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Berasain L, Beati P, Trigila AP, Rubinstein M, Franchini LF. Accelerated evolution in the human lineage led to gain and loss of transcriptional enhancers in the RBFOX1 locus. SCIENCE ADVANCES 2024; 10:eadl1049. [PMID: 38924416 PMCID: PMC11204294 DOI: 10.1126/sciadv.adl1049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 05/22/2024] [Indexed: 06/28/2024]
Abstract
A long-standing goal of evolutionary biology is to decode how changes in gene regulatory networks contribute to human-specific traits. Human accelerated regions (HARs) are prime candidates for driving gene regulatory modifications in human development. The RBFOX1 locus is densely populated with HARs, providing a set of potential regulatory elements that could have changed its expression in the human lineage. Here, we examined the role of RBFOX1-HARs using transgenic zebrafish reporter assays and identified 15 transcriptional enhancers that are active in the developing nervous system, 9 of which displayed differential activity between the human and chimpanzee sequences. The engineered loss of two selected RBFOX1-HARs in knockout mouse models modified Rbfox1 expression at specific developmental stages and tissues in the brain, influencing the expression and splicing of a high number of Rbfox1 target genes. Our results provided insight into the spatial and temporal changes in gene expression driven by RBFOX1-HARs.
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Affiliation(s)
- Lara Berasain
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) “Dr. Hector N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428, Argentina
| | - Paula Beati
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) “Dr. Hector N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428, Argentina
| | - Anabella P. Trigila
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) “Dr. Hector N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428, Argentina
| | - Marcelo Rubinstein
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) “Dr. Hector N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1428, Argentina
| | - Lucía F. Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) “Dr. Hector N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428, Argentina
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Yang WQ, Ge JY, Zhang X, Zhu WY, Lin L, Shi Y, Xu B, Liu RJ. THUMPD2 catalyzes the N2-methylation of U6 snRNA of the spliceosome catalytic center and regulates pre-mRNA splicing and retinal degeneration. Nucleic Acids Res 2024; 52:3291-3309. [PMID: 38165050 PMCID: PMC11014329 DOI: 10.1093/nar/gkad1243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024] Open
Abstract
The mechanisms by which the relatively conserved spliceosome manages the enormously large number of splicing events that occur in humans (∼200 000 versus ∼300 in yeast) are poorly understood. Here, we show deposition of one RNA modification-N2-methylguanosine (m2G) on the G72 of U6 snRNA (the catalytic center of the spliceosome) promotes efficient pre-mRNA splicing activity in human cells. This modification was identified to be conserved among vertebrates. Further, THUMPD2 was demonstrated as the methyltransferase responsible for U6 m2G72 by explicitly recognizing the U6-specific sequences and structural elements. The knock-out of THUMPD2 eliminated U6 m2G72 and impaired the pre-mRNA splicing activity, resulting in thousands of changed alternative splicing events of endogenous pre-mRNAs in human cells. Notably, the aberrantly spliced pre-mRNA population elicited the nonsense-mediated mRNA decay pathway. We further show that THUMPD2 was associated with age-related macular degeneration and retinal function. Our study thus demonstrates how an RNA epigenetic modification of the major spliceosome regulates global pre-mRNA splicing and impacts physiology and disease.
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Affiliation(s)
- Wen-Qing Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jian-Yang Ge
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaofeng Zhang
- Division of Reproduction and Genetics, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science and Technology of China, 230027 Hefei, China
| | - Wen-Yu Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lin Lin
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yigong Shi
- Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Hangzhou 310064,Zhejiang Province, China
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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3
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AlAbdi L, Shamseldin HE, Khouj E, Helaby R, Aljamal B, Alqahtani M, Almulhim A, Hamid H, Hashem MO, Abdulwahab F, Abouyousef O, Jaafar A, Alshidi T, Al-Owain M, Alhashem A, Al Tala S, Khan AO, Mardawi E, Alkuraya H, Faqeih E, Afqi M, Alkhalifi S, Rahbeeni Z, Hagos ST, Al-Ahmadi W, Nadeef S, Maddirevula S, Khabar KSA, Putra A, Angelov A, Park C, Reyes-Ramos AM, Umer H, Ullah I, Driguez P, Fukasawa Y, Cheung MS, Gallouzi IE, Alkuraya FS. Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases. Genome Med 2023; 15:114. [PMID: 38098057 PMCID: PMC10720148 DOI: 10.1186/s13073-023-01270-8] [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: 07/27/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Long-read whole genome sequencing (lrWGS) has the potential to address the technical limitations of exome sequencing in ways not possible by short-read WGS. However, its utility in autosomal recessive Mendelian diseases is largely unknown. METHODS In a cohort of 34 families in which the suspected autosomal recessive diseases remained undiagnosed by exome sequencing, lrWGS was performed on the Pacific Bioscience Sequel IIe platform. RESULTS Likely causal variants were identified in 13 (38%) of the cohort. These include (1) a homozygous splicing SV in TYMS as a novel candidate gene for lethal neonatal lactic acidosis, (2) a homozygous non-coding SV that we propose impacts STK25 expression and causes a novel neurodevelopmental disorder, (3) a compound heterozygous SV in RP1L1 with complex inheritance pattern in a family with inherited retinal disease, (4) homozygous deep intronic variants in LEMD2 and SNAP91 as novel candidate genes for neurodevelopmental disorders in two families, and (5) a promoter SNV in SLC4A4 causing non-syndromic band keratopathy. Surprisingly, we also encountered causal variants that could have been identified by short-read exome sequencing in 7 families. The latter highlight scenarios that are especially challenging at the interpretation level. CONCLUSIONS Our data highlight the continued need to address the interpretation challenges in parallel with efforts to improve the sequencing technology itself. We propose a path forward for the implementation of lrWGS sequencing in the setting of autosomal recessive diseases in a way that maximizes its utility.
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Affiliation(s)
- Lama AlAbdi
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ebtissal Khouj
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Bayan Aljamal
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mashael Alqahtani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Aisha Almulhim
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Halima Hamid
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais O Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Abouyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amal Jaafar
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Alshidi
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Collage of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Collage of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Pediatric Department, Division of Genetic and Metabolic Medicine, Prince Sultan Medical Military City, Riyadh, Saudi Arabia
| | - Saeed Al Tala
- Pediatric Department, Neonatal Unit, Armed Forces Hospital, Khamis Mushayt, Saudi Arabia
| | - Arif O Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Elham Mardawi
- Maternal Fetal Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia
| | - Hisham Alkuraya
- Vitreoretinal Surgery and Ocular Genetics, Global Eye Care/Specialized Medical Center Hospital, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Section of Medical Genetics, King Fahad Medical City, Children's Specialist Hospital, Riyadh, Saudi Arabia
| | - Manal Afqi
- Metabolic and Genetic Center, King Salman Bin Abdulaziz Medical City, Almadinah Almunwarah, Saudi Arabia
| | - Salwa Alkhalifi
- Newborn Screening, Ministry of Health, Eastern Province, Saudi Arabia
| | - Zuhair Rahbeeni
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Samya T Hagos
- Department of Clinical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Wijdan Al-Ahmadi
- Department of Molecular Biomedicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Seba Nadeef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Khalid S A Khabar
- Department of Molecular Biomedicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Alexander Putra
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Angel Angelov
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Changsook Park
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ana M Reyes-Ramos
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Husen Umer
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ikram Ullah
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Patrick Driguez
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Yoshinori Fukasawa
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Ming Sin Cheung
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal, Saudi Arabia
| | - Imed Eddine Gallouzi
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- KAUST Smart-Health Initiative King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Shinozuka T, Kanda M, Sato Y, Shimizu D, Tanaka C, Umeda S, Inokawa Y, Hattori N, Hayashi M, Nakayama G, Kodera Y. Increased STX3 transcript and protein levels were associated with poor prognosis in two independent cohorts of esophageal squamous cell carcinoma patients. Cancer Med 2023; 12:22185-22195. [PMID: 38014487 PMCID: PMC10757105 DOI: 10.1002/cam4.6770] [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: 05/31/2023] [Revised: 11/07/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Some conventional prognostic biomarkers for esophageal squamous cell carcinoma (ESCC) have the disadvantage that they have only been investigated at the level of either mRNA or protein levels or only in individual cohorts. Associations between Syntaxin 3 (STX3) expression and malignancy have been reported in several tumor types but not in ESCC. Here, we investigated the levels of both STX3 mRNA and protein, and its prognostic potential in two independent cohorts of patients with ESCC. METHODS STX3 mRNA levels were examined in surgical specimens by quantitative PCR in a cohort that included 176 ESCC patients. STX3 protein levels were investigated in surgically resected ESCC tissues by immunohistochemistry using tissue microarrays in a different cohort of 177 ESCC patients. Correlations were analyzed between the expression of STX3 mRNA and protein with clinicopathological factors and long-term prognosis. RESULTS Quantitative PCR indicated a significant association between high level of STX3 mRNA expression and lymph node involvement, pathological stage, and poor overall survival. The multivariate analysis demonstrated that high STX3 mRNA expression was independently associated with poor overall survival outcomes. Immunohistochemistry revealed that STX3 protein expression in ESCC tissues and high STX3 protein expression were also significantly correlated with unfavorable overall survival. CONCLUSIONS Overexpression of STX3 mRNA and protein may serve as potential prognostic biomarkers for ESCC patients.
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Affiliation(s)
- Takahiro Shinozuka
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Mitsuro Kanda
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Yusuke Sato
- Department of Thoracic SurgeryAkita University Graduate School of MedicineAkitaJapan
| | - Dai Shimizu
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Chie Tanaka
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Shinichi Umeda
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Yoshikuni Inokawa
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Norifumi Hattori
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Masamichi Hayashi
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Goro Nakayama
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Yasuhiro Kodera
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
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Hayashi K, Nozaki S, Tokushima K, Tanaka F, Hirai Y. Role of syntaxin3 an apical polarity protein in poorly polarized keratinocytes: regulation of asymmetric barrier formations in the skin epidermis. Cell Tissue Res 2023; 393:523-535. [PMID: 37351635 DOI: 10.1007/s00441-023-03798-y] [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: 01/09/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023]
Abstract
The skin epidermis exhibits an asymmetric structure composed of multilayered keratinocytes and those in the outer layers form two-way physical barriers, cornified cell envelope (CCE), and tight junctions (TJs). While undifferentiated keratinocytes in the basal layer continuously deliver daughter cells outward, which undergo successive differentiation with losing their polarized characteristics, they retain the expression of several polarity proteins. In the present study, we revealed that the t-SNARE protein syntaxin3, a critical element for the formation of the apical compartment in simple epithelial cells, is required to confer the ability to organize the physical barriers on "poorly polarized" keratinocytes in epidermal outer layers. HaCaT keratinocytes with genetic ablation of syntaxin3 readily succumbed to hydrogen peroxide-induced cell death. Additionally, they lost the ability to organize TJ and CCE structures, accompanied by notable downregulation of transglutaminase1 and caspase14 (a cornification regulator) expression. These syntaxin3-knockout cells appeared to restore oxidative stress tolerance and functional TJ formation ability, in response to the inducible re-expression of exogenous syntaxin3. While plausible mechanisms underlying these phenomena remain unclear, syntaxin3, an apical polarity protein in the simple epithelia, has emerged as a potentially crucial element for barrier formation in poorly polarized keratinocytes in polarized epidermal tissue.
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Affiliation(s)
- Kaho Hayashi
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, Gakuen-Uegahara, Sanda, 669-1330, Japan
| | - Sae Nozaki
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, Gakuen-Uegahara, Sanda, 669-1330, Japan
| | - Kanako Tokushima
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, Gakuen-Uegahara, Sanda, 669-1330, Japan
| | - Fumika Tanaka
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, Gakuen-Uegahara, Sanda, 669-1330, Japan
| | - Yohei Hirai
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, Gakuen-Uegahara, Sanda, 669-1330, Japan.
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Warner H, Mahajan S, van den Bogaart G. Rerouting trafficking circuits through posttranslational SNARE modifications. J Cell Sci 2022; 135:276344. [PMID: 35972760 DOI: 10.1242/jcs.260112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are membrane-associated trafficking proteins that confer identity to lipid membranes and facilitate membrane fusion. These functions are achieved through the complexing of Q-SNAREs with a specific cognate target R-SNARE, leading to the fusion of their associated membranes. These SNARE complexes then dissociate so that the Q-SNAREs and R-SNAREs can repeat this cycle. Whilst the basic function of SNAREs has been long appreciated, it is becoming increasingly clear that the cell can control the localisation and function of SNARE proteins through posttranslational modifications (PTMs), such as phosphorylation and ubiquitylation. Whilst numerous proteomic methods have shown that SNARE proteins are subject to these modifications, little is known about how these modifications regulate SNARE function. However, it is clear that these PTMs provide cells with an incredible functional plasticity; SNARE PTMs enable cells to respond to an ever-changing extracellular environment through the rerouting of membrane traffic. In this Review, we summarise key findings regarding SNARE regulation by PTMs and discuss how these modifications reprogramme membrane trafficking pathways.
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Affiliation(s)
- Harry Warner
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands
| | - Shweta Mahajan
- Division of Immunobiology, Center for Inflammation and Tolerance, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Geert van den Bogaart
- Department of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG Groningen, The Netherlands
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Dong C, Liu W, Zhang Y, Song Y, Du J, Huang Z, Wang T, Yu Z, Ma X. Identification of Common Hub Genes in Human Dermal Fibroblasts Stimulated by Mechanical Stretch at Both the Early and Late Stages. Front Surg 2022; 9:846161. [PMID: 35510126 PMCID: PMC9058084 DOI: 10.3389/fsurg.2022.846161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/16/2022] [Indexed: 11/25/2022] Open
Abstract
Background Mechanical stretch is vital for soft tissue regeneration and development and is utilized by plastic surgeons for tissue expansion. Identifying the common hub genes in human dermal fibroblasts (HDFs) stimulated by mechanical stretch at different stages will help elucidate the mechanisms involved and improve the efficiency of tissue expansion. Methods A gene expression dataset (GSE58389) was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) in HDFs between cyclic mechanical stretching and static samples were identified at 5 and 24 h. Common DEGs overlapped in both the 5 h and 24 h groups. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to determine the functions of the DEGs. Protein-protein interaction networks were constructed using the STRING database. The top 10 hub genes were selected using the plug-in Cytohubba within Cytoscape. The regulatory network of hub genes was predicted using NetworkAnalyst. Results A total of 669 and 249 DEGs were identified at the early (5 h) and late stages (24 h), respectively. Of these, 152 were present at both stages and were designated as common DEGs. The top enriched GO terms were “regulation of autophagy” at the early stage, and “sterol biosynthetic processes” at the late stage. The top KEGG terms were “pyrimidine metabolism” and “synaptic vesicle cycle” at the early and late stages, respectively. Seven common DEGs [DEAD-box helicase 17 (DDX17), exocyst complex component 7 (EXOC7), CASK interacting protein 1 (CASKIN1), ribonucleoprotein PTB-binding 1 (RAVER1), late cornified envelope 1D (LCE1D), LCE1C, and polycystin 1, transient receptor potential channel interacting (PKD1)] and three common DEGs [5′-3′ exoribonuclease 2 (XRN2), T-complex protein 1 (TCP1), and syntaxin 3 (STX3)] were shown to be upregulated and downregulated hub genes, respectively. The GO terms of the common hub genes were “skin development” and “mRNA processing.” After constructing the regulatory network, hsa-mir-92a-3p, hsa-mir-193b-3p, RNA polymerase II subunit A (POLR2A), SMAD family member 5 (SMAD5), and MYC-associated zinc finger protein (MAZ) were predicted as potential targets in both stages. Conclusion At the early stage, there were clear changes in gene expression related to DNA and chromatin alterations; at late stages, gene expression associated with cholesterol metabolism was suppressed. Common DEGs related to skin development, transcriptional regulation, and cytoskeleton rearrangement identified in both stages were found to be potential targets for promoting HDF growth and alignment under mechanical stretch.
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Arango Duque G, Dion R, Matte C, Fabié A, Descoteaux J, Stäger S, Descoteaux A. Sec22b Regulates Inflammatory Responses by Controlling the Nuclear Translocation of NF-κB and the Secretion of Inflammatory Mediators. THE JOURNAL OF IMMUNOLOGY 2021; 207:2297-2309. [PMID: 34580108 DOI: 10.4049/jimmunol.2100258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/17/2021] [Indexed: 01/24/2023]
Abstract
Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) regulate the vesicle transport machinery in phagocytic cells. Within the secretory pathway, Sec22b is an endoplasmic reticulum-Golgi intermediate compartment (ERGIC)-resident SNARE that controls phagosome maturation and function in macrophages and dendritic cells. The secretory pathway controls the release of cytokines and may also impact the secretion of NO, which is synthesized by the Golgi-active inducible NO synthase (iNOS). Whether ERGIC SNARE Sec22b controls NO and cytokine secretion is unknown. Using murine bone marrow-derived dendritic cells, we demonstrated that inducible NO synthase colocalizes with ERGIC/Golgi markers, notably Sec22b and its partner syntaxin 5, in the cytoplasm and at the phagosome. Pharmacological blockade of the secretory pathway hindered NO and cytokine release, and inhibited NF-κB translocation to the nucleus. Importantly, RNA interference-mediated silencing of Sec22b revealed that NO and cytokine production were abrogated at the protein and mRNA levels. This correlated with reduced nuclear translocation of NF-κB. We also found that Sec22b co-occurs with NF-κB in both the cytoplasm and nucleus, pointing to a role for this SNARE in the shuttling of NF-κB. Collectively, our data unveiled a novel function for the ERGIC/Golgi, and its resident SNARE Sec22b, in the production and release of inflammatory mediators.
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Affiliation(s)
- Guillermo Arango Duque
- INRS-Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Laval, Quebec, Canada
| | - Renaud Dion
- INRS-Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Laval, Quebec, Canada
| | - Christine Matte
- INRS-Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Laval, Quebec, Canada
| | - Aymeric Fabié
- INRS-Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Laval, Quebec, Canada
| | - Julien Descoteaux
- INRS-Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Laval, Quebec, Canada
| | - Simona Stäger
- INRS-Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Laval, Quebec, Canada
| | - Albert Descoteaux
- INRS-Centre Armand-Frappier Santé Biotechnologie, Université du Québec, Laval, Quebec, Canada
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Karouta C, Kucharski R, Hardy K, Thomson K, Maleszka R, Morgan I, Ashby R. Transcriptome-based insights into gene networks controlling myopia prevention. FASEB J 2021; 35:e21846. [PMID: 34405458 DOI: 10.1096/fj.202100350rr] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/11/2022]
Abstract
Myopia (short-sightedness), usually caused by excessive elongation of the eye during development, has reached epidemic proportions worldwide. In animal systems including the chicken model, several treatments have been shown to inhibit ocular elongation and experimental myopia. Although diverse in their apparent mechanism of action, each one leads to a reduction in the rate of ocular growth. We hypothesize that a defined set of retinal molecular changes may underlie growth inhibition, irrespective of the treatment agent used. Accordingly, across five well-established but diverse methods of inhibiting myopia, significant overlap is seen in the retinal transcriptome profile (transcript levels and alternative splicing events) in chicks when analyzed by RNA-seq. Within the two major pathway networks enriched during growth inhibition, that of cell signaling and circadian entrainment, transcription factors form the largest functional grouping. Importantly, a large percentage of those genes forming the defined retinal response are downstream targets of the transcription factor EGR1 which itself shows a universal response to all five growth-inhibitory treatments. This supports EGR1's previously implicated role in ocular growth regulation. Finally, by contrasting our data with human linkage and GWAS studies on refractive error, we confirm the applicability of our study to the human condition. Together, these findings suggest that a universal set of transcriptome changes, which sit within a well-defined retinal network that cannot be bypassed, is fundamental to growth regulation, thus paving a way for designing novel targets for myopia therapies.
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Affiliation(s)
- Cindy Karouta
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Robert Kucharski
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia.,Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Kristine Hardy
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Kate Thomson
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Ryszard Maleszka
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Ian Morgan
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Regan Ashby
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia.,Research School of Biology, Australian National University, Canberra, ACT, Australia
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10
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Janecke AR, Liu X, Adam R, Punuru S, Viestenz A, Strauß V, Laass M, Sanchez E, Adachi R, Schatz MP, Saboo US, Mittal N, Rohrschneider K, Escher J, Ganesh A, Al Zuhaibi S, Al Murshedi F, AlSaleem B, Alfadhel M, Al Sinani S, Alkuraya FS, Huber LA, Müller T, Heidelberger R, Janz R. Pathogenic STX3 variants affecting the retinal and intestinal transcripts cause an early-onset severe retinal dystrophy in microvillus inclusion disease subjects. Hum Genet 2021; 140:1143-1156. [PMID: 33974130 PMCID: PMC8263458 DOI: 10.1007/s00439-021-02284-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/15/2021] [Indexed: 01/12/2023]
Abstract
Biallelic STX3 variants were previously reported in five individuals with the severe congenital enteropathy, microvillus inclusion disease (MVID). Here, we provide a significant extension of the phenotypic spectrum caused by STX3 variants. We report ten individuals of diverse geographic origin with biallelic STX3 loss-of-function variants, identified through exome sequencing, single-nucleotide polymorphism array-based homozygosity mapping, and international collaboration. The evaluated individuals all presented with MVID. Eight individuals also displayed early-onset severe retinal dystrophy, i.e., syndromic-intestinal and retinal-disease. These individuals harbored STX3 variants that affected both the retinal and intestinal STX3 transcripts, whereas STX3 variants affected only the intestinal transcript in individuals with solitary MVID. That STX3 is essential for retinal photoreceptor survival was confirmed by the creation of a rod photoreceptor-specific STX3 knockout mouse model which revealed a time-dependent reduction in the number of rod photoreceptors, thinning of the outer nuclear layer, and the eventual loss of both rod and cone photoreceptors. Together, our results provide a link between STX3 loss-of-function variants and a human retinal dystrophy. Depending on the genomic site of a human loss-of-function STX3 variant, it can cause MVID, the novel intestinal-retinal syndrome reported here or, hypothetically, an isolated retinal dystrophy.
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Affiliation(s)
- Andreas R Janecke
- Department of Pediatrics I, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria.
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria.
| | - Xiaoqin Liu
- Department of Neurobiology and Anatomy, MSB 7.046, McGovern Medical School at the University of Texas HSC (UTHealth), 6431 Fannin Street, Houston, TX, 77030, USA
| | - Rüdiger Adam
- University Children's Hospital, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Sumanth Punuru
- Department of Neurobiology and Anatomy, MSB 7.046, McGovern Medical School at the University of Texas HSC (UTHealth), 6431 Fannin Street, Houston, TX, 77030, USA
| | - Arne Viestenz
- Department of Ophthalmology, University Medical Center Halle, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Valeria Strauß
- Klinik für Kinder- und Jugendmedizin, Universitätsklinikum Halle, Halle, Germany
| | - Martin Laass
- Klinik und Poliklinik f. Kinder- u. Jugendmedizin, University of Dresden, Dresden, Germany
| | - Elizabeth Sanchez
- Department of Pulmonary Medicine, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roberto Adachi
- Department of Pulmonary Medicine, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martha P Schatz
- Department of Ophthalmology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Ujwala S Saboo
- Department of Ophthalmology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Naveen Mittal
- Department of Department of Pediatrics, Division of Pediatric Gastroenterology, University of Texas Health Science Center, San Antonio, TX, USA
| | | | - Johanna Escher
- Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Anuradha Ganesh
- Department of Ophthalmology, Sultan Qaboos University Hospital, Muscat, Oman
| | - Sana Al Zuhaibi
- Department of Ophthalmology, Sultan Qaboos University Hospital, Muscat, Oman
| | - Fathiya Al Murshedi
- Genetic and Developmental Medicine Clinic, Sultan Qaboos University Hospital, Muscat, Oman
| | - Badr AlSaleem
- King Fahad Medical City, Children's Specialized Hospital, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Genetics Division and Medical Genomic Research Lab, King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
| | - Siham Al Sinani
- Department of Child Health, Sultan Qaboos University Hospital, Muscat, Oman
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Lukas A Huber
- Division of Cell Biology, Medical University of Innsbruck, Innsbruck, Austria
| | - Thomas Müller
- Department of Pediatrics I, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
| | - Ruth Heidelberger
- Department of Neurobiology and Anatomy, MSB 7.046, McGovern Medical School at the University of Texas HSC (UTHealth), 6431 Fannin Street, Houston, TX, 77030, USA.
| | - Roger Janz
- Department of Neurobiology and Anatomy, MSB 7.046, McGovern Medical School at the University of Texas HSC (UTHealth), 6431 Fannin Street, Houston, TX, 77030, USA
- Center for Scientific Review, National Institutes of Health, Bethesda, MD, USA
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11
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Farnsworth DR, Posner M, Miller AC. Single cell transcriptomics of the developing zebrafish lens and identification of putative controllers of lens development. Exp Eye Res 2021; 206:108535. [PMID: 33705730 PMCID: PMC8092445 DOI: 10.1016/j.exer.2021.108535] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/31/2021] [Accepted: 03/02/2021] [Indexed: 01/10/2023]
Abstract
The vertebrate lens is a valuable model system for investigating the gene expression changes that coordinate tissue differentiation due to its inclusion of two spatially separated cell types, the outer epithelial cells and the deeper denucleated fiber cells that they support. Zebrafish are a useful model system for studying lens development given the organ's rapid development in the first several days of life in an accessible, transparent embryo. While we have strong foundational knowledge of the diverse lens crystallin proteins and the basic gene regulatory networks controlling lens development, no study has detailed gene expression in a vertebrate lens at single cell resolution. Here we report an atlas of lens gene expression in zebrafish embryos and larvae at single cell resolution through five days of development, identifying a number of novel putative regulators of lens development. Our data address open questions about the temperospatial expression of α-crystallins during lens development that will support future studies of their function and provide the first detailed view of β- and γ-crystallin expression in and outside the lens. We describe divergent expression in transcription factor genes that occur as paralog pairs in the zebrafish. Finally, we examine the expression dynamics of cytoskeletal, membrane associated, RNA-binding, and transcription factor genes, identifying a number of novel patterns. Overall these data provide a foundation for identifying and characterizing lens developmental regulatory mechanisms and revealing targets for future functional studies with potential therapeutic impact.
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Affiliation(s)
| | - Mason Posner
- Department of Biology and Toxicology, Ashland University, Ashland, OH, USA.
| | - Adam C Miller
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
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12
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Cancer-driving mutations and variants of components of the membrane trafficking core machinery. Life Sci 2020; 264:118662. [PMID: 33127517 DOI: 10.1016/j.lfs.2020.118662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
The core machinery for vesicular membrane trafficking broadly comprises of coat proteins, RABs, tethering complexes and SNAREs. As cellular membrane traffic modulates key processes of mitogenic signaling, cell migration, cell death and autophagy, its dysregulation could potentially results in increased cell proliferation and survival, or enhanced migration and invasion. Changes in the levels of some components of the core machinery of vesicular membrane trafficking, likely due to gene amplifications and/or alterations in epigenetic factors (such as DNA methylation and micro RNA) have been extensively associated with human cancers. Here, we provide an overview of association of membrane trafficking with cancer, with a focus on mutations and variants of coat proteins, RABs, tethering complex components and SNAREs that have been uncovered in human cancer cells/tissues. The major cellular and molecular cancer-driving or suppression mechanisms associated with these components of the core membrane trafficking machinery shall be discussed.
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13
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Yang Y, Sun X, Chi C, Liu Y, Lin C, Xie D, Shen X, Lin X. Upregulation of long noncoding RNA LINC00152 promotes proliferation and metastasis of esophageal squamous cell carcinoma. Cancer Manag Res 2019; 11:4643-4654. [PMID: 31191025 PMCID: PMC6535442 DOI: 10.2147/cmar.s198905] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/20/2019] [Indexed: 12/30/2022] Open
Abstract
Purpose: Esophageal cancer is a major cause of cancer-related mortality worldwide. The long noncoding RNA LINC00152 has been confirmed to play an oncogenic role in many cancers. However, the expression pattern and function of LINC00152 in human esophageal squamous cell carcinoma (ESCC) remain unclear. Materials and methods: We evaluated LINC00152 expression in ESCC by qPCR and in situ hybridization. Proliferation, apoptosis, cell cycle, migration and invasion were examined in ESCC cells knocked down for LINC00152 knockdown by siRNA. Furthermore, an mRNA microarray was performed in ESCC cells with LINC00152 knockdown. Results: LINC00152 was significantly upregulated in human ESCC clinical samples (P<0.001) and cell lines (P=0.008), and LINC00152 overexpression was related to lymphatic metastasis (P=0.03) and advanced pTNM classification (P=0.005). Furthermore, ESCC patients with LINC00152 overexpression had significantly shorter overall survival (P=0.007), and LINC00152 overexpression was an independent risk factor for overall survival of ESCC patients. LINC00152 knockdown inhibited the proliferation, migration and invasion of ESCC cells in vitro. In addition, mechanistic investigations through mRNA array and immunoblot analyses demonstrated that LINC00152 regulated the expression of several cell cycle-related proteins and SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) interactions in vesicular transport pathway proteins. Conclusion: Our research indicated that LINC00152 exhibits oncogenic functions in ESCC and may represent a potential new target for ESCC therapy.
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Affiliation(s)
- Yi Yang
- Department of Clinical Skills Experiments Center, Wenzhou Medical University, Wenzhou, Zhejiang 325035, People's Republic of China
| | - Xiangwei Sun
- Department of General Surgery, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325003, People's Republic of China
| | - Chuang Chi
- Department of Thoracic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325003, People's Republic of China
| | - Yu Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325003, People's Republic of China
| | - Chaoxi Lin
- Department of Thoracic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325003, People's Republic of China
| | - Deyao Xie
- Department of Thoracic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325003, People's Republic of China
| | - Xian Shen
- Department of General Surgery, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325003, People's Republic of China
| | - Xiaoming Lin
- Department of Thoracic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325003, People's Republic of China
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14
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Coppola U, Caccavale F, Scelzo M, Holland ND, Ristoratore F, D’Aniello S. Ran GTPase, an eukaryotic gene novelty, is involved in amphioxus mitosis. PLoS One 2018; 13:e0196930. [PMID: 30300344 PMCID: PMC6177115 DOI: 10.1371/journal.pone.0196930] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 04/23/2018] [Indexed: 01/19/2023] Open
Abstract
Ran (ras-related nuclear protein) is a small GTPase belonging to the RAS superfamily that is specialized in nuclear trafficking. Through different accessory proteins, Ran plays key roles in several processes including nuclear import-export, mitotic progression and spindle assembly. Consequently, Ran dysfunction has been linked to several human pathologies. This work illustrates the high degree of amino acid conservation of Ran orthologues across evolution, reflected in its conserved role in nuclear trafficking. Moreover, we studied the evolutionary scenario of the pre-metazoan genetic linkage between Ran and Stx, and we hypothesized that chromosomal proximity of these two genes across metazoans could be related to a regulatory logic or a functional linkage. We studied, for the first time, Ran expression during amphioxus development and reported its presence in the neural vesicle, mouth, gill slits and gut corresponding to body regions involved in active cell division.
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Affiliation(s)
- Ugo Coppola
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, Napoli, Italy
| | - Filomena Caccavale
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, Napoli, Italy
| | - Marta Scelzo
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, Napoli, Italy
- Laboratory of Developmental Biology of Villefranche sur Mer, UMR7009 CNRS/UPMC Observatoire Océanologique, Villefranche sur Mer, France
| | - Nicholas D. Holland
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, United States of America
| | - Filomena Ristoratore
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, Napoli, Italy
| | - Salvatore D’Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Villa Comunale, Napoli, Italy
- * E-mail:
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