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Lu J, Zhu P, Zhang X, Zeng L, Xu B, Zhou P. tRNA-derived fragments: Unveiling new roles and molecular mechanisms in cancer progression. Int J Cancer 2024; 155:1347-1360. [PMID: 38867475 DOI: 10.1002/ijc.35041] [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: 11/09/2023] [Revised: 04/17/2024] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
tRNA-derived fragments (tRFs) are novel small noncoding RNAs (sncRNAs) that range from approximately 14 to 50 nt. They are generated by the cleavage of mature tRNAs or precursor tRNAs (pre-tRNAs) at specific sites. Based on their origin and length, tRFs can be classified into three categories: (1) tRF-1 s; (2) tRF-3 s, tRF-5 s, and internal tRFs (i-tRFs); and (3) tRNA halves. They play important roles in stress response, signal transduction, and gene expression processes. Recent studies have identified differential expression of tRFs in various tumors. Aberrantly expressed tRFs have critical clinical value and show promise as new biomarkers for tumor diagnosis and prognosis and as therapeutic targets. tRFs regulate the malignant progression of tumors via various mechanisms, primarily including modulation of noncoding RNA biogenesis, global chromatin organization, gene expression regulation, modulation of protein translation, regulation of epigenetic modification, and alternative splicing regulation. In conclusion, tRF-mediated regulatory pathways could present new avenues for tumor treatment, and tRFs could serve as promising therapeutic targets for cancer therapy.
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Affiliation(s)
- Jingjing Lu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Clinical Medical Research Center, Affiliated Hospital of Nantong University, Nantong, China
| | - Ping Zhu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiufen Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Oncology Institute, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Linzi Zeng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Bujie Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ping Zhou
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
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2
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Trigg NA, Conine CC. Epididymal acquired sperm microRNAs modify post-fertilization embryonic gene expression. Cell Rep 2024; 43:114698. [PMID: 39226174 DOI: 10.1016/j.celrep.2024.114698] [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: 02/21/2024] [Revised: 06/18/2024] [Accepted: 08/14/2024] [Indexed: 09/05/2024] Open
Abstract
Sperm small RNAs have emerged as important non-genetic contributors to embryogenesis and offspring health. A subset of sperm small RNAs is thought to be acquired during epididymal transit. However, the identity of the specific small RNAs transferred remains unclear. Here, we employ Cre/Lox genetics to generate germline- and epididymal-specific Dgcr8 knockout (KO) mice to investigate the dynamics of sperm microRNAs (miRNAs) and their functions post-fertilization. Testicular sperm from germline Dgcr8 KO mice has reduced levels of 116 miRNAs. Enthrallingly, following epididymal transit, the abundance of 72% of these miRNAs is restored. Conversely, sperm from epididymal Dgcr8 KO mice displayed reduced levels of 27 miRNAs. This loss of epididymal miRNAs in sperm was accompanied by transcriptomic changes in embryos fertilized by this sperm, which was rescued by microinjection of epididymal miRNAs. These findings ultimately demonstrate the acquisition of miRNAs from the soma by sperm during epididymal transit and their subsequent regulation of embryonic gene expression.
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Affiliation(s)
- Natalie A Trigg
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Women's Health and Reproductive Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Colin C Conine
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Women's Health and Reproductive Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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3
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Velázquez-Flores MÁ, Ruiz Esparza-Garrido R. Fragments derived from non-coding RNAs: how complex is genome regulation? Genome 2024; 67:292-306. [PMID: 38684113 DOI: 10.1139/gen-2023-0136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The human genome is highly dynamic and only a small fraction of it codes for proteins, but most of the genome is transcribed, highlighting the importance of non-coding RNAs on cellular functions. In addition, it is now known the generation of non-coding RNA fragments under particular cellular conditions and their functions have revealed unexpected mechanisms of action, converging, in some cases, with the biogenic pathways and action machineries of microRNAs or Piwi-interacting RNAs. This led us to the question why the cell produces so many apparently redundant molecules to exert similar functions and regulate apparently convergent processes? However, non-coding RNAs fragments can also function similarly to aptamers, with secondary and tertiary conformations determining their functions. In the present work, it was reviewed and analyzed the current information about the non-coding RNAs fragments, describing their structure and biogenic pathways, with special emphasis on their cellular functions.
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Affiliation(s)
- Miguel Ángel Velázquez-Flores
- Laboratorio de RNAs No Codificantes de la Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX, México
| | - Ruth Ruiz Esparza-Garrido
- Investigadora por México, Laboratorio de RNAs No Codificantes de la Unidad de Investigación Médica en Genética Humana, Hospital de Pediatría del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social (IMSS), CDMX, México
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4
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Liu S, Holmes AD, Katzman S, Sharma U. A sperm-enriched 5'fragment of tRNA-Valine regulates preimplantation embryonic transcriptome and development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.08.607197. [PMID: 39211093 PMCID: PMC11361008 DOI: 10.1101/2024.08.08.607197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Sperm small RNAs have been implicated in intergenerational epigenetic inheritance of paternal environmental effects; however, their biogenesis and functions remain poorly understood. We previously identified a 5' fragment of tRNA-Valine-CAC-2 (tRFValCAC) as one of the most abundant small RNA in mature sperm. tRFValCAC is specifically enriched in sperm during post-testicular maturation in the epididymis, and we found that it is delivered to sperm from epididymis epithelial cells via extracellular vesicles. Here, we investigated the mechanistic basis of tRFValCAC delivery to sperm and its functions in the early embryo. We show that tRFValCAC interacts with an RNA binding protein, heterogeneous nuclear ribonucleoprotein A/B (hnRNPAB), in the epididymis, and this interaction regulates the sorting and packing of tRFValCAC into extracellular vesicles. In the embryo, we found that tRFValCAC regulates early embryonic mRNA processing and splicing. Inhibition of tRFValCAC in preimplantation embryos altered the transcript abundance of genes involved in RNA splicing and mRNA processing. Importantly, tRFValCAC-inhibited embryos showed altered mRNA splicing, including alternative splicing of various splicing factors and genes important for proper preimplantation embryonic development. Finally, we find that inhibition of tRFValCAC in zygotes delayed preimplantation embryonic development. Together, our results reveal a novel function of a sperm-enriched tRF in regulating alternating splicing and preimplantation embryonic development and shed light on the mechanism of sperm small RNA-mediated epigenetic inheritance.
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Affiliation(s)
- Simeiyun Liu
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
| | - Andrew D. Holmes
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
| | - Sol Katzman
- Genomics Institute, University of California, Santa Cruz, California, 95064
| | - Upasna Sharma
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
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5
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Plewka P, Szczesniak MW, Stepien A, Pasieka R, Wanowska E, Makalowska I, Raczynska KD. Novel function of U7 snRNA in the repression of HERV1/LTR12s and lincRNAs in human cells. Nucleic Acids Res 2024:gkae738. [PMID: 39189459 DOI: 10.1093/nar/gkae738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 08/07/2024] [Accepted: 08/19/2024] [Indexed: 08/28/2024] Open
Abstract
U7 snRNA is part of the U7 snRNP complex, required for the 3' end processing of replication-dependent histone pre-mRNAs in S phase of the cell cycle. Here, we show that U7 snRNA plays another function in inhibiting the expression of a subset of long terminal repeats of human endogenous retroviruses (HERV1/LTR12s) and LTR12-containing long intergenic noncoding RNAs (lincRNAs), both bearing sequence motifs that perfectly match the 5' end of U7 snRNA. We demonstrate that U7 snRNA inhibits LTR12 and lincRNA transcription and propose a mechanism in which U7 snRNA hampers the binding/activity of the NF-Y transcription factor to CCAAT motifs within LTR12 elements. Thereby, U7 snRNA plays a protective role in maintaining the silencing of deleterious genetic elements in selected types of cells.
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Affiliation(s)
- Patrycja Plewka
- Department of Gene Expression, Laboratory of RNA Processing, Institute of Molecular Biology and Biotechnology, Faculty of Biology and Center for Advanced Technology, Adam Mickiewicz University, Poznan, Poland
| | - Michal W Szczesniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Agata Stepien
- Department of Gene Expression, Laboratory of RNA Processing, Institute of Molecular Biology and Biotechnology, Faculty of Biology and Center for Advanced Technology, Adam Mickiewicz University, Poznan, Poland
| | - Robert Pasieka
- Department of Gene Expression, Laboratory of RNA Processing, Institute of Molecular Biology and Biotechnology, Faculty of Biology and Center for Advanced Technology, Adam Mickiewicz University, Poznan, Poland
| | - Elzbieta Wanowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Izabela Makalowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Katarzyna Dorota Raczynska
- Department of Gene Expression, Laboratory of RNA Processing, Institute of Molecular Biology and Biotechnology, Faculty of Biology and Center for Advanced Technology, Adam Mickiewicz University, Poznan, Poland
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6
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Nie J, Chen H, Zhao X. Advancement and Potential Applications of Epididymal Organoids. Biomolecules 2024; 14:1026. [PMID: 39199413 PMCID: PMC11352229 DOI: 10.3390/biom14081026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/04/2024] [Accepted: 08/08/2024] [Indexed: 09/01/2024] Open
Abstract
The epididymis, a key reproductive organ, is crucial for sperm concentration, maturation, and storage. Despite a comprehensive understanding of many of its functions, several aspects of the complex processes within the epididymis remain obscure. Dysfunction in this organ is intricately connected to the formation of the microenvironment, disruptions in sperm maturation, and the progression of male infertility. Thus, elucidating the functional mechanisms of the epididymal epithelium is imperative. Given the variety of cell types present within the epididymal epithelium, utilizing a three-dimensional (3D) in vitro model provides a holistic and practical framework for exploring the multifaceted roles of the epididymis. Organoid cell culture, involving the co-cultivation of pluripotent or adult stem cells with growth factors on artificial matrix scaffolds, effectively recreates the in vivo cell growth microenvironment, thereby offering a promising avenue for studying the epididymis. The field of epididymal organoids is relatively new, with few studies focusing on their formation and even fewer detailing the generation of organoids that exhibit epididymis-specific structures and functions. Ongoing challenges in both clinical applications and mechanistic studies underscore the importance of this research. This review summarizes the established methodologies for inducing the in vitro cultivation of epididymal cells, outlines the various approaches for the development of epididymal organoids, and explores their potential applications in the field of male reproductive biology.
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Affiliation(s)
| | | | - Xiuling Zhao
- Institute of Reproductive Medicine, Medical School, Nantong University, Nantong 226019, China; (J.N.)
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7
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Kameni SL, Dlamini NH, Feugang JM. Exploring the full potential of sperm function with nanotechnology tools. Anim Reprod 2024; 21:e20240033. [PMID: 39176004 PMCID: PMC11340799 DOI: 10.1590/1984-3143-ar2024-0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 06/20/2024] [Indexed: 08/24/2024] Open
Abstract
Sperm quality is essential to guarantee the success of assisted reproduction. However, selecting high-quality sperm and maintaining it during (cryo)preservation for high efficiency remains challenging in livestock reproduction. A comprehensive understanding of sperm biology allows for better assessment of sperm quality, which could replace conventional sperm analyses used today to predict fertility with low accuracy. Omics approaches have revealed numerous biomarkers associated with various sperm phenotypic traits such as quality, survival during storage, freezability, and fertility. At the same time, nanotechnology is emerging as a new biotechnology with high potential for use in preparing sperm intended to improve reproduction in livestock. The unique physicochemical properties of nanoparticles make them exciting tools for targeting (e.g., sperm damage and sexing) and non-targeting bioapplications. Recent advances in sperm biology have led to the discovery of numerous biomarkers, making it possible to target specific subpopulations of spermatozoa within the ejaculate. In this review, we explore potential biomarkers associated with sperm phenotypes and highlight the benefits of combining these biomarkers with nanoparticles to further improve sperm preparation and technology.
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Affiliation(s)
- Serge Leugoué Kameni
- Mississippi State University, Department of Animal and Dairy Sciences, Mississippi State, MS, USA
| | - Notsile Hleliwe Dlamini
- Mississippi State University, Department of Animal and Dairy Sciences, Mississippi State, MS, USA
| | - Jean Magloire Feugang
- Mississippi State University, Department of Animal and Dairy Sciences, Mississippi State, MS, USA
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8
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Kilama J, Dahlen CR, Reynolds LP, Amat S. Contribution of the seminal microbiome to paternal programming. Biol Reprod 2024; 111:242-268. [PMID: 38696371 PMCID: PMC11327320 DOI: 10.1093/biolre/ioae068] [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: 01/13/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/04/2024] Open
Abstract
The field of Developmental Origins of Health and Disease has primarily focused on maternal programming of offspring health. However, emerging evidence suggests that paternal factors, including the seminal microbiome, could potentially play important roles in shaping the developmental trajectory and long-term offspring health outcomes. Historically, the microbes present in the semen were regarded as inherently pathogenic agents. However, this dogma has recently been challenged by the discovery of a diverse commensal microbial community within the semen of healthy males. In addition, recent studies suggest that the transmission of semen-associated microbes into the female reproductive tract during mating has potentials to not only influence female fertility and embryo development but could also contribute to paternal programming in the offspring. In this review, we summarize the current knowledge on the seminal microbiota in both humans and animals followed by discussing their potential involvement in paternal programming of offspring health. We also propose and discuss potential mechanisms through which paternal influences are transmitted to offspring via the seminal microbiome. Overall, this review provides insights into the seminal microbiome-based paternal programing, which will expand our understanding of the potential paternal programming mechanisms which are currently focused primarily on the epigenetic modifications, oxidative stresses, and cytokines.
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Affiliation(s)
- Justine Kilama
- Department of Microbiological Sciences, North Dakota State University, NDSU Department 7520, Fargo, ND 58108-6050, USA
| | - Carl R Dahlen
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, NDSU Department 7630, Fargo, ND 58108-6050, USA
| | - Lawrence P Reynolds
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, NDSU Department 7630, Fargo, ND 58108-6050, USA
| | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, NDSU Department 7520, Fargo, ND 58108-6050, USA
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9
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Ding C, Wang N, Peng A, Wang Z, Li B, Zhang X, Zeng J, Zhou Y. Potential Diagnostic Biomarkers of tRNA-Derived Small RNAs in PBMCs for Nonproliferative Diabetic Retinopathy in Patients With Type 2 Diabetes Mellitus. Transl Vis Sci Technol 2024; 13:32. [PMID: 39167377 PMCID: PMC11343001 DOI: 10.1167/tvst.13.8.32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 07/01/2024] [Indexed: 08/23/2024] Open
Abstract
Purpose This study aimed to reveal the altered expressions of transfer RNA (tRNA)-derived small RNAs (tsRNAs) in peripheral blood mononuclear cells and identify potential diagnostic biomarkers for nonproliferative diabetic retinopathy (NPDR) from patients with type 2 diabetes mellitus. Methods Fifty-three patients diagnosed with type 2 diabetes mellitus were enrolled, including 25 patients with NPDR and 28 patients without diabetic retinopathy (DR) as the control group. A small RNA microarray was performed to screen the differentially expressed tsRNAs. Reverse transcriptase quantitative polymerase chain reaction was used to validate the significantly altered tsRNAs in a screening cohort and a verification cohort. The target genes, their enriched functions, and signaling pathways were predicted by bioinformatics analyses. Results In total, 668 upregulated and 485 downregulated tsRNAs were found in the NPDR group by microarray. Eight tsRNAs were validated preliminarily to be altered significantly by reverse transcriptase quantitative polymerase chain reaction, and their target genes were enriched in cellular macromolecule metabolic process and ubiquitin-mediated proteolysis. The verification experiments confirmed the increased levels of 5'tiRNA-35-PheGAA-8, tRF3-28-PheGAA-1, and tRF3b-PheGAA-6, and the decreased levels of mt-tRF3-19-ArgTCG, mt-tRF3-20-ArgTCG, and mt-tRF3-21-ArgTCG in patients with NPDR, which may serve as potential biomarkers with clinical significance. Conclusions The study recognized the tsRNA expression changes in peripheral blood mononuclear cells from patients with NPDR and discovered potential diagnostic biomarkers that hold clinical significance. Translational Relevance The significantly altered tsRNAs identified in the study may serve as potential diagnostic biomarkers for patients with NPDR as well as possible molecular targets of the occurrence and development of DR.
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Affiliation(s)
- Chun Ding
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, China
| | - Nan Wang
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, China
| | - Aohua Peng
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, China
| | - Zicong Wang
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, China
| | - Bingyan Li
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, China
| | - Xian Zhang
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, China
| | - Jun Zeng
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, China
| | - Yedi Zhou
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, China
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10
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Scacchetti A, Shields EJ, Trigg NA, Lee GS, Wilusz JE, Conine CC, Bonasio R. A ligation-independent sequencing method reveals tRNA-derived RNAs with blocked 3' termini. Mol Cell 2024:S1097-2765(24)00584-7. [PMID: 39096899 DOI: 10.1016/j.molcel.2024.07.008] [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: 06/09/2023] [Revised: 12/12/2023] [Accepted: 07/10/2024] [Indexed: 08/05/2024]
Abstract
Despite the numerous sequencing methods available, the diversity in RNA size and chemical modification makes it difficult to capture all RNAs in a cell. We developed a method that combines quasi-random priming with template switching to construct sequencing libraries from RNA molecules of any length and with any type of 3' modifications, allowing for the sequencing of virtually all RNA species. Our ligation-independent detection of all types of RNA (LIDAR) is a simple, effective tool to identify and quantify all classes of coding and non-coding RNAs. With LIDAR, we comprehensively characterized the transcriptomes of mouse embryonic stem cells, neural progenitor cells, mouse tissues, and sperm. LIDAR detected a much larger variety of tRNA-derived RNAs (tDRs) compared with traditional ligation-dependent sequencing methods and uncovered tDRs with blocked 3' ends that had previously escaped detection. Therefore, LIDAR can capture all RNAs in a sample and uncover RNA species with potential regulatory functions.
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Affiliation(s)
- Alessandro Scacchetti
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Emily J Shields
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Urology and Institute of Neuropathology, Medical Center - University of Freiburg, 79106 Freiburg, Germany
| | - Natalie A Trigg
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Grace S Lee
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Colin C Conine
- Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Roberto Bonasio
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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11
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Basel A, Bhadsavle SS, Scaturro KZ, Parkey GK, Gaytan MN, Patel JJ, Thomas KN, Golding MC. Parental Alcohol Exposures Associate with Lasting Mitochondrial Dysfunction and Accelerated Aging in a Mouse Model. Aging Dis 2024:AD.2024.0722. [PMID: 39122451 DOI: 10.14336/ad.2024.0722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/20/2024] [Indexed: 08/12/2024] Open
Abstract
Although detrimental changes in mitochondrial morphology and function are widely described symptoms of fetal alcohol exposure, no studies have followed these mitochondrial deficits into adult life or determined if they predispose individuals with fetal alcohol spectrum disorders (FASDs) to accelerated biological aging. Here, we used a multiplex preclinical mouse model to compare markers of cellular senescence and age-related outcomes induced by maternal, paternal, and dual-parental alcohol exposures. We find that even in middle life (postnatal day 300), the adult offspring of alcohol-exposed parents exhibited significant increases in markers of stress-induced premature cellular senescence in the brain and liver, including an upregulation of cell cycle inhibitory proteins and increased senescence-associated β-galactosidase activity. Strikingly, in the male offspring, we observe an interaction between maternal and paternal alcohol use, with histological indicators of accelerated age-related liver disease in the dual-parental offspring exceeding those induced by either maternal or paternal alcohol use alone. Our studies indicate that chronic parental alcohol use causes enduring mitochondrial dysfunction in offspring, resulting in a reduced NAD+/NAHD ratio and altered expression of the NAD+-dependent deacetylases SIRT1 and SIRT3. These observations suggest that some aspects of FASDs may be linked to accelerated aging due to programmed changes in the regulation of mitochondrial function and cellular bioenergetics.
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12
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Skerrett-Byrne DA, Stanger SJ, Trigg NA, Anderson AL, Sipilä P, Bernstein IR, Lord T, Schjenken JE, Murray HC, Verrills NM, Dun MD, Pang TY, Nixon B. Phosphoproteomic analysis of the adaption of epididymal epithelial cells to corticosterone challenge. Andrology 2024; 12:1038-1057. [PMID: 38576152 DOI: 10.1111/andr.13636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND The epididymis has long been of interest owing to its role in promoting the functional maturation of the male germline. More recent evidence has also implicated the epididymis as an important sensory tissue responsible for remodeling of the sperm epigenome, both under physiological conditions and in response to diverse forms of environmental stress. Despite this knowledge, the intricacies of the molecular pathways involved in regulating the adaptation of epididymal tissue to paternal stressors remains to be fully resolved. OBJECTIVE The overall objective of this study was to investigate the direct impact of corticosterone challenge on a tractable epididymal epithelial cell line (i.e., mECap18 cells), in terms of driving adaptation of the cellular proteome and phosphoproteome signaling networks. MATERIALS AND METHODS The newly developed phosphoproteomic platform EasyPhos coupled with sequencing via an Orbitrap Exploris 480 mass spectrometer, was applied to survey global changes in the mECap18 cell (phospho)proteome resulting from sub-chronic (10-day) corticosterone challenge. RESULTS The imposed corticosterone exposure regimen elicited relatively subtle modifications of the global mECap18 proteome (i.e., only 73 out of 4171 [∼1.8%] proteins displayed altered abundance). By contrast, ∼15% of the mECap18 phosphoproteome was substantially altered following corticosterone challenge. In silico analysis of the corresponding parent proteins revealed an activation of pathways linked to DNA damage repair and oxidative stress responses as well as a reciprocal inhibition of pathways associated with organismal death. Corticosterone challenge also induced the phosphorylation of several proteins linked to the biogenesis of microRNAs. Accordingly, orthogonal validation strategies confirmed an increase in DNA damage, which was ameliorated upon selective kinase inhibition, and an altered abundance profile of a subset of microRNAs in corticosterone-treated cells. CONCLUSIONS Together, these data confirm that epididymal epithelial cells are reactive to corticosterone challenge, and that their response is tightly coupled to the opposing action of cellular kinases and phosphatases.
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Affiliation(s)
- David A Skerrett-Byrne
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Simone J Stanger
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Natalie A Trigg
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Amanda L Anderson
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Petra Sipilä
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, and Turku Center for Disease Modeling, University of Turku, Turku, Finland
| | - Ilana R Bernstein
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Tessa Lord
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - John E Schjenken
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Heather C Murray
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Nicole M Verrills
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Matthew D Dun
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia
- Precision Medicine Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
| | - Terence Y Pang
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC, Australia
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, VIC, Australia
| | - Brett Nixon
- Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, New Lambton, NSW, Australia
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13
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Blaze J, Browne CJ, Futamura R, Javidfar B, Zachariou V, Nestler EJ, Akbarian S. tRNA epitranscriptomic alterations associated with opioid-induced reward-seeking and long-term opioid withdrawal in male mice. Neuropsychopharmacology 2024; 49:1276-1284. [PMID: 38332016 PMCID: PMC11224224 DOI: 10.1038/s41386-024-01813-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
DNA cytosine methylation has been documented as a potential epigenetic mechanism of transcriptional regulation underlying opioid use disorder. However, methylation of RNA cytosine residues, which would drive another level of biological influence as an epitranscriptomic mechanism of gene and protein regulation has not been studied in the context of addiction. Here, we probed whether chronic morphine exposure could alter tRNA cytosine methylation (m5C) and resulting expression levels in the medial prefrontal cortex (mPFC), a brain region crucial for reward processing and executive function that exhibits opioid-induced molecular restructuring. We identified dynamic changes in glycine tRNA (tRNAGlyGCC) cytosine methylation, corresponding to altered expression levels of this tRNA at multiple timepoints following 15 days of daily morphine. Additionally, a robust increase in methylation, coupled with decreased expression, was present after 30 days of withdrawal, suggesting that repeated opioid administration produces changes to the tRNA regulome long after discontinuation. Furthermore, forebrain-wide knockout of neuronal Nsun2, a tRNA methyltransferase, was associated with disruption of opioid conditioned place preference, and this effect was recapitulated by regional mPFC Nsun2 knockout. Taken together, these studies provide a foundational link between the regulation of tRNA cytosine methylation and opioid reward and highlight the tRNA machinery as a potential therapeutic target in addiction.
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Affiliation(s)
- Jennifer Blaze
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Caleb J Browne
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain Health Imaging Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Rita Futamura
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Behnam Javidfar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Venetia Zachariou
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacology, Physiology, and Biophysics, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Eric J Nestler
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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14
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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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15
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Pozzi A. Ancestry affects the transcription of small mitochondrial RNAs in human lymphocytes. Mitochondrion 2024; 77:101907. [PMID: 38777221 DOI: 10.1016/j.mito.2024.101907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 04/29/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
Mitochondrial mutations have been linked to changes in phenotypes such as fertility or longevity, however, these changes have been often inconsistent across populations for unknown reasons. A hypothesis that could explain this inconsistency is that some still uncharacterized mitochondrial products are mediating the phenotypic changes across populations. It has been hypothesized that one such product could be the small RNAs encoded in the mitochondrial genome, thus this work will provide new evidence for their existence and function. By using data from the 1000 genome project and knowledge from previously characterized nuclear small RNAs, this study found that 10 small RNAs encoded in tRNA fragments are consistently expressed in 450 individuals from five different populations. Furthermore, this study demonstrated that the expression of some small mitochondrial RNAs is different in individuals of African ancestry, similar to what was observed before in nuclear and mitochondria mRNAs. Lastly, we investigate the causes behind these differences in expression, showing that at least one of the mt-tRFs might be regulated by TRMT10B. The analyses presented in this work further support the small mitochondrial RNAs as functional molecules, and their population-specific expression supports the hypothesis that they act as a mediator between the nucleus and mitochondria differently across populations.
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Affiliation(s)
- Andrea Pozzi
- Faculty of Biology, Ludwig-Maximilians-Universität Munich, München, Germany; Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
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16
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Fazeli A, Godakumara K. The evolving roles of extracellular vesicles in embryo-maternal communication. Commun Biol 2024; 7:754. [PMID: 38906986 PMCID: PMC11192758 DOI: 10.1038/s42003-024-06442-9] [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: 01/11/2024] [Accepted: 06/12/2024] [Indexed: 06/23/2024] Open
Abstract
Mammalian reproduction relies on precise maternal-fetal communication, wherein immune modifications foster tolerance toward the semi-allogeneic embryo. Extracellular vesicles (EVs), including exosomes and microvesicles, have emerged as crucial mediators, transporting molecules like microRNAs securely. EVs influence various reproductive stages, from gamete maturation to implantation, and impact pathologies like pregnancy loss. In the embryo-maternal dialogue, EVs notably affect oviductal interactions, gene expression, and the embryo-endometrial interface, crucial for successful implantation. Key queries persist about EV uptake, cargo delivery, and the specific biomolecules driving communication. Their potential in diagnostics, therapeutics, and understanding environmental impacts on fertility signals an exciting future, reliant on collaborative efforts for transformative strides in reproductive health.
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Affiliation(s)
- Alireza Fazeli
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia.
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, Tartu University, Tartu, Estonia.
- Division of Clinical Medicine, School of Medicine & Population Health, University of Sheffield, Sheffield, UK.
| | - Kasun Godakumara
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
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17
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Liu X, Duan C, Yin X, Zhang L, Chen M, Zhao W, Li X, Liu Y, Zhang Y. Inhibition of Prolactin Affects Epididymal Morphology by Decreasing the Secretion of Estradiol in Cashmere Bucks. Animals (Basel) 2024; 14:1778. [PMID: 38929397 PMCID: PMC11201029 DOI: 10.3390/ani14121778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/31/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Yanshan Cashmere bucks are seasonal breeding animals and an important national genetic resource. This study aimed to investigate the involvement of prolactin (PRL) in the epididymal function of bucks. Twenty eleven-month-old Cashmere bucks were randomly divided into a control (CON) group and a bromocriptine (BCR, a prolactin inhibitor, 0.06 mg/kg body weight (BW)) treatment group. The experiment was conducted from September to October 2020 in Qinhuangdao City, China, and lasted for 30 days. Blood was collected on the last day before the BCR treatment (day 0) and on the 15th and 30th days after the BCR treatment (days 15 and 30). On the 30th day, all bucks were transported to the local slaughterhouse, where epididymal samples were collected immediately after slaughter. The left epididymis was preserved in 4% paraformaldehyde for histological observation, and the right epididymis was immediately preserved in liquid nitrogen for RNA sequencing (RNA-seq). The results show that the PRL inhibitor reduced the serum PRL and estradiol (E2) concentrations (p < 0.05) and tended to decrease luteinizing hormone (LH) concentrations (p = 0.052) by the 30th day, but no differences (p > 0.05) occurred by either day 0 or 15. There were no differences (p > 0.05) observed in the follicle-stimulating hormone (FSH), testosterone (T), and dihydrotestosterone (DHT) concentrations between the two groups. The PRL receptor (PRLR) protein was mainly located in the cytoplasm and intercellular substance of the epididymal epithelial cells. The PRL inhibitor decreased (p < 0.05) the expression of the PRLR protein in the epididymis. In the BCR group, the height of the epididymal epithelium in the caput and cauda increased, as did the diameter of the epididymal duct in the caput (p < 0.05). However, the diameter of the cauda epididymal duct decreased (p < 0.05). Thereafter, a total of 358 differentially expressed genes (DEGs) were identified in the epididymal tissues, among which 191 were upregulated and 167 were downregulated. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that ESR2, MAPK10, JUN, ACTL7A, and CALML4 were mainly enriched in the estrogen signaling pathway, steroid binding, calcium ion binding, the GnRH signaling pathway, the cAMP signaling pathway, and the chemical carcinogenesis-reactive oxygen species pathway, which are related to epididymal function. In conclusion, the inhibition of PRL may affect the structure of the epididymis by reducing the expression of the PRLR protein and the secretion of E2. ESR2, MAPK10, JUN, ACTL7A, and CALML4 could be the key genes of PRL in its regulation of epididymal reproductive function.
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Affiliation(s)
- Xiaona Liu
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China; (X.L.); (C.D.); (L.Z.); (M.C.); (W.Z.)
| | - Chunhui Duan
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China; (X.L.); (C.D.); (L.Z.); (M.C.); (W.Z.)
| | - Xuejiao Yin
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066004, China; (X.Y.); (X.L.)
| | - Lechao Zhang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China; (X.L.); (C.D.); (L.Z.); (M.C.); (W.Z.)
| | - Meijing Chen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China; (X.L.); (C.D.); (L.Z.); (M.C.); (W.Z.)
| | - Wen Zhao
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China; (X.L.); (C.D.); (L.Z.); (M.C.); (W.Z.)
| | - Xianglong Li
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066004, China; (X.Y.); (X.L.)
| | - Yueqin Liu
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China; (X.L.); (C.D.); (L.Z.); (M.C.); (W.Z.)
| | - Yingjie Zhang
- College of Animal Science and Technology, Hebei Agricultural University, Baoding 071001, China; (X.L.); (C.D.); (L.Z.); (M.C.); (W.Z.)
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18
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Sutovsky P, Hamilton LE, Zigo M, Ortiz D’Avila Assumpção ME, Jones A, Tirpak F, Agca Y, Kerns K, Sutovsky M. Biomarker-based human and animal sperm phenotyping: the good, the bad and the ugly†. Biol Reprod 2024; 110:1135-1156. [PMID: 38640912 PMCID: PMC11180624 DOI: 10.1093/biolre/ioae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/28/2024] [Accepted: 04/17/2024] [Indexed: 04/21/2024] Open
Abstract
Conventional, brightfield-microscopic semen analysis provides important baseline information about sperm quality of an individual; however, it falls short of identifying subtle subcellular and molecular defects in cohorts of "bad," defective human and animal spermatozoa with seemingly normal phenotypes. To bridge this gap, it is desirable to increase the precision of andrological evaluation in humans and livestock animals by pursuing advanced biomarker-based imaging methods. This review, spiced up with occasional classic movie references but seriously scholastic at the same time, focuses mainly on the biomarkers of altered male germ cell proteostasis resulting in post-testicular carryovers of proteins associated with ubiquitin-proteasome system. Also addressed are sperm redox homeostasis, epididymal sperm maturation, sperm-seminal plasma interactions, and sperm surface glycosylation. Zinc ion homeostasis-associated biomarkers and sperm-borne components, including the elements of neurodegenerative pathways such as Huntington and Alzheimer disease, are discussed. Such spectrum of biomarkers, imaged by highly specific vital fluorescent molecular probes, lectins, and antibodies, reveals both obvious and subtle defects of sperm chromatin, deoxyribonucleic acid, and accessory structures of the sperm head and tail. Introduction of next-generation image-based flow cytometry into research and clinical andrology will soon enable the incorporation of machine and deep learning algorithms with the end point of developing simple, label-free methods for clinical diagnostics and high-throughput phenotyping of spermatozoa in humans and economically important livestock animals.
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Affiliation(s)
- Peter Sutovsky
- Division of Animal Sciences, University of Missouri, Columbia MO, USA
- Department of Obstetrics, Gynecology and Women’s Health, University of Missouri, Columbia MO, USA
| | - Lauren E Hamilton
- Division of Animal Sciences, University of Missouri, Columbia MO, USA
| | - Michal Zigo
- Division of Animal Sciences, University of Missouri, Columbia MO, USA
| | - Mayra E Ortiz D’Avila Assumpção
- Division of Animal Sciences, University of Missouri, Columbia MO, USA
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, SP, Brazil
| | - Alexis Jones
- Division of Animal Sciences, University of Missouri, Columbia MO, USA
| | - Filip Tirpak
- Division of Animal Sciences, University of Missouri, Columbia MO, USA
| | - Yuksel Agca
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Karl Kerns
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Miriam Sutovsky
- Division of Animal Sciences, University of Missouri, Columbia MO, USA
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19
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Phillips D, Noble D. Bubbling beyond the barrier: exosomal RNA as a vehicle for soma-germline communication. J Physiol 2024; 602:2547-2563. [PMID: 37936475 DOI: 10.1113/jp284420] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
'Weismann's barrier' has restricted theories of heredity to the transmission of genomic variation for the better part of a century. However, the discovery and elucidation of epigenetic mechanisms of gene regulation such as DNA methylation and histone modifications has renewed interest in studies on the inheritance of acquired traits and given them mechanistic plausibility. Although it is now clear that these mechanisms allow many environmentally acquired traits to be transmitted to the offspring, how phenotypic information is communicated from the body to its gametes has remained a mystery. Here, we discuss recent evidence that such communication is mediated by somatic RNAs that travel inside extracellular vesicles to the gametes where they reprogram the offspring epigenome and phenotype. How gametes learn about bodily changes has implications not only for the clinic, but also for evolutionary theory by bringing together intra- and intergenerational mechanisms of phenotypic plasticity and adaptation.
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Affiliation(s)
- Daniel Phillips
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Denis Noble
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford, UK
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20
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Cai C, Chen Q. Father's diet influences son's metabolic health through sperm RNA. Nature 2024; 630:571-573. [PMID: 38839997 DOI: 10.1038/d41586-024-01502-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
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21
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Tomar A, Gomez-Velazquez M, Gerlini R, Comas-Armangué G, Makharadze L, Kolbe T, Boersma A, Dahlhoff M, Burgstaller JP, Lassi M, Darr J, Toppari J, Virtanen H, Kühnapfel A, Scholz M, Landgraf K, Kiess W, Vogel M, Gailus-Durner V, Fuchs H, Marschall S, Hrabě de Angelis M, Kotaja N, Körner A, Teperino R. Epigenetic inheritance of diet-induced and sperm-borne mitochondrial RNAs. Nature 2024; 630:720-727. [PMID: 38839949 PMCID: PMC11186758 DOI: 10.1038/s41586-024-07472-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 04/26/2024] [Indexed: 06/07/2024]
Abstract
Spermatozoa harbour a complex and environment-sensitive pool of small non-coding RNAs (sncRNAs)1, which influences offspring development and adult phenotypes1-7. Whether spermatozoa in the epididymis are directly susceptible to environmental cues is not fully understood8. Here we used two distinct paradigms of preconception acute high-fat diet to dissect epididymal versus testicular contributions to the sperm sncRNA pool and offspring health. We show that epididymal spermatozoa, but not developing germ cells, are sensitive to the environment and identify mitochondrial tRNAs (mt-tRNAs) and their fragments (mt-tsRNAs) as sperm-borne factors. In humans, mt-tsRNAs in spermatozoa correlate with body mass index, and paternal overweight at conception doubles offspring obesity risk and compromises metabolic health. Sperm sncRNA sequencing of mice mutant for genes involved in mitochondrial function, and metabolic phenotyping of their wild-type offspring, suggest that the upregulation of mt-tsRNAs is downstream of mitochondrial dysfunction. Single-embryo transcriptomics of genetically hybrid two-cell embryos demonstrated sperm-to-oocyte transfer of mt-tRNAs at fertilization and suggested their involvement in the control of early-embryo transcription. Our study supports the importance of paternal health at conception for offspring metabolism, shows that mt-tRNAs are diet-induced and sperm-borne and demonstrates, in a physiological setting, father-to-offspring transfer of sperm mitochondrial RNAs at fertilization.
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MESH Headings
- Animals
- Female
- Humans
- Male
- Mice
- Body Mass Index
- Diet, High-Fat/adverse effects
- Embryo, Mammalian/cytology
- Embryo, Mammalian/embryology
- Embryo, Mammalian/metabolism
- Epididymis/cytology
- Epigenesis, Genetic/genetics
- Fertilization/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Developmental
- Mice, Inbred C57BL
- Mitochondria/genetics
- Mitochondria/metabolism
- Mitochondria/pathology
- Obesity/genetics
- Obesity/metabolism
- Obesity/etiology
- Oocytes/metabolism
- Overweight/genetics
- Overweight/metabolism
- Paternal Inheritance/genetics
- RNA, Mitochondrial/genetics
- RNA, Mitochondrial/metabolism
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Spermatozoa/metabolism
- Testis/cytology
- Transcription, Genetic
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Affiliation(s)
- A Tomar
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - M Gomez-Velazquez
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - R Gerlini
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - G Comas-Armangué
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - L Makharadze
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - T Kolbe
- Unit of in vivo and in vitro Models, Center for Biological Sciences, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
- IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Austria
| | - A Boersma
- Unit of in vivo and in vitro Models, Center for Biological Sciences, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - M Dahlhoff
- Unit of in vivo and in vitro Models, Center for Biological Sciences, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - J P Burgstaller
- Institute of Animal Breeding and Genetics, Department of Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
- Group Molecular Reproduction, IFA-Tulln, Tulln, Austria
| | - M Lassi
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - J Darr
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - J Toppari
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
- Center for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - H Virtanen
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
- Center for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - A Kühnapfel
- University of Leipzig, Medical Faculty, Institute for Medical Informatics, Statistics and Epidemiology, Leipzig, Germany
| | - M Scholz
- University of Leipzig, Medical Faculty, Institute for Medical Informatics, Statistics and Epidemiology, Leipzig, Germany
| | - K Landgraf
- Center for Pediatric Research Leipzig (CPL), Hospital for Children & Adolescents, University of Leipzig, Leipzig, Germany
| | - W Kiess
- Center for Pediatric Research Leipzig (CPL), Hospital for Children & Adolescents, University of Leipzig, Leipzig, Germany
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - M Vogel
- Center for Pediatric Research Leipzig (CPL), Hospital for Children & Adolescents, University of Leipzig, Leipzig, Germany
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - V Gailus-Durner
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - H Fuchs
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - S Marschall
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - M Hrabě de Angelis
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Freising, Germany
| | - N Kotaja
- Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - A Körner
- Center for Pediatric Research Leipzig (CPL), Hospital for Children & Adolescents, University of Leipzig, Leipzig, Germany
- LIFE Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic Obesity and Vascular Research (HI-MAG), Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - R Teperino
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany.
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22
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Wu D, Zhang K, Guan K, Khan FA, Pandupuspitasari NS, Negara W, Sun F, Huang C. Future in the past: paternal reprogramming of offspring phenotype and the epigenetic mechanisms. Arch Toxicol 2024; 98:1685-1703. [PMID: 38460001 DOI: 10.1007/s00204-024-03713-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/20/2024] [Indexed: 03/11/2024]
Abstract
That certain preconceptual paternal exposures reprogram the developmental phenotypic plasticity in future generation(s) has conceptualized the "paternal programming of offspring health" hypothesis. This transgenerational effect is transmitted primarily through sperm epigenetic mechanisms-DNA methylation, non-coding RNAs (ncRNAs) and associated RNA modifications, and histone modifications-and potentially through non-sperm-specific mechanisms-seminal plasma and circulating factors-that create 'imprinted' memory of ancestral information. The epigenetic landscape in sperm is highly responsive to environmental cues, due to, in part, the soma-to-germline communication mediated by epididymosomes. While human epidemiological studies and experimental animal studies have provided solid evidences in support of transgenerational epigenetic inheritance, how ancestral information is memorized as epigenetic codes for germline transmission is poorly understood. Particular elusive is what the downstream effector pathways that decode those epigenetic codes into persistent phenotypes. In this review, we discuss the paternal reprogramming of offspring phenotype and the possible underlying epigenetic mechanisms. Cracking these epigenetic mechanisms will lead to a better appreciation of "Paternal Origins of Health and Disease" and guide innovation of intervention algorithms to achieve 'healthier' outcomes in future generations. All this will revolutionize our understanding of human disease etiology.
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Affiliation(s)
- Di Wu
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Kejia Zhang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Kaifeng Guan
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Faheem Ahmed Khan
- Research Center for Animal Husbandry, National Research and Innovation Agency, Jakarta Pusat, 10340, Indonesia
| | | | - Windu Negara
- Research Center for Animal Husbandry, National Research and Innovation Agency, Jakarta Pusat, 10340, Indonesia
| | - Fei Sun
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China.
| | - Chunjie Huang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China.
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23
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van Wijnen AJ, Lewallen EA. Natural selection and evolution: evolving concepts. ACADEMIA BIOLOGY 2024; 2:10.20935/AcadBiol6245. [PMID: 38873024 PMCID: PMC11175172 DOI: 10.20935/acadbiol6245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Many recent studies in evolutionary biology have expanded and refined definitions of biological evolution and natural selection. Current evolutionary models incorporate different adaptive and non-adaptive processes based on molecular genetic changes and how DNA is modified over time in unicellular species, or in germline versus somatic cells in metazoan species. Cogent arguments can be raised for the view that natural selection should be considered a biological law, consistent with quantitative mathematical equations that describe the fitness of individuals, as well as variations within and among populations. Evolution is an overarching framework that incorporates the laws of natural selection and clarifies why phenotypic variation can increase in prevalence and result in species adaptations. The conceptual framework for biological evolution incorporates many cohesive principles that collectively have a predictive value. This framework will continue to evolve with improvements in high-resolution technologies that enable us to examine both adaptive and non-adaptive changes that drive biological phenotypes.
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Affiliation(s)
- Andre J. van Wijnen
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Eric A. Lewallen
- Department of Biological Sciences, Hampton University, Hampton, VA, 23668, USA
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24
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Sun C, Guo R, Ye X, Tang S, Chen M, Zhou P, Yang M, Liao C, Li H, Lin B, Zang C, Qi Y, Han D, Sun Y, Li N, Zhu D, Xu K, Hu H. Wybutosine hypomodification of tRNAphe activates HERVK and impairs neuronal differentiation. iScience 2024; 27:109748. [PMID: 38706838 PMCID: PMC11066470 DOI: 10.1016/j.isci.2024.109748] [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: 09/19/2023] [Revised: 02/23/2024] [Accepted: 04/11/2024] [Indexed: 05/07/2024] Open
Abstract
We previously reported that loss of function of TYW1 led to cerebral palsy with severe intellectual disability through reduced neural proliferation. However, whether TYW1 loss affects neural differentiation is unknown. In this study, we first demonstrated that TYW1 loss blocked the formation of OHyW in tRNAphe and therefore affected the translation efficiency of UUU codon. Using the brain organoid model, we showed impaired neuron differentiation when TYW1 was depleted. Interestingly, retrotransposons were differentially regulated in TYW1-/- hESCs (human embryonic stem cells). In particular, one kind of human-specific endogenous retrovirus-K (HERVK/HML2), whose reactivation impaired human neurodevelopment, was significantly up-regulated in TYW1-/- hESCs. Consistently, a UUU codon-enriched protein, SMARCAD1, which was a key factor in controlling endogenous retroviruses, was reduced. Taken together, TYW1 loss leads to up-regulation of HERVK in hESCs by down-regulated SMARCAD1, thus impairing neuron differentiation.
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Affiliation(s)
- Chuanbo Sun
- Laboratory of Medical Systems Biology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Ruirui Guo
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
- School of Basic Medical Science, Gansu Medical College, Pingliang 744000, Gansu, China
| | - Xiangyan Ye
- Laboratory of Medical Systems Biology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Shiyi Tang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Manqi Chen
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Pei Zhou
- Laboratory of Medical Systems Biology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Miaomiao Yang
- Laboratory of Medical Systems Biology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Caihua Liao
- Laboratory of Medical Systems Biology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Hong Li
- Laboratory of Medical Systems Biology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Bing Lin
- Laboratory of Medical Systems Biology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Congwen Zang
- Laboratory of Medical Systems Biology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Yifei Qi
- Laboratory of Medical Systems Biology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Dingding Han
- Laboratory of Medical Systems Biology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Yi Sun
- Department of Neonatology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, Guangdong Province 510180, China
| | - Na Li
- Laboratory of Medical Systems Biology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Dengna Zhu
- Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Kaishou Xu
- Department of Rehabilitation, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510120, China
| | - Hao Hu
- Laboratory of Medical Systems Biology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, China
- Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
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25
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Zhang G, Sun Y, Guan M, Liu M, Sun S. Single-cell and spatial transcriptomic investigation reveals the spatiotemporal specificity of the beta-defensin gene family during mouse sperm maturation. Cell Commun Signal 2024; 22:267. [PMID: 38745232 PMCID: PMC11092205 DOI: 10.1186/s12964-024-01637-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 04/27/2024] [Indexed: 05/16/2024] Open
Abstract
Low sperm motility is a significant contributor to male infertility. beta-defensins have been implicated in host defence and the acquisition of sperm motility; however, the regulatory mechanisms governing their gene expression patterns and functions remain poorly understood. In this study, we performed single-cell RNA and spatial transcriptome sequencing to investigate the cellular composition of testicular and epididymal tissues and examined their gene expression characteristics. In the epididymis, we found that epididymal epithelial cells display a region specificity of gene expression in different epididymal segments, including the beta-defensin family genes. In particular, Defb15, Defb18, Defb20, Defb25 and Defb48 are specific to the caput; Defb22, Defb23 and Defb26 to the corpus; Defb2 and Defb9 to the cauda of the epididymis. To confirm this, we performed mRNA fluorescence in situ hybridisation (FISH) targeting certain exon region of beta-defensin genes, and found some of their expression matched the sequencing results and displayed a close connection with epididimosome marker gene Cd63. In addition, we paid attention to the Sertoli cells and Leydig cells in the testis, along with fibroblasts and smooth muscle cells in the epididymis, by demonstrating their gene expression profile and spatial information. Our study provides a single-cell and spatial landscape for analysing the gene expression characteristics of testicular and epididymal environments and has important implications for the study of spermatogenesis and sperm maturation.
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Affiliation(s)
| | - Yuanchao Sun
- Qingdao Agricultural University, Qingdao, China
- Qingdao University, Qingdao, China
| | - Minkai Guan
- Qingdao Agricultural University, Qingdao, China
| | | | - Shiduo Sun
- Northwest A&F University, Yangling, China
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26
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Li D, Gao X, Ma X, Wang M, Cheng C, Xue T, Gao F, Shen Y, Zhang J, Liu Q. Aging-induced tRNA Glu-derived fragment impairs glutamate biosynthesis by targeting mitochondrial translation-dependent cristae organization. Cell Metab 2024; 36:1059-1075.e9. [PMID: 38458203 DOI: 10.1016/j.cmet.2024.02.011] [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: 05/14/2023] [Revised: 10/31/2023] [Accepted: 02/15/2024] [Indexed: 03/10/2024]
Abstract
Mitochondrial cristae, infoldings of the mitochondrial inner membrane, undergo aberrant changes in their architecture with age. However, the underlying molecular mechanisms and their contribution to brain aging are largely elusive. Here, we observe an age-dependent accumulation of Glu-5'tsRNA-CTC, a transfer-RNA-derived small RNA (tsRNA), derived from nuclear-encoded tRNAGlu in the mitochondria of glutaminergic neurons. Mitochondrial Glu-5'tsRNA-CTC disrupts the binding of mt-tRNALeu and leucyl-tRNA synthetase2 (LaRs2), impairing mt-tRNALeu aminoacylation and mitochondria-encoded protein translation. Mitochondrial translation defects disrupt cristae organization, leading to damaged glutaminase (GLS)-dependent glutamate formation and reduced synaptosomal glutamate levels. Moreover, reduction of Glu-5'tsRNA-CTC protects aged brains from age-related defects in mitochondrial cristae organization, glutamate metabolism, synaptic structures, and memory. Thus, beyond illustrating a physiological role for normal mitochondrial cristae ultrastructure in maintaining glutamate levels, our study defines a pathological role for tsRNAs in brain aging and age-related memory decline.
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Affiliation(s)
- Dingfeng Li
- Department of Neurology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230001, China; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China; CAS Key Laboratory of Brain Function and Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Xinyi Gao
- Department of Neurology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230001, China; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China; CAS Key Laboratory of Brain Function and Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Xiaolin Ma
- Department of Neurology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230001, China; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China; CAS Key Laboratory of Brain Function and Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Ming Wang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China; CAS Key Laboratory of Brain Function and Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Chuandong Cheng
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Tian Xue
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China; CAS Key Laboratory of Brain Function and Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Feng Gao
- Department of Neurology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230001, China
| | - Yong Shen
- Department of Neurology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230001, China; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China; CAS Key Laboratory of Brain Function and Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China; Neurodegenerative Disorder Research Center, Anhui Province Key Laboratory of Biomedical Aging Research, University of Science and Technology of China, Hefei 230026, China
| | - Juan Zhang
- Department of Neurology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230001, China; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China; CAS Key Laboratory of Brain Function and Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China.
| | - Qiang Liu
- Department of Neurology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230001, China; Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China; CAS Key Laboratory of Brain Function and Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China; Neurodegenerative Disorder Research Center, Anhui Province Key Laboratory of Biomedical Aging Research, University of Science and Technology of China, Hefei 230026, China; Key Laboratory of Immune Response and Immunotherapy, University of Science and Technology of China, Hefei 230001, China.
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27
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Hamilton M, Russell S, Swanson GM, Krawetz SA, Menezes K, Moskovtsev SI, Librach C. A comprehensive analysis of spermatozoal RNA elements in idiopathic infertile males undergoing fertility treatment. Sci Rep 2024; 14:10316. [PMID: 38705876 PMCID: PMC11070429 DOI: 10.1038/s41598-024-60586-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/24/2024] [Indexed: 05/07/2024] Open
Abstract
Current approaches to diagnosing male infertility inadequately assess the complexity of the male gamete. Beyond the paternal haploid genome, spermatozoa also deliver coding and non-coding RNAs to the oocyte. While sperm-borne RNAs have demonstrated potential involvement in embryo development, the underlying mechanisms remain unclear. In this study, 47 sperm samples from normozoospermic males undergoing fertility treatment using donor oocytes were sequenced and analyzed to evaluate associations between sperm RNA elements (exon-sized sequences) and blastocyst progression. A total of 366 RNA elements (REs) were significantly associated with blastocyst rate (padj < 0.05), some of which were linked to genes related to critical developmental processes, including mitotic spindle formation and both ectoderm and mesoderm specification. Of note, 27 RE-associated RNAs are predicted targets of our previously reported list of developmentally significant miRNAs. Inverse RE-miRNA expression patterns were consistent with miRNA-mediated down-regulation. This study provides a comprehensive set of REs which differ by the patient's ability to produce blastocysts. This knowledge can be leveraged to improve clinical screening of male infertility and ultimately reduce time to pregnancy.
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Affiliation(s)
| | | | - Grace M Swanson
- Department of Obstetrics and Gynecology, Center for Molecular Medicine & Genetics, C.S. Mott Center, Wayne State University School of Medicine, Detroit, USA
| | - Stephen A Krawetz
- Department of Obstetrics and Gynecology, Center for Molecular Medicine & Genetics, C.S. Mott Center, Wayne State University School of Medicine, Detroit, USA
| | | | - Sergey I Moskovtsev
- CReATe Fertility Centre, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Clifford Librach
- CReATe Fertility Centre, Toronto, ON, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, Canada
- Department of Physiology and Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
- Sunnybrook Research Institute, Toronto, ON, Canada
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28
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Argaw-Denboba A, Schmidt TSB, Di Giacomo M, Ranjan B, Devendran S, Mastrorilli E, Lloyd CT, Pugliese D, Paribeni V, Dabin J, Pisaniello A, Espinola S, Crevenna A, Ghosh S, Humphreys N, Boruc O, Sarkies P, Zimmermann M, Bork P, Hackett JA. Paternal microbiome perturbations impact offspring fitness. Nature 2024; 629:652-659. [PMID: 38693261 PMCID: PMC11096121 DOI: 10.1038/s41586-024-07336-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
The gut microbiota operates at the interface of host-environment interactions to influence human homoeostasis and metabolic networks1-4. Environmental factors that unbalance gut microbial ecosystems can therefore shape physiological and disease-associated responses across somatic tissues5-9. However, the systemic impact of the gut microbiome on the germline-and consequently on the F1 offspring it gives rise to-is unexplored10. Here we show that the gut microbiota act as a key interface between paternal preconception environment and intergenerational health in mice. Perturbations to the gut microbiota of prospective fathers increase the probability of their offspring presenting with low birth weight, severe growth restriction and premature mortality. Transmission of disease risk occurs via the germline and is provoked by pervasive gut microbiome perturbations, including non-absorbable antibiotics or osmotic laxatives, but is rescued by restoring the paternal microbiota before conception. This effect is linked with a dynamic response to induced dysbiosis in the male reproductive system, including impaired leptin signalling, altered testicular metabolite profiles and remapped small RNA payloads in sperm. As a result, dysbiotic fathers trigger an elevated risk of in utero placental insufficiency, revealing a placental origin of mammalian intergenerational effects. Our study defines a regulatory 'gut-germline axis' in males, which is sensitive to environmental exposures and programmes offspring fitness through impacting placenta function.
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Affiliation(s)
- Ayele Argaw-Denboba
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Thomas S B Schmidt
- European Molecular Biology Laboratory (EMBL), Structural & Computational Biology Unit, Heidelberg, Germany
| | - Monica Di Giacomo
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Bobby Ranjan
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Saravanan Devendran
- European Molecular Biology Laboratory (EMBL), Structural & Computational Biology Unit, Heidelberg, Germany
| | - Eleonora Mastrorilli
- European Molecular Biology Laboratory (EMBL), Structural & Computational Biology Unit, Heidelberg, Germany
| | - Catrin T Lloyd
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Danilo Pugliese
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Violetta Paribeni
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Juliette Dabin
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Alessandra Pisaniello
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Sergio Espinola
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Alvaro Crevenna
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Subhanita Ghosh
- MRC London Institute for Medical Science (LMS), London, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Neil Humphreys
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Olga Boruc
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy
| | - Peter Sarkies
- MRC London Institute for Medical Science (LMS), London, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Michael Zimmermann
- European Molecular Biology Laboratory (EMBL), Structural & Computational Biology Unit, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory (EMBL), Structural & Computational Biology Unit, Heidelberg, Germany
- Department of Bioinformatics, Biozentrum, University of Würzburg, Würzburg, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
| | - Jamie A Hackett
- European Molecular Biology Laboratory (EMBL), Epigenetics & Neurobiology Unit, Rome, Italy.
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29
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Muthukumar S, Li CT, Liu RJ, Bellodi C. Roles and regulation of tRNA-derived small RNAs in animals. Nat Rev Mol Cell Biol 2024; 25:359-378. [PMID: 38182846 DOI: 10.1038/s41580-023-00690-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2023] [Indexed: 01/07/2024]
Abstract
A growing class of small RNAs, known as tRNA-derived RNAs (tdRs), tRNA-derived small RNAs or tRNA-derived fragments, have long been considered mere intermediates of tRNA degradation. These small RNAs have recently been implicated in an evolutionarily conserved repertoire of biological processes. In this Review, we discuss the biogenesis and molecular functions of tdRs in mammals, including tdR-mediated gene regulation in cell metabolism, immune responses, transgenerational inheritance, development and cancer. We also discuss the accumulation of tRNA-derived stress-induced RNAs as a distinct adaptive cellular response to pathophysiological conditions. Furthermore, we highlight new conceptual advances linking RNA modifications with tdR activities and discuss challenges in studying tdR biology in health and disease.
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Affiliation(s)
- Sowndarya Muthukumar
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Cai-Tao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden.
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30
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Riyahi J, Taslimi Z, Gelfo F, Petrosini L, Haghparast A. Trans-generational effects of parental exposure to drugs of abuse on offspring memory functions. Neurosci Biobehav Rev 2024; 160:105644. [PMID: 38548003 DOI: 10.1016/j.neubiorev.2024.105644] [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: 01/14/2024] [Revised: 03/10/2024] [Accepted: 03/22/2024] [Indexed: 04/01/2024]
Abstract
Recent evidence reported that parental-derived phenotypes can be passed on to the next generations. Within the inheritance of epigenetic characteristics allowing the transmission of information related to the ancestral environment to the offspring, the specific case of the trans-generational effects of parental drug addiction has been extensively studied. Drug addiction is a chronic disorder resulting from complex interactions among environmental, genetic, and drug-related factors. Repeated exposures to drugs induce epigenetic changes in the reward circuitry that in turn mediate enduring changes in brain function. Addictive drugs can exert their effects trans-generally and influence the offspring of addicted parents. Although there is growing evidence that shows a wide range of behavioral, physiological, and molecular phenotypes in inter-, multi-, and trans-generational studies, transmitted phenotypes often vary widely even within similar protocols. Given the breadth of literature findings, in the present review, we restricted our investigation to learning and memory performances, as examples of the offspring's complex behavioral outcomes following parental exposure to drugs of abuse, including morphine, cocaine, cannabinoids, nicotine, heroin, and alcohol.
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Affiliation(s)
- Javad Riyahi
- Department of Cognitive and Behavioral Science and Technology in Sport, Faculty of Sport Sciences and Health, Shahid Beheshti University, Tehran, Iran
| | - Zahra Taslimi
- Behavioral Disorders and Substance Abuse Research Center, Hamadan University of Medical Sciences, Hamadan, Iran; Fertility and Infertility Research Center, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Francesca Gelfo
- IRCCS Santa Lucia Foundation, Rome, Italy; Department of Human Sciences, Guglielmo Marconi University, Rome, Italy
| | | | - Abbas Haghparast
- Neuroscience Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; School of Cognitive Sciences, Institute for Research in Fundamental Sciences, Tehran, Iran; Department of Basic Sciences, Iranian Academy of Medical Sciences, Tehran, Iran.
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31
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Harris JC, Trigg NA, Goshu B, Yokoyama Y, Dohnalová L, White EK, Harman A, Murga-Garrido SM, Ting-Chun Pan J, Bhanap P, Thaiss CA, Grice EA, Conine CC, Kambayashi T. The microbiota and T cells non-genetically modulate inherited phenotypes transgenerationally. Cell Rep 2024; 43:114029. [PMID: 38573852 PMCID: PMC11102039 DOI: 10.1016/j.celrep.2024.114029] [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: 07/12/2023] [Revised: 01/21/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
The host-microbiota relationship has evolved to shape mammalian physiology, including immunity, metabolism, and development. Germ-free models are widely used to study microbial effects on host processes such as immunity. Here, we find that both germ-free and T cell-deficient mice exhibit a robust sebum secretion defect persisting across multiple generations despite microbial colonization and T cell repletion. These phenotypes are inherited by progeny conceived during in vitro fertilization using germ-free sperm and eggs, demonstrating that non-genetic information in the gametes is required for microbial-dependent phenotypic transmission. Accordingly, gene expression in early embryos derived from gametes from germ-free or T cell-deficient mice is strikingly and similarly altered. Our findings demonstrate that microbial- and immune-dependent regulation of non-genetic information in the gametes can transmit inherited phenotypes transgenerationally in mice. This mechanism could rapidly generate phenotypic diversity to enhance host adaptation to environmental perturbations.
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Affiliation(s)
- Jordan C Harris
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Natalie A Trigg
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Bruktawit Goshu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuichi Yokoyama
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lenka Dohnalová
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ellen K White
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adele Harman
- Transgenic Core, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sofía M Murga-Garrido
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jamie Ting-Chun Pan
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Preeti Bhanap
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christoph A Thaiss
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Elizabeth A Grice
- Department of Dermatology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Colin C Conine
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Departments of Genetics and Pediatrics - Penn Epigenetics Institute, Institute of Regenerative Medicine, and Center for Research on Reproduction and Women's Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Taku Kambayashi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
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32
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Costa DL. Grandchildren's Longevity and Their Grandfathers' POW Trauma in the U.S. Civil War. Demography 2024; 61:337-361. [PMID: 38393987 DOI: 10.1215/00703370-11191183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
I document the transmission of a grandfather's net nutritional deprivation and psychosocial stress in young adulthood across multiple generations using the grandfather's ex-prisoner of war (ex-POW) status in the U.S. Civil War (1861-1865). Using a newly created dataset, I uncover an association between a grandfather's ex-POW status and the longevity after age 45 of his sons and male-line grandsons but not of his daughters, granddaughters, female-line grandsons, children-in-law, or grandchildren-in-law. Male-line grandsons lost roughly a year of life at age 45 (4% of remaining life expectancy) if descended from ex-POWs who suffered severe captivity conditions than if descended from non-POWs. If their grandfathers faced a less harsh captivity, male-line grandsons lost less than a year of life compared with those descended from non-POWs. I find that the grandfather's age at exposure and the grandson's education, as well as the son's and the grandson's poor late gestational conditions (proxied by season of birth), mediate this relationship. I rule out socioeconomic status, marriage and mortality selection, and cultural or psychological transmission from grandfathers to grandsons as explanations. I cannot rule out an epigenetic explanation.
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Affiliation(s)
- Dora L Costa
- Department of Economics, University of California, Los Angeles, Los Angeles, CA, USA
- National Bureau of Economic Research, Cambridge, MA, USA
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Chen E, da Cruz RS, Nascimento A, Joshi M, Pereira DG, Dominguez O, Fernandes G, Smith M, Paiva SPC, de Assis S. Paternal DDT exposure induces sex-specific programming of fetal growth, placenta development and offspring's health phenotypes in a mouse model. Sci Rep 2024; 14:7567. [PMID: 38555297 PMCID: PMC10981700 DOI: 10.1038/s41598-024-58176-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/26/2024] [Indexed: 04/02/2024] Open
Abstract
Mounting evidence suggests that environmentally induced epigenetic inheritance occurs in mammals and that traits in the progeny can be shaped by parental environmental experiences. Epidemiological studies link parental exposure to environmental toxicants, such as the pesticide DDT, to health phenotypes in the progeny, including low birth and increased risk of chronic diseases later in life. Here, we show that the progeny of male mice exposed to DDT in the pre-conception period are born smaller and exhibit sexual dimorphism in metabolic function, with male, but not female, offspring developing severe glucose intolerance compared to controls. These phenotypes in DDT offspring were linked to reduced fetal growth and placenta size as well as placenta-specific reduction of glycogen levels and the nutrient sensor and epigenetic regulator OGT, with more pronounced phenotypes observed in male placentas. However, placenta-specific genetic reduction of OGT only partially replicates the metabolic phenotype observed in offspring of DDT-exposed males. Our findings reveal a role for paternal pre-conception environmental experiences in shaping placenta development and in fetal growth restriction. While many questions remain, our data raise the tantalizing possibility that placenta programming could be a mediator of environmentally induced intergenerational epigenetic inheritance of phenotypes and needs to be further evaluated.
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Affiliation(s)
- Elaine Chen
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
| | - Raquel Santana da Cruz
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
| | - Aallya Nascimento
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
| | - Meghali Joshi
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
| | - Duane Gischewski Pereira
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
| | - Odalys Dominguez
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
| | - Gabriela Fernandes
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
| | - Megan Smith
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
| | - Sara P C Paiva
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
- Department of Obstetrics and Gynecology, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Sonia de Assis
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA.
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34
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Ali N, Amelkina O, Santymire RM, Koepfli KP, Comizzoli P, Vazquez JM. Semen proteome and transcriptome of the endangered black-footed ferret (Mustela nigripes) show association with the environment and fertility outcome. Sci Rep 2024; 14:7063. [PMID: 38528039 DOI: 10.1038/s41598-024-57096-w] [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: 09/17/2023] [Accepted: 03/14/2024] [Indexed: 03/27/2024] Open
Abstract
The ex situ population of the endangered black-footed ferret (Mustela nigripes) has been experiencing declines in reproductive success over the past 30 years of human-managed care. A potential cause may be environmental-dependent inbreeding depression with diet being one of the contributing factors since ferrets are not fed their natural diet of prairie dogs. Here, we generated and analyzed semen proteome and transcriptome data from both wild and ex situ ferrets maintained on various diets. We identified 1757 proteins across all samples, with 149 proteins unique to the semen of wild ferrets and forming a ribosomal predicted protein-protein interaction cluster. Wild ferrets also differed from ex situ ferrets in their transcriptomic profile, showing enrichment in ribosomal RNA processing and potassium ion transport. Successful fertility outcomes documented for ex situ ferrets showed the strongest association with the semen transcriptome, with enrichment in genes involved in translation initiation and focal adhesion. Fertility also synergized with the effect of diet on differentially expressed transcriptomes, mainly affecting genes enriched in mitochondrial function. Our data and functional networks are important for understanding the causes and mechanisms of declining fertility in the ex situ ferret population and can be used as a resource for future conservation efforts.
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Affiliation(s)
- Nadya Ali
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA.
| | - Olga Amelkina
- Smithsonian's National Zoo and Conservation Biology Institute, Washington D.C., USA.
| | | | - Klaus-Peter Koepfli
- Smithsonian's National Zoo and Conservation Biology Institute, Washington D.C., USA.
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA.
| | - Pierre Comizzoli
- Smithsonian's National Zoo and Conservation Biology Institute, Washington D.C., USA
| | - Juan M Vazquez
- Department of Integrative Biology, University of California, Berkeley, USA.
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35
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Zhang Q, Zhao X, Sun M, Dong D. Novel insights into transfer RNA-derived small RNA (tsRNA) in cardio-metabolic diseases. Life Sci 2024; 341:122475. [PMID: 38309576 DOI: 10.1016/j.lfs.2024.122475] [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: 10/13/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
Cardio-metabolic diseases, including a cluster of metabolic disorders and their secondary affections on cardiovascular physiology, are gradually brought to the forefront by researchers due to their high prevalence and mortality, as well as an unidentified pathogenesis. tRNA-derived small RNAs (tsRNAs), cleaved by several specific enzymes and once considered as some "metabolic junks" in the past, have been proved to possess numerous functions in human bodies. More interestingly, such a potential also seems to influence the progression of cardio-metabolic diseases to some extent. In this review, the biogenesis, classification and mechanisms of tsRNAs will be discussed based on some latest studies, and their relations with several cardio-metabolic diseases will be highlighted in sequence. Lastly, some future prospects, such as their clinical applications as biomarkers and therapeutic targets will also be mentioned, in order to provide researchers with a comprehensive understanding of the research status of tsRNAs as well as its association with cardio-metabolic diseases, thus presenting as a beacon to indicate directions for the next stage of study.
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Affiliation(s)
- Qingya Zhang
- Innovation Institute, China Medical University, Shenyang 110122, Liaoning, China
| | - Xiaopeng Zhao
- College of Exercise and Health, Shenyang Sport University, Shenyang 110102, Liaoning, China
| | - Mingli Sun
- College of Exercise and Health, Shenyang Sport University, Shenyang 110102, Liaoning, China
| | - Dan Dong
- College of Basic Medical Science, China Medical University, Shenyang 110122, Liaoning, China.
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36
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Zhao Y, Wang K, Zhao C, Liu N, Wang Z, Yang W, Cheng Z, Zhou L, Wang K. The function of tRNA-derived small RNAs in cardiovascular diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102114. [PMID: 38314096 PMCID: PMC10835008 DOI: 10.1016/j.omtn.2024.102114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
tRNA-derived small RNAs (tsRNAs) constitute a subgroup of small noncoding RNAs (ncRNAs) originating from tRNA molecules. Their rich content, evolutionary conservatism, high stability, and widespread existence makes them significant in disease research. These characteristics have positioned tsRNAs as key players in various physiological and pathological processes. tsRNA actively participates in regulating many cellular processes, such as cell death, proliferation, and metabolism. tsRNAs could be promising diagnostic markers for cardiovascular diseases (CVDs). tsRNAs have been identified in serums, suggesting their utility as early indicators for the diagnosis of CVDs. Moreover, the regulatory roles of tsRNAs in CVDs make them promising targets for therapeutic intervention. This review provides a succinct overview of the characteristics, classification, and regulatory functions of tsRNAs in the context of CVDs. By shedding light on the intricate roles of tsRNAs, this knowledge could pave the way for the development of innovative diagnostic tools and therapeutic strategies for CVDs.
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Affiliation(s)
- Yan Zhao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Kai Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Chun Zhao
- College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Ning Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Zhihong Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Wenting Yang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Zewei Cheng
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Luyu Zhou
- College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Kun Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
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37
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Huang T, Zhao Y, Jiang G, Yang Z. tsRNA: A Promising Biomarker in Breast Cancer. J Cancer 2024; 15:2613-2626. [PMID: 38577588 PMCID: PMC10988313 DOI: 10.7150/jca.93531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024] Open
Abstract
tRNA-derived small RNAs (tsRNAs) are a novel class of non-coding small RNAs, generated from specific cleavage sites of tRNA or pre-tRNA. tsRNAs can directly participate in RNA silencing, transcription, translation, and other processes. Their dysregulation is closely related to the occurrence and development of various cancers. Breast cancer is one of the most common and fastest-growing malignant tumors in humans. tsRNAs have been found to be dysregulated in breast cancer, serving as a new target for exploring the pathogenesis of breast cancer. They are also considered new tumor markers, providing a basis for diagnosis and treatment. This article reviews the generation, classification, mechanism of action, function of tsRNAs, and their biological effects and related mechanisms in breast cancer, in the hope of providing a new direction for the diagnosis and treatment of breast cancer.
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Affiliation(s)
- Ting Huang
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Yuexin Zhao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Guoqin Jiang
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Zhixue Yang
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
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38
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Fan Y, Pavani KC, Smits K, Van Soom A, Peelman L. tRNA Glu-derived fragments from embryonic extracellular vesicles modulate bovine embryo hatching. J Anim Sci Biotechnol 2024; 15:23. [PMID: 38424649 PMCID: PMC10905895 DOI: 10.1186/s40104-024-00997-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/14/2024] [Indexed: 03/02/2024] Open
Abstract
Transfer RNA-derived small RNAs (tsRNAs) have been shown to be involved in early embryo development and repression of endogenous retroelements in embryos and stem cells. However, it is unknown whether tsRNAs also regulate embryo hatching. In this study, we mined the sequencing data of a previous experiment in which we demonstrated that the microRNA (miRNA) cargo of preimplantation embryonic extracellular vesicles (EVs) influences embryo development. We thus profiled the tsRNA cargo of EVs secreted by blastocysts and non-blastocysts. The majority of tsRNAs was identified as tRNA halves originating from the 5´ ends of tRNAs. Among the 148 differentially expressed tsRNAs, the 19 nt tRNA fragment (tRF) tDR-14:32-Glu-CTC-1 was found to be significantly up-regulated in EVs derived from non-blastocysts. RT-qPCR assays confirmed its significant up-regulation in non-blastocyst embryos and their conditioned medium compared to the blastocyst group (P < 0.05). Inhibition of tDR-14:32-Glu-CTC-1 by supplementing antagomirs to the conditioned medium improved embryo hatching (P < 0.05). Transcriptomic analysis of embryos treated with tDR-14:32-Glu-CTC-1 antagomirs further showed differential expression of genes that are associated with embryo hatching and implantation. In summary, tDR-14:32-Glu-CTC-1 is up-regulated in non-blastocyst embryos and their secretions, and inhibition of tDR-14:32-Glu-CTC-1 promotes embryo hatching, while influencing embryo implantation-related genes and pathways. These results indicate that embryonic EVs containing specific tRFs may regulate preimplantation embryo development.
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Affiliation(s)
- Yuan Fan
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820, Merelbeke, Belgium
| | - Krishna Chaitanya Pavani
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
- Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Katrien Smits
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Ann Van Soom
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Luc Peelman
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820, Merelbeke, Belgium.
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39
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Tosar JP, Castellano M, Costa B, Cayota A. Small RNA structural biochemistry in a post-sequencing era. Nat Protoc 2024; 19:595-602. [PMID: 38057624 DOI: 10.1038/s41596-023-00936-2] [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: 02/23/2023] [Accepted: 08/25/2023] [Indexed: 12/08/2023]
Abstract
High-throughput sequencing has had an enormous impact on small RNA research during the past decade. However, sequencing only offers a one-dimensional view of the transcriptome and is often highly biased. Additionally, the 'sequence, map and annotate' approach, used widely in small RNA research, can lead to flawed interpretations of the data, lacking biological plausibility, due in part to database issues. Even in the absence of technical biases, the loss of three-dimensional information is a major limitation to understanding RNA stability, turnover and function. For example, noncoding RNA-derived fragments seem to exist mainly as dimers, tetramers or as nicked forms of their parental RNAs, contrary to widespread assumptions. In this perspective, we will discuss main sources of bias during small RNA-sequencing, present several useful bias-reducing strategies and provide guidance on the interpretation of small RNA-sequencing results, with emphasis on RNA fragmentomics. As sequencing offers a one-dimensional projection of a four-dimensional reality, prior structure-level knowledge is often needed to make sense of the data. Consequently, while less-biased sequencing methods are welcomed, integration of orthologous experimental techniques is also strongly recommended.
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Affiliation(s)
- Juan Pablo Tosar
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay.
- Analytical Biochemistry Unit, Center for Nuclear Research, School of Science, Universidad de la República, Montevideo, Uruguay.
| | - Mauricio Castellano
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Biochemistry Department, School of Science, Universidad de la República, Montevideo, Uruguay
| | - Bruno Costa
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Analytical Biochemistry Unit, Center for Nuclear Research, School of Science, Universidad de la República, Montevideo, Uruguay
| | - Alfonso Cayota
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Hospital de Clínicas, Universidad de la República, Montevideo, Uruguay
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40
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Jimenez-Gonzalez A, Ansaloni F, Nebendahl C, Alavioon G, Murray D, Robak W, Sanges R, Müller F, Immler S. Paternal starvation affects metabolic gene expression during zebrafish offspring development and lifelong fitness. Mol Ecol 2024; 33:e17296. [PMID: 38361456 DOI: 10.1111/mec.17296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/03/2024] [Accepted: 01/12/2024] [Indexed: 02/17/2024]
Abstract
Dietary restriction in the form of fasting is a putative key to a healthier and longer life, but these benefits may come at a trade-off with reproductive fitness and may affect the following generation(s). The potential inter- and transgenerational effects of long-term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split-egg clutch design to explore the male-specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected, we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 h post-fertilisation in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra-embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism-associated genes. These similarities suggest a physiologically relevant, directed and potentially adaptive response transmitted by the father, independently from the offspring's nutritional state, which was defined by the mother.
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Affiliation(s)
- Ada Jimenez-Gonzalez
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Federico Ansaloni
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | | | - Ghazal Alavioon
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
| | - David Murray
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Centre for Environment, Fisheries, and Aquaculture Science, Lowestoft, UK
| | - Weronika Robak
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Remo Sanges
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Simone Immler
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich, UK
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Senaldi L, Hassan N, Cullen S, Balaji U, Trigg N, Gu J, Finkelstein H, Phillips K, Conine C, Smith-Raska M. Khdc3 Regulates Metabolism Across Generations in a DNA-Independent Manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582278. [PMID: 38464133 PMCID: PMC10925209 DOI: 10.1101/2024.02.27.582278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Genetic variants can alter the profile of heritable molecules such as small RNAs in sperm and oocytes, and in this manner ancestral genetic variants can have a significant effect on offspring phenotypes even if they are not themselves inherited. Here we show that wild type female mice descended from ancestors with a mutation in the mammalian germ cell gene Khdc3 have hepatic metabolic defects that persist over multiple generations. We find that genetically wild type females descended from Khdc3 mutants have transcriptional dysregulation of critical hepatic metabolic genes, which persist over multiple generations and pass through both female and male lineages. This was associated with dysregulation of hepatically-metabolized molecules in the blood of these wild type mice with mutational ancestry. The oocytes of Khdc3-null females, as well as their wild type descendants, had dysregulation of multiple small RNAs, suggesting that these epigenetic changes in the gametes transmit the phenotype between generations. Our results demonstrate that ancestral mutation in Khdc3 can produce transgenerational inherited phenotypes, potentially indefinitely.
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Affiliation(s)
- Liana Senaldi
- Division of Neonatology, Department of Pediatrics, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA
| | - Nora Hassan
- Division of Neonatology, Department of Pediatrics, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
| | - Sean Cullen
- Division of Neonatology, Department of Pediatrics, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA
| | - Uthra Balaji
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA
| | - Natalie Trigg
- Departments of Genetics and Paediatrics, University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jinghua Gu
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA
| | - Hailey Finkelstein
- Division of Neonatology, Department of Pediatrics, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
| | - Kathryn Phillips
- Division of Neonatology, Department of Pediatrics, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
| | - Colin Conine
- Departments of Genetics and Paediatrics, University of Pennsylvania Perelman School of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Matthew Smith-Raska
- Division of Neonatology, Department of Pediatrics, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
- Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA
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Sato A, Mihirogi Y, Wood C, Suzuki Y, Truebano M, Bishop J. Heterogeneity in maternal mRNAs within clutches of eggs in response to thermal stress during the embryonic stage. BMC Ecol Evol 2024; 24:21. [PMID: 38347459 PMCID: PMC10860308 DOI: 10.1186/s12862-024-02203-8] [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: 06/18/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND The origin of variation is of central interest in evolutionary biology. Maternal mRNAs govern early embryogenesis in many animal species, and we investigated the possibility that heterogeneity in maternal mRNA provisioning of eggs can be modulated by environmental stimuli. RESULTS We employed two sibling species of the ascidian Ciona, called here types A and B, that are adapted to different temperature regimes and can be hybridized. Previous study showed that hybrids using type B eggs had higher susceptibility to thermal stress than hybrids using type A eggs. We conducted transcriptome analyses of multiple single eggs from crosses using eggs of the different species to compare the effects of maternal thermal stress on heterogeneity in egg provisioning, and followed the effects across generations. We found overall decreases of heterogeneity of egg maternal mRNAs associated with maternal thermal stress. When the eggs produced by the F1 AB generation were crossed with type B sperm and the progeny ('ABB' generation) reared unstressed until maturation, the overall heterogeneity of the eggs produced was greater in a clutch from an individual with a heat-stressed mother compared to one from a non-heat-stressed mother. By examining individual genes, we found no consistent overall effect of thermal stress on heterogeneity of expression in genes involved in developmental buffering. In contrast, heterogeneity of expression in signaling molecules was directly affected by thermal stress. CONCLUSIONS Due to the absence of batch replicates and variation in the number of reads obtained, our conclusions are very limited. However, contrary to the predictions of bet-hedging, the results suggest that maternal thermal stress at the embryo stage is associated with reduced heterogeneity of maternal mRNA provision in the eggs subsequently produced by the stressed individual, but there is then a large increase in heterogeneity in eggs of the next generation, although itself unstressed. Despite its limitations, our study presents a proof of concept, identifying a model system, experimental approach and analytical techniques capable of providing a significant advance in understanding the impact of maternal environment on developmental heterogeneity.
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Affiliation(s)
- Atsuko Sato
- Department of Biology, Ochanomizu University, Otsuka, Bunkyo-Ku, Tokyo, 112-8610, Japan.
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK.
- Human Life Innovation Center, Ochanomizu University, Otsuka, Bunkyo-Ku, Tokyo, 112-8610, Japan.
- Graduate School of Life Sciences, Tohoku University, 6-3, Aramaki Aza Aoba, Aoba-Ku, Sendai, 980-8578, Japan.
| | - Yukie Mihirogi
- Department of Biology, Ochanomizu University, Otsuka, Bunkyo-Ku, Tokyo, 112-8610, Japan
| | - Christine Wood
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwano-Ha, Chiba, 277-8561, Japan
| | - Manuela Truebano
- Marine Biology and Ecology Research Center, School of Biological and Marine Sciences, Plymouth University, Drake Circus, Plymouth, PL4 8AA, UK
| | - John Bishop
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
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Mehta P, Singh R. Small RNAs: an ideal choice as sperm quality biomarkers. FRONTIERS IN REPRODUCTIVE HEALTH 2024; 6:1329760. [PMID: 38406667 PMCID: PMC10884189 DOI: 10.3389/frph.2024.1329760] [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: 10/29/2023] [Accepted: 01/17/2024] [Indexed: 02/27/2024] Open
Abstract
Spermatozoa were classically known as vehicles for the delivery of the paternal genome to the oocyte. However, in 1962, spermatozoa were discovered to carry significant amounts of RNA in them, which raised questions about the significance of these molecules in such a highly specialized cell. Scientific research in the last six decades has investigated the biological significance of sperm RNAs by various means. Irrespective of what sperm RNAs do, their presence in spermatozoa has attracted attention for their exploitation as biomarkers of fertility. Research in this direction started in the year 2000 and is still underway. A major hurdle in this research is the definition of the standard human sperm RNAome. Only a few normozoospermic samples have been analyzed to define the normal sperm RNAome. In this article, we provide a perspective on the suitability of sperm RNAs as biomarkers of fertility and the importance of defining the normal sperm RNAome before we can succeed in identifying RNA-based biomarkers of sperm quality and fertility. The identification of sperm RNA biomarkers of fertility can be exploited for quality screening of donor sperm samples, explain infertility in idiopathic cases, and RNA therapeutics for the treatment of male infertility.
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Affiliation(s)
- Poonam Mehta
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India
- Division of Endocrinology, Academy of Scientific and Industrial Research (AcSIR), Ghaziabad, India
| | - Rajender Singh
- Division of Endocrinology, Central Drug Research Institute, Lucknow, India
- Division of Endocrinology, Academy of Scientific and Industrial Research (AcSIR), Ghaziabad, India
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44
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van den Berg JS, Molina NM, Altmäe S, Arends B, Steba GS. A systematic review identifying seminal plasma biomarkers and their predictive ability on IVF and ICSI outcomes. Reprod Biomed Online 2024; 48:103622. [PMID: 38128376 DOI: 10.1016/j.rbmo.2023.103622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 06/30/2023] [Accepted: 10/12/2023] [Indexed: 12/23/2023]
Abstract
The diverse nature and high molecule concentration of seminal plasma (SP) makes this fluid a good potential source for a potential biomarker that could predict assisted reproductive technology (ART) outcomes. Currently, semen quality parameters cannot accurately predict ART outcomes. A systematic literature search was conducted to identify human SP biomarkers with potential predictive ability for the outcomes of IVF and intracytoplasmic sperm injection. Observational cohort and case-control studies describing the association between biomarkers in human SP and the outcome of infertile men attending for ART were included. Forty-three studies were selected, reporting on 89 potential SP biomarkers (grouped as oxidative stress, proteins glycoproteins, metabolites, immune system components, metals and trace elements and nucleic acids). The present review supports 32 molecules in SP as potentially relevant biomarkers for predicting ART outcomes; 23 molecules were reported once and nine molecules were reported in more than one study; IL-18 and TGF-β1-IL-18 ratio were confirmed in distinct studies. This review presents the most comprehensive overview of relevant SP biomarkers to predict ART outcomes to date, which is of clinical interest for infertility investigations and assisted reproduction; nevertheless, its potential is under-exploited. This review could serve as starting point for designing an all-encompassing study for biomarkers in SP and their predictive ability for ART outcomes, and for developing a non-invasive diagnostic tool.
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Affiliation(s)
- Jonna S van den Berg
- Department of Reproductive Medicine and Gynaecology, Division Female and Baby, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Nerea M Molina
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Granada, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Signe Altmäe
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Granada, Spain; Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain; Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Brigitte Arends
- Department of Reproductive Medicine and Gynaecology, Division Female and Baby, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Gaby Sarina Steba
- Department of Reproductive Medicine and Gynaecology, Division Female and Baby, University Medical Centre Utrecht, Utrecht, the Netherlands.
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45
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Maitin-Shepard M, Werner EF, Feig LA, Chavarro JE, Mumford SL, Wylie B, Rando OJ, Gaskins AJ, Sakkas D, Arora M, Kudesia R, Lujan ME, Braun J, Mozaffarian D. Food, nutrition, and fertility: from soil to fork. Am J Clin Nutr 2024; 119:578-589. [PMID: 38101699 DOI: 10.1016/j.ajcnut.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/22/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023] Open
Abstract
Food and nutrition-related factors, including foods and nutrients consumed, dietary patterns, use of dietary supplements, adiposity, and exposure to food-related environmental contaminants, have the potential to impact semen quality and male and female fertility; obstetric, fetal, and birth outcomes; and the health of future generations, but gaps in evidence remain. On 9 November 2022, Tufts University's Friedman School of Nutrition Science and Policy and the school's Food and Nutrition Innovation Institute hosted a 1-d meeting to explore the evidence and evidence gaps regarding the relationships between food, nutrition, and fertility. Topics addressed included male fertility, female fertility and gestation, and intergenerational effects. This meeting report summarizes the presentations and deliberations from the meeting. Regarding male fertility, a positive association exists with a healthy dietary pattern, with high-quality evidence for semen quality and lower quality evidence for clinical outcomes. Folic acid and zinc supplementation have been found to not impact male fertility. In females, body weight status and other nutrition-related factors are linked to nearly half of all ovulation disorders, a leading cause of female infertility. Females with obesity have worse fertility treatment, pregnancy-related, and birth outcomes. Environmental contaminants found in food, water, or its packaging, including lead, perfluorinated alkyl substances, phthalates, and phenols, adversely impact female reproductive outcomes. Epigenetic research has found that maternal and paternal dietary-related factors can impact outcomes for future generations. Priority evidence gaps identified by meeting participants relate to the effects of nutrition and dietary patterns on fertility, gaps in communication regarding fertility optimization through changes in nutritional and environmental exposures, and interventions impacting germ cell mechanisms through dietary effects. Participants developed research proposals to address the priority evidence gaps. The workshop findings serve as a foundation for future prioritization of scientific research to address evidence gaps related to food, nutrition, and fertility.
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Affiliation(s)
| | - Erika F Werner
- Tufts University School of Medicine, Boston, MA, United States
| | - Larry A Feig
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA, United States
| | - Jorge E Chavarro
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Sunni L Mumford
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, United States
| | - Blair Wylie
- Collaborative for Women's Environmental Health, Columbia University, New York, NY, United States
| | - Oliver J Rando
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Audrey J Gaskins
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, United States
| | | | - Manish Arora
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Marla E Lujan
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States
| | - Joseph Braun
- Department of Epidemiology, Brown University, Providence, RI, United States
| | - Dariush Mozaffarian
- Tufts University School of Medicine, Boston, MA, United States; Food is Medicine Institute, Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, United States.
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46
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Zhang Y, Labrecque R, Tremblay P, Plessis C, Dufour P, Martin H, Sirard MA. Sperm-borne tsRNAs and miRNAs analysis in relation to dairy cattle fertility. Theriogenology 2024; 215:241-248. [PMID: 38100996 DOI: 10.1016/j.theriogenology.2023.11.029] [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: 03/24/2023] [Revised: 10/16/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023]
Abstract
Sperm small non-coding RNAs (sncRNAs), such as microRNAs (miRNAs) and tRNA-derived small RNAs (tsRNAs), have been found to have implications for male fertility and play a role in the intergenerational transmission of specific phenotypes by influencing the early embryo's physiological processes in various animal species. This study postulates that there exists a correlation between sperm small non-coding RNAs (sncRNAs) and bull fertility, which in turn can influence the fertility of offspring through the modulation of early embryo development. To investigate this hypothesis, we generated comparative libraries of sperm sncRNAs from sires exhibiting high (n = 3) versus low bull fertility (n = 3), as well as high (n = 3) versus low daughter fertility (n = 3), as determined by the industry-standard Bull fertility index and Daughter fertility index. In total, 12 tsRNAs carried by sperm (11 down-regulated and 1 up-regulated) were found to be associated with bull fertility, while 19 tsRNAs (11 down-regulated and 8 up-regulated) were found to be associated with daughter fertility (q < 0.05, Log2foldchange>±1.5, base mean > 50). Notably, tRX-Glu-NNN-3811 exhibited potential as a biomarker for predicting fertility in both male and female dairy cattle. Moreover, a total of six miRNAs sperm-borne (two up-regulated and four down-regulated) and 35 miRNAs (27 up-regulated and eight down-regulated) exhibited a significant correlation with both bull fertility and daughter fertility individually (p < 0.05, base mean > 50, log2foldchange>±1.5), two microRNAs, namely miR-2385-5p (down-regulated) and miR-98 (up-regulated), exhibit a significant association (p < 0.05, base mean > 50, log2foldchange>±1.5) with the fertility of both bulls and daughter. The targets of these two microRNAs were subsequently identified and integrated with the transcriptomic database of the embryonic cells at the two-cell stage, which is known to be indicative of embryonic competence. The KEGG analysis revealed a potential correlation between these targets and choline metabolism, a crucial factor in embryonic epigenetic programming. In summary, the findings of this study indicate that sperm-borne small non-coding RNAs (sncRNAs) hold promise as biomarkers for predicting and enhancing fertility in dairy cattle. Furthermore, it is plausible that these sncRNAs may exert their effects on daughter fertility by targeting genes in the early embryo.
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Affiliation(s)
- Ying Zhang
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Faculté des Sciences de l'Agriculture et de l'Alimentation, Département des Sciences Animales, Pavillon, INAF, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Rémi Labrecque
- SEMEX Boviteq, 3450 Rue Sicotte, Saint-Hyacinthe, QC J2S, Canada
| | - Patricia Tremblay
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Faculté des Sciences de l'Agriculture et de l'Alimentation, Département des Sciences Animales, Pavillon, INAF, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Clément Plessis
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Faculté des Sciences de l'Agriculture et de l'Alimentation, Département des Sciences Animales, Pavillon, INAF, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Pascal Dufour
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Faculté des Sciences de l'Agriculture et de l'Alimentation, Département des Sciences Animales, Pavillon, INAF, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Hélène Martin
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Faculté des Sciences de l'Agriculture et de l'Alimentation, Département des Sciences Animales, Pavillon, INAF, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Marc André Sirard
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Faculté des Sciences de l'Agriculture et de l'Alimentation, Département des Sciences Animales, Pavillon, INAF, Université Laval, Québec, Québec, G1V 0A6, Canada.
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47
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Kimmins S, Anderson RA, Barratt CLR, Behre HM, Catford SR, De Jonge CJ, Delbes G, Eisenberg ML, Garrido N, Houston BJ, Jørgensen N, Krausz C, Lismer A, McLachlan RI, Minhas S, Moss T, Pacey A, Priskorn L, Schlatt S, Trasler J, Trasande L, Tüttelmann F, Vazquez-Levin MH, Veltman JA, Zhang F, O'Bryan MK. Frequency, morbidity and equity - the case for increased research on male fertility. Nat Rev Urol 2024; 21:102-124. [PMID: 37828407 DOI: 10.1038/s41585-023-00820-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2023] [Indexed: 10/14/2023]
Abstract
Currently, most men with infertility cannot be given an aetiology, which reflects a lack of knowledge around gamete production and how it is affected by genetics and the environment. A failure to recognize the burden of male infertility and its potential as a biomarker for systemic illness exists. The absence of such knowledge results in patients generally being treated as a uniform group, for whom the strategy is to bypass the causality using medically assisted reproduction (MAR) techniques. In doing so, opportunities to prevent co-morbidity are missed and the burden of MAR is shifted to the woman. To advance understanding of men's reproductive health, longitudinal and multi-national centres for data and sample collection are essential. Such programmes must enable an integrated view of the consequences of genetics, epigenetics and environmental factors on fertility and offspring health. Definition and possible amelioration of the consequences of MAR for conceived children are needed. Inherent in this statement is the necessity to promote fertility restoration and/or use the least invasive MAR strategy available. To achieve this aim, protocols must be rigorously tested and the move towards personalized medicine encouraged. Equally, education of the public, governments and clinicians on the frequency and consequences of infertility is needed. Health options, including male contraceptives, must be expanded, and the opportunities encompassed in such investment understood. The pressing questions related to male reproductive health, spanning the spectrum of andrology are identified in the Expert Recommendation.
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Affiliation(s)
- Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- The Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
- The Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, Quebec, Canada
| | - Richard A Anderson
- MRC Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
| | - Christopher L R Barratt
- Division of Systems Medicine, School of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Hermann M Behre
- Center for Reproductive Medicine and Andrology, University Hospital, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Sarah R Catford
- Hudson Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Obstetrics and Gynaecology, The Royal Women's Hospital, Melbourne, Victoria, Australia
| | | | - Geraldine Delbes
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Sante Biotechnologie, Laval, Quebec, Canada
| | - Michael L Eisenberg
- Department of Urology and Obstetrics and Gynecology, Stanford University, Stanford, CA, USA
| | - Nicolas Garrido
- IVI Foundation, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Brendan J Houston
- School of BioSciences and Bio21 Institute, The University of Melbourne, Parkville, Melbourne, Australia
| | - Niels Jørgensen
- Department of Growth and Reproduction, International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Csilla Krausz
- Department of Experimental and Clinical Biomedical Sciences, 'Mario Serio', University of Florence, University Hospital of Careggi Florence, Florence, Italy
| | - Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Robert I McLachlan
- Hudson Institute of Medical Research and the Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia
- Monash IVF Group, Richmond, Victoria, Australia
| | - Suks Minhas
- Department of Surgery and Cancer Imperial, London, UK
| | - Tim Moss
- Healthy Male and the Department of Obstetrics and Gynaecology, Monash University, Melbourne, Victoria, Australia
| | - Allan Pacey
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Lærke Priskorn
- Department of Growth and Reproduction, International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Stefan Schlatt
- Centre for Reproductive Medicine and Andrology, University of Münster, Münster, Germany
| | - Jacquetta Trasler
- Departments of Paediatrics, Human Genetics and Pharmacology & Therapeutics, McGill University and Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Leonardo Trasande
- Center for the Investigation of Environmental Hazards, Department of Paediatrics, NYU Grossman School of Medicine, New York, NY, USA
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Mónica Hebe Vazquez-Levin
- Instituto de Biología y Medicina Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Fundación IBYME, Buenos Aires, Argentina
| | - Joris A Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Moira K O'Bryan
- School of BioSciences and Bio21 Institute, The University of Melbourne, Parkville, Melbourne, Australia.
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48
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Chen Y, Liu X, Chen W, Zhu L. RNS2 is required for the biogenesis of a wounding responsive 16 nts tsRNA in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2024; 114:6. [PMID: 38265739 DOI: 10.1007/s11103-023-01399-5] [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: 06/01/2023] [Accepted: 12/05/2023] [Indexed: 01/25/2024]
Abstract
tRNA-derived small RNAs (tsRNAs), a new category of regulatory small non-coding RNA existing in almost all branches of life, have recently attracted broad attention. Increasing evidence has shown that tsRNAs are not random degradation debris of tRNAs, but products cleaved by specific endoribonucleases, with versatile functions in response to various developmental and environmental cues. However, it is still unclear about the diversity, biogenesis and function of tsRNAs in plants. In this study, we comprehensively profiled 10-60 nts small RNAs in Arabidopsis thaliana leaf with or without wounding stress and identified four 16 nts tiny tRFs (tRNA-derived fragments) sharply increased after wounding, namely tRF5'Ala. Notably, genetic, biochemical and bioinformatic data indicated that RNS2, a member of class II RNase T2 enzymes, was the main endoribonuclease responsible for the biogenesis of tRF5'Ala. Moreover, tRF5'Ala was highly abundant and conserved in Arabidopsis and rice pollen. However, tRF5'Ala did not associate with AGO 1 in vivo or display any inhibitory effect on the translation of a luciferase mRNA in vitro. Altogether, our study highlights the discovery of a novel class of tiny tsRNAs drastically increased under wounding stress as well as their generation by RNS2, which provides a new insight into tsRNAs research in plants.
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Affiliation(s)
- Yan Chen
- Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, 230 Waihuanxi Road, Guangzhou, 510006, China
| | - Xiaobin Liu
- Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou Higher Education Mega Center, 230 Waihuanxi Road, Guangzhou, 510006, China
| | - Weiqiang Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- Prescription Laboratory of Xinjiang Traditional Uyghur Medicine, Xinjiang Institute of Traditional Uyghur Medicine, Urmuqi, 830000, China.
| | - Lei Zhu
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, 6100041, China.
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49
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Silva JR, Souza-Fabjan JMG, Bento TFM, Silva RC, Moura CRF, Bartlewski PM, Batista RITP. The effects of heat stress on intrauterine development, reproductive function, and ovarian gene expression of F1 female mice as well as gene expression of F2 embryos†. Biol Reprod 2024; 110:33-47. [PMID: 37812452 DOI: 10.1093/biolre/ioad133] [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: 05/12/2023] [Revised: 08/30/2023] [Accepted: 10/01/2023] [Indexed: 10/10/2023] Open
Abstract
Exposure to heat stress (HS) in utero was postulated to trigger an adaptive molecular response that can be transmitted to the next generation. Hence, this study assessed the impact of HS exposure at different stages of the gestational period of mice on the female F1 population and their offspring. Heat stress exposure (41°C and 65% relative humidity-RH) occurred during the first half (FP), the second half (SP), or the entire pregnancy (TP). A control group (C) was maintained in normothermic conditions (25°C, 45% RH) throughout the experiment. Heat stress had a significant negative effect on intrauterine development, mainly when HS exposure occurred in the first half of pregnancy (FP and TP groups). Postnatal growth of FP and TP mice was hindered until 4 weeks of age. The total number of follicles per ovary did not vary (P > 0.05) between the control and HS-exposed groups. Mean numbers of primordial follicles were lower (P < 0.05) in the sexually mature FP than those in SP and TP F1 females. However, the mean number of viable embryos after superovulation was lower (P < 0.05) in TP compared with C group. The expression of genes associated with physiological and cellular response to HS, autophagy, and apoptosis was significantly affected in the ovarian tissue of F1 females and F2 in vivo-derived blastocysts in all HS-exposed groups. In conclusion, exposure to HS during pregnancy compromised somatic development and reproductive parameters as well as altered gene expression profile that was then transmitted to the next generation of mice.
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Affiliation(s)
- José R Silva
- Programa de Pós-Graduação em Ciência e Biotecnologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Joanna M G Souza-Fabjan
- Programa de Pós-Graduação em Ciência e Biotecnologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
- Faculdade de Veterinária, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Tays F M Bento
- Programa de Pós-Graduação em Ciência e Biotecnologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Robson Campos Silva
- Departamento de Ciências Básicas, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG, Brazil
| | - Cristiane R F Moura
- Departamento de Ciências Básicas, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG, Brazil
| | - Pawel M Bartlewski
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Ribrio I T P Batista
- Programa de Pós-Graduação em Ciência e Biotecnologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
- Faculdade de Veterinária, Universidade Federal Fluminense, Niterói, RJ, Brazil
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50
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Lismer A, Shao X, Dumargne MC, Lafleur C, Lambrot R, Chan D, Toft G, Bonde JP, MacFarlane AJ, Bornman R, Aneck-Hahn N, Patrick S, Bailey JM, de Jager C, Dumeaux V, Trasler JM, Kimmins S. The Association between Long-Term DDT or DDE Exposures and an Altered Sperm Epigenome-a Cross-Sectional Study of Greenlandic Inuit and South African VhaVenda Men. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:17008. [PMID: 38294233 PMCID: PMC10829569 DOI: 10.1289/ehp12013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/26/2023] [Accepted: 12/20/2023] [Indexed: 02/01/2024]
Abstract
BACKGROUND The organochlorine dichlorodiphenyltrichloroethane (DDT) is banned worldwide owing to its negative health effects. It is exceptionally used as an insecticide for malaria control. Exposure occurs in regions where DDT is applied, as well as in the Arctic, where its endocrine disrupting metabolite, p , p ' -dichlorodiphenyldichloroethylene (p , p ' -DDE) accumulates in marine mammals and fish. DDT and p , p ' -DDE exposures are linked to birth defects, infertility, cancer, and neurodevelopmental delays. Of particular concern is the potential of DDT use to impact the health of generations to come via the heritable sperm epigenome. OBJECTIVES The objective of this study was to assess the sperm epigenome in relation to p , p ' -DDE serum levels between geographically diverse populations. METHODS In the Limpopo Province of South Africa, we recruited 247 VhaVenda South African men and selected 50 paired blood serum and semen samples, and 47 Greenlandic Inuit blood and semen paired samples were selected from a total of 193 samples from the biobank of the INUENDO cohort, an EU Fifth Framework Programme Research and Development project. Sample selection was based on obtaining a range of p , p ' -DDE serum levels (mean = 870.734 ± 134.030 ng / mL ). We assessed the sperm epigenome in relation to serum p , p ' -DDE levels using MethylC-Capture-sequencing (MCC-seq) and chromatin immunoprecipitation followed by sequencing (ChIP-seq). We identified genomic regions with altered DNA methylation (DNAme) and differential enrichment of histone H3 lysine 4 trimethylation (H3K4me3) in sperm. RESULTS Differences in DNAme and H3K4me3 enrichment were identified at transposable elements and regulatory regions involved in fertility, disease, development, and neurofunction. A subset of regions with sperm DNAme and H3K4me3 that differed between exposure groups was predicted to persist in the preimplantation embryo and to be associated with embryonic gene expression. DISCUSSION These findings suggest that DDT and p , p ' -DDE exposure impacts the sperm epigenome in a dose-response-like manner and may negatively impact the health of future generations through epigenetic mechanisms. Confounding factors, such as other environmental exposures, genetic diversity, and selection bias, cannot be ruled out. https://doi.org/10.1289/EHP12013.
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Affiliation(s)
- Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Marie-Charlotte Dumargne
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Christine Lafleur
- University of Montreal Hospital Research Centre, Montreal, Quebec, Canada
| | - Romain Lambrot
- University of Montreal Hospital Research Centre, Montreal, Quebec, Canada
| | - Donovan Chan
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Gunnar Toft
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Jens Peter Bonde
- Department of Occupational and Environmental Medicine, Bispebjerg University Hospital, Copenhagen, Denmark
- Institute of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Amanda J. MacFarlane
- Agriculture Food and Nutrition Evidence Center, Texas A&M University, Fort Worth, Texas, USA
| | - Riana Bornman
- Environmental Chemical Pollution and Health Research Unit, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Natalie Aneck-Hahn
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Sean Patrick
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Janice M. Bailey
- Research Centre on Reproduction and Intergenerational Health, Department of Animal Sciences, Université Laval, Quebec, Quebec, Canada
| | - Christiaan de Jager
- Environmental Chemical Pollution and Health Research Unit, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
- University of Pretoria Institute for Sustainable Malaria Control, School of Health Systems and Public Health, Faculty of Health Sciences, University of Pretoria, South Africa
| | - Vanessa Dumeaux
- Department of Anatomy and Cell Biology, Western University, London, Ontario, Canada
- Department of Oncology, Western University, London, Ontario, Canada
| | - Jacquetta M. Trasler
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
- Department of Pediatrics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
- University of Montreal Hospital Research Centre, Montreal, Quebec, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, University of Montreal, Quebec, Canada
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