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Kuczyńska A, Michałek M, Ogrodowicz P, Kempa M, Witaszak N, Dziurka M, Gruszka D, Daszkowska-Golec A, Szarejko I, Krajewski P, Mikołajczak K. Drought-induced molecular changes in crown of various barley phytohormone mutants. PLANT SIGNALING & BEHAVIOR 2024; 19:2371693. [PMID: 38923879 PMCID: PMC11210921 DOI: 10.1080/15592324.2024.2371693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
One of the main signal transduction pathways that modulate plant growth and stress responses, including drought, is the action of phytohormones. Recent advances in omics approaches have facilitated the exploration of plant genomes. However, the molecular mechanisms underlying the response in the crown of barley, which plays an essential role in plant performance under stress conditions and regeneration after stress treatment, remain largely unclear. The objective of the present study was the elucidation of drought-induced molecular reactions in the crowns of different barley phytohormone mutants. We verified the hypothesis that defects of gibberellins, brassinosteroids, and strigolactones action affect the transcriptomic, proteomic, and hormonal response of barley crown to the transitory drought influencing plant development under stress. Moreover, we assumed that due to the strong connection between strigolactones and branching the hvdwarf14.d mutant, with dysfunctional receptor of strigolactones, manifests the most abundant alternations in crowns and phenotype under drought. Finally, we expected to identify components underlying the core response to drought which are independent of the genetic background. Large-scale analyses were conducted using gibberellins-biosynthesis, brassinosteroids-signaling, and strigolactones-signaling mutants, as well as reference genotypes. Detailed phenotypic evaluation was also conducted. The obtained results clearly demonstrated that hormonal disorders caused by mutations in the HvGA20ox2, HvBRI1, and HvD14 genes affected the multifaceted reaction of crowns to drought, although the expression of these genes was not induced by stress. The study further detected not only genes and proteins that were involved in the drought response and reacted specifically in mutants compared to the reaction of reference genotypes and vice versa, but also the candidates that may underlie the genotype-universal stress response. Furthermore, candidate genes involved in phytohormonal interactions during the drought response were identified. We also found that the interplay between hormones, especially gibberellins and auxins, as well as strigolactones and cytokinins may be associated with the regulation of branching in crowns exposed to drought. Overall, the present study provides novel insights into the molecular drought-induced responses that occur in barley crowns.
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Affiliation(s)
- Anetta Kuczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Martyna Michałek
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Piotr Ogrodowicz
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Michał Kempa
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Natalia Witaszak
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Michał Dziurka
- Faculty of Natural Sciences, The Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Krakow, Poland
| | - Damian Gruszka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Agata Daszkowska-Golec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Iwona Szarejko
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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Sahrhage M, Paul NB, Beißbarth T, Haubrock M. The importance of DNA sequence for nucleosome positioning in transcriptional regulation. Life Sci Alliance 2024; 7:e202302380. [PMID: 38830772 PMCID: PMC11147951 DOI: 10.26508/lsa.202302380] [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: 09/18/2023] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
Nucleosome positioning is a key factor for transcriptional regulation. Nucleosomes regulate the dynamic accessibility of chromatin and interact with the transcription machinery at every stage. Influences to steer nucleosome positioning are diverse, and the according importance of the DNA sequence in contrast to active chromatin remodeling has been the subject of long discussion. In this study, we evaluate the functional role of DNA sequence for all major elements along the process of transcription. We developed a random forest classifier based on local DNA structure that assesses the sequence-intrinsic support for nucleosome positioning. On this basis, we created a simple data resource that we applied genome-wide to the human genome. In our comprehensive analysis, we found a special role of DNA in mediating the competition of nucleosomes with cis-regulatory elements, in enabling steady transcription, for positioning of stable nucleosomes in exons, and for repelling nucleosomes during transcription termination. In contrast, we relate these findings to concurrent processes that generate strongly positioned nucleosomes in vivo that are not mediated by sequence, such as energy-dependent remodeling of chromatin.
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Affiliation(s)
- Malte Sahrhage
- Department of Medical Bioinformatics, University Medical Center, Göttingen, Germany
| | - Niels Benjamin Paul
- Department of Medical Bioinformatics, University Medical Center, Göttingen, Germany
- Department of Cardiology and Pneumology, University Medical Center, Göttingen, Germany
| | - Tim Beißbarth
- Department of Medical Bioinformatics, University Medical Center, Göttingen, Germany
| | - Martin Haubrock
- Department of Medical Bioinformatics, University Medical Center, Göttingen, Germany
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3
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Giraudi PJ, Laraño AA, Monego SD, Pravisani R, Bonazza D, Gondolesi G, Tiribelli C, Baralle F, Baccarani U, Licastro D. Genome-wide DNA methylation and transcriptomic analysis of liver tissues subjected to early ischemia/reperfusion injury upon human liver transplantation. Ann Hepatol 2024; 29:101506. [PMID: 38710471 DOI: 10.1016/j.aohep.2024.101506] [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: 02/23/2024] [Revised: 03/11/2024] [Accepted: 03/27/2024] [Indexed: 05/08/2024]
Abstract
INTRODUCTION AND OBJECTIVES Epigenetic changes represent a mechanism connecting external stresses with long-term modifications of gene expression programs. In solid organ transplantation, ischemia-reperfusion injury (IRI) appears to induce epigenomic changes in the graft, although the currently available data are extremely limited. The present study aimed to characterize variations in DNA methylation and their effects on the transcriptome in liver transplantation from brain-dead donors. PATIENTS AND METHODS 12 liver grafts were evaluated through serial biopsies at different timings in the procurement-transplantation process: T0 (warm procurement, in donor), T1 (bench surgery), and T2 (after reperfusion, in recipient). DNA methylation (DNAm) and transcriptome profiles of biopsies were analyzed using microarrays and RNAseq. RESULTS Significant variations in DNAm were identified, particularly between T2 and T0. Functional enrichment of the best 1000 ranked differentially methylated promoters demonstrated that 387 hypermethylated and 613 hypomethylated promoters were involved in spliceosomal assembly and response to biotic stimuli, and inflammatory immune responses, respectively. At the transcriptome level, T2 vs. T0 showed an upregulation of 337 and downregulation of 61 genes, collectively involved in TNF-α, NFKB, and interleukin signaling. Cell enrichment analysis individuates macrophages, monocytes, and neutrophils as the most significant tissue-cell type in the response. CONCLUSIONS In the process of liver graft procurement-transplantation, IRI induces significant epigenetic changes that primarily act on the signaling pathways of inflammatory responses dependent on TNF-α, NFKB, and interleukins. Our DNAm datasets are the early IRI methylome literature and will serve as a launch point for studying the impact of epigenetic modification in IRI.
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Affiliation(s)
- Pablo J Giraudi
- Metabolic Liver Disease Unit, Fondazione Italiana Fegato, Trieste, Italy.
| | - Allen A Laraño
- Metabolic Liver Disease Unit, Fondazione Italiana Fegato, Trieste, Italy; Research Institute for Tropical Medicine, Department of Health, Muntinlupa City, Philippines
| | | | - Riccardo Pravisani
- Liver-Kidney Transplant Unit, Department of Medicine, University of Udine, Italy
| | - Deborah Bonazza
- Anatomia ed Istologia Patologica, Cattinara Hospital, ASUGI, Trieste, Italy
| | - Gabriel Gondolesi
- Instituto de Medicina Traslacional, Trasplante y Bioingeniería, Universidad Favaloro, Buenos Aires, Argentina
| | - Claudio Tiribelli
- Metabolic Liver Disease Unit, Fondazione Italiana Fegato, Trieste, Italy
| | - Francisco Baralle
- Metabolic Liver Disease Unit, Fondazione Italiana Fegato, Trieste, Italy
| | - Umberto Baccarani
- Liver-Kidney Transplant Unit, Department of Medicine, University of Udine, Italy
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Lorgen-Ritchie M, Chalmers L, Clarkson M, Taylor JF, MacKenzie S, Migaud H, Martin SAM. Impact of freshwater rearing history on Atlantic salmon gill response to viral stimulation post seawater transfer. FISH & SHELLFISH IMMUNOLOGY 2024; 150:109653. [PMID: 38801843 DOI: 10.1016/j.fsi.2024.109653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 05/29/2024]
Abstract
Land-based recirculating aquaculture systems (RAS) have risen in prevalence in recent years for Atlantic salmon production, enabling intensive production which allows increased growth and environmental control, but also having the potential for reducing water use and eutrophication. The Atlantic salmon has an anadromous life history with juvenile stages in freshwater (FW) and on-growing in seawater (SW), enabled by a transformational process known as smoltification. The timing of smoltification and transfer of smolts from FW to SW is critical under commercial production with high mortalities during this period. The impact of FW rearing system on immune function following seawater transfer (SWT) is not well understood. In this study parr were raised in either RAS or a traditional open-LOCH system until smolting and then transferred to a common marine environment. Two-weeks post-SWT fish were immune stimulated with a viral mimic (poly I:C) for 24 h to assess the ability to mount an antiviral immune response, assessed by whole transcriptome analysis of gill tissue, an important immune organ in fish. We show that unstimulated smolts reared in the LOCH had higher immune gene expression than those reared in RAS as determined by functional analysis. However, following stimulation, smolts reared in the RAS mounted a greater magnitude of response with a suite of immune genes displaying higher fold induction of transcription compared to LOCH reared smolts. We suggest RAS smolts have a lower steady state immune-associated transcriptome likely due to an unvarying environment, in terms of environmental factors and lack of exposure to pathogens, which shows a compensatory mechanism following stimulation allowing immune 'catch-up' with those reared in the LOCH. Alternatively, the RAS fish are experiencing an excessive response to the immune stimulation.
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Affiliation(s)
- Marlene Lorgen-Ritchie
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Lynn Chalmers
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Michael Clarkson
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - John F Taylor
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Simon MacKenzie
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Herve Migaud
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK.
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Díez AR, Szakonyi D, Lozano-Juste J, Duque P. Alternative splicing as a driver of natural variation in abscisic acid response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:9-27. [PMID: 38659400 DOI: 10.1111/tpj.16773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 04/01/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
Abscisic acid (ABA) is a crucial player in plant responses to the environment. It accumulates under stress, activating downstream signaling to implement molecular responses that restore homeostasis. Natural variance in ABA sensitivity remains barely understood, and the ABA pathway has been mainly studied at the transcriptional level, despite evidence that posttranscriptional regulation, namely, via alternative splicing, contributes to plant stress tolerance. Here, we identified the Arabidopsis accession Kn-0 as less sensitive to ABA than the reference Col-0, as shown by reduced effects of the hormone on seedling establishment, root branching, and stomatal closure, as well as by decreased induction of ABA marker genes. An in-depth comparative transcriptome analysis of the ABA response in the two variants revealed lower expression changes and fewer genes affected for the least ABA-sensitive ecotype. Notably, Kn-0 exhibited reduced levels of the ABA-signaling SnRK2 protein kinases and lower basal expression of ABA-reactivation genes, consistent with our finding that Kn-0 contains less endogenous ABA than Col-0. ABA also markedly affected alternative splicing, primarily intron retention, with Kn-0 being less responsive regarding both the number and magnitude of alternative splicing events, particularly exon skipping. We find that alternative splicing introduces a more ecotype-specific layer of ABA regulation and identify ABA-responsive splicing changes in key ABA pathway regulators that provide a functional and mechanistic link to the differential sensitivity of the two ecotypes. Our results offer new insight into the natural variation of ABA responses and corroborate a key role for alternative splicing in implementing ABA-mediated stress responses.
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Affiliation(s)
- Alba R Díez
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
| | - Dóra Szakonyi
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV), Consejo Superior de Investigaciones Científicas (CSIC), 46022, Valencia, Spain
| | - Paula Duque
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
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Bell I, Khan H, Stutt N, Horn M, Hydzik T, Lum W, Rea V, Clapham E, Hoeg L, Van Raay TJ. Nkd1 functions downstream of Axin2 to attenuate Wnt signaling. Mol Biol Cell 2024; 35:ar93. [PMID: 38656801 DOI: 10.1091/mbc.e24-02-0059-t] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
Wnt signaling is a crucial developmental pathway involved in early development as well as stem-cell maintenance in adults and its misregulation leads to numerous diseases. Thus, understanding the regulation of this pathway becomes vitally important. Axin2 and Nkd1 are widely utilized negative feedback regulators in Wnt signaling where Axin2 functions to destabilize cytoplasmic β-catenin, and Nkd1 functions to inhibit the nuclear localization of β-catenin. Here, we set out to further understand how Axin2 and Nkd1 regulate Wnt signaling by creating axin2gh1/gh1, nkd1gh2/gh2 single mutants and axin2gh1/gh1;nkd1gh2/gh2 double mutant zebrafish using sgRNA/Cas9. All three Wnt regulator mutants were viable and had impaired heart looping, neuromast migration defects, and behavior abnormalities in common, but there were no signs of synergy in the axin2gh1/gh1;nkd1gh2/gh2 double mutants. Further, Wnt target gene expression by qRT-PCR and RNA-seq, and protein expression by mass spectrometry demonstrated that the double axin2gh1/gh1;nkd1gh2/gh2 mutant resembled the nkd1gh2/gh2 phenotype demonstrating that Nkd1 functions downstream of Axin2. In support of this, the data further demonstrates that Axin2 uniquely alters the properties of β-catenin-dependent transcription having novel readouts of Wnt activity compared with nkd1gh2/gh2 or the axin2gh1/gh1;nkd1gh2/gh2 double mutant. We also investigated the sensitivity of the Wnt regulator mutants to exacerbated Wnt signaling, where the single mutants displayed characteristic heightened Wnt sensitivity, resulting in an eyeless phenotype. Surprisingly, this phenotype was rescued in the double mutant, where we speculate that cross-talk between Wnt/β-catenin and Wnt/Planar Cell Polarity pathways could lead to altered Wnt signaling in some scenarios. Collectively, the data emphasizes both the commonality and the complexity in the feedback regulation of Wnt signaling.
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Affiliation(s)
- Ian Bell
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Haider Khan
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Nathan Stutt
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Matthew Horn
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Teesha Hydzik
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Whitney Lum
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Victoria Rea
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Emma Clapham
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
| | - Lisa Hoeg
- Department of Bioinformatics, University of Guelph, Guelph, Ontario, N1G 2W1 Canada
| | - Terence J Van Raay
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G 2W1 Ontario, Canada
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7
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Liao H, Lu D, Reisinger SN, Kleeman EA, van de Garde N, Gubert C, Hannan AJ. Mimicking bacterial infection in male mice changes sperm small RNA profiles and multigenerationally alters offspring behavior and physiology. Brain Behav Immun 2024; 119:520-538. [PMID: 38636562 DOI: 10.1016/j.bbi.2024.04.017] [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: 12/21/2023] [Revised: 03/22/2024] [Accepted: 04/16/2024] [Indexed: 04/20/2024] Open
Abstract
Paternal pre-conceptual exposures, including stress, diet, substance abuse, parasite infection, and viral immune activation via Poly I:C, have been reported to influence the brains and behavior of offspring through sperm epigenetic changes. However, the effects of paternal (F0) pre-conceptual exposure to bacterial-induced immune activation on the behavior and physiology of F1 and F2 generations remain unexplored. We examined this using C57BL/6J mice. Eight-week-old males (F0) received a single intraperitoneal injection of the bacterial mimetic lipopolysaccharide (LPS: 5 mg/kg) or 0.9 % saline (vehicle control) before mating with naïve females at four weeks post-injection. Comprehensive behavioral assessments were conducted to investigate anxiety, social behaviors, depressive-like behaviors and cognition in both the F1 and F2 generations within the age range of 8 to 14 weeks. Results demonstrated that only female offspring of LPS-exposed fathers exhibited reduced anxiety levels in the light/dark box, large open field, and novelty-suppressed feeding test. These F1 female offspring also exhibited heightened sociability in the 3-chambered social interaction test and a reduced preference for saccharin in the saccharin preference test. Additionally, the F1 male offspring of LPS-challenged males demonstrated an increased total distance traveled in the light/dark box and a longer distance covered in the light zone. They also exhibited diminished preference for social novelty in the 3-chambered social interaction test and an elevated novel arm preference index in the Y-maze. In the F2 generation, male descendants of LPS-treated fathers showed reduced latency to feed in the novelty-suppressed feeding test. Additionally, the F2 generation of LPS-challenged fathers, but not the F1 generation, displayed enhanced immune response in both sexes after an acute LPS immune challenge (5 mg/kg). Analysis of sperm small noncoding RNA profiles from LPS-treated F0 mice revealed significant changes at 4 weeks after administration of LPS. These changes included three microRNAs, eight PIWI-interacting RNAs, and two transfer RNAs, exhibiting significant upregulation (mmu-miR-146a-5p, mmu-piR-27082 and mmu-piR-29102) or downregulation (mmu-miR-5110, mmu-miR-467e-3p, mmu-piR-22583, mmu-piR-23548, mmu-piR-36341, mmu-piR-50293, mmu-piR-16583, mmu-piR-36507, Mus_musculus_tRNA-Ile-AAT-2-1 and Mus_musculus_tRNA-Tyr-GTA-1-1). Additionally, we detected 52 upregulated small noncoding RNAs (including 9 miRNAs, 41 piRNAs, and 2 tRNAs) and 7 downregulated small noncoding RNAs (3 miRNAs, 3 piRNAs, and 1 tRNA) in the sperm of F1 offspring from LPS-treated males. These findings provide compelling evidence for the involvement of epigenetic mechanisms in the modulation of brain function and immunity, and associated behavioral and immunological traits, across generations, in response to bacterial infection.
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Affiliation(s)
- Huan Liao
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia.
| | - Da Lu
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Sonali N Reisinger
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Elizabeth A Kleeman
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Nicholas van de Garde
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Carolina Gubert
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Anthony J Hannan
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia; Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia.
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Rödel A, Weig I, Tiedemann S, Schwartz U, Längst G, Moehle C, Grasser M, Grasser KD. Arabidopsis mRNA export factor MOS11: molecular interactions and role in abiotic stress responses. THE NEW PHYTOLOGIST 2024; 243:180-194. [PMID: 38650347 DOI: 10.1111/nph.19773] [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: 11/20/2023] [Accepted: 04/01/2024] [Indexed: 04/25/2024]
Abstract
Transcription and export (TREX) is a multi-subunit complex that links synthesis, processing and export of mRNAs. It interacts with the RNA helicase UAP56 and export factors such as MOS11 and ALYs to facilitate nucleocytosolic transport of mRNAs. Plant MOS11 is a conserved, but sparsely researched RNA-binding export factor, related to yeast Tho1 and mammalian CIP29/SARNP. Using biochemical approaches, the domains of Arabidopsis thaliana MOS11 required for interaction with UAP56 and RNA-binding were identified. Further analyses revealed marked genetic interactions between MOS11 and ALY genes. Cell fractionation in combination with transcript profiling demonstrated that MOS11 is required for export of a subset of mRNAs that are shorter and more GC-rich than MOS11-independent transcripts. The central α-helical domain of MOS11 proved essential for physical interaction with UAP56 and for RNA-binding. MOS11 is involved in the nucleocytosolic transport of mRNAs that are upregulated under stress conditions and accordingly mos11 mutant plants turned out to be sensitive to elevated NaCl concentrations and heat stress. Collectively, our analyses identify functional interaction domains of MOS11. In addition, the results establish that mRNA export is critically involved in the plant response to stress conditions and that MOS11 plays a prominent role at this.
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Affiliation(s)
- Amelie Rödel
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Ina Weig
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Sophie Tiedemann
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Uwe Schwartz
- NGS Analysis Center, Biology and Pre-Clinical Medicine, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Gernot Längst
- Institute for Biochemistry III, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Christoph Moehle
- Center of Excellence for Fluorescent Bioanalytics (KFB), University of Regensburg, Am Biopark 9, D-93053, Regensburg, Germany
| | - Marion Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
| | - Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Center, University of Regensburg, Universitätsstr. 31, D-93053, Regensburg, Germany
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Mehrotra P, Maschalidi S, Boeckaerts L, Maueröder C, Tixeira R, Pinney J, Burgoa Cardás J, Sukhov V, Incik Y, Anderson CJ, Hu B, Keçeli BN, Goncalves A, Vande Walle L, Van Opdenbosch N, Sergushichev A, Hoste E, Jain U, Lamkanfi M, Ravichandran KS. Oxylipins and metabolites from pyroptotic cells act as promoters of tissue repair. Nature 2024:10.1038/s41586-024-07585-9. [PMID: 38926576 DOI: 10.1038/s41586-024-07585-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 05/17/2024] [Indexed: 06/28/2024]
Abstract
Pyroptosis is a lytic cell death mode that helps limit the spread of infections and is also linked to pathology in sterile inflammatory diseases and autoimmune diseases1-4. During pyroptosis, inflammasome activation and the engagement of caspase-1 lead to cell death, along with the maturation and secretion of the inflammatory cytokine interleukin-1β (IL-1β). The dominant effect of IL-1β in promoting tissue inflammation has clouded the potential influence of other factors released from pyroptotic cells. Here, using a system in which macrophages are induced to undergo pyroptosis without IL-1β or IL-1α release (denoted Pyro-1), we identify unexpected beneficial effects of the Pyro-1 secretome. First, we noted that the Pyro-1 supernatants upregulated gene signatures linked to migration, cellular proliferation and wound healing. Consistent with this gene signature, Pyro-1 supernatants boosted migration of primary fibroblasts and macrophages, and promoted faster wound closure in vitro and improved tissue repair in vivo. In mechanistic studies, lipidomics and metabolomics of the Pyro-1 supernatants identified the presence of both oxylipins and metabolites, linking them to pro-wound-healing effects. Focusing specifically on the oxylipin prostaglandin E2 (PGE2), we find that its synthesis is induced de novo during pyroptosis, downstream of caspase-1 activation and cyclooxygenase-2 activity; further, PGE2 synthesis occurs late in pyroptosis, with its release dependent on gasdermin D pores opened during pyroptosis. As for the pyroptotic metabolites, they link to immune cell infiltration into the wounds, and polarization to CD301+ macrophages. Collectively, these data advance the concept that the pyroptotic secretome possesses oxylipins and metabolites with tissue repair properties that may be harnessed therapeutically.
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Affiliation(s)
- Parul Mehrotra
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
- KSBS, Indian Institute of Technology, New Delhi, India.
| | - Sophia Maschalidi
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Laura Boeckaerts
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Christian Maueröder
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Rochelle Tixeira
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | - Javier Burgoa Cardás
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Vladimir Sukhov
- ITMO University, St Petersburg, Russia
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Yunus Incik
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Christopher J Anderson
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Bing Hu
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Burcu N Keçeli
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | | | - Nina Van Opdenbosch
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Alexey Sergushichev
- ITMO University, St Petersburg, Russia
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Esther Hoste
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Umang Jain
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Mohamed Lamkanfi
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Kodi S Ravichandran
- VIB-UGent Center for Inflammation Research, Ghent, Belgium.
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
- University of Virginia, Charlottesville, VA, USA.
- Division of Immunobiology, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
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10
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Boukas L, Luperchio TR, Razi A, Hansen KD, Bjornsson HT. Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice. Genome Res 2024; 34:696-710. [PMID: 38702196 PMCID: PMC11216309 DOI: 10.1101/gr.278416.123] [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: 08/17/2023] [Accepted: 04/15/2024] [Indexed: 05/06/2024]
Abstract
Many Mendelian developmental disorders caused by coding variants in epigenetic regulators have now been discovered. Epigenetic regulators are broadly expressed, and each of these disorders typically shows phenotypic manifestations from many different organ systems. An open question is whether the chromatin disruption-the root of the pathogenesis-is similar in the different disease-relevant cell types. This is possible in principle, because all these cell types are subject to effects from the same causative gene, which has the same kind of function (e.g., methylates histones) and is disrupted by the same germline variant. We focus on mouse models for Kabuki syndrome types 1 and 2 and find that the chromatin accessibility changes in neurons are mostly distinct from changes in B or T cells. This is not because the neuronal accessibility changes occur at regulatory elements that are only active in neurons. Neurons, but not B or T cells, show preferential chromatin disruption at CpG islands and at regulatory elements linked to aging. A sensitive analysis reveals that regulatory elements disrupted in B/T cells do show chromatin accessibility changes in neurons, but these are very subtle and of uncertain functional significance. Finally, we are able to identify a small set of regulatory elements disrupted in all three cell types. Our findings reveal the cellular-context-specific effect of variants in epigenetic regulators and suggest that blood-derived episignatures, although useful diagnostically, may not be well suited for understanding the mechanistic basis of neurodevelopment in Mendelian disorders of the epigenetic machinery.
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Affiliation(s)
- Leandros Boukas
- Department of Pediatrics, Children's National Hospital, Washington, DC 20010, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Teresa Romeo Luperchio
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Afrooz Razi
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Kasper D Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21218, USA
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Faculty of Medicine, University of Iceland, 101 Reykjavík, Iceland
- Landspitali University Hospital, 101 Reykjavík, Iceland
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11
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Eriksson ANM, Dubiel J, Alcaraz AJ, Doering JA, Wiseman S. Far from Their Origins: A Transcriptomic Investigation on How 2,4-Di-tert-butyl-6-(5-chloro-2H-benzotriazol-2-yl) Phenol Affects Rainbow Trout Alevins. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2024. [PMID: 38923588 DOI: 10.1002/etc.5943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/08/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
Benzotriazole ultraviolet stabilizers (BUVSs) are a group of widely used chemicals added to a variety of consumer (e.g., plastics) and industrial (e.g., metal coating) goods. Although detected globally as an environmentally persistent pollutant, BUVSs have received relatively little toxicological attention and only recently have been acknowledged to affect development and the endocrine system in vivo. In our previous study, altered behavior, indicative of potential neurotoxicity, was observed among rainbow trout alevins (day 14 posthatching) that were microinjected as embryos with a single environmentally relevant dose of 2,4-di-tert-butyl-6-(5-chloro-2H-benzotriazol-2-yl) phenol (UV-327). In the present follow-up study, we performed whole-transcriptome profiling (RNA sequencing) of newly hatched alevins from the same batch. The primary aim was to identify biomarkers related to behavior and neurology. Dose-specifically, 1 to 176 differentially expressed genes (DEGs) were identified. In the group presenting altered behavior (273.4 ng g-1), 176 DEGs were identified, yet only a fraction was related to neurological functions, including water, calcium, and potassium homeostasis; acetylcholine transmission and signaling; as well insulin and energy metabolism. The second objective was to estimate the transcriptomic point of departure (tPOD) and assess if point estimate(s) are protective of altered behavior. A tPOD was established at 35 to 94 ng UV-327 g-1 egg, making this tPOD protective of behavioral alterations. Holistically, these transcriptomic alterations provide a foundation for future research on how BUVSs can influence rainbow trout alevin development, while providing support to the hypothesis that UV-327 can influence neurogenesis and subsequent behavioral endpoints. The exact structural and functional changes caused by embryonic exposure to UV-327 remain enigmatic and will require extensive investigation before being deciphered and understood toxicologically. Environ Toxicol Chem 2024;00:1-12. © 2024 The Author(s). Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
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Affiliation(s)
- Andreas N M Eriksson
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Justin Dubiel
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Alper James Alcaraz
- National Institute of Environmental Health Sciences, Bethesda, Maryland, USA
| | - Jon A Doering
- Department of Environmental Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Steve Wiseman
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
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12
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Funaya S, Takahashi Y, Suzuki MG, Suzuki Y, Aoki F. H3.1/3.2 regulate the initial progression of the gene expression program. Nucleic Acids Res 2024; 52:6158-6170. [PMID: 38567720 PMCID: PMC11194095 DOI: 10.1093/nar/gkae214] [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: 11/24/2023] [Revised: 02/07/2024] [Accepted: 03/13/2024] [Indexed: 06/25/2024] Open
Abstract
In mice, transcription from the zygotic genome is initiated at the mid-one-cell stage, and occurs promiscuously in many areas of the genome, including intergenic regions. Regulated transcription from selected genes is established during the two-cell stage. This dramatic change in the gene expression pattern marks the initiation of the gene expression program and is essential for early development. We investigated the involvement of the histone variants H3.1/3.2 in the regulation of changes in gene expression pattern during the two-cell stage. Immunocytochemistry analysis showed low nuclear deposition of H3.1/3.2 in the one-cell stage, followed by a rapid increase in the late two-cell stage. Where chromatin structure is normally closed between the one- and two-cell stages, it remained open until the late two-cell stage when H3.1/3.2 were knocked down by small interfering RNA. Hi-C analysis showed that the formation of the topologically associating domain was disrupted in H3.1/3.2 knockdown (KD) embryos. Promiscuous transcription was also maintained in the late two-cell stage in H3.1/3.2 KD embryos. These results demonstrate that H3.1/3.2 are involved in the initial process of the gene expression program after fertilization, through the formation of a closed chromatin structure to execute regulated gene expression during the two-cell stage.
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Affiliation(s)
- Satoshi Funaya
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Yusuke Takahashi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Masataka G Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Fugaku Aoki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
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13
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Li K, Shu D, Li H, Lan A, Zhang W, Tan Z, Huang M, Tomasi ML, Jin A, Yu H, Shen M, Liu S. SMAD4 depletion contributes to endocrine resistance by integrating ER and ERBB signaling in HR + HER2- breast cancer. Cell Death Dis 2024; 15:444. [PMID: 38914552 PMCID: PMC11196642 DOI: 10.1038/s41419-024-06838-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 06/26/2024]
Abstract
Endocrine resistance poses a significant clinical challenge for patients with hormone receptor-positive and human epithelial growth factor receptor 2-negative (HR + HER2-) breast cancer. Dysregulation of estrogen receptor (ER) and ERBB signaling pathways is implicated in resistance development; however, the integration of these pathways remains unclear. While SMAD4 is known to play diverse roles in tumorigenesis, its involvement in endocrine resistance is poorly understood. Here, we investigate the role of SMAD4 in acquired endocrine resistance in HR + HER2- breast cancer. Genome-wide CRISPR screening identifies SMAD4 as a regulator of 4-hydroxytamoxifen (OHT) sensitivity in T47D cells. Clinical data analysis reveals downregulated SMAD4 expression in breast cancer tissues, correlating with poor prognosis. Following endocrine therapy, SMAD4 expression is further suppressed. Functional studies demonstrate that SMAD4 depletion induces endocrine resistance in vitro and in vivo by enhancing ER and ERBB signaling. Concomitant inhibition of ER and ERBB signaling leads to aberrant autophagy activation. Simultaneous inhibition of ER, ERBB, and autophagy pathways synergistically impacts SMAD4-depleted cells. Our findings unveil a mechanism whereby endocrine therapy-induced SMAD4 downregulation drives acquired resistance by integrating ER and ERBB signaling and suggest a rational treatment strategy for endocrine-resistant HR + HER2- breast cancer patients.
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MESH Headings
- Humans
- Smad4 Protein/metabolism
- Smad4 Protein/genetics
- Female
- Breast Neoplasms/metabolism
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Breast Neoplasms/drug therapy
- Signal Transduction/drug effects
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Receptor, ErbB-2/metabolism
- Receptor, ErbB-2/genetics
- Receptors, Estrogen/metabolism
- Cell Line, Tumor
- Animals
- Tamoxifen/pharmacology
- Tamoxifen/therapeutic use
- Tamoxifen/analogs & derivatives
- Mice
- Antineoplastic Agents, Hormonal/pharmacology
- Antineoplastic Agents, Hormonal/therapeutic use
- Mice, Nude
- Gene Expression Regulation, Neoplastic/drug effects
- Autophagy/drug effects
- ErbB Receptors/metabolism
- ErbB Receptors/genetics
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Affiliation(s)
- Kang Li
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Dan Shu
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Han Li
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Ailin Lan
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Wenjie Zhang
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Zhaofu Tan
- Department of Dermatology and Venereology, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Man Huang
- Department of Breast Center, Chongqing University Three Gorges Hospital, Wanzhou, 404000, Chongqing, China
| | - Maria Lauda Tomasi
- Department of Medicine, Cedars-Sinai Medical Center, DAVIS Research Building 3096A, 8700 Beverly Blv, Los Angeles, CA, 90048, USA
| | - Aishun Jin
- Department of Immunology, School of Basic Medical Sciences, Chongqing Medical University, 400010, Chongqing, China
| | - Haochen Yu
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China.
| | - Meiying Shen
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China.
| | - Shengchun Liu
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China.
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14
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Yanagiya R, Miyatake Y, Watanabe N, Shimizu T, Kanamori A, Ueno M, Okabe S, Carreras J, Nakayama S, Hasegawa A, Kameda K, Kamakura T, Nakagawa S, Yamauchi T, Maeda T, Ishii K, Matsuura T, Handa H, Hirao A, Ishizawa K, Onizuka M, Mashima T, Nakamura N, Ando K, Kotani A. Amino acid influx via LAT1 regulates iron demand and sensitivity to PPMX-T003 of aggressive natural killer cell leukemia. Leukemia 2024:10.1038/s41375-024-02296-6. [PMID: 38914715 DOI: 10.1038/s41375-024-02296-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/15/2024] [Accepted: 05/22/2024] [Indexed: 06/26/2024]
Abstract
Aggressive natural killer cell leukemia (ANKL) is a rare hematological malignancy with a fulminant clinical course. Our previous study revealed that ANKL cells proliferate predominantly in the liver sinusoids and strongly depend on transferrin supplementation. In addition, we demonstrated that liver-resident ANKL cells are sensitive to PPMX-T003, an anti-human transferrin receptor 1 inhibitory antibody, whereas spleen-resident ANKL cells are resistant to transferrin receptor 1 inhibition. However, the microenvironmental factors that regulate the iron dependency of ANKL cells remain unclear. In this study, we first revealed that the anti-neoplastic effect of PPMX-T003 was characterized by DNA double-strand breaks in a DNA replication-dependent manner, similar to conventional cytotoxic agents. We also found that the influx of extracellular amino acids via LAT1 stimulated sensitivity to PPMX-T003. Taken together, we discovered that the amount of extracellular amino acid influx through LAT1 was the key environmental factor determining the iron dependency of ANKL cells via adjustment of their mTOR/Myc activity, which provides a good explanation for the different sensitivity to PPMX-T003 between liver- and spleen-resident ANKL cells, as the liver sinusoid contains abundant amino acids absorbed from the gut.
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Affiliation(s)
- Ryo Yanagiya
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Japan
- Department of Neurology, Hematology, Diabetology, Endocrinology, and Metabolism (3rd Department of Internal Medicine), Faculty of Medicine, Yamagata University, Yamagata, Japan
- Department of Regulation of Infectious Cancers, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yuji Miyatake
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Natsumi Watanabe
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Takanobu Shimizu
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Akane Kanamori
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Masaya Ueno
- Division of Molecular Genetics, Cancer and Stem Cell Research Program, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
- WPI Nano Life Science Institute (WPI Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Sachiko Okabe
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Joaquim Carreras
- Department of Pathology, Tokai University School of Medicine, Isehara, Japan
| | - Shunya Nakayama
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
- Laboratory of Veterinary Physiology, College of Bioresource Science, Nihon University, Kanagawa, Japan
| | - Ami Hasegawa
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Kazuaki Kameda
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Takeshi Kamakura
- Department of Regulation of Infectious Cancers, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Takuji Yamauchi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Takahiro Maeda
- Division of Precision Medicine, Kyushu University Hospital, Fukuoka, Japan
| | | | | | - Hiroshi Handa
- Department of Hematology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Atsushi Hirao
- Division of Molecular Genetics, Cancer and Stem Cell Research Program, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, Japan
- WPI Nano Life Science Institute (WPI Nano LSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Kenichi Ishizawa
- Department of Neurology, Hematology, Diabetology, Endocrinology, and Metabolism (3rd Department of Internal Medicine), Faculty of Medicine, Yamagata University, Yamagata, Japan
- Faculty of Health Sciences, Tohoku Fukushi University, Sendai, Japan
| | - Makoto Onizuka
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Japan
| | - Tetsuo Mashima
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Naoya Nakamura
- Department of Pathology, Tokai University School of Medicine, Isehara, Japan
| | - Kiyoshi Ando
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Japan
- Department of Hematology, Hiroshima University, Hiroshima, Japan
- Department of Hematological Malignancy, Institute of Medical Science, Tokai University, Isehara, Japan
| | - Ai Kotani
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan.
- Department of Regulation of Infectious Cancers, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
- Department of Hematological Malignancy, Institute of Medical Science, Tokai University, Isehara, Japan.
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15
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Ewald JD, Lu Y, Ellis CE, Worton J, Kolic J, Sasaki S, Zhang D, Dos Santos T, Spigelman AF, Bautista A, Dai XQ, Lyon JG, Smith NP, Wong JM, Rajesh V, Sun H, Sharp SA, Rogalski JC, Moravcova R, Cen HH, Manning Fox JE, Consortium HDAS, Atlas E, Bruin JE, Mulvihill EE, Verchere CB, Foster LJ, Gloyn AL, Johnson JD, Pepper AR, Lynn FC, Xia J, MacDonald PE. HumanIslets: An integrated platform for human islet data access and analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599613. [PMID: 38948734 PMCID: PMC11212983 DOI: 10.1101/2024.06.19.599613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Comprehensive molecular and cellular phenotyping of human islets can enable deep mechanistic insights for diabetes research. We established the Human Islet Data Analysis and Sharing (HI-DAS) consortium to advance goals in accessibility, usability, and integration of data from human islets isolated from donors with and without diabetes at the Alberta Diabetes Institute (ADI) IsletCore. Here we introduce HumanIslets.com , an open resource for the research community. This platform, which presently includes data on 547 human islet donors, allows users to access linked datasets describing molecular profiles, islet function and donor phenotypes, and to perform various statistical and functional analyses at the donor, islet and single-cell levels. As an example of the analytic capacity of this resource we show a dissociation between cell culture effects on transcript and protein expression, and an approach to correct for exocrine contamination found in hand-picked islets. Finally, we provide an example workflow and visualization that highlights links between type 2 diabetes status, SERCA3b Ca 2+ -ATPase levels at the transcript and protein level, insulin secretion and islet cell phenotypes. HumanIslets.com provides a growing and adaptable set of resources and tools to support the metabolism and diabetes research community.
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16
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Hu L, Zhang XT, Zeng X, Xiong LX, Ai Q, Liu CJ, Yang WW, Wu Y, Guo X, Li GQ, Liu L. ISAba1 mediated intrinsic chromosomal oxacillinase amplification confers carbapenem resistance in Acinetobacter baumannii. Int J Antimicrob Agents 2024:107258. [PMID: 38914142 DOI: 10.1016/j.ijantimicag.2024.107258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 05/19/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024]
Abstract
Tandem amplification of carbapenemase genes increases gene copy number and enhances carbapenem resistance. These amplifications are often heterogeneous, transient, and located on plasmids, which also contribute to heteroresistance. Amplification of encoding genes is especially important for enzymes with low hydrolysis activity, which are often overlooked. Here, we reported an intrinsic oxacillinase oxaAb amplification flanked by ISAba1. The amplification is in the chromosome and contains up to twenty-five repeats. We provided genomic, transcriptomic, and proteomic evidence that the amplification resulted in oxacillinase overproduction. Notably, no point mutations of oxaAb were found during the amplification process. Strains of A. baumannii with intrinsic amplified or external transformed ISAba1-oxaAb exhibited higher meropenem hydrolysis activity. Furthermore, the number of repeats in the amplification decreased gradually over a period of 21 days cultured with carbapenem withdrawal. However, upon re-exposure to meropenem, the ISAba1 flanked oxaAb responded rapidly, with repeat numbers reaching or exceeding pre-carbapenem withdrawal levels within 24 hours. Taken together, these findings suggest that ISAba1-mediated gene amplification and overproduction of intrinsic low-activity oxacillinase oxaAb resulted in carbapenem resistance.
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Affiliation(s)
- Limiao Hu
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Xiao-Tuan Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Xi Zeng
- Department of Gastroenterology, the First Affiliated Hospital of Shaoyang University, Shaoyang, 422000, China
| | - Lu-Xi Xiong
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Qi Ai
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Cai-Juan Liu
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Wei-Wei Yang
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Yuan Wu
- Department of Clinical Laboratory Medicine, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, China.
| | - Xuemin Guo
- Meizhou People's Hospital, Meizhou, 514031, China; Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translation Research of Hakka Population, Meizhou, 514031, China.
| | - Guo-Qing Li
- Department of Gastroenterology, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, China; Hunan Provincial Key Laboratory of Basic and Clinical Pharmacological Research for Gastroenterological Tumors, Hengyang, 421001, China.
| | - Logen Liu
- Hunan Provincial Key Laboratory of Basic and Clinical Pharmacological Research for Gastroenterological Tumors, Hengyang, 421001, China; Clinical Research Center, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, China;.
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17
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Barlit H, Romero AM, Gülhan A, Patnaik PK, Tyshkovskiy A, Martínez-Pastor MT, Gladyshev VN, Puig S, Labunskyy VM. Ribosome profiling reveals the role of yeast RNA-binding proteins Cth1 and Cth2 in translational regulation. iScience 2024; 27:109868. [PMID: 38779483 PMCID: PMC11109004 DOI: 10.1016/j.isci.2024.109868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/12/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Iron serves as a cofactor for enzymes involved in several steps of protein translation, but the control of translation during iron limitation is not understood at the molecular level. Here, we report a genome-wide analysis of protein translation in response to iron deficiency in yeast using ribosome profiling. We show that iron depletion affects global protein synthesis and leads to translational repression of multiple genes involved in iron-related processes. Furthermore, we demonstrate that the RNA-binding proteins Cth1 and Cth2 play a central role in this translational regulation by repressing the activity of the iron-dependent Rli1 ribosome recycling factor and inhibiting mitochondrial translation and heme biosynthesis. Additionally, we found that iron deficiency represses MRS3 mRNA translation through increased expression of antisense long non-coding RNA. Together, our results reveal complex gene expression and protein synthesis remodeling in response to low iron, demonstrating how this important metal affects protein translation at multiple levels.
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Affiliation(s)
- Hanna Barlit
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Antonia M. Romero
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Ali Gülhan
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Praveen K. Patnaik
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - María T. Martínez-Pastor
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Valencia, Spain
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sergi Puig
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Vyacheslav M. Labunskyy
- Department of Dermatology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
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18
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Bedolla A, Wegman E, Weed M, Stevens MK, Ware K, Paranjpe A, Alkhimovitch A, Ifergan I, Taranov A, Peter JD, Gonzalez RMS, Robinson JE, McClain L, Roskin KM, Greig NH, Luo Y. Adult microglial TGFβ1 is required for microglia homeostasis via an autocrine mechanism to maintain cognitive function in mice. Nat Commun 2024; 15:5306. [PMID: 38906887 PMCID: PMC11192737 DOI: 10.1038/s41467-024-49596-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 06/11/2024] [Indexed: 06/23/2024] Open
Abstract
While TGF-β signaling is essential for microglial function, the cellular source of TGF-β1 ligand and its spatial regulation remains unclear in the adult CNS. Our data supports that microglia but not astrocytes or neurons are the primary producers of TGF-β1 ligands needed for microglial homeostasis. Microglia-Tgfb1 KO leads to the activation of microglia featuring a dyshomeostatic transcriptome that resembles disease-associated, injury-associated, and aged microglia, suggesting microglial self-produced TGF-β1 ligands are important in the adult CNS. Astrocytes in MG-Tgfb1 inducible (i)KO mice show a transcriptome profile that is closely aligned with an LPS-associated astrocyte profile. Additionally, using sparse mosaic single-cell microglia KO of TGF-β1 ligand we established an autocrine mechanism for signaling. Here we show that MG-Tgfb1 iKO mice present cognitive deficits, supporting that precise spatial regulation of TGF-β1 ligand derived from microglia is required for the maintenance of brain homeostasis and normal cognitive function in the adult brain.
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Affiliation(s)
- Alicia Bedolla
- Department of Molecular and Cellular Biosciences, University of Cincinnati, Cincinnati, OH, USA
- Neuroscience Graduate Program, University of Cincinnati, Cincinnati, OH, USA
| | - Elliot Wegman
- Department of Molecular and Cellular Biosciences, University of Cincinnati, Cincinnati, OH, USA
| | - Max Weed
- Department of Molecular and Cellular Biosciences, University of Cincinnati, Cincinnati, OH, USA
| | | | - Kierra Ware
- Department of Molecular and Cellular Biosciences, University of Cincinnati, Cincinnati, OH, USA
| | - Aditi Paranjpe
- Information Services for Research, Cincinnati Children's Hospital Medical Center, Cincinnati, USA
| | - Anastasia Alkhimovitch
- Department of Molecular and Cellular Biosciences, University of Cincinnati, Cincinnati, OH, USA
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Igal Ifergan
- Department of Molecular and Cellular Biosciences, University of Cincinnati, Cincinnati, OH, USA
- Neuroscience Graduate Program, University of Cincinnati, Cincinnati, OH, USA
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Aleksandr Taranov
- Department of Molecular and Cellular Biosciences, University of Cincinnati, Cincinnati, OH, USA
- Neuroscience Graduate Program, University of Cincinnati, Cincinnati, OH, USA
| | - Joshua D Peter
- Department of Molecular and Cellular Biosciences, University of Cincinnati, Cincinnati, OH, USA
| | - Rosa Maria Salazar Gonzalez
- Division of Experimental Hematology and Cancer Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, US
| | - J Elliott Robinson
- Division of Experimental Hematology and Cancer Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, US
| | - Lucas McClain
- Department of Molecular and Cellular Biosciences, University of Cincinnati, Cincinnati, OH, USA
| | - Krishna M Roskin
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, US
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, USA
| | - Nigel H Greig
- Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Yu Luo
- Department of Molecular and Cellular Biosciences, University of Cincinnati, Cincinnati, OH, USA.
- Neuroscience Graduate Program, University of Cincinnati, Cincinnati, OH, USA.
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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19
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Molière A, Park JYC, Goyala A, Vayndorf EM, Zhang B, Hsiung KC, Jung Y, Kwon S, Statzer C, Meyer D, Nguyen R, Chadwick J, Thompson MA, Schumacher B, Lee SJV, Essmann CL, MacArthur MR, Kaeberlein M, David D, Gems D, Ewald CY. Improved resilience and proteostasis mediate longevity upon DAF-2 degradation in old age. GeroScience 2024:10.1007/s11357-024-01232-x. [PMID: 38900346 DOI: 10.1007/s11357-024-01232-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Little is known about the possibility of reversing age-related biological changes when they have already occurred. To explore this, we have characterized the effects of reducing insulin/IGF-1 signaling (IIS) during old age. Reduction of IIS throughout life slows age-related decline in diverse species, most strikingly in the nematode Caenorhabditis elegans. Here we show that even at advanced ages, auxin-induced degradation of DAF-2 in single tissues, including neurons and the intestine, is still able to markedly increase C. elegans lifespan. We describe how reversibility varies among senescent changes. While senescent pathologies that develop in mid-life were not reversed, there was a rejuvenation of the proteostasis network, manifesting as a restoration of the capacity to eliminate otherwise intractable protein aggregates that accumulate with age. Moreover, resistance to several stressors was restored. These results support several new conclusions. (1) Loss of resilience is not solely a consequence of pathologies that develop in earlier life. (2) Restoration of proteostasis and resilience by inhibiting IIS is a plausible cause of the increase in lifespan. And (3), most interestingly, some aspects of the age-related transition from resilience to frailty can be reversed to a certain extent. This raises the possibility that the effect of IIS and related pathways on resilience and frailty during aging in higher animals might possess some degree of reversibility.
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Affiliation(s)
- Adrian Molière
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, CH-8603, Schwerzenbach, Switzerland
| | - Ji Young Cecilia Park
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, CH-8603, Schwerzenbach, Switzerland
| | - Anita Goyala
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, CH-8603, Schwerzenbach, Switzerland
| | - Elena M Vayndorf
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195-7470, USA
| | - Bruce Zhang
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Kuei Ching Hsiung
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Yoonji Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Sujeong Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Cyril Statzer
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, CH-8603, Schwerzenbach, Switzerland
| | - David Meyer
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University Hospital and University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Richard Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195-7470, USA
| | | | | | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University Hospital and University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Seung-Jae V Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Clara L Essmann
- Bioinformatics and Molecular Genetics, Institute of Biology III, Faculty of Biology, Albert-Ludwigs-University Freiburg, 79108, Freiburg, Germany
| | - Michael R MacArthur
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195-7470, USA
| | | | - David Gems
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Collin Y Ewald
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, CH-8603, Schwerzenbach, Switzerland.
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20
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Sato Y, Mino S, Thompson F, Sawabe T. Core Transcriptome of Hydrogen Producing Marine Vibrios Reveals Contribution of Glycolysis in Their Efficient Hydrogen Production. Curr Microbiol 2024; 81:230. [PMID: 38896159 DOI: 10.1007/s00284-024-03764-z] [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: 04/11/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024]
Abstract
Pyruvate (Pyr) is the end product of the glycolysis pathway. Pyr is also renewable and is further metabolized to produce formate, which is the precursor of H2, via pyruvate formate lyase (PFL) under anaerobic conditions. The formate is excluded and re-imported via the formate channel and is then converted to H2 via the formate hydrogenlyase (FHL) complex. In H2 producing marine vibrios, such as Vibrio tritonius and Vibrio porteresiae in the Porteresiae clade of the family Vibrionaceae, apparent but inefficient H2 production from Pyr has been observed. To elucidate the molecular mechanism of why this inefficient H2 production is observed in Pry-metabolized marine vibrio cells and how glycolysis affects those H2 productions of marine vibrios, the "Core Transcriptome" approach to find common gene expressions of those two major H2 producing Vibrio species in Pyr metabolism was first applied. In the Pyr-metabolized vibrio cells, genes for the "Phosphoenolpyruvate (PEP)-Pyruvate-Oxalate (PPO)" node, due to energy saving, and PhoB-, RhaR-, and DeoR-regulons were regulated. Interestingly, a gene responsible for oxalate/formate family antiporter was up-regulated in Pyr-metabolized cells compared to those of Glc-metabolized cells, which provides new insights into the uses of alternative formate exclusion mechanics due to energy deficiencies in Pyr-metabolized marine vibrios cells. We further discuss the contribution of the Embden-Meyerhof-Parnas (EMP) pathway to efficient H2 production in marine vibrios.
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Affiliation(s)
- Yoshihiro Sato
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
| | - Fabiano Thompson
- Laboratory of Microbiology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
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21
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Doyle C, Callaghan B, Roodnat AW, Armstrong L, Lester K, Simpson DA, Atkinson SD, Sheridan C, McKenna DJ, Willoughby CE. The TGFβ Induced MicroRNAome of the Trabecular Meshwork. Cells 2024; 13:1060. [PMID: 38920689 PMCID: PMC11201560 DOI: 10.3390/cells13121060] [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: 05/01/2024] [Revised: 06/08/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
Primary open-angle glaucoma (POAG) is a progressive optic neuropathy with a complex, multifactorial aetiology. Raised intraocular pressure (IOP) is the most important clinically modifiable risk factor for POAG. All current pharmacological agents target aqueous humour dynamics to lower IOP. Newer therapeutic agents are required as some patients with POAG show a limited therapeutic response or develop ocular and systemic side effects to topical medication. Elevated IOP in POAG results from cellular and molecular changes in the trabecular meshwork driven by increased levels of transforming growth factor β (TGFβ) in the anterior segment of the eye. Understanding how TGFβ affects both the structural and functional changes in the outflow pathway and IOP is required to develop new glaucoma therapies that target the molecular pathology in the trabecular meshwork. In this study, we evaluated the effects of TGF-β1 and -β2 treatment on miRNA expression in cultured human primary trabecular meshwork cells. Our findings are presented in terms of specific miRNAs (miRNA-centric), but given miRNAs work in networks to control cellular pathways and processes, a pathway-centric view of miRNA action is also reported. Evaluating TGFβ-responsive miRNA expression in trabecular meshwork cells will further our understanding of the important pathways and changes involved in the pathogenesis of glaucoma and could lead to the development of miRNAs as new therapeutic modalities in glaucoma.
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Affiliation(s)
- Chelsey Doyle
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Breedge Callaghan
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Anton W. Roodnat
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Lee Armstrong
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Karen Lester
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - David A. Simpson
- Wellcome Wolfson Institute for Experimental Medicine, Queens’ University, Belfast BT9 7BL, UK;
| | - Sarah D. Atkinson
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Carl Sheridan
- Department of Eye and Vision Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK;
| | - Declan J. McKenna
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
| | - Colin E. Willoughby
- Centre for Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine Campus, Coleraine BT52 1SA, UK; (C.D.); (A.W.R.); (L.A.); (S.D.A.); (D.J.M.)
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22
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Brida KL, Jorgensen ET, Phillips RA, Newman CE, Tuscher JJ, Morring EK, Zipperly ME, Ianov L, Montgomery KD, Tippani M, Hyde TM, Maynard KR, Martinowich K, Day JJ. Reelin marks cocaine-activated striatal ensembles, promotes neuronal excitability, and regulates cocaine reward. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599348. [PMID: 38948801 PMCID: PMC11212904 DOI: 10.1101/2024.06.17.599348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Drugs of abuse activate defined neuronal ensembles in brain reward structures such as the nucleus accumbens (NAc), which are thought to promote the enduring synaptic, circuit, and behavioral consequences of drug exposure. While the molecular and cellular effects arising from experience with drugs like cocaine are increasingly well understood, the mechanisms that sculpt NAc ensemble participation are largely unknown. Here, we leveraged unbiased single-nucleus transcriptional profiling to identify expression of the secreted glycoprotein Reelin (encoded by the Reln gene) as a marker of cocaine-activated neuronal ensembles within the rat NAc. Multiplexed in situ detection confirmed selective expression of the immediate early gene Fos in Reln+ neurons after cocaine experience, and also revealed enrichment of Reln mRNA in Drd1 + medium spiny neurons (MSNs) in both the rat and human brain. Using a novel CRISPR interference strategy enabling selective Reln knockdown in the adult NAc, we observed altered expression of genes linked to calcium signaling, emergence of a transcriptional trajectory consistent with loss of cocaine sensitivity, and a striking decrease in MSN intrinsic excitability. At the behavioral level, loss of Reln prevented cocaine locomotor sensitization, abolished cocaine place preference memory, and decreased cocaine self-administration behavior. Together, these results identify Reelin as a critical mechanistic link between ensemble participation and cocaine-induced behavioral adaptations.
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23
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Nacev BA, Dabas Y, Paul MR, Pacheco C, Mitchener M, Perez Y, Fang Y, Soshnev AA, Barrows D, Carroll T, Socci ND, St Jean SC, Tiwari S, Gruss MJ, Monette S, Tap WD, Garcia BA, Muir T, Allis CD. Cancer-associated Histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation. Nat Commun 2024; 15:5155. [PMID: 38886411 PMCID: PMC11183192 DOI: 10.1038/s41467-024-49486-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
Dysregulated epigenetic states are a hallmark of cancer and often arise from genetic alterations in epigenetic regulators. This includes missense mutations in histones, which, together with associated DNA, form nucleosome core particles. However, the oncogenic mechanisms of most histone mutations are unknown. Here, we demonstrate that cancer-associated histone mutations at arginines in the histone H3 N-terminal tail disrupt repressive chromatin domains, alter gene regulation, and dysregulate differentiation. We find that histone H3R2C and R26C mutants reduce transcriptionally repressive H3K27me3. While H3K27me3 depletion in cells expressing these mutants is exclusively observed on the minor fraction of histone tails harboring the mutations, the same mutants recurrently disrupt broad H3K27me3 domains in the chromatin context, including near developmentally regulated promoters. H3K27me3 loss leads to de-repression of differentiation pathways, with concordant effects between H3R2 and H3R26 mutants despite different proximity to the PRC2 substrate, H3K27. Functionally, H3R26C-expressing mesenchymal progenitor cells and murine embryonic stem cell-derived teratomas demonstrate impaired differentiation. Collectively, these data show that cancer-associated H3 N-terminal arginine mutations reduce PRC2 activity and disrupt chromatin-dependent developmental functions, a cancer-relevant phenotype.
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Affiliation(s)
- Benjamin A Nacev
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA.
| | - Yakshi Dabas
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, 10065, USA
| | - Christian Pacheco
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Michelle Mitchener
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Yekaterina Perez
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yan Fang
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Alexey A Soshnev
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Douglas Barrows
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, 10065, USA
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, 10065, USA
| | - Nicholas D Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Samantha C St Jean
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sagarika Tiwari
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA
| | - Michael J Gruss
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA
| | - Sebastien Monette
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tom Muir
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
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24
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Yi S, Singh SS, Rozen-Gagnon K, Luna JM. Mapping RNA-protein interactions with subcellular resolution using colocalization CLIP. RNA (NEW YORK, N.Y.) 2024; 30:920-937. [PMID: 38658162 PMCID: PMC11182006 DOI: 10.1261/rna.079890.123] [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: 11/16/2023] [Accepted: 04/04/2024] [Indexed: 04/26/2024]
Abstract
RNA-binding proteins (RBPs) are essential for RNA metabolism and profoundly impact health and disease. The subcellular organization of RBP interaction networks with target RNAs remains largely unexplored. Here, we develop colocalization CLIP (coCLIP), a method that combines cross-linking and immunoprecipitation (CLIP) with proximity labeling, to explore in-depth the subcellular RNA interactions of the RBP human antigen R (HuR). Using this method, we uncover HuR's dynamic and location-specific interactions with RNA, revealing alterations in sequence preferences and interactions in the nucleus, cytosol, or stress granule (SG) compartments. We uncover HuR's unique binding preferences within SGs during arsenite stress, illuminating intricate interactions that conventional methodologies cannot capture. Overall, coCLIP provides a powerful method for revealing RBP-RNA interactions based on localization and lays the foundation for an advanced understanding of RBP models that incorporate subcellular location as a critical determinant of their functions.
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Affiliation(s)
- Soon Yi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Shashi S Singh
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Kathryn Rozen-Gagnon
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Joseph M Luna
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
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25
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Mishra A, Jajodia A, Weston E, Jayavelu ND, Garcia M, Hossack D, Hawkins RD. Identification of functional enhancer variants associated with type I diabetes in CD4+ T cells. Front Immunol 2024; 15:1387253. [PMID: 38947339 PMCID: PMC11211866 DOI: 10.3389/fimmu.2024.1387253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 04/09/2024] [Indexed: 07/02/2024] Open
Abstract
Type I diabetes is an autoimmune disease mediated by T-cell destruction of β cells in pancreatic islets. Currently, there is no known cure, and treatment consists of daily insulin injections. Genome-wide association studies and twin studies have indicated a strong genetic heritability for type I diabetes and implicated several genes. As most strongly associated variants are noncoding, there is still a lack of identification of functional and, therefore, likely causal variants. Given that many of these genetic variants reside in enhancer elements, we have tested 121 CD4+ T-cell enhancer variants associated with T1D. We found four to be functional through massively parallel reporter assays. Three of the enhancer variants weaken activity, while the fourth strengthens activity. We link these to their cognate genes using 3D genome architecture or eQTL data and validate them using CRISPR editing. Validated target genes include CLEC16A and SOCS1. While these genes have been previously implicated in type 1 diabetes and other autoimmune diseases, we show that enhancers controlling their expression harbor functional variants. These variants, therefore, may act as causal type 1 diabetic variants.
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Affiliation(s)
- Arpit Mishra
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States
| | - Ajay Jajodia
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States
| | - Eryn Weston
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States
| | - Naresh Doni Jayavelu
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States
| | - Mariana Garcia
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States
| | - Daniel Hossack
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States
| | - R. David Hawkins
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA, United States
- Benaroya Research Institute at Virginia Mason, Seattle, WA, United States
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26
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Tsuda K, Maeno A, Otake A, Kato K, Tanaka W, Hibara KI, Nonomura KI. YABBY and diverged KNOX1 genes shape nodes and internodes in the stem. Science 2024; 384:1241-1247. [PMID: 38870308 DOI: 10.1126/science.adn6748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/03/2024] [Indexed: 06/15/2024]
Abstract
Plant stems comprise nodes and internodes that specialize in solute exchange and elongation. However, their boundaries are not well defined, and how these basic units arise remains elusive. In rice with clear nodes and internodes, we found that one subclade of class I knotted1-like homeobox (KNOX1) genes for shoot meristem indeterminacy restricts node differentiation and allows internode formation by repressing YABBY genes for leaf development and genes from another node-specific KNOX1 subclade. YABBYs promote nodal vascular differentiation and limit stem elongation. YABBY and node-specific KNOX1 genes specify the pulvinus, which further elaborates the nodal structure for gravitropism. Notably, this KNOX1 subclade organization is specific to seed plants. We propose that nodes and internodes are distinct domains specified by YABBY-KNOX1 cross-regulation that diverged in early seed plants.
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Affiliation(s)
- Katsutoshi Tsuda
- Plant Cytogenetics Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540, Japan
| | - Akiteru Maeno
- Plant Cytogenetics Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Ayako Otake
- Plant Cytogenetics Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Kae Kato
- Plant Cytogenetics Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Wakana Tanaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Ken-Ichiro Hibara
- Graduate School of Agricultural Regional Vitalization, Kibi International University, Minamiawaji, Hyogo 656-0484, Japan
| | - Ken-Ichi Nonomura
- Plant Cytogenetics Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540, Japan
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27
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Lehle JD, Lin YH, Gomez A, Chavez L, McCarrey JR. Endocrine disruptor-induced epimutagenesis in vitro : Insight into molecular mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574355. [PMID: 38746310 PMCID: PMC11092511 DOI: 10.1101/2024.01.05.574355] [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
Endocrine disrupting chemicals (EDCs) such as bisphenol S (BPS) are xenobiotic compounds that can disrupt endocrine signaling following exposure due to steric similarities to endogenous hormones within the body. EDCs have been shown to induce disruptions in normal epigenetic programming (epimutations) that accompany dysregulation of normal gene expression patterns that appear to predispose disease states. Most interestingly, the prevalence of epimutations following exposure to many different EDCs often persists over multiple subsequent generations, even with no further exposure to the causative EDC. Many previous studies have described both the direct and prolonged effects of EDC exposure in animal models, but many questions remain about molecular mechanisms by which EDCs initially induce epimutations or contribute to the propagation of EDC-induced epimutations either within the exposed generation or to subsequent generations. Additional questions remain regarding the extent to which there may be differences in cell-type specific susceptibilities to various EDCs, and whether this susceptibility is correlative with expression of relevant hormone receptors and/or the location of relevant hormone response elements (HREs) in the genome. To address these questions, we exposed cultured mouse pluripotent (induced pluripotent stem [iPS]), somatic (Sertoli and granulosa), and germ (primordial germ cell like [PGCLC]) cells to BPS and measured changes in DNA methylation levels at the epigenomic level and gene expression at the transcriptomic level. We found that there was indeed a difference in cell-type specific susceptibility to EDC-induced epimutagenesis and that this susceptibility correlated with differential expression of relevant hormone receptors and, in many cases, tended to generate epimutations near relevant HREs within the genome. Additionally, however, we also found that BPS can induce epimutations in a cell type that does not express relevant receptors and in genomic regions that do not contain relevant HREs, suggesting that both canonical and non-canonical signaling mechanisms can be disrupted by BPS exposure. Most interestingly, we found that when iPS cells were exposed to BPS and then induced to differentiate into PGCLCs, the prevalence of epimutations and differentially expressed genes (DEGs) initially induced in the iPSCs was largely retained in the resulting PGCLCs, however, >90% of the specific epimutations and DEGs were not conserved but were rather replaced by novel epimutations and DEGs following the iPSC to PGCLC transition. These results are consistent with a unique concept that many EDC-induced epimutations may normally be corrected by germline and/or embryonic epigenetic reprogramming but that due to disruption of the underlying chromatin architecture induced by the EDC exposure, many novel epimutations may emerge during the reprogramming process as well. Thus, it appears that following exposure to a disruptive agent such as an EDC, a prevalence of epimutations may transcend epigenetic reprogramming even though most individual epimutations are not conserved during this process.
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28
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Corujo-Simon E, Bates LE, Yanagida A, Jones K, Clark S, von Meyenn F, Reik W, Nichols J. Human trophectoderm becomes multi-layered by internalization at the polar region. Dev Cell 2024:S1534-5807(24)00362-9. [PMID: 38889726 DOI: 10.1016/j.devcel.2024.05.028] [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: 10/11/2023] [Revised: 02/02/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024]
Abstract
To implant in the uterus, mammalian embryos form blastocysts comprising trophectoderm (TE) surrounding an inner cell mass (ICM), confined to the polar region by the expanding blastocoel. The mode of implantation varies between species. Murine embryos maintain a single layered TE until they implant in the characteristic thick deciduum, whereas human blastocysts attach via polar TE directly to the uterine wall. Using immunofluorescence (IF) of rapidly isolated ICMs, blockade of RNA and protein synthesis in whole embryos, or 3D visualization of immunostained embryos, we provide evidence of multi-layering in human polar TE before implantation. This may be required for rapid uterine invasion to secure the developing human embryo and initiate formation of the placenta. Using sequential fluorescent labeling, we demonstrate that the majority of inner TE in human blastocysts arises from existing outer cells, with no evidence of conversion from the ICM in the context of the intact embryo.
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Affiliation(s)
- Elena Corujo-Simon
- Wellcome - MRC Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK.
| | - Lawrence Edward Bates
- Wellcome - MRC Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Ayaka Yanagida
- Wellcome - MRC Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Kenneth Jones
- Wellcome - MRC Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Stephen Clark
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | | | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Jennifer Nichols
- Wellcome - MRC Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
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29
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Ingelman H, Heffernan JK, Harris A, Brown SD, Shaikh KM, Saqib AY, Pinheiro MJ, de Lima LA, Martinez KR, Gonzalez-Garcia RA, Hawkins G, Daleiden J, Tran L, Zeleznik H, Jensen RO, Reynoso V, Schindel H, Jänes J, Simpson SD, Köpke M, Marcellin E, Valgepea K. Autotrophic adaptive laboratory evolution of the acetogen Clostridium autoethanogenum delivers the gas-fermenting strain LAbrini with superior growth, products, and robustness. N Biotechnol 2024; 83:S1871-6784(24)00023-2. [PMID: 38871051 DOI: 10.1016/j.nbt.2024.06.002] [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: 04/12/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 06/15/2024]
Abstract
Microbes able to convert gaseous one-carbon (C1) waste feedstocks are increasingly important to transition to the sustainable production of renewable chemicals and fuels. Acetogens are interesting biocatalysts since gas fermentation using Clostridium autoethanogenum has been commercialised. However, most acetogen strains need complex nutrients, display slow growth, and are not robust for bioreactor fermentations. In this work, we used three different and independent adaptive laboratory evolution (ALE) strategies to evolve the wild-type C. autoethanogenum to grow faster, without yeast extract and to be robust in operating continuous bioreactor cultures. Multiple evolved strains with improved phenotypes were isolated on minimal media with one strain, named "LAbrini", exhibiting superior performance regarding the maximum specific growth rate, product profile, and robustness in continuous cultures. Whole-genome sequencing of the evolved strains identified 25 mutations. Of particular interest are two genes that acquired seven different mutations across the three ALE strategies, potentially as a result of convergent evolution. Reverse genetic engineering of mutations in potentially sporulation-related genes CLAU_3129 (spo0A) and CLAU_1957 recovered all three superior features of our ALE strains through triggering significant proteomic rearrangements. This work provides a robust C. autoethanogenum strain "LAbrini" to accelerate phenotyping and genetic engineering and to better understand acetogen metabolism.
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Affiliation(s)
- Henri Ingelman
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - James K Heffernan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | | | | | | | - Asfand Yar Saqib
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Marina J Pinheiro
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Lorena Azevedo de Lima
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia
| | - Karen Rodriguez Martinez
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | - Ricardo A Gonzalez-Garcia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia
| | | | | | | | | | | | | | | | - Jürgen Jänes
- Institute of Molecular Systems Biology, ETH Zürich, 8049 Zürich, Switzerland
| | | | | | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 St. Lucia, Australia.
| | - Kaspar Valgepea
- ERA Chair in Gas Fermentation Technologies, Institute of Bioengineering, University of Tartu, 50411 Tartu, Estonia.
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30
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Yu X, Zhou J, Ye W, Xu J, Li R, Huang L, Chai Y, Wen M, Xu S, Zhou Y. Time-course swRNA-seq uncovers a hierarchical gene regulatory network in controlling the response-repair-remodeling after wounding. Commun Biol 2024; 7:694. [PMID: 38844830 PMCID: PMC11156874 DOI: 10.1038/s42003-024-06352-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/17/2024] [Indexed: 06/09/2024] Open
Abstract
Wounding initiates intricate responses crucial for tissue repair and regeneration. Yet, the gene regulatory networks governing wound healing remain poorly understood. Here, employing single-worm RNA sequencing (swRNA-seq) across 12 time-points, we delineated a three-stage wound repair process in C. elegans: response, repair, and remodeling. Integrating diverse datasets, we constructed a dynamic regulatory network comprising 241 transcription regulators and their inferred targets. We identified potentially seven autoregulatory TFs and five cross-autoregulatory loops involving pqm-1 and jun-1. We revealed that TFs might interact with chromatin factors and form TF-TF combinatory modules via intrinsically disordered regions to enhance response robustness. We experimentally validated six regulators functioning in transcriptional and translocation-dependent manners. Notably, nhr-76, daf-16, nhr-84, and oef-1 are potentially required for efficient repair, while elt-2 may act as an inhibitor. These findings elucidate transcriptional responses and hierarchical regulatory networks during C. elegans wound repair, shedding light on mechanisms underlying tissue repair and regeneration.
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Affiliation(s)
- Xinghai Yu
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, 430072, China
| | - Jinghua Zhou
- Center for Stem Cell and Regenerative Medicine and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Wenkai Ye
- Center for Stem Cell and Regenerative Medicine and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jingxiu Xu
- Center for Stem Cell and Regenerative Medicine and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Rui Li
- Institute of Hydrobiology, Chinese Academy of Science, Wuhan, 430072, China
| | - Li Huang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, 430072, China
| | - Yi Chai
- The Zhejiang University-University of Edinburgh Institute, 718 East Haizhou Rd., Haining, Zhejiang, 314400, China
| | - Miaomiao Wen
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, 430072, China
| | - Suhong Xu
- Center for Stem Cell and Regenerative Medicine and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
- The Zhejiang University-University of Edinburgh Institute, 718 East Haizhou Rd., Haining, Zhejiang, 314400, China.
| | - Yu Zhou
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, 430072, China.
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China.
- State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, China.
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
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31
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Teague CD, Markovic T, Zhou X, Martinez-Rivera FJ, Minier-Toribio A, Zinsmaier A, Pulido NV, Schmidt KH, Lucerne KE, Godino A, van der Zee YY, Ramakrishnan A, Futamura R, Browne CJ, Holt LM, Yim YY, Azizian CH, Walker DM, Shen L, Dong Y, Zhang B, Nestler EJ. Circuit-Wide Gene Network Analysis Reveals Sex-Specific Roles for Phosphodiesterase 1b in Cocaine Addiction. J Neurosci 2024; 44:e1327232024. [PMID: 38637154 PMCID: PMC11154853 DOI: 10.1523/jneurosci.1327-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 03/21/2024] [Accepted: 04/01/2024] [Indexed: 04/20/2024] Open
Abstract
Cocaine use disorder is a significant public health issue without an effective pharmacological treatment. Successful treatments are hindered in part by an incomplete understanding of the molecular mechanisms that underlie long-lasting maladaptive plasticity and addiction-like behaviors. Here, we leverage a large RNA sequencing dataset to generate gene coexpression networks across six interconnected regions of the brain's reward circuitry from mice that underwent saline or cocaine self-administration. We identify phosphodiesterase 1b (Pde1b), a Ca2+/calmodulin-dependent enzyme that increases cAMP and cGMP hydrolysis, as a central hub gene within a nucleus accumbens (NAc) gene module that was bioinformatically associated with addiction-like behavior. Chronic cocaine exposure increases Pde1b expression in NAc D2 medium spiny neurons (MSNs) in male but not female mice. Viral-mediated Pde1b overexpression in NAc reduces cocaine self-administration in female rats but increases seeking in both sexes. In female mice, overexpressing Pde1b in D1 MSNs attenuates the locomotor response to cocaine, with the opposite effect in D2 MSNs. Overexpressing Pde1b in D1/D2 MSNs had no effect on the locomotor response to cocaine in male mice. At the electrophysiological level, Pde1b overexpression reduces sEPSC frequency in D1 MSNs and regulates the excitability of NAc MSNs. Lastly, Pde1b overexpression significantly reduced the number of differentially expressed genes (DEGs) in NAc following chronic cocaine, with discordant effects on gene transcription between sexes. Together, we identify novel gene modules across the brain's reward circuitry associated with addiction-like behavior and explore the role of Pde1b in regulating the molecular, cellular, and behavioral responses to cocaine.
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Affiliation(s)
- Collin D Teague
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Tamara Markovic
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Freddyson J Martinez-Rivera
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Angelica Minier-Toribio
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Alexander Zinsmaier
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Nathalia V Pulido
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Kyra H Schmidt
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Kelsey E Lucerne
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Arthur Godino
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Yentl Y van der Zee
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Rita Futamura
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Caleb J Browne
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Leanne M Holt
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Yun Young Yim
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Corrine H Azizian
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Deena M Walker
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon 97239
| | - Li Shen
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Yan Dong
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Eric J Nestler
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029
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32
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Lichner Z, Ding M, Khare T, Dan Q, Benitez R, Praszner M, Song X, Saleeb R, Hinz B, Pei Y, Szászi K, Kapus A. Myocardin-Related Transcription Factor Mediates Epithelial Fibrogenesis in Polycystic Kidney Disease. Cells 2024; 13:984. [PMID: 38891116 PMCID: PMC11172104 DOI: 10.3390/cells13110984] [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: 04/19/2024] [Revised: 05/21/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Polycystic kidney disease (PKD) is characterized by extensive cyst formation and progressive fibrosis. However, the molecular mechanisms whereby the loss/loss-of-function of Polycystin 1 or 2 (PC1/2) provokes fibrosis are largely unknown. The small GTPase RhoA has been recently implicated in cystogenesis, and we identified the RhoA/cytoskeleton/myocardin-related transcription factor (MRTF) pathway as an emerging mediator of epithelium-induced fibrogenesis. Therefore, we hypothesized that MRTF is activated by PC1/2 loss and plays a critical role in the fibrogenic reprogramming of the epithelium. The loss of PC1 or PC2, induced by siRNA in vitro, activated RhoA and caused cytoskeletal remodeling and robust nuclear MRTF translocation and overexpression. These phenomena were also manifested in PKD1 (RC/RC) and PKD2 (WS25/-) mice, with MRTF translocation and overexpression occurring predominantly in dilated tubules and the cyst-lining epithelium, respectively. In epithelial cells, a large cohort of PC1/PC2 downregulation-induced genes was MRTF-dependent, including cytoskeletal, integrin-related, and matricellular/fibrogenic proteins. Epithelial MRTF was necessary for the paracrine priming of the fibroblast-myofibroblast transition. Thus, MRTF acts as a prime inducer of epithelial fibrogenesis in PKD. We propose that RhoA is a common upstream inducer of both histological hallmarks of PKD: cystogenesis and fibrosis.
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Affiliation(s)
- Zsuzsanna Lichner
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Toronto, ON M5B 1T8, Canada; (Z.L.); (T.K.); (R.S.); (K.S.)
| | - Mei Ding
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Toronto, ON M5B 1T8, Canada; (Z.L.); (T.K.); (R.S.); (K.S.)
| | - Tarang Khare
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Toronto, ON M5B 1T8, Canada; (Z.L.); (T.K.); (R.S.); (K.S.)
- Enrich Bioscience, Toronto, ON M5B 1T8, Canada
| | - Qinghong Dan
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Toronto, ON M5B 1T8, Canada; (Z.L.); (T.K.); (R.S.); (K.S.)
| | - Raquel Benitez
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Toronto, ON M5B 1T8, Canada; (Z.L.); (T.K.); (R.S.); (K.S.)
| | - Mercédesz Praszner
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Toronto, ON M5B 1T8, Canada; (Z.L.); (T.K.); (R.S.); (K.S.)
| | - Xuewen Song
- Division of Nephrology, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Rola Saleeb
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Toronto, ON M5B 1T8, Canada; (Z.L.); (T.K.); (R.S.); (K.S.)
- Department of Laboratory Medicine and Pathobiology, Temerty School of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Boris Hinz
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Toronto, ON M5B 1T8, Canada; (Z.L.); (T.K.); (R.S.); (K.S.)
- Faculty of Dentistry, University of Toronto, Toronto, ON M5G 1G6, Canada
| | - York Pei
- Division of Nephrology, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Katalin Szászi
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Toronto, ON M5B 1T8, Canada; (Z.L.); (T.K.); (R.S.); (K.S.)
- Department of Laboratory Medicine and Pathobiology, Temerty School of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Surgery, University of Toronto, Toronto, ON M5T 1P5, Canada
| | - András Kapus
- Keenan Research Centre for Biomedical Science, St. Michael’s Hospital, Toronto, ON M5B 1T8, Canada; (Z.L.); (T.K.); (R.S.); (K.S.)
- Department of Surgery, University of Toronto, Toronto, ON M5T 1P5, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
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33
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Martin MV, Aguilar-Rosas S, Franke K, Pieterse M, Langelaar JV, Schreurs R, Bijlsma MF, Besselink MG, Koster J, Timens W, Khasraw M, Ashley DM, Keir ST, Ottensmeier CH, King EV, Verheij J, Waasdorp C, Valk PJM, Engels SAG, Oostenbach E, van Dinter JT, Hofman DA, Mok JY, van Esch WJE, Wilmink H, Monkhorst K, Verheul HMW, Poel D, Hiltermann TJN, Kempen LCLTV, Groen HJM, Aerts JGJV, Heesch SV, Löwenberg B, Plasterk R, Kloosterman WP. The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy. Cancer Immunol Res 2024; 12:759-778. [PMID: 38573707 DOI: 10.1158/2326-6066.cir-23-0158] [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: 02/21/2023] [Revised: 09/22/2023] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
Identification of immunogenic cancer neoantigens as targets for therapy is challenging. Here, we integrate the whole-genome and long-read transcript sequencing of cancers to identify the collection of neo-open reading frame peptides (NOP) expressed in tumors. We termed this collection of NOPs the tumor framome. NOPs represent tumor-specific peptides that are different from wild-type proteins and may be strongly immunogenic. We describe a class of hidden NOPs that derive from structural genomic variants involving an upstream protein coding gene driving expression and translation of noncoding regions of the genome downstream of a rearrangement breakpoint, i.e., where no gene annotation or evidence for transcription exists. The entire collection of NOPs represents a vast number of possible neoantigens particularly in tumors with many structural genomic variants and a low number of missense mutations. We show that NOPs are immunogenic and epitopes derived from NOPs can bind to MHC class I molecules. Finally, we provide evidence for the presence of memory T cells specific for hidden NOPs in peripheral blood from a patient with lung cancer. This work highlights NOPs as a major source of possible neoantigens for personalized cancer immunotherapy and provides a rationale for analyzing the complete cancer genome and transcriptome as a basis for the detection of NOPs.
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Affiliation(s)
| | | | - Katka Franke
- CureVac Netherlands B.V., Amsterdam, the Netherlands
| | - Mark Pieterse
- CureVac Netherlands B.V., Amsterdam, the Netherlands
| | | | | | - Maarten F Bijlsma
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Marc G Besselink
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
- Amsterdam UMC, location University of Amsterdam, Department of Surgery, Amsterdam, the Netherlands
| | - Jan Koster
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University, Medical Center Groningen, the Netherlands
| | - Mustafa Khasraw
- Duke University Medical Center, Duke University, Durham, North Carolina
| | - David M Ashley
- Preston Robert Tisch Brain Tumor Center, Department of Neurosurgery, Duke University, Durham, North Carolina
| | - Stephen T Keir
- Duke University Medical Center, Duke University, Durham, North Carolina
| | - Christian H Ottensmeier
- Liverpool Head and Neck Centre, Institute of Systems, Molecular and Integrative Biology, University of Liverpool and Clatterbridge Cancer Center NHS Foundation Trust, Liverpool, UK
| | - Emma V King
- Department of Otorhinolaryngology, Head and Neck Surgery, Poole Hospital, Poole, UK
| | - Joanne Verheij
- Amsterdam UMC, location University of Amsterdam, Department of Pathology, Amsterdam, the Netherlands
| | - Cynthia Waasdorp
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | - Peter J M Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sem A G Engels
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Ellen Oostenbach
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Jip T van Dinter
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Damon A Hofman
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Juk Yee Mok
- Sanquin Reagents, Sanquin, Amsterdam, the Netherlands
| | | | - Hanneke Wilmink
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
- Amsterdam UMC, location University of Amsterdam, Department of Medical Oncology, Amsterdam, the Netherlands
| | - Kim Monkhorst
- Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Dennis Poel
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the, Netherlands
| | - T Jeroen N Hiltermann
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Léon C L T van Kempen
- Department of Pathology and Medical Biology, University of Groningen, University, Medical Center Groningen, the Netherlands
- University of Antwerp, Antwerp University Hospital, Edegem, Belgium
| | - Harry J M Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, the Netherlands
| | | | | | - Bob Löwenberg
- CureVac Netherlands B.V., Amsterdam, the Netherlands
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Martin P, Szkop KJ, Robert F, Bhattacharyya S, Beauchamp RL, Brenner J, Redmond NE, Huang S, Erdin S, Larsson O, Ramesh V. TSC2 loss in neural progenitor cells suppresses translation of ASD/NDD-associated transcripts in an mTORC1- and MNK1/2-reversible fashion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597393. [PMID: 38895292 PMCID: PMC11185676 DOI: 10.1101/2024.06.04.597393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Tuberous sclerosis complex (TSC), an inherited neurodevelopmental (ND) disorder with frequent manifestations of epilepsy and autism spectrum disorder (ASD). TSC is caused by mutations in TSC1 or TSC2 tumor suppressor genes, with encoded proteins hamartin/TSC1 and tuberin/TSC2 forming a functional complex inhibiting mechanistic target of rapamycin complex-1 (mTORC1) signaling, leading to FDA-approved allosteric mTORC1-selective rapamycin analogs for TSC tumors. Rapalogs are effective for TSC-associated hamartomas, however, they are not effective for treating ND manifestations. mTORC1 signaling plays an essential role in protein synthesis through mTORC1-eIF4F and MNK-eIF4E-mediated mRNA translation. Further, the effects on mRNA translation by specific mTORC1 and MNK inhibitors such as RMC-6272 and eFT-508 in TSC have never been explored. Here, employing CRISPR-modified, isogenic TSC2 patient-derived neural progenitor cells (NPCs), we have examined mRNA translation upon loss of TSC2 . Our results reveal dysregulated translation in TSC2 -Null NPCs, which significantly overlap with the translatome from TSC1 -Null NPCs, which we reported recently. Most notably, numerous non-monogenic ASD-NDD- and epilepsy-associated genes identified in patients harboring putative loss-of-function mutations, including protein truncating, or damaging missense variants, were translationally suppressed in TSC2 -Null NPCs, and their translation were reversed upon RMC-6272 or eFT-508 treatment. Our study here establishes the importance of mTORC1-eIF4F and MNK-eIF4E-mediated mRNA translation in TSC, ASD and other neurodevelopmental disorders and lay the groundwork for evaluating drugs in clinical development that target these pathways as a treatment strategy for TSC as well as ASD/NDD.
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Sztuka M, Kotlarz K, Mielczarek M, Hajduk P, Liu J, Szyda J. Nextflow vs. plain bash: different approaches to the parallelization of SNP calling from the whole genome sequence data. NAR Genom Bioinform 2024; 6:lqae040. [PMID: 38686136 PMCID: PMC11057021 DOI: 10.1093/nargab/lqae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/28/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
This study compared computational approaches to parallelization of an SNP calling workflow. The data comprised DNA from five Holstein-Friesian cows sequenced with the Illumina platform. The pipeline consisted of quality control, alignment to the reference genome, post-alignment, and SNP calling. Three approaches to parallelization were compared: (i) a plain Bash script in which a pipeline for each cow was executed as separate processes invoked at the same time, (ii) a Bash script wrapped in a single Nextflow process and (iii) a Nextflow script with each component of the pipeline defined as a separate process. The results demonstrated that on average, the multi-process Nextflow script performed 15-27% faster depending on the number of assigned threads, with the biggest execution time advantage over the plain Bash approach observed with 10 threads. In terms of RAM usage, the most substantial variation was observed for the multi-process Nextflow, for which it increased with the number of assigned threads, while RAM consumption of the other setups did not depend much on the number of threads assigned for computations. Due to intermediate and log files generated, disk usage was markedly higher for the multi-process Nextflow than for the plain Bash and for the single-process Nextflow.
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Affiliation(s)
- Marek Sztuka
- Wroclaw University of Environmental and Life Sciences, Department of Genetics, the Biostatistics Group Kozuchowska 7, Wroclaw PL-51631, Poland
| | - Krzysztof Kotlarz
- Wroclaw University of Environmental and Life Sciences, Department of Genetics, the Biostatistics Group Kozuchowska 7, Wroclaw PL-51631, Poland
- University Cancer Diagnostic Center, Poznan University of Medical Science, Fredry 10, Poznan 61-701, Poland
| | - Magda Mielczarek
- Wroclaw University of Environmental and Life Sciences, Department of Genetics, the Biostatistics Group Kozuchowska 7, Wroclaw PL-51631, Poland
- University Cancer Diagnostic Center, Poznan University of Medical Science, Fredry 10, Poznan 61-701, Poland
| | - Piotr Hajduk
- Wroclaw University of Environmental and Life Sciences, Department of Genetics, the Biostatistics Group Kozuchowska 7, Wroclaw PL-51631, Poland
| | - Jakub Liu
- University Cancer Diagnostic Center, Poznan University of Medical Science, Fredry 10, Poznan 61-701, Poland
- Wroclaw University of Environmental and Life Sciences, Department of Genetics, the Biostatistics Group Kozuchowska 7, Wroclaw PL-51631, Poland
| | - Joanna Szyda
- Wroclaw University of Environmental and Life Sciences, Department of Genetics, the Biostatistics Group Kozuchowska 7, Wroclaw PL-51631, Poland
- University Cancer Diagnostic Center, Poznan University of Medical Science, Fredry 10, Poznan 61-701, Poland
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Suwakulsiri W, Xu R, Rai A, Chen M, Shafiq A, Greening DW, Simpson RJ. Transcriptomic analysis and fusion gene identifications of midbody remnants released from colorectal cancer cells reveals they are molecularly distinct from exosomes and microparticles. Proteomics 2024; 24:e2300058. [PMID: 38470197 DOI: 10.1002/pmic.202300058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/13/2024]
Abstract
Previously, we reported that human primary (SW480) and metastatic (SW620) colorectal (CRC) cells release three classes of membrane-encapsulated extracellular vesicles (EVs); midbody remnants (MBRs), exosomes (Exos), and microparticles (MPs). We reported that MBRs were molecularly distinct at the protein level. To gain further biochemical insights into MBRs, Exos, and MPs and their emerging role in CRC, we performed, and report here, for the first time, a comprehensive transcriptome and long noncoding RNA sequencing analysis and fusion gene identification of these three EV classes using the next-generation RNA sequencing technique. Differential transcript expression analysis revealed that MBRs have a distinct transcriptomic profile compared to Exos and MPs with a high enrichment of mitochondrial transcripts lncRNA/pseudogene transcripts that are predicted to bind to ribonucleoprotein complexes, spliceosome, and RNA/stress granule proteins. A salient finding from this study is a high enrichment of several fusion genes in MBRs compared to Exos, MPs, and cell lysates from their parental cells such as MSH2 (gene encoded DNA mismatch repair protein MSH2). This suggests potential EV-liquid biopsy targets for cancer detection. Importantly, the expression of cancer progression-related transcripts found in EV classes derived from SW480 (EGFR) and SW620 (MET and MACCA1) cell lines reflects their parental cell types. Our study is the report of RNA and fusion gene compositions within MBRs (including Exos and MPs) that could have an impact on EV functionality in cancer progression and detection using EV-based RNA/ fusion gene candidates for cancer biomarkers.
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Affiliation(s)
- Wittaya Suwakulsiri
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science (LIMS), School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
- School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Darlington, New South Wales, Australia
| | - Rong Xu
- Nanobiotechnology Laboratory, Australia Centre for Blood Diseases, Centre Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Alin Rai
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Maoshan Chen
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Centre, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Adnan Shafiq
- Department of Cell & Developmental Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - David W Greening
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard J Simpson
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science (LIMS), School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
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37
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Lane RE, Korbie D, Khanna KK, Mohamed A, Hill MM, Trau M. Defining the relationship between cellular and extracellular vesicle (EV) content in breast cancer via an integrative multi-omic analysis. Proteomics 2024; 24:e2300089. [PMID: 38168906 DOI: 10.1002/pmic.202300089] [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: 05/18/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 01/05/2024]
Abstract
Much recent research has been dedicated to exploring the utility of extracellular vesicles (EVs) as circulating disease biomarkers. Underpinning this work is the assumption that the molecular cargo of EVs directly reflects the originating cell. Few attempts have been made, however, to empirically validate this on the -omic level. To this end, we have performed an integrative multi-omic analysis of a panel of breast cancer cell lines and corresponding EVs. Whole transcriptome analysis validated that the cellular transcriptome remained stable when cultured cells are transitioned to low serum or serum-free medium for EV collection. Transcriptomic profiling of the isolated EVs indicated a positive correlation between transcript levels in cells and EVs, including disease-associated transcripts. Analysis of the EV proteome verified that HER2 protein is present in EVs, however neither the estrogen (ER) nor progesterone (PR) receptor proteins are detected regardless of cellular expression. Using multivariate analysis, we derived an EV protein signature to infer cellular patterns of ER and HER2 expression, though the ER protein could not be directly detected. Integrative analyses affirmed that the EV proteome and transcriptome captured key phenotypic hallmarks of the originating cells, supporting the potential of EVs for non-invasive monitoring of breast cancers.
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Affiliation(s)
- Rebecca E Lane
- Australian Institute for Bioengineering and Nanotechnology, Centre for Personalised Nanomedicine, The University of Queensland, St Lucia, Queensland, Australia
| | - Darren Korbie
- Australian Institute for Bioengineering and Nanotechnology, Centre for Personalised Nanomedicine, The University of Queensland, St Lucia, Queensland, Australia
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Ahmed Mohamed
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Michelle M Hill
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Matt Trau
- Australian Institute for Bioengineering and Nanotechnology, Centre for Personalised Nanomedicine, The University of Queensland, St Lucia, Queensland, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
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38
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Welch N, Mishra S, Bellar A, Kannan P, Gopan A, Goudarzi M, King J, Luknis M, Musich R, Agrawal V, Bena J, Koch CJ, Li L, Willard B, Shah YM, Dasarathy S. Differential impact of sex on regulation of skeletal muscle mitochondrial function and protein homeostasis by hypoxia-inducible factor-1α in normoxia. J Physiol 2024; 602:2763-2806. [PMID: 38761133 PMCID: PMC11178475 DOI: 10.1113/jp285339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 04/19/2024] [Indexed: 05/20/2024] Open
Abstract
Hypoxia-inducible factor (HIF)-1α is continuously synthesized and degraded in normoxia. During hypoxia, HIF1α stabilization restricts cellular/mitochondrial oxygen utilization. Cellular stressors can stabilize HIF1α even during normoxia. However, less is known about HIF1α function(s) and sex-specific effects during normoxia in the basal state. Since skeletal muscle is the largest protein store in mammals and protein homeostasis has high energy demands, we determined HIF1α function at baseline during normoxia in skeletal muscle. Untargeted multiomics data analyses were followed by experimental validation in differentiated murine myotubes with loss/gain of function and skeletal muscle from mice without/with post-natal muscle-specific Hif1a deletion (Hif1amsd). Mitochondrial oxygen consumption studies using substrate, uncoupler, inhibitor, titration protocols; targeted metabolite quantification by gas chromatography-mass spectrometry; and post-mitotic senescence markers using biochemical assays were performed. Multiomics analyses showed enrichment in mitochondrial and cell cycle regulatory pathways in Hif1a deleted cells/tissue. Experimentally, mitochondrial oxidative functions and ATP content were higher with less mitochondrial free radical generation with Hif1a deletion. Deletion of Hif1a also resulted in higher concentrations of TCA cycle intermediates and HIF2α proteins in myotubes. Overall responses to Hif1amsd were similar in male and female mice, but changes in complex II function, maximum respiration, Sirt3 and HIF1β protein expression and muscle fibre diameter were sex-dependent. Adaptive responses to hypoxia are mediated by stabilization of constantly synthesized HIF1α. Despite rapid degradation, the presence of HIF1α during normoxia contributes to lower mitochondrial oxidative efficiency and greater post-mitotic senescence in skeletal muscle. In vivo responses to HIF1α in skeletal muscle were differentially impacted by sex. KEY POINTS: Hypoxia-inducible factor -1α (HIF1α), a critical transcription factor, undergoes continuous synthesis and proteolysis, enabling rapid adaptive responses to hypoxia by reducing mitochondrial oxygen consumption. In mammals, skeletal muscle is the largest protein store which is determined by a balance between protein synthesis and breakdown and is sensitive to mitochondrial oxidative function. To investigate the functional consequences of transient HIF1α expression during normoxia in the basal state, myotubes and skeletal muscle from male and female mice with HIF1α knockout were studied using complementary multiomics, biochemical and metabolite assays. HIF1α knockout altered the electron transport chain, mitochondrial oxidative function, signalling molecules for protein homeostasis, and post-mitotic senescence markers, some of which were differentially impacted by sex. The cost of rapid adaptive responses mediated by HIF1α is lower mitochondrial oxidative efficiency and post-mitotic senescence during normoxia.
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Affiliation(s)
- Nicole Welch
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Saurabh Mishra
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Annette Bellar
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Pugazhendhi Kannan
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Amrit Gopan
- KEM Hospital, Seth GS Medical College, Mumbai, India
| | - Maryam Goudarzi
- Respiratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jasmine King
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Mathew Luknis
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Ryan Musich
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - Vandana Agrawal
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
| | - James Bena
- Quantitative Health, Cleveland Clinic, Cleveland, Ohio, USA
| | | | - Ling Li
- Proteomics and Metabolomics Core, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Belinda Willard
- Proteomics and Metabolomics Core, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yatrik M Shah
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Srinivasan Dasarathy
- Departments of Inflammation and Immunity, Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA
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MacFawn I, Farris J, Pifer P, Margaryan NV, Akhter H, Wang L, Dziadowicz S, Denvir J, Hu G, Frisch SM. Grainyhead-like-2, an epithelial master programmer, promotes interferon induction and suppresses breast cancer recurrence. Mol Immunol 2024; 170:156-169. [PMID: 38692097 PMCID: PMC11106721 DOI: 10.1016/j.molimm.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024]
Abstract
Type-I and -III interferons play a central role in immune rejection of pathogens and tumors, thus promoting immunogenicity and suppressing tumor recurrence. Double strand RNA is an important ligand that stimulates tumor immunity via interferon responses. Differentiation of embryonic stem cells to pluripotent epithelial cells activates the interferon response during development, raising the question of whether epithelial vs. mesenchymal gene signatures in cancer potentially regulate the interferon pathway as well. Here, using genomics and signaling approaches, we show that Grainyhead-like-2 (GRHL2), a master programmer of epithelial cell identity, promotes type-I and -III interferon responses to double-strand RNA. GRHL2 enhanced the activation of IRF3 and relA/NF-kB and the expression of IRF1; a functional GRHL2 binding site in the IFNL1 promoter was also identified. Moreover, time to recurrence in breast cancer correlated positively with GRHL2 protein expression, indicating that GRHL2 is a tumor recurrence suppressor, consistent with its enhancement of interferon responses. These observations demonstrate that epithelial cell identity supports interferon responses in the context of cancer.
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Affiliation(s)
- Ian MacFawn
- Department of Immunology, University of Pittsburgh, 5051 Centre Avenue, Pittsburgh, PA 15213, USA; UPMC Hillman Cancer Center, 5115 Centre Avenue, Pittsburgh, PA 15232, USA
| | - Joshua Farris
- Wake Forest University, Department of Radiation Oncology, 1 Medical Center Blvd., Winston-Salem, NC 27157, USA
| | - Phillip Pifer
- Department of Radiation Oncology, WVU Cancer Institute, 1 Medical Drive, Morgantown, WV, USA
| | - Naira V Margaryan
- WVU Cancer Institute, West Virginia University, 64 Medical Center Drive, Morgantown, WV 26506, USA
| | - Halima Akhter
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, 64 Medical Center Drive, Box 9142, Morgantown, WV 26505, USA
| | - Lei Wang
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, 64 Medical Center Drive, Box 9142, Morgantown, WV 26505, USA
| | - Sebastian Dziadowicz
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, 64 Medical Center Drive, Box 9142, Morgantown, WV 26505, USA
| | - James Denvir
- Byrd Biotechnology Center, Marshall University, One John Marshall Drive, Huntington, WV 25701, USA
| | - Gangqing Hu
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, 64 Medical Center Drive, Box 9142, Morgantown, WV 26505, USA.
| | - Steven M Frisch
- Department of Biochemistry and Molecular Medicine, 64 Medical Center Drive, Box 9142, West Virginia University, Morgantown, WV 26506.
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Behrens K, Kauppi M, Viney EM, Kueh AJ, Hyland CD, Willson TA, Salleh L, de Graaf CA, Babon JJ, Herold MJ, Nicola NA, Alexander WS. Differential in vivo roles of Mpl cytoplasmic tyrosine residues in murine hematopoiesis and myeloproliferative disease. Leukemia 2024; 38:1342-1352. [PMID: 38491305 PMCID: PMC11147766 DOI: 10.1038/s41375-024-02219-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 03/18/2024]
Abstract
Thrombopoietin (Tpo), which binds to its specific receptor, the Mpl protein, is the major cytokine regulator of megakaryopoiesis and circulating platelet number. Tpo binding to Mpl triggers activation of Janus kinase 2 (Jak2) and phosphorylation of the receptor, as well as activation of several intracellular signalling cascades that mediate cellular responses. Three tyrosine (Y) residues in the C-terminal region of the Mpl intracellular domain have been implicated as sites of phosphorylation required for regulation of major Tpo-stimulated signalling pathways: Mpl-Y565, Mpl-Y599 and Mpl-Y604. Here, we have introduced mutations in the mouse germline and report a consistent physiological requirement for Mpl-Y599, mutation of which resulted in thrombocytopenia, deficient megakaryopoiesis, low hematopoietic stem cell (HSC) number and function, and attenuated responses to myelosuppression. We further show that in models of myeloproliferative neoplasms (MPN), where Mpl is required for pathogenesis, thrombocytosis was dependent on intact Mpl-Y599. In contrast, Mpl-Y565 was required for negative regulation of Tpo responses; mutation of this residue resulted in excess megakaryopoiesis at steady-state and in response to myelosuppression, and exacerbated thrombocytosis associated with MPN.
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Affiliation(s)
- Kira Behrens
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Maria Kauppi
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Elizabeth M Viney
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Andrew J Kueh
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia
- School of Cancer Medicine, La Trobe University, Heidelberg, VIC, 3084, Australia
| | - Craig D Hyland
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Tracy A Willson
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Liam Salleh
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Carolyn A de Graaf
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jeffrey J Babon
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Marco J Herold
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia
- School of Cancer Medicine, La Trobe University, Heidelberg, VIC, 3084, Australia
| | - Nicos A Nicola
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Warren S Alexander
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
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Sun P, Yuan H, Pan J, Wu Z, Li W, Wang X, Kuang H, Chen J. A WOX homolog disrupted by a transposon led to the loss of spines and contributed to the domestication of lettuce. THE NEW PHYTOLOGIST 2024; 242:2857-2871. [PMID: 38584520 DOI: 10.1111/nph.19738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/22/2024] [Indexed: 04/09/2024]
Abstract
The loss of spines is one of the most important domestication traits for lettuce (Lactuca sativa). However, the genetics and regulation of spine development in lettuce remain unclear. We examined the genetics of spines in lettuce using a segregating population derived from a cross between cultivated and wild lettuce (Lactuca serriola). A gene encoding WUSCHEL-related homeobox transcription factor, named as WOX-SPINE1 (WS1), was identified as the candidate gene controlling the spine development in lettuce, and its function on spines was verified. A CACTA transposon was found to be inserted into the first exon of the ws1 allele, knocking out its function and leading to the lack of spines in cultivated lettuce. All lettuce cultivars investigated have the nonfunctional ws1 gene, and a selection sweep was found at the WS1 locus, suggesting its important role in lettuce domestication. The expression levels of WS1 were associated with the density of spines among different accessions of wild lettuce. At least two independent loss-of-function mutations in the ws1 gene caused the loss of spines in wild lettuce. These findings provide new insights into the development of spines and facilitate the exploitation of wild genetic resources in future lettuce breeding programs.
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Affiliation(s)
- Peinan Sun
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Huanran Yuan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Jiangpeng Pan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhihao Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Weibo Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Xin Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Hanhui Kuang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
| | - Jiongjiong Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, China
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Hasan A, Macias JJ, Wood B, Malone-Perez M, Park G, Foster CA, Frazer JK. Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1733-1743. [PMID: 38656392 PMCID: PMC11163880 DOI: 10.4049/jimmunol.2300495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/23/2024] [Indexed: 04/26/2024]
Abstract
The thymus is the site of T lymphocyte development and T cell education to recognize foreign, but not self, Ags. B cells also reside and develop in the thymus, although their functions are less clear. During "thymic involution," a process of lymphoid atrophy and adipose replacement linked to sexual maturation, thymocytes decline. However, thymic B cells decrease far less than T cells, such that B cells comprise ∼1% of human neonatal thymocytes but up to ∼10% in adults. All jawed vertebrates possess a thymus, and we and others have shown zebrafish (Danio rerio) also have thymic B cells. In this article, we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte-specific, fluorophore-labeled transgenic lines, quantifying the changes in thymic T- and B-lymphocytes pre- versus postinvolution. Our results prove that, as in humans, zebrafish thymic B cells increase relative to T cells postinvolution. We also performed RNA sequencing on D. rerio thymic and marrow lymphocytes of four novel double-transgenic lines, identifying distinct populations of immature T and B cells. Collectively, this is, to our knowledge, the first comprehensive analysis of zebrafish thymic involution, demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies.
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Affiliation(s)
- Ameera Hasan
- Dept. of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jose J. Macias
- Dept. of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Brashé Wood
- Pediatrics, Section of Pediatric Hematology-Oncology, and University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Megan Malone-Perez
- Pediatrics, Section of Pediatric Hematology-Oncology, and University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Gilseung Park
- Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Clay A. Foster
- Pediatrics, Section of Pediatric Hematology-Oncology, and University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - J. Kimble Frazer
- Dept. of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Pediatrics, Section of Pediatric Hematology-Oncology, and University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
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43
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Pekayvaz K, Losert C, Knottenberg V, Gold C, van Blokland IV, Oelen R, Groot HE, Benjamins JW, Brambs S, Kaiser R, Gottschlich A, Hoffmann GV, Eivers L, Martinez-Navarro A, Bruns N, Stiller S, Akgöl S, Yue K, Polewka V, Escaig R, Joppich M, Janjic A, Popp O, Kobold S, Petzold T, Zimmer R, Enard W, Saar K, Mertins P, Huebner N, van der Harst P, Franke LH, van der Wijst MGP, Massberg S, Heinig M, Nicolai L, Stark K. Multiomic analyses uncover immunological signatures in acute and chronic coronary syndromes. Nat Med 2024; 30:1696-1710. [PMID: 38773340 PMCID: PMC11186793 DOI: 10.1038/s41591-024-02953-4] [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: 05/02/2023] [Accepted: 03/26/2024] [Indexed: 05/23/2024]
Abstract
Acute and chronic coronary syndromes (ACS and CCS) are leading causes of mortality. Inflammation is considered a key pathogenic driver of these diseases, but the underlying immune states and their clinical implications remain poorly understood. Multiomic factor analysis (MOFA) allows unsupervised data exploration across multiple data types, identifying major axes of variation and associating these with underlying molecular processes. We hypothesized that applying MOFA to multiomic data obtained from blood might uncover hidden sources of variance and provide pathophysiological insights linked to clinical needs. Here we compile a longitudinal multiomic dataset of the systemic immune landscape in both ACS and CCS (n = 62 patients in total, n = 15 women and n = 47 men) and validate this in an external cohort (n = 55 patients in total, n = 11 women and n = 44 men). MOFA reveals multicellular immune signatures characterized by distinct monocyte, natural killer and T cell substates and immune-communication pathways that explain a large proportion of inter-patient variance. We also identify specific factors that reflect disease state or associate with treatment outcome in ACS as measured using left ventricular ejection fraction. Hence, this study provides proof-of-concept evidence for the ability of MOFA to uncover multicellular immune programs in cardiovascular disease, opening new directions for mechanistic, biomarker and therapeutic studies.
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Grants
- Deutsche Forschungsgemeinschaft (German Research Foundation)
- Deutsches Zentrum fr Herz-Kreislaufforschung (Deutsches Zentrum fr Herz-Kreislaufforschung e.V.)
- Deutsche Herzstiftung e.V., Frankfurt a.M. Institutional Strategy LMUexcellent of LMU Munich Else-Krner-Fresenius Stiftung DFG Clinician Scientist Programme PRIME DZHK Sule B Antrag DZHK B 21-014 SE
- Was supported by the Helmholtz Association under the joint research school ;Munich School for Data Science MUDS
- DFG GO 3823/1-1, grant number: 510821390 Frderprogramm fr Forschung und Lehre der Medizinischen Fakultt der LMU the Bavarian Cancer Research Center (BZKF) Else Kroner-Fresenius-Stiftung
- Was supported by a grant from the Frderprogramm fur Forschung und Lehre (FFoLe) of the Ludwig Maximilian University (LMU) of Munich.
- DFG SFB 1123, Z02
- DFG EN 1093/2-1
- DFG KO5055-2-1 and KO5055/3-1 the Bavarian Cancer Research Center (BZKF) the international doctoral program i-Target: immunotargeting of cancer the Melanoma Research Alliance (grant number 409510), Marie Sklodowska-Curie Training Network for Optimizing Adoptive T Cell Therapy of Cancer (funded by the Horizon 2020 programme of the European Union; grant 955575), Else Kroner-Fresenius-Stiftung (IOLIN), German Cancer Aid (AvantCAR.de), the Wilhelm-Sander-Stiftung, Ernst Jung Stiftung, Institutional Strategy LMUexcellent of LMU Munich (within the framework of the German Excellence Initiative), the Go-Bio-Initiative, the m4-Award of the Bavarian Ministry for Economical Affairs, Bundesministerium fur Bildung und Forschung, European Research Council (Starting Grant 756017 and PoC Grant 101100460, by the SFB-TRR 338/1 2021452881907, Fritz-Bender Foundation, Deutsche Jose#x0301; Carreras Leuk#x00E4;mie Stiftung, Hector Foundation, the Bavarian Research Foundation, the Bruno and Helene J#x00F6;ster Foundation (360#x00B0; CAR)
- T.P. from the DFG (PE 2704/3-1)
- DFG SFB1243, A14 DFG EN 1093/2-1,
- DZHK Säule B Antrag DZHK B 21-014 SE
- DZHK Säule B Antrag DZHK B 21-014 SE DFG SFB-1470-B03 the Chan Zuckerberg Foundation ERC Advanced Grant under the European Union Horizon 2020 Research and Innovation Program (AdG788970)
- Deutsche Forschungsgemeinschaft (DFG) SFB 914, B02 and Z01 DFG SFB 1123, B06 DFG SFB1321, P10 DFG FOR 2033 ERC-2018-ADG German Centre for Cardiovascular Research (DZHK) MHA 1.4VD
- DZHK project 81Z0600106 Supported by the Chan Zuckerberg Foundation
- DZHK S#x00E4;ule B Antrag DZHK B 21-014 SE Deutsche Herzstiftung e.V., Frankfurt a.M. DFG SFB 1123, B06 DFG NI 2219/2-1 Corona Foundation German Centre for Cardiovascular Research (DZHK) Clinician Scientist Programme the Ernst und Berta Grimmke Stiftung the GTH Junior research grant
- DZHK partner site project Deutsche Forschungsgemeinschaft (DFG) SFB 914, B02 DFG SFB 1123, A07 DFG SFB 359, A03 ERC grant 947611
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Affiliation(s)
- Kami Pekayvaz
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.
| | - Corinna Losert
- Institute of Computational Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Computer Science, TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
| | | | - Christoph Gold
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Irene V van Blokland
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Roy Oelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Hilde E Groot
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jan Walter Benjamins
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Sophia Brambs
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Rainer Kaiser
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Adrian Gottschlich
- Department of Medicine III, LMU University Hospital, Munich, Germany
- Division of Clinical Pharmacology, LMU University Hospital, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Gordon Victor Hoffmann
- Division of Clinical Pharmacology, LMU University Hospital, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Luke Eivers
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | | | - Nils Bruns
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Susanne Stiller
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Sezer Akgöl
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Keyang Yue
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Vivien Polewka
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Raphael Escaig
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
| | - Markus Joppich
- Department of Informatics, Ludwig-Maximilian University, Munich, Germany
| | - Aleksandar Janjic
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilian University, Munich, Germany
| | - Oliver Popp
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Sebastian Kobold
- Division of Clinical Pharmacology, LMU University Hospital, Member of the German Center for Lung Research (DZL), Munich, Germany
- German Cancer Consortium (DKTK), a partnership between DKFZ and LMU University Hospital, Partner Site Munich, Munich, Germany
- Einheit für Klinische Pharmakologie (EKLiP), Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Tobias Petzold
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Department of Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum der Charité (DHZC), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Charite-Universitätsmedizin Berlin, Berlin, Germany
| | - Ralf Zimmer
- Department of Informatics, Ludwig-Maximilian University, Munich, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilian University, Munich, Germany
| | - Kathrin Saar
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Norbert Huebner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
- Charite-Universitätsmedizin Berlin, Berlin, Germany
| | - Pim van der Harst
- Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lude H Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Monique G P van der Wijst
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Steffen Massberg
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Matthias Heinig
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.
- Institute of Computational Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany.
- Department of Computer Science, TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
| | - Leo Nicolai
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.
| | - Konstantin Stark
- Medizinische Klinik und Poliklinik I, LMU University Hospital, Munich, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.
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Zhang T, Gao S, Zhang SW, Cui XD. m 6Aexpress-enet: Predicting the regulatory expression m 6A sites by an enet-regularization negative binomial regression model. Methods 2024; 226:61-70. [PMID: 38631404 DOI: 10.1016/j.ymeth.2024.04.011] [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: 03/02/2024] [Revised: 04/04/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
As the most abundant mRNA modification, m6A controls and influences many aspects of mRNA metabolism including the mRNA stability and degradation. However, the role of specific m6A sites in regulating gene expression still remains unclear. In additional, the multicollinearity problem caused by the correlation of methylation level of multiple m6A sites in each gene could influence the prediction performance. To address the above challenges, we propose an elastic-net regularized negative binomial regression model (called m6Aexpress-enet) to predict which m6A site could potentially regulate its gene expression. Comprehensive evaluations on simulated datasets demonstrate that m6Aexpress-enet could achieve the top prediction performance. Applying m6Aexpress-enet on real MeRIP-seq data from human lymphoblastoid cell lines, we have uncovered the complex regulatory pattern of predicted m6A sites and their unique enrichment pathway of the constructed co-methylation modules. m6Aexpress-enet proves itself as a powerful tool to enable biologists to discover the mechanism of m6A regulatory gene expression. Furthermore, the source code and the step-by-step implementation of m6Aexpress-enet is freely accessed at https://github.com/tengzhangs/m6Aexpress-enet.
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Affiliation(s)
- Teng Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an, 710027 Shaanxi, China; School of Computer, Jiangsu University of Science and Technology, ZhenJiang, 212100 JiangSu, China
| | - Shang Gao
- School of Computer, Jiangsu University of Science and Technology, ZhenJiang, 212100 JiangSu, China
| | - Shao-Wu Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an, 710027 Shaanxi, China.
| | - Xiao-Dong Cui
- School of Marine Science and Technology Northwestern Polytechnical University, Xi'an, 710027 Shaanxi, China.
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45
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Yang Q, Zhou X, Fang J, Lin A, Zhang H, Cheng Q, Liu Z, Luo P, Zhang J. Development and validation of a radiosensitivity model to evaluate radiotherapy benefits in pan-cancer. Cancer Sci 2024; 115:1820-1833. [PMID: 38571294 PMCID: PMC11145160 DOI: 10.1111/cas.16168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/05/2024] Open
Abstract
Radiotherapy, one of the most fundamental cancer treatments, is confronted with the dilemma of treatment failure due to radioresistance. To predict the radiosensitivity and improve tumor treatment efficiency in pan-cancer, we developed a model called Radiation Intrinsic Sensitivity Evaluation (RISE). The RISE model was built using cell line-based mRNA sequencing data from five tumor types with varying radiation sensitivity. Through four cell-derived datasets, two public tissue-derived cohorts, and one local cohort of 42 nasopharyngeal carcinoma patients, we demonstrated that RISE could effectively predict the level of radiation sensitivity (area under the ROC curve [AUC] from 0.666 to 1 across different datasets). After the verification by the colony formation assay and flow cytometric analysis of apoptosis, our four well-established radioresistant cell models successfully proved higher RISE values in radioresistant cells by RT-qPCR experiments. We also explored the prognostic value of RISE in five independent TCGA cohorts consisting of 1137 patients who received radiation therapy and found that RISE was an independent adverse prognostic factor (pooled multivariate Cox regression hazard ratio [HR]: 1.84, 95% CI 1.39-2.42; p < 0.01). RISE showed a promising ability to evaluate the radiotherapy benefit while predicting the prognosis of cancer patients, enabling clinicians to make individualized radiotherapy strategies in the future and improve the success rate of radiotherapy.
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Affiliation(s)
- Qi Yang
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Xinyi Zhou
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Jianbo Fang
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Anqi Lin
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Hongman Zhang
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Quan Cheng
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Zaoqu Liu
- Department of Interventional RadiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenanChina
| | - Peng Luo
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
| | - Jian Zhang
- Department of Oncology, Zhujiang HospitalSouthern Medical UniversityGuangzhouChina
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46
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Figueroa KP, Gross C, Buena-Atienza E, Paul S, Gandelman M, Kakar N, Sturm M, Casadei N, Admard J, Park J, Zühlke C, Hellenbroich Y, Pozojevic J, Balachandran S, Händler K, Zittel S, Timmann D, Erdlenbruch F, Herrmann L, Feindt T, Zenker M, Klopstock T, Dufke C, Scoles DR, Koeppen A, Spielmann M, Riess O, Ossowski S, Haack TB, Pulst SM. A GGC-repeat expansion in ZFHX3 encoding polyglycine causes spinocerebellar ataxia type 4 and impairs autophagy. Nat Genet 2024; 56:1080-1089. [PMID: 38684900 DOI: 10.1038/s41588-024-01719-5] [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: 11/03/2023] [Accepted: 03/18/2024] [Indexed: 05/02/2024]
Abstract
Despite linkage to chromosome 16q in 1996, the mutation causing spinocerebellar ataxia type 4 (SCA4), a late-onset sensory and cerebellar ataxia, remained unknown. Here, using long-read single-strand whole-genome sequencing (LR-GS), we identified a heterozygous GGC-repeat expansion in a large Utah pedigree encoding polyglycine (polyG) in zinc finger homeobox protein 3 (ZFHX3), also known as AT-binding transcription factor 1 (ATBF1). We queried 6,495 genome sequencing datasets and identified the repeat expansion in seven additional pedigrees. Ultrarare DNA variants near the repeat expansion indicate a common distant founder event in Sweden. Intranuclear ZFHX3-p62-ubiquitin aggregates were abundant in SCA4 basis pontis neurons. In fibroblasts and induced pluripotent stem cells, the GGC expansion led to increased ZFHX3 protein levels and abnormal autophagy, which were normalized with small interfering RNA-mediated ZFHX3 knockdown in both cell types. Improving autophagy points to a therapeutic avenue for this novel polyG disease. The coding GGC-repeat expansion in an extremely G+C-rich region was not detectable by short-read whole-exome sequencing, which demonstrates the power of LR-GS for variant discovery.
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Affiliation(s)
- Karla P Figueroa
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
| | - Caspar Gross
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
| | - Elena Buena-Atienza
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
| | - Sharan Paul
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
| | - Mandi Gandelman
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
| | - Naseebullah Kakar
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
- Department of Biotechnology, FLS&I, BUITEMS, Quetta, Pakistan
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
| | - Joohyun Park
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Christine Zühlke
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Yorck Hellenbroich
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Jelena Pozojevic
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Saranya Balachandran
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Kristian Händler
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
| | - Simone Zittel
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dagmar Timmann
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), Essen University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Friedrich Erdlenbruch
- Department of Neurology and Center for Translational Neuro- and Behavioral Sciences (C-TNBS), Essen University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Laura Herrmann
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg and Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Thomas Klopstock
- Department of Neurology with Friedrich-Baur-Institute, University Hospital of Ludwig-Maximilians-Universität München, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Claudia Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Daniel R Scoles
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
| | | | - Malte Spielmann
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg, Lübeck, Kiel, Lübeck, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- NGS Competence Center Tübingen, Tübingen, Germany.
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen, Tübingen, Germany
| | - Stefan M Pulst
- Department of Neurology, University of Utah, Salt Lake City, UT, USA.
- Clinical Neurosciences Center, University of Utah Hospitals and Clinics, Salt Lake City, UT, USA.
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Zeng X, Wang TW, Yamaguchi K, Hatakeyama S, Yamazaki S, Shimizu E, Imoto S, Furukawa Y, Johmura Y, Nakanishi M. M2 macrophage-derived TGF-β induces age-associated loss of adipogenesis through progenitor cell senescence. Mol Metab 2024; 84:101943. [PMID: 38657734 PMCID: PMC11079528 DOI: 10.1016/j.molmet.2024.101943] [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: 11/24/2023] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024] Open
Abstract
OBJECTIVES Adipose tissue is an endocrine and energy storage organ composed of several different cell types, including mature adipocytes, stromal cells, endothelial cells, and a variety of immune cells. Adipose tissue aging contributes to the pathogenesis of metabolic dysfunction and is likely induced by crosstalk between adipose progenitor cells (APCs) and immune cells, but the underlying molecular mechanisms remain largely unknown. In this study, we revealed the biological role of p16high senescent APCs, and investigated the crosstalk between each cell type in the aged white adipose tissue. METHODS We performed the single-cell RNA sequencing (scRNA-seq) analysis on the p16high adipose cells sorted from aged p16-CreERT2/Rosa26-LSL-tdTomato mice. We also performed the time serial analysis on the age-dependent bulk RNA-seq datasets of human and mouse white adipose tissues to infer the transcriptome alteration of adipogenic potential within aging. RESULTS We show that M2 macrophage-derived TGF-β induces APCs senescence which impairs adipogenesis in vivo. p16high senescent APCs increase with age and show loss of adipogenic potential. The ligand-receptor interaction analysis reveals that M2 macrophages are the donors for TGF-β and the senescent APCs are the recipients. Indeed, treatment of APCs with TGF-β1 induces senescent phenotypes through mitochondrial ROS-mediated DNA damage in vitro. TGF-β1 injection into gonadal white adipose tissue (gWAT) suppresses adipogenic potential and induces fibrotic genes as well as p16 in APCs. A gWAT atrophy is observed in cancer cachexia by APCs senescence, whose induction appeared to be independent of TGF-β induction. CONCLUSIONS Our results suggest that M2 macrophage-derived TGF-β induces age-related lipodystrophy by APCs senescence. The TGF-β treatment induced DNA damage, mitochondrial ROS, and finally cellular senescence in APCs.
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Affiliation(s)
- Xinyi Zeng
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Teh-Wei Wang
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Seira Hatakeyama
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Satoshi Yamazaki
- Division of Stem Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Eigo Shimizu
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yoshikazu Johmura
- Division of Cancer and Senescence Biology, Cancer Research Institute, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
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48
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De Bem THC, Bridi A, Tinning H, Sampaio RV, Malo-Estepa I, Wang D, Vasconcelos EJR, Nociti RP, de Ávila ACFCM, Rodrigues Sangalli J, Motta IG, Arantes Ataíde G, da Silva JCB, Fumie Watanabe Y, Gonella-Diaza A, da Silveira JC, Pugliesi G, Vieira Meirelles F, Forde N. Biosensor capability of the endometrium is mediated in part, by altered miRNA cargo from conceptus-derived extracellular vesicles. FASEB J 2024; 38:e23639. [PMID: 38742798 DOI: 10.1096/fj.202302423rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 04/09/2024] [Accepted: 04/18/2024] [Indexed: 05/16/2024]
Abstract
We tested the hypothesis that the biosensor capability of the endometrium is mediated in part, by the effect of different cargo contained in the extracellular vesicles secreted by the conceptus during the peri-implantation period of pregnancy. We transferred Bos taurus taurus embryos of different origin, in vivo (high developmental potential (IV)), in vitro (intermediate developmental potential (IVF)), or cloned (low developmental potential (NT)), into Bos taurus indicus recipients. Extracellular vesicles (EVs) recovered from Day 16 conceptus-conditioned medium were characterized and their microRNA (miRNA) cargo sequenced alongside RNA sequencing of their respective endometria. There were substantial differences in the endometrial response to in vivo versus in vitro and in vivo versus cloned conceptuses (1153 and 334DEGs respectively) with limited differences between in vitro Vs cloned conceptuses (36 DEGs). The miRNA cargo contained in conceptus-derived EVs was similar between all three groups (426 miRNA in common). Only 8 miRNAs were different between in vivo and cloned conceptuses, while only 6 miRNAs were different between in vivo and in vitro-derived conceptuses. Treatment of endometrial epithelial cells with mimic or inhibitors for miR-128 and miR-1298 changed the proteomic content of target cells (96 and 85, respectively) of which mRNAs are altered in the endometrium in vivo (PLXDC2, COPG1, HSPA12A, MCM5, TBL1XR1, and TTF). In conclusion, we have determined that the biosensor capability of the endometrium is mediated in part, by its response to different EVs miRNA cargo produced by the conceptus during the peri-implantation period of pregnancy.
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Affiliation(s)
- Tiago H C De Bem
- Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, Brazil
| | - Alessandra Bridi
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, Brazil
| | - Haidee Tinning
- Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - Rafael Vilar Sampaio
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, Brazil
| | - Irene Malo-Estepa
- Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - Dapeng Wang
- LeedsOmics, University of Leeds, Leeds, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Ricardo Perecin Nociti
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, Brazil
| | - Ana C F C M de Ávila
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, Brazil
| | - Juliano Rodrigues Sangalli
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, Brazil
| | - Igor Garcia Motta
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, Brazil
| | - Gilmar Arantes Ataíde
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, Brazil
| | - Júlio C B da Silva
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, Brazil
| | | | - Angela Gonella-Diaza
- North Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Juliano C da Silveira
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, Brazil
| | - Guilherme Pugliesi
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, Brazil
| | - Flávio Vieira Meirelles
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, Brazil
| | - Niamh Forde
- Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
- LeedsOmics, University of Leeds, Leeds, UK
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49
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Elovitz M, Anton L, Cristancho A, Ferguson B, Joseph A, Ravel J. Vaginal microbes alter epithelial transcriptome and induce epigenomic modifications providing insight into mechanisms for susceptibility to adverse reproductive outcomes. RESEARCH SQUARE 2024:rs.3.rs-4385224. [PMID: 38854063 PMCID: PMC11160883 DOI: 10.21203/rs.3.rs-4385224/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The cervicovaginal microbiome is highly associated with women's health, with microbial communities dominated by Lactobacillus species considered optimal. Conversely, a lack of lactobacilli and a high abundance of strict and facultative anaerobes, including Gardnerella vaginalis, have been associated with adverse reproductive outcomes. However, how host-microbial interactions alter specific molecular pathways and impact cervical and vaginal epithelial function remains unclear. Using RNA-sequencing, we characterized the in vitro cervicovaginal epithelial transcriptional response to different vaginal bacteria and their culture supernatants. We showed that G. vaginalis upregulates genes associated with an activated innate immune response. Unexpectedly, G. vaginalis specifically induced inflammasome pathways through activation of NLRP3-mediated increases in caspase-1, IL-1β and cell death, while live L. crispatus had minimal transcriptomic changes on epithelial cells. L. crispatus culture supernatants resulted in a shift in the epigenomic landscape of cervical epithelial cells that was confirmed by ATAC-sequencing showing reduced chromatin accessibility. This study reveals new insights into host-microbe interactions in the lower reproductive tract and suggests potential therapeutic strategies leveraging the vaginal microbiome to improve reproductive health.
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50
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Desroches-Castan A, Koca D, Liu H, Roelants C, Resmini L, Ricard N, Bouvard C, Chaumontel N, Tharaux PL, Tillet E, Battail C, Lenoir O, Bailly S. BMP9 is a key player in endothelial identity and its loss is sufficient to induce arteriovenous malformations. Cardiovasc Res 2024; 120:782-795. [PMID: 38502919 DOI: 10.1093/cvr/cvae052] [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: 04/11/2023] [Revised: 10/10/2023] [Accepted: 12/18/2023] [Indexed: 03/21/2024] Open
Abstract
AIMS BMP9 is a high affinity ligand of ALK1 and endoglin receptors that are mutated in the rare genetic vascular disorder hereditary hemorrhagic telangiectasia (HHT). We have previously shown that loss of Bmp9 in the 129/Ola genetic background leads to spontaneous liver fibrosis via capillarization of liver sinusoidal endothelial cells (LSEC) and kidney lesions. We aimed to decipher the molecular mechanisms downstream of BMP9 to better characterize its role in vascular homeostasis in different organs. METHODS AND RESULTS For this, we performed an RNA-seq analysis on LSEC from adult WT and Bmp9-KO mice and identified over 2000 differentially expressed genes. Gene ontology analysis showed that Bmp9 deletion led to a decrease in BMP and Notch signalling, but also LSEC capillary identity while increasing their cell cycle. The gene ontology term 'glomerulus development' was also negatively enriched in Bmp9-KO mice vs. WT supporting a role for BMP9 in kidney vascularization. Through different imaging approaches (electron microscopy, immunostainings), we found that loss of Bmp9 led to vascular enlargement of the glomeruli capillaries associated with alteration of podocytes. Importantly, we also showed for the first time that the loss of Bmp9 led to spontaneous arteriovenous malformations (AVMs) in the liver, gastrointestinal tract, and uterus. CONCLUSION Altogether, these results demonstrate that BMP9 plays an important role in vascular quiescence both locally in the liver by regulating endothelial capillary differentiation markers and cell cycle but also at distance in many organs via its presence in the circulation. It also reveals that loss of Bmp9 is sufficient to induce spontaneous AVMs, supporting a key role for BMP9 in the pathogenesis of HHT.
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Affiliation(s)
- Agnes Desroches-Castan
- Laboratoire Biosanté U1292, Université Grenoble Alpes, Inserm, CEA, 17 avenue des Martyrs, 38054 Grenoble, France
| | - Dzenis Koca
- Laboratoire Biosanté U1292, Université Grenoble Alpes, Inserm, CEA, 17 avenue des Martyrs, 38054 Grenoble, France
| | - Hequn Liu
- Laboratoire Biosanté U1292, Université Grenoble Alpes, Inserm, CEA, 17 avenue des Martyrs, 38054 Grenoble, France
| | - Caroline Roelants
- Laboratoire Biosanté U1292, Université Grenoble Alpes, Inserm, CEA, 17 avenue des Martyrs, 38054 Grenoble, France
| | - Léa Resmini
- Université Paris Cité, Inserm, PARCC, Paris, France
| | - Nicolas Ricard
- Laboratoire Biosanté U1292, Université Grenoble Alpes, Inserm, CEA, 17 avenue des Martyrs, 38054 Grenoble, France
| | - Claire Bouvard
- Laboratoire Biosanté U1292, Université Grenoble Alpes, Inserm, CEA, 17 avenue des Martyrs, 38054 Grenoble, France
| | - Nicolas Chaumontel
- Laboratoire Biosanté U1292, Université Grenoble Alpes, Inserm, CEA, 17 avenue des Martyrs, 38054 Grenoble, France
| | | | - Emmanuelle Tillet
- Laboratoire Biosanté U1292, Université Grenoble Alpes, Inserm, CEA, 17 avenue des Martyrs, 38054 Grenoble, France
| | - Christophe Battail
- Laboratoire Biosanté U1292, Université Grenoble Alpes, Inserm, CEA, 17 avenue des Martyrs, 38054 Grenoble, France
| | | | - Sabine Bailly
- Laboratoire Biosanté U1292, Université Grenoble Alpes, Inserm, CEA, 17 avenue des Martyrs, 38054 Grenoble, France
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