1
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Vishnevsky OV, Bocharnikov AV, Ignatieva EV. Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks. Int J Mol Sci 2024; 25:1011. [PMID: 38256085 PMCID: PMC10816497 DOI: 10.3390/ijms25021011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) is a central genome-wide method for in vivo analyses of DNA-protein interactions in various cellular conditions. Numerous studies have demonstrated the complex contextual organization of ChIP-seq peak sequences and the presence of binding sites for transcription factors in them. We assessed the dependence of the ChIP-seq peak score on the presence of different contextual signals in the peak sequences by analyzing these sequences from several ChIP-seq experiments using our fully enumerative GPU-based de novo motif discovery method, Argo_CUDA. Analysis revealed sets of significant IUPAC motifs corresponding to the binding sites of the target and partner transcription factors. For these ChIP-seq experiments, multiple regression models were constructed, demonstrating a significant dependence of the peak scores on the presence in the peak sequences of not only highly significant target motifs but also less significant motifs corresponding to the binding sites of the partner transcription factors. A significant correlation was shown between the presence of the target motifs FOXA2 and the partner motifs HNF4G, which found experimental confirmation in the scientific literature, demonstrating the important contribution of the partner transcription factors to the binding of the target transcription factor to DNA and, consequently, their important contribution to the peak score.
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Affiliation(s)
- Oleg V. Vishnevsky
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia;
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Andrey V. Bocharnikov
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Elena V. Ignatieva
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia;
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
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2
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Pasquariello R, Anipchenko P, Pennarossa G, Crociati M, Zerani M, Brevini TA, Gandolfi F, Maranesi M. Carotenoids in female and male reproduction. PHYTOCHEMISTRY 2022; 204:113459. [PMID: 36183866 DOI: 10.1016/j.phytochem.2022.113459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Carotenoids are among the best-known pigments in nature, confer color to plants and animals, and are mainly derived from photosynthetic bacteria, fungi, algae, plants. Mammals cannot synthesize carotenoids. Carotenoids' source is only alimentary and after their assumption, they are mainly converted in retinal, retinol and retinoic acid, collectively known also as pro-vitamins and vitamin A, which play an essential role in tissue growth and regulate different aspects of the reproductive functions. However, their mechanisms of action and potential therapeutic effects are still unclear. This review aims to clarify the role of carotenoids in the male and female reproductive functions in species of veterinary interest. In female, carotenoids and their derivatives regulate not only folliculogenesis and oogenesis but also steroidogenesis. Moreover, they improve fertility by decreasing the risk of embryonic mortality. In male, retinol and retinoic acids activate molecular pathways related to spermatogenesis. Deficiencies of these vitamins have been correlated with degeneration of testis parenchyma with consequent absence of the mature sperm. Carotenoids have also been considered anti-antioxidants as they ameliorate the effect of free radicals. The mechanisms of action seem to be exerted by activating Kit and Stra8 pathways in both female and male. In conclusion, carotenoids have potentially beneficial effects for ameliorating ovarian and testes function.
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Affiliation(s)
- Rolando Pasquariello
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università Degli Studi di Milano, 20133, Milan, Italy
| | - Polina Anipchenko
- Department of Veterinary Medicine, University of Perugia, Via S. Costanzo 4, 06126, Perugia, Italy
| | - Georgia Pennarossa
- Laboratory of Biomedical Embryology, Department of Veterinary Medicine and Animal Sciences, Università Degli Studi di Milano, 26900, Lodi, Italy.
| | - Martina Crociati
- Department of Veterinary Medicine, University of Perugia, Via S. Costanzo 4, 06126, Perugia, Italy; Centre for Perinatal and Reproductive Medicine, University of Perugia, 06129, Perugia, Italy
| | - Massimo Zerani
- Department of Veterinary Medicine, University of Perugia, Via S. Costanzo 4, 06126, Perugia, Italy
| | - Tiziana Al Brevini
- Laboratory of Biomedical Embryology, Department of Veterinary Medicine and Animal Sciences, Università Degli Studi di Milano, 26900, Lodi, Italy
| | - Fulvio Gandolfi
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università Degli Studi di Milano, 20133, Milan, Italy
| | - Margherita Maranesi
- Department of Veterinary Medicine, University of Perugia, Via S. Costanzo 4, 06126, Perugia, Italy
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3
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A novel posttranslational modification of histone, H3 S-sulfhydration, is down-regulated in asthenozoospermic sperm. J Assist Reprod Genet 2021; 38:3175-3193. [PMID: 34664184 PMCID: PMC8666411 DOI: 10.1007/s10815-021-02314-x] [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: 06/29/2021] [Accepted: 09/07/2021] [Indexed: 11/14/2022] Open
Abstract
Oxidative stress is one of the major causes leading to male infertility including asthenozoospermia. Hydrogen sulfide (H2S) has been widely recognized to be a potent antioxidant whose role is partially implemented by protein S-sulfhydration. However, protein S-sulfhydration has not been reported in germ cells. Therefore, we investigated whether asthenozoospermia could be associated with sperm protein S-sulfhydration. S-sulfhydrated proteins in human sperm were enriched via biotin-switch assay and analyzed using LC-MS/MS spectrometry. Two hundred forty-four S-sulfhydrated proteins were identified. Importantly, we validated that sperm histones H3.1 and H3.3 were the S-sulfhydrated proteins. Their S-sulfhydrated amino acid residue was Cysteine111. Abundances of S-sulfhydrated H3 (sH3) and S-sulfhydrated H3.3 (sH3.3) were significantly down-regulated in asthenozoospermic sperm, compared with the fertile controls, and were significantly correlated with progressive motility. Retinoic acid (RA) up-regulated level of sH3.3 in primary round spermatids and the C18-4 cells (a mouse spermatogonial stem cell line). Overexpression of the mutant H3.3 (Cysteine111 was replaced with serine) affected expression of 759 genes and raised growth rate of C18-4 cells. For the first time, S-sulfhydration H3 and H3.3 were demonstrated in the present study. Our results highlight that aberrant S-sulfhydration of H3 is a new pathophysiological basis in male infertility.
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Suzuki S, McCarrey JR, Hermann BP. Differential RA responsiveness among subsets of mouse late progenitor spermatogonia. Reproduction 2021; 161:645-655. [PMID: 33835049 PMCID: PMC8105290 DOI: 10.1530/rep-21-0031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/07/2021] [Indexed: 01/11/2023]
Abstract
Initiation of spermatogonial differentiation in the mouse testis begins with the response to retinoic acid (RA) characterized by activation of KIT and STRA8 expression. In the adult, spermatogonial differentiation is spatiotemporally coordinated by a pulse of RA every 8.6 days that is localized to stages VII-VIII of the seminiferous epithelial cycle. Dogmatically, progenitor spermatogonia that express retinoic acid receptor gamma (RARG) at these stages will differentiate in response to RA, but this has yet to be tested functionally. Previous single-cell RNA-seq data identified phenotypically and functionally distinct subsets of spermatogonial stem cells (SSCs) and progenitor spermatogonia, where late progenitor spermatogonia were defined by expression of RARG and Dppa3. Here, we found late progenitor spermatogonia (RARGhigh KIT-) were further divisible into two subpopulations based on Dppa3 reporter expression (Dppa3-ECFP or Dppa3-EGFP) and were observed across all stages of the seminiferous epithelial cycle. However, nearly all Dppa3+ spermatogonia were differentiating (KIT+) late in the seminiferous epithelial cycle (stages X-XII), while Dppa3- late progenitors remained abundant, suggesting that Dppa3+ and Dppa3- late progenitors differentially responded to RA. Following acute RA treatment (2-4 h), significantly more Dppa3+ late progenitors induced KIT, including at the midpoint of the cycle (stages VI-IX), than Dppa3- late progenitors. Subsequently, single-cell analyses indicated a subset of Dppa3+ late progenitors expressed higher levels of Rxra, which we confirmed by RXRA whole-mount immunostaining. Together, these results indicate RARG alone is insufficient to initiate a spermatogonial response to RA in the adult mouse testis and suggest differential RXRA expression may discriminate responding cells.
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Affiliation(s)
- Shinnosuke Suzuki
- Department of Biology, University of Texas at San Antonio, San Antonio, Texas 78249 USA
| | - John R. McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, Texas 78249 USA
| | - Brian P. Hermann
- Department of Biology, University of Texas at San Antonio, San Antonio, Texas 78249 USA
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5
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Nasimi M, Jorsaraei SGA, Fattahi E, Tabari MG, Neyshaburi EZ. SCF Improves In Vitro Differentiation of SSCs Through Transcriptionally Up-regulating PRTM1, STRA8, c-KIT, PIWIL2, and OCT4 Genes. Reprod Sci 2021; 28:963-972. [PMID: 33492648 DOI: 10.1007/s43032-020-00326-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022]
Abstract
Several lines of evidence strongly suggest that retinoic acid (RA) and stem cell factor (SCF)/c-Kit signal transduction pathways are involved in the differentiation of spermatogonial stem cells (SSCs). This study was aimed to investigate the effect of RA and SCF on in vitro differentiation of SSCs via evaluation of the mRNA expression of meiosis-specific genes in cultured testicular tissues. Testicular tissue samples were obtained from bilaterally vasectomized rats and also healthy adult rats and then were cultured for 25, 30, and 35 days on different conditions. The cultured testicular pieces were sectioned and stained with PAS to histological analysis. The total RNA was extracted from cultured testicular samples, and the expression of ACR, PRTM1, SYCP3, STRA8, c-KIT, PIWIL2, and OCT4 genes at mRNA level was quantified using real-time polymerase chain reaction (qPCR) procedure. After 1-month surgery, bilateral testicular weight showed a significant decrease in vasectomized adult rats compared with healthy adult rats (P < 0.05). Reduction in the diameter of the seminiferous tubules and depletion of advanced germinal elements in vasectomized rats compared with healthy adult rats were also observed. Our findings also demonstrated that the mRNA expression level of PRTM1, STRA8, c-KIT, PIWIL2, and OCT4 genes in cultured testicular tissues significantly up-regulated in experimental group II compared with the control group (P < 0.001). Our findings lead us to conclude that SCF improves in vitro differentiation of SSCs in the OA rats, at least partially, by transcriptionally upregulating PRTM1, STRA8, c-KIT, PIWIL2, and OCT4 genes.
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Affiliation(s)
- Mahnaz Nasimi
- Department of Biology, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | - Seyed Gholam Ali Jorsaraei
- Department of Anatomy and Embryology, Infertility and Health Reproductive Research Center, Babol University of Medical Sciences, P.O. Box: 4136747176, Babol, Iran.
| | - Esmail Fattahi
- Department of Biology, Ayatollah Amoli Branch, Islamic Azad University, Amol, Iran
| | | | - Ebrahim Zabihi Neyshaburi
- Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, Babol, Iran.,Department of Pharmacology and Toxicology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
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6
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Xie Y, Wei BH, Ni FD, Yang WX. Conversion from spermatogonia to spermatocytes: Extracellular cues and downstream transcription network. Gene 2020; 764:145080. [PMID: 32858178 DOI: 10.1016/j.gene.2020.145080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/16/2020] [Accepted: 08/19/2020] [Indexed: 12/15/2022]
Abstract
Spermatocyte (spc) formation from spermatogonia (spg) differentiation is the first step of spermatogenesis which produces prodigious spermatozoa for a lifetime. After decades of studies, several factors involved in the functioning of a mouse were discovered both inside and outside spg. Considering the peculiar expression and working pattern of each factor, this review divides the whole conversion of spg to spc into four consecutive development processes with a focus on extracellular cues and downstream transcription network in each one. Potential coordination among Dmrt1, Sohlh1/2 and BMP families mediates Ngn3 upregulation, which marks progenitor spg, with other changes. After that, retinoic acid (RA), as a master regulator, promotes A1 spg formation with its helpers and Sall4. A1-to-B spg transition is under the control of Kitl and impulsive RA signaling together with early and late transcription factors Stra8 and Dmrt6. Finally, RA and its responsive effectors conduct the entry into meiosis. The systematic transcription network from outside to inside still needs research to supplement or settle the controversials in each process. As a step further ahead, this review provides possible drug targets for infertility therapy by cross-linking humans and mouse model.
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Affiliation(s)
- Yi Xie
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bang-Hong Wei
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fei-Da Ni
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wan-Xi Yang
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
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7
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Persistent Human KIT Receptor Signaling Disposes Murine Placenta to Premature Differentiation Resulting in Severely Disrupted Placental Structure and Functionality. Int J Mol Sci 2020; 21:ijms21155503. [PMID: 32752102 PMCID: PMC7432075 DOI: 10.3390/ijms21155503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022] Open
Abstract
Activating mutations in the human KIT receptor is known to drive severe hematopoietic disorders and tumor formation spanning various entities. The most common mutation is the substitution of aspartic acid at position 816 to valine (D816V), rendering the receptor constitutively active independent of ligand binding. As the role of the KIT receptor in placental signaling cascades is poorly understood, we analyzed the impact of KITD816V expression on placental development using a humanized mouse model. Placentas from KITD816V animals present with a grossly changed morphology, displaying a reduction in labyrinth and spongiotrophoblast layer and an increase in the Parietal Trophoblast Giant Cell (P-TGC) layer. Elevated differentiation to P-TGCs was accompanied with reduced differentiation to other Trophoblast Giant Cell (TGC) subtypes and by severe decrease in proliferation. The embryos display growth retardation and die in utero. KITD816V-trophoblast stem cells (TSC) differentiate much faster compared to wild type (WT) controls. In undifferentiated KITD816V-TSCs, levels of Phosphorylated Extracellular-signal Regulated Kinase (P-ERK) and Phosphorylated Protein Kinase B (P-AKT) are comparable to wildtype cultures differentiating for 3–6 days. Accordingly, P-TGC markers Placental Lactogen 1 (PL1) and Proliferin (PLF) are upregulated as well. The results reveal that KIT signaling orchestrates the fine-tuned differentiation of the placenta, with special emphasis on P-TGC differentiation. Appropriate control of KIT receptor action is therefore essential for placental development and nourishment of the embryo.
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8
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Song L, Zigmond ZM, Martinez L, Lassance-Soares RM, Macias AE, Velazquez OC, Liu ZJ, Salama A, Webster KA, Vazquez-Padron RI. c-Kit suppresses atherosclerosis in hyperlipidemic mice. Am J Physiol Heart Circ Physiol 2019; 317:H867-H876. [PMID: 31441677 PMCID: PMC6843012 DOI: 10.1152/ajpheart.00062.2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/18/2019] [Accepted: 08/13/2019] [Indexed: 12/14/2022]
Abstract
Atherosclerosis is the most common underlying cause of cardiovascular morbidity and mortality worldwide. c-Kit (CD117) is a member of the receptor tyrosine kinase family, which regulates differentiation, proliferation, and survival of multiple cell types. Recent studies have shown that c-Kit and its ligand stem cell factor (SCF) are present in arterial endothelial cells and smooth muscle cells (SMCs). The role of c-Kit in cardiovascular disease remains unclear. The aim of the current study is to determine the role of c-Kit in atherogenesis. For this purpose, atherosclerotic plaques were quantified in c-Kit-deficient mice (KitMut) after they were fed a high-fat diet (HFD) for 16 wk. KitMut mice demonstrated substantially greater atherosclerosis compared with control (KitWT) littermates (P < 0.01). Transplantation of c-Kit-positive bone marrow cells into KitMut mice failed to rescue the atherogenic phenotype, an indication that increased atherosclerosis was associated with reduced arterial c-Kit. To investigate the mechanism, SMC organization and morphology were analyzed in the aorta by histopathology and electron microscopy. SMCs were more abundant, disorganized, and vacuolated in aortas of c-Kit mutant mice compared with controls (P < 0.05). Markers of the "contractile" SMC phenotype (calponin, SM22α) were downregulated with pharmacological and genetic c-Kit inhibition (P < 0.05). The absence of c-Kit increased lipid accumulation and significantly reduced the expression of the ATP-binding cassette transporter G1 (ABCG1) necessary for lipid efflux in SMCs. Reconstitution of c-Kit in cultured KitMut SMCs resulted in increased spindle-shaped morphology, reduced proliferation, and elevated levels of contractile markers, all indicators of their restored contractile phenotype (P < 0.05).NEW & NOTEWORTHY This study describes the novel vasculoprotective role of c-Kit against atherosclerosis and its function in the preservation of the SMC contractile phenotype.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily G, Member 1/genetics
- ATP Binding Cassette Transporter, Subfamily G, Member 1/metabolism
- Animals
- Aorta/metabolism
- Aorta/ultrastructure
- Aortic Diseases/etiology
- Aortic Diseases/metabolism
- Aortic Diseases/pathology
- Aortic Diseases/prevention & control
- Atherosclerosis/etiology
- Atherosclerosis/metabolism
- Atherosclerosis/pathology
- Atherosclerosis/prevention & control
- Calcium-Binding Proteins/genetics
- Calcium-Binding Proteins/metabolism
- Cells, Cultured
- Disease Models, Animal
- Foam Cells/metabolism
- Foam Cells/pathology
- Humans
- Hyperlipidemias/complications
- Hyperlipidemias/metabolism
- Mice, Knockout, ApoE
- Microfilament Proteins/genetics
- Microfilament Proteins/metabolism
- Muscle Proteins/genetics
- Muscle Proteins/metabolism
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/ultrastructure
- Mutation
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/ultrastructure
- Phenotype
- Plaque, Atherosclerotic
- Promoter Regions, Genetic
- Proto-Oncogene Proteins c-kit/genetics
- Proto-Oncogene Proteins c-kit/metabolism
- Signal Transduction
- Calponins
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Affiliation(s)
- Lei Song
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, Florida
| | - Zachary M Zigmond
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, Florida
| | - Laisel Martinez
- Department of Surgery, University of Miami, Miller School of Medicine, Miami, Florida
| | | | - Alejandro E Macias
- Department of Surgery, University of Miami, Miller School of Medicine, Miami, Florida
| | - Omaida C Velazquez
- Department of Surgery, University of Miami, Miller School of Medicine, Miami, Florida
| | - Zhao-Jun Liu
- Department of Surgery, University of Miami, Miller School of Medicine, Miami, Florida
| | - Alghidak Salama
- Department of Surgery, University of Miami, Miller School of Medicine, Miami, Florida
| | - Keith A Webster
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, Florida
| | - Roberto I Vazquez-Padron
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, Florida
- Department of Surgery, University of Miami, Miller School of Medicine, Miami, Florida
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9
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Li X, Long XY, Xie YJ, Zeng X, Chen X, Mo ZC. The roles of retinoic acid in the differentiation of spermatogonia and spermatogenic disorders. Clin Chim Acta 2019; 497:54-60. [PMID: 31302099 DOI: 10.1016/j.cca.2019.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/20/2019] [Accepted: 07/10/2019] [Indexed: 12/21/2022]
Abstract
Male fertility depends on the regulatory balance between germ cell self-renewal and differentiation, and the spatial and temporal patterns of this balance must be maintained throughout the life cycle. Retinoic acid and its receptors are important factors in spermatogenesis. Spermatogonia cells can self-proliferate and differentiate and have unique meiotic capabilities; they halve their genetic material and produce monomorphic sperm to pass genetic material to the next generation. A number of studies have found that the spermatogenesis process is halted in animals with vitamin A deficiency and that most germ cells are degraded, but they tend to recover after treatment with RA or vitamin A. This literature review discusses our understanding of how RA regulates sperm cell differentiation and meiosis and also reviews the functional information and details of RA.
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Affiliation(s)
- Xuan Li
- Clinical Anatomy & Reproductive Medicine Application Institute, Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Xiang-Yang Long
- Department of Urology, The Second Affiliated Hospital, University of South China, Hengyang 421001, China
| | - Yuan-Jie Xie
- Clinical Anatomy & Reproductive Medicine Application Institute, Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Xin Zeng
- Clinical Anatomy & Reproductive Medicine Application Institute, Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Xi Chen
- Clinical Anatomy & Reproductive Medicine Application Institute, Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang 421001, China.
| | - Zhong-Cheng Mo
- Clinical Anatomy & Reproductive Medicine Application Institute, Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang 421001, China.
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10
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Sisakhtnezhad S. In silico analysis of single‐cell RNA sequencing data from 3 and 7 days old mouse spermatogonial stem cells to identify their differentially expressed genes and transcriptional regulators. J Cell Biochem 2018; 119:7556-7569. [DOI: 10.1002/jcb.27066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/23/2018] [Indexed: 02/06/2023]
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11
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Li X, Fok KL, Guo J, Wang Y, Liu Z, Chen Z, Wang C, Ruan YC, Yu SS, Zhao H, Wu J, Jiang X, Chan HC. Retinoic acid promotes stem cell differentiation and embryonic development by transcriptionally activating CFTR. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:605-615. [DOI: 10.1016/j.bbamcr.2018.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 01/03/2018] [Accepted: 01/07/2018] [Indexed: 01/11/2023]
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12
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Sisakhtnezhad S, Heshmati P. Comparative analysis of single-cell RNA sequencing data from mouse spermatogonial and mesenchymal stem cells to identify differentially expressed genes and transcriptional regulators of germline cells. J Cell Physiol 2018; 233:5231-5242. [PMID: 29194616 DOI: 10.1002/jcp.26303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022]
Abstract
Identifying effective internal factors for regulating germline commitment during development and for maintaining spermatogonial stem cells (SSCs) self-renewal is important to understand the molecular basis of spermatogenesis process, and to develop new protocols for the production of the germline cells from other cell sources. Therefore, this study was designed to investigate single-cell RNA-sequencing data for identification of differentially expressed genes (DEGs) in 12 mouse-derived single SSCs (mSSCs) in compare with 16 mouse-derived single mesenchymal stem cells. We also aimed to find transcriptional regulators of DEGs. Collectively, 1,584 up-regulated DEGs were identified that are associated with 32 biological processes. Moreover, investigation of the expression profiles of genes including in spermatogenesis process revealed that Dazl, Ddx4, Sall4, Fkbp6, Tex15, Tex19.1, Rnf17, Piwil2, Taf7l, Zbtb16, and Cadm1 are presented in the first 30 up-regulated DEGs. We also found 12 basal transcription factors (TFs) and three sequence-specific TFs that control the expression of DEGs. Our findings also indicated that MEIS1, SMC3, TAF1, KAT2A, STAT3, GTF3C2, SIN3A, BDP1, PHC1, and EGR1 are the main central regulators of DEGs in mSSCs. In addition, we collectively detected two significant protein complexes in the protein-protein interactions network for DEGs regulators. Finally, this study introduces the major upstream kinases for the main central regulators of DEGs and the components of core protein complexes. In conclusion, this study provides a molecular blueprint to uncover the molecular mechanisms behind the biology of SSCs and offers a list of candidate factors for cell type conversion approaches and production of germ cells.
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Affiliation(s)
| | - Parvin Heshmati
- Faculty of Dentistry, Department of Endodontics, Kermanshah University of Medical Sciences, Kermanshah, Iran
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13
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DMRTC2, PAX7, BRACHYURY/T and TERT Are Implicated in Male Germ Cell Development Following Curative Hormone Treatment for Cryptorchidism-Induced Infertility. Genes (Basel) 2017; 8:genes8100267. [PMID: 29019938 PMCID: PMC5664117 DOI: 10.3390/genes8100267] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 09/25/2017] [Accepted: 10/05/2017] [Indexed: 12/14/2022] Open
Abstract
Defective mini-puberty results in insufficient testosterone secretion that impairs the differentiation of gonocytes into dark-type (Ad) spermatogonia. The differentiation of gonocytes into Ad spermatogonia can be induced by administration of the gonadotropin-releasing hormone agonist, GnRHa (Buserelin, INN)). Nothing is known about the mechanism that underlies successful GnRHa treatment in the germ cells. Using RNA-sequencing of testicular biopsies, we recently examined RNA profiles of testes with and without GnRHa treatment. Here, we focused on the expression patterns of known gene markers for gonocytes and spermatogonia, and found that DMRTC2, PAX7, BRACHYURY/T, and TERT were associated with defective mini-puberty and were responsive to GnRHa. These results indicate novel testosterone-dependent genes and provide valuable insight into the transcriptional response to both defective mini-puberty and curative GnRHa treatment, which prevents infertility in man with one or both undescended (cryptorchid) testes.
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