis and gene set enriched analysis identified three different tumour clusters (CL): CL-A, CL-B, CL-C. CL-A showed the overexpression of ARGFX, BIRC8, NANOS2, and SSTR4 genes. Its most characterizing signatures were those related to cell-junctions, and activation of mTOR and WNT pathway. CL-A was also enriched in T CD8 + lymphocytes. CL-B showed the overexpression of PCSK1, QPCT, ST18, and TPH1 genes. Its most characterizing signatures were those related to adipogenesis, neuroendocrine metabolism, and splice site machinery-related processes. CL-B was also enriched in T CD4 + lymphocytes. CL-C showed the overexpression of ALB, ANG, ARG1, and HP genes. Its most characterizing signatures were complement/coagulation and xenobiotic metabolism. CL-C was also enriched in M1/2 macrophages. These CL-based differences may have therapeutic implications in refining the management of I-NET patients. At last, we described a specific gene-set for differentiating I-NET from pancreatic NET. DISCUSSION Our data represent an additional step for refining the molecular taxonomy of I-NET, identifying novel transcriptome subgroups with different biology and therapeutic opportunities.
Collapse
Affiliation(s)
- Paola Mattiolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Anastasios Gkountakos
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Giovanni Centonze
- Pathology Unit 1, Pathology and Laboratory Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Michele Bevere
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Paola Piccoli
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Serena Ammendola
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Corrado Pedrazzani
- Division of General and Hepatobiliary Surgery, Department of Surgical Sciences, Dentistry, Gynecology, and Pediatrics, University and Hospital Trust of Verona, Verona, Italy
| | - Luca Landoni
- General and Pancreatic Surgery Department, Pancreas Institute, University and Hospital Trust of Verona, Verona, Italy
| | - Sara Cingarlini
- Department of Medicine, Section of Medical Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Michele Milella
- Department of Medicine, Section of Medical Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Massimo Milione
- Pathology Unit 1, Pathology and Laboratory Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy; ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy; ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Michele Simbolo
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy.
| |
Collapse
|
46
|
Botella J, Schytz CT, Pehrson TF, Hokken R, Laugesen S, Aagaard P, Suetta C, Christensen B, Ørtenblad N, Nielsen J. Increased mitochondrial surface area and cristae density in the skeletal muscle of strength athletes. J Physiol 2023; 601:2899-2915. [PMID: 37042493 DOI: 10.1113/jp284394] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/05/2023] [Indexed: 04/13/2023] Open
Abstract
Mitochondria are the cellular organelles responsible for resynthesising the majority of ATP. In skeletal muscle, there is an increased ATP turnover during resistance exercise to sustain the energetic demands of muscle contraction. Despite this, little is known regarding the mitochondrial characteristics of chronically strength-trained individuals and any potential pathways regulating the strength-specific mitochondrial remodelling. Here, we investigated the mitochondrial structural characteristics in skeletal muscle of strength athletes and age-matched untrained controls. The mitochondrial pool in strength athletes was characterised by increased mitochondrial cristae density, decreased mitochondrial size, and increased surface-to-volume ratio, despite similar mitochondrial volume density. We also provide a fibre-type and compartment-specific assessment of mitochondria morphology in human skeletal muscle, which reveals across groups a compartment-specific influence on mitochondrial morphology that is largely independent of fibre type. Furthermore, we show that resistance exercise leads to signs of mild mitochondrial stress, without an increase in the number of damaged mitochondria. Using publicly available transcriptomic data we show that acute resistance exercise increases the expression of markers of mitochondrial biogenesis, fission and mitochondrial unfolded protein responses (UPRmt ). Further, we observed an enrichment of the UPRmt in the basal transcriptome of strength-trained individuals. Together, these findings show that strength athletes possess a unique mitochondrial remodelling, which minimises the space required for mitochondria. We propose that the concurrent activation of markers of mitochondrial biogenesis and mitochondrial remodelling pathways (fission and UPRmt ) with resistance exercise may be partially responsible for the observed mitochondrial phenotype of strength athletes. KEY POINTS: Untrained individuals and strength athletes possess comparable skeletal muscle mitochondrial volume density. In contrast, strength athletes' mitochondria are characterised by increased cristae density, decreased size and increased surface-to-volume ratio. Type I fibres have an increased number of mitochondrial profiles with minor differences in the mitochondrial morphological characteristics compared with type II fibres. The mitochondrial morphology is distinct across the subcellular compartments in both groups, with subsarcolemmal mitochondria being bigger in size when compared with intermyofibrillar. Acute resistance exercise leads to signs of mild morphological mitochondrial stress accompanied by increased gene expression of markers of mitochondrial biogenesis, fission and mitochondrial unfolded protein response (UPRmt ).
Collapse
Affiliation(s)
- Javier Botella
- Institute for Mental and Physical Health and Clinical Translation, Metabolic Research Unit, School of Medicine, Deakin University, Geelong, Australia
| | - Camilla T Schytz
- Department of Sports Science and Clinical Biomechanics, University of Southern Denmark, Odense, Denmark
| | - Thomas F Pehrson
- Department of Sports Science and Clinical Biomechanics, University of Southern Denmark, Odense, Denmark
| | - Rune Hokken
- Department of Sports Science and Clinical Biomechanics, University of Southern Denmark, Odense, Denmark
| | - Simon Laugesen
- Department of Sports Science and Clinical Biomechanics, University of Southern Denmark, Odense, Denmark
| | - Per Aagaard
- Department of Sports Science and Clinical Biomechanics, University of Southern Denmark, Odense, Denmark
| | - Charlotte Suetta
- Geriatric Research Unit, Department of Geriatric and Palliative Medicine, Copenhagen University Hospital, Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | - Britt Christensen
- Department of Endocrinology and Internal Medicine, NBG/THG, Aarhus University Hospital, Aarhus, Denmark
| | - Niels Ørtenblad
- Department of Sports Science and Clinical Biomechanics, University of Southern Denmark, Odense, Denmark
| | - Joachim Nielsen
- Department of Sports Science and Clinical Biomechanics, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
47
|
Kumsta R, Zang JCS, Hummel EM, Müller S, Moser DA, Herpertz S, Kessler H. Treatment-associated mRNA co-expression changes in monocytes of patients with posttraumatic stress disorder. Front Psychiatry 2023; 14:1181321. [PMID: 37426106 PMCID: PMC10326517 DOI: 10.3389/fpsyt.2023.1181321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/05/2023] [Indexed: 07/11/2023] Open
Abstract
PTSD is a prevalent mental disorder that results from exposure to extreme and stressful life events and comes at high costs for both the individual and society. Therapeutic treatment presents the best way to deal with PTSD-the mechanisms underlying change after treatment, however, remain poorly understood. While stress and immune associated gene expression changes have been associated with PTSD development, studies investigating treatment effects at the molecular level so far tended to focus on DNA methylation. Here we use gene-network analysis on whole-transcriptome RNA-Seq data isolated from CD14+ monocytes of female PTSD patients (N = 51) to study pre-treatment signatures of therapy response and therapy-related changes at the level of gene expression. Patients who exhibited significant symptom improvement after therapy showed higher baseline expression in two modules involved in inflammatory processes (including notable examples IL1R2 and FKBP5) and blood coagulation. After therapy, expression of an inflammatory module was increased, and expression of a wound healing module was decreased. This supports findings reporting an association between PTSD and dysregulations of the inflammatory and the hemostatic system and mark both as potentially treatment sensitive.
Collapse
Affiliation(s)
- Robert Kumsta
- Department of Genetic Psychology, Faculty of Psychology, Ruhr University Bochum, Bochum, Germany
- Department of Behavioural and Cognitive Sciences, Laboratory for Stress and Gene-Environment Interplay, University of Luxemburg, Esch-sur-Alzette, Luxemburg
| | - Johannes C. S. Zang
- Department of Genetic Psychology, Faculty of Psychology, Ruhr University Bochum, Bochum, Germany
| | - Elisabeth M. Hummel
- Department of Genetic Psychology, Faculty of Psychology, Ruhr University Bochum, Bochum, Germany
| | - Svenja Müller
- Department of Genetic Psychology, Faculty of Psychology, Ruhr University Bochum, Bochum, Germany
| | - Dirk A. Moser
- Department of Genetic Psychology, Faculty of Psychology, Ruhr University Bochum, Bochum, Germany
| | - Stephan Herpertz
- Department of Psychosomatic Medicine and Psychotherapy, LWL-University Hospital Ruhr-University Bochum, Bochum, Germany
| | - Henrik Kessler
- Department of Psychosomatic Medicine and Psychotherapy, LWL-University Hospital Ruhr-University Bochum, Bochum, Germany
- Department of Psychosomatic Medicine and Psychotherapy, Fulda Hospital, University Medicine Marburg Campus Fulda, Fulda, Germany
| |
Collapse
|
48
|
Usui-Ouchi A, Giles S, Harkins-Perry S, Mills EA, Bonelli R, Wei G, Ouchi Y, Ebihara N, Nakao S, Friedlander M, Eade KT. Integrating human iPSC-derived macrophage progenitors into retinal organoids to generate a mature retinal microglial niche. Glia 2023. [PMID: 37335016 DOI: 10.1002/glia.24428] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/21/2023]
Abstract
In the retina, microglia are resident immune cells that are essential for development and function. Retinal microglia play a central role in mediating pathological degeneration in diseases such as glaucoma, retinitis pigmentosa, age-related neurodegeneration, ischemic retinopathy, and diabetic retinopathy. Current models of mature human retinal organoids (ROs) derived from iPS cell (hiPSC) do not contain resident microglia integrated into retinal layers. Increasing cellular diversity in ROs by including resident microglia would more accurately represent the native retina and better model diseases in which microglia play a key role. In this study, we develop a new 3D in vitro tissue model of microglia-containing retinal organoids by co-culturing ROs and hiPSC-derived macrophage precursor cells (MPCs). We optimized the parameters for successful integration of MPCs into retinal organoids. We show that while in the ROs, MPCs migrate to the equivalent of the outer plexiform layer where retinal microglia cells reside in healthy retinal tissue. While there, they develop a mature morphology characterized by small cell bodies and long branching processes which is only observed in vivo. During this maturation process these MPCs cycle through an activated phase followed by a stable mature microglial phase as seen by the down regulation of pro-inflammatory cytokines and upregulation of anti-inflammatory cytokines. Finally, we characterized mature ROs with integrated MPCs using RNAseq showing an enrichment of cell-type specific microglia markers. We propose that this co-culture system may be useful for understanding the pathogenesis of retinal diseases involving retinal microglia and for drug discovery directly in human tissue.
Collapse
Affiliation(s)
- Ayumi Usui-Ouchi
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
- Department of Ophthalmology, Juntendo University Urayasu Hospital, Urayasu, Japan
| | - Sarah Giles
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
- The Lowy Medical Research Institute, La Jolla, California, USA
| | - Sarah Harkins-Perry
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
- The Lowy Medical Research Institute, La Jolla, California, USA
| | | | - Roberto Bonelli
- The Lowy Medical Research Institute, La Jolla, California, USA
| | - Guoqin Wei
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Yasuo Ouchi
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
- Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Nobuyuki Ebihara
- Department of Ophthalmology, Juntendo University Urayasu Hospital, Urayasu, Japan
| | - Shintaro Nakao
- Department of Ophthalmology, Juntendo University, Tokyo, Japan
| | - Martin Friedlander
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
- The Lowy Medical Research Institute, La Jolla, California, USA
| | - Kevin T Eade
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
- The Lowy Medical Research Institute, La Jolla, California, USA
| |
Collapse
|
49
|
Almeida CF, Robriquet F, Vetter TA, Huang N, Neinast R, Hernandez-Rosario L, Rajakumar D, Arnold WD, McBride KL, Flanigan KM, Weiss RB, Wein N. Promising AAV.U7snRNAs vectors targeting DMPK improve DM1 hallmarks in patient-derived cell lines. Front Cell Dev Biol 2023; 11:1181040. [PMID: 37397246 PMCID: PMC10309041 DOI: 10.3389/fcell.2023.1181040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/18/2023] [Indexed: 07/04/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is the most common form of muscular dystrophy in adults and affects mainly the skeletal muscle, heart, and brain. DM1 is caused by a CTG repeat expansion in the 3'UTR region of the DMPK gene that sequesters muscleblind-like proteins, blocking their splicing activity and forming nuclear RNA foci. Consequently, many genes have their splicing reversed to a fetal pattern. There is no treatment for DM1, but several approaches have been explored, including antisense oligonucleotides (ASOs) aiming to knock down DMPK expression or bind to the CTGs expansion. ASOs were shown to reduce RNA foci and restore the splicing pattern. However, ASOs have several limitations and although being safe treated DM1 patients did not demonstrate improvement in a human clinical trial. AAV-based gene therapies have the potential to overcome such limitations, providing longer and more stable expression of antisense sequences. In the present study, we designed different antisense sequences targeting exons 5 or 8 of DMPK and the CTG repeat tract aiming to knock down DMPK expression or promote steric hindrance, respectively. The antisense sequences were inserted in U7snRNAs, which were then vectorized in AAV8 particles. Patient-derived myoblasts treated with AAV8. U7snRNAs showed a significant reduction in the number of RNA foci and re-localization of muscle-blind protein. RNA-seq analysis revealed a global splicing correction in different patient-cell lines, without alteration in DMPK expression.
Collapse
Affiliation(s)
- Camila F. Almeida
- Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Florence Robriquet
- Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Tatyana A. Vetter
- Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Nianyuan Huang
- Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH, United States
| | - Reid Neinast
- Center for Cardiovascular Research, Nationwide Children’s Hospital, Columbus, OH, United States
| | | | - Dhanarajan Rajakumar
- Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH, United States
| | - W. David Arnold
- Department of Neurology, The Ohio State University, Columbus, OH, United States
- Department of Physical Medicine and Rehabilitation, University of Missouri School of Medicine, Columbia, MO, United States
| | - Kim L. McBride
- Center for Cardiovascular Research, Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada
| | - Kevin M. Flanigan
- Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Neurology, The Ohio State University, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States
| | - Robert B. Weiss
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Nicolas Wein
- Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH, United States
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States
| |
Collapse
|
50
|
McKee CA, Polino AJ, King MW, Musiek ES. Circadian clock protein BMAL1 broadly influences autophagy and endolysosomal function in astrocytes. Proc Natl Acad Sci U S A 2023; 120:e2220551120. [PMID: 37155839 PMCID: PMC10194014 DOI: 10.1073/pnas.2220551120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
An emerging role for the circadian clock in autophagy and lysosome function has opened new avenues for exploration in the field of neurodegeneration. The daily rhythms of circadian clock proteins may coordinate gene expression programs involved not only in daily rhythms but in many cellular processes. In the brain, astrocytes are critical for sensing and responding to extracellular cues to support neurons. The core clock protein BMAL1 serves as the primary positive circadian transcriptional regulator and its depletion in astrocytes not only disrupts circadian function but also leads to a unique cell-autonomous activation phenotype. We report here that astrocyte-specific deletion of Bmal1 influences endolysosome function, autophagy, and protein degradation dynamics. In vitro, Bmal1-deficient astrocytes exhibit increased endocytosis, lysosome-dependent protein cleavage, and accumulation of LAMP1- and RAB7-positive organelles. In vivo, astrocyte-specific Bmal1 knockout (aKO) brains show accumulation of autophagosome-like structures within astrocytes by electron microscopy. Transcriptional analysis of isolated astrocytes from young and aged Bmal1 aKO mice indicates broad dysregulation of pathways involved in lysosome function which occur independently of TFEB activation. Since a clear link has been established between neurodegeneration and endolysosome dysfunction over the course of aging, this work implicates BMAL1 as a key regulator of these crucial astrocyte functions in health and disease.
Collapse
Affiliation(s)
- Celia A. McKee
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO63110
- Center on Biological Rhythms and Sleep, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Alexander J. Polino
- Department of Cell Biology and Physiology, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Melvin W. King
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO63110
- Center on Biological Rhythms and Sleep, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Erik S. Musiek
- Department of Neurology, Washington University School of Medicine in St. Louis, St. Louis, MO63110
- Center on Biological Rhythms and Sleep, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| |
Collapse
|