1
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Seixas S, Kolbe AR, Gomes S, Sucena M, Sousa C, Vaz Rodrigues L, Teixeira G, Pinto P, Tavares de Abreu T, Bárbara C, Semedo J, Mota L, Carvalho AS, Matthiesen R, Marques PI, Pérez-Losada M. Comparative analysis of the bronchoalveolar microbiome in Portuguese patients with different chronic lung disorders. Sci Rep 2021; 11:15042. [PMID: 34294826 PMCID: PMC8298389 DOI: 10.1038/s41598-021-94468-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/09/2021] [Indexed: 01/04/2023] Open
Abstract
The lung is inhabited by a diverse microbiome that originates from the oropharynx by a mechanism of micro-aspiration. Its bacterial biomass is usually low; however, this condition shifts in lung cancer (LC), chronic obstructive pulmonary disease (COPD) and interstitial lung disease (ILD). These chronic lung disorders (CLD) may coexist in the same patient as comorbidities and share common risk factors, among which the microbiome is included. We characterized the microbiome of 106 bronchoalveolar lavages. Samples were initially subdivided into cancer and non-cancer and high-throughput sequenced for the 16S rRNA gene. Additionally, we used a cohort of 25 CLD patients where crossed comorbidities were excluded. Firmicutes, Proteobacteria and Bacteroidetes were the most prevalent phyla independently of the analyzed group. Streptococcus and Prevotella were associated with LC and Haemophilus was enhanced in COPD versus ILD. Although no significant discrepancies in microbial diversity were observed between cancer and non-cancer samples, statistical tests suggested a gradient across CLD where COPD and ILD displayed the highest and lowest alpha diversities, respectively. Moreover, COPD and ILD were separated in two clusters by the unweighted UniFrac distance (P value = 0.0068). Our results support the association of Streptoccocus and Prevotella with LC and of Haemophilus with COPD, and advocate for specific CLD signatures.
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Affiliation(s)
- Susana Seixas
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal. .,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal.
| | - Allison R Kolbe
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Sílvia Gomes
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal
| | - Maria Sucena
- Pneumology Department, Centro Hospitalar de São João (CHSJ), Porto, Portugal
| | - Catarina Sousa
- Pneumology Department, Centro Hospitalar de São João (CHSJ), Porto, Portugal
| | - Luís Vaz Rodrigues
- Department of Pneumology, Unidade Local de Saúde da Guarda (USLGuarda), Guarda, Portugal
| | - Gilberto Teixeira
- Department of Pneumology, Centro Hospitalar Do Baixo Vouga (CHBV), Aveiro, Portugal
| | - Paula Pinto
- Unidade de Pneumologia de Intervenção, Hospital Pulido Valente, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon, Portugal.,Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Tiago Tavares de Abreu
- Unidade de Pneumologia de Intervenção, Hospital Pulido Valente, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon, Portugal
| | - Cristina Bárbara
- Unidade de Pneumologia de Intervenção, Hospital Pulido Valente, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon, Portugal.,Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Júlio Semedo
- Unidade de Pneumologia de Intervenção, Hospital Pulido Valente, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon, Portugal
| | - Leonor Mota
- Unidade de Pneumologia de Intervenção, Hospital Pulido Valente, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon, Portugal
| | - Ana Sofia Carvalho
- Computational and Experimental Biology Group, CEDOC, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Rune Matthiesen
- Computational and Experimental Biology Group, CEDOC, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Patrícia Isabel Marques
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal
| | - Marcos Pérez-Losada
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
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Cerván-Martín M, Bossini-Castillo L, Rivera-Egea R, Garrido N, Luján S, Romeu G, Santos-Ribeiro S, Castilla JA, Gonzalvo MDC, Clavero A, Vicente FJ, Guzmán-Jiménez A, Burgos M, Barrionuevo FJ, Jiménez R, Sánchez-Curbelo J, López-Rodrigo O, Peraza MF, Pereira-Caetano I, Marques PI, Carvalho F, Barros A, Bassas L, Seixas S, Gonçalves J, Larriba S, Lopes AM, Carmona FD, Palomino-Morales RJ. Effect and in silico characterization of genetic variants associated with severe spermatogenic disorders in a large Iberian cohort. Andrology 2021; 9:1151-1165. [PMID: 33784440 DOI: 10.1111/andr.13009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/08/2021] [Accepted: 03/24/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Severe spermatogenic failure (SpF) represents the most extreme manifestation of male infertility, as it decreases drastically the semen quality leading to either severe oligospermia (SO, <5 million spermatozoa/mL semen) or non-obstructive azoospermia (NOA, complete lack of spermatozoa in the ejaculate without obstructive causes). OBJECTIVES The main objective of the present study is to analyze in the Iberian population the effect of 6 single-nucleotide polymorphisms (SNPs) previously associated with NOA in Han Chinese through genome-wide association studies (GWAS) and to establish their possible functional relevance in the development of specific SpF patterns. MATERIALS AND METHODS We genotyped 674 Iberian infertile men (including 480 NOA and 194 SO patients) and 1058 matched unaffected controls for the GWAS-associated variants PRMT6-rs12097821, PEX10-rs2477686, CDC42BPA-rs3000811, IL17A-rs13206743, ABLIM1-rs7099208, and SOX5-rs10842262. Their association with SpF, SO, NOA, and different NOA phenotypes was evaluated by logistic regression models, and their functional relevance was defined by comprehensive interrogation of public resources. RESULTS ABLIM1-rs7099208 was associated with SpF under both additive (OR = 0.86, p = 0.036) and dominant models (OR = 0.78, p = 0.026). The CDC42BPA-rs3000811 minor allele frequency was significantly increased in the subgroup of NOA patients showing maturation arrest (MA) of germ cells compared to the remaining NOA cases under the recessive model (OR = 4.45, p = 0.044). The PEX10-rs2477686 SNP was associated with a negative testicular sperm extraction (TESE) outcome under the additive model (OR = 1.32, p = 0.034). The analysis of functional annotations suggested that these variants affect the testis-specific expression of nearby genes and that lincRNA may play a role in SpF. CONCLUSIONS Our data support the association of three previously reported NOA risk variants in Asians (ABLIM1-rs7099208, CDC42BPA-rs3000811, and PEX10-rs2477686) with different manifestations of SpF in Iberians of European descent, likely by influencing gene expression and lincRNA deregulation.
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Affiliation(s)
- Miriam Cerván-Martín
- Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, Granada, Spain.,Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Lara Bossini-Castillo
- Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, Granada, Spain.,Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Rocío Rivera-Egea
- Andrology Laboratory and Sperm Bank, IVIRMA Valencia, Valencia, Spain.,IVI Foundation, Health Research Institute La Fe, Valencia, Spain
| | - Nicolás Garrido
- IVI Foundation, Health Research Institute La Fe, Valencia, Spain.,Servicio de Urología, Hospital Universitari i Politecnic La Fe e Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Saturnino Luján
- Servicio de Urología, Hospital Universitari i Politecnic La Fe e Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Gema Romeu
- Servicio de Urología, Hospital Universitari i Politecnic La Fe e Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Samuel Santos-Ribeiro
- IVI-RMA Lisbon, Lisbon, Portugal.,Department of Obstetrics and Gynecology, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | | | - José A Castilla
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain.,UGC Obstetricia y Ginecología, Unidad de Reproducción, HU Virgen de las Nieves, Granada, Spain.,CEIFER Biobanco - NextClinics, Granada, Spain
| | - María Del Carmen Gonzalvo
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain.,UGC Obstetricia y Ginecología, Unidad de Reproducción, HU Virgen de las Nieves, Granada, Spain
| | - Ana Clavero
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain.,UGC Obstetricia y Ginecología, Unidad de Reproducción, HU Virgen de las Nieves, Granada, Spain
| | - Francisco Javier Vicente
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain.,UGC de Urología, HU Virgen de las Nieves, Granada, Spain
| | - Andrea Guzmán-Jiménez
- Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, Granada, Spain
| | - Miguel Burgos
- Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, Granada, Spain
| | | | - Rafael Jiménez
- Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, Granada, Spain
| | - Josvany Sánchez-Curbelo
- Laboratory of Seminology and Embryology, Andrology Service-Fundació Puigvert, Barcelona, Spain
| | - Olga López-Rodrigo
- Laboratory of Seminology and Embryology, Andrology Service-Fundació Puigvert, Barcelona, Spain
| | - María Fernanda Peraza
- Laboratory of Seminology and Embryology, Andrology Service-Fundació Puigvert, Barcelona, Spain
| | - Iris Pereira-Caetano
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | - Patrícia Isabel Marques
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Filipa Carvalho
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Alberto Barros
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Lluís Bassas
- Laboratory of Seminology and Embryology, Andrology Service-Fundació Puigvert, Barcelona, Spain
| | - Susana Seixas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - João Gonçalves
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal.,Nova Medical School, ToxOmics - Centro de Toxicogenómica e Saúde Humana, Lisbon, Portugal
| | - Sara Larriba
- Human Molecular Genetics Group, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Alexandra Manuel Lopes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Francisco David Carmona
- Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, Granada, Spain.,Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Rogelio Jesús Palomino-Morales
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain.,Departamento de Bioquímica y Biología Molecular I, Universidad de Granada, Granada, Spain
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3
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Gomes S, Cavadas B, Ferreira JC, Marques PI, Monteiro C, Sucena M, Sousa C, Vaz Rodrigues L, Teixeira G, Pinto P, Tavares de Abreu T, Bárbara C, Semedo J, Mota L, Carvalho AS, Matthiesen R, Pereira L, Seixas S. Profiling of lung microbiota discloses differences in adenocarcinoma and squamous cell carcinoma. Sci Rep 2019; 9:12838. [PMID: 31492894 PMCID: PMC6731246 DOI: 10.1038/s41598-019-49195-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 08/19/2019] [Indexed: 12/31/2022] Open
Abstract
The lung is a complex ecosystem of host cells and microbes often disrupted in pathological conditions. Although bacteria have been hypothesized as agents of carcinogenesis, little is known about microbiota profile of the most prevalent cancer subtypes: adenocarcinoma (ADC) and squamous cell carcinoma (SCC). To characterize lung cancer (LC) microbiota a first a screening was performed through a pooled sequencing approach of 16S ribosomal RNA gene (V3-V6) using a total of 103 bronchoalveaolar lavage fluid samples. Then, identified taxa were used to inspect 1009 cases from The Cancer Genome Atlas and to annotate tumor unmapped RNAseq reads. Microbial diversity was analyzed per cancer subtype, history of cigarette smoking and airflow obstruction, among other clinical data. We show that LC microbiota is enriched in Proteobacteria and more diverse in SCC than ADC, particularly in males and heavier smokers. High frequencies of Proteobacteria were found to discriminate a major cluster, further subdivided into well-defined communities’ associated with either ADC or SCC. Here, a SCC subcluster differing from other cases by a worse survival was correlated with several Enterobacteriaceae. Overall, this study provides first evidence for a correlation between lung microbiota and cancer subtype and for its influence on patient life expectancy.
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Affiliation(s)
- Sílvia Gomes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Bruno Cavadas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Joana Catarina Ferreira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Patrícia Isabel Marques
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Catarina Monteiro
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Maria Sucena
- Pneumology Department, Centro Hospitalar de São João (CHSJ), Porto, Portugal
| | - Catarina Sousa
- Pneumology Department, Centro Hospitalar de São João (CHSJ), Porto, Portugal
| | - Luís Vaz Rodrigues
- Department of Pneumology, Unidade Local de Saúde da Guarda (USLG), Guarda, Portugal
| | - Gilberto Teixeira
- Department of Pneumology; Centro Hospitalar do Baixo Vouga (CHBV), Aveiro, Portugal
| | - Paula Pinto
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte (CHLN), Lisbon, Portugal.,Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Tiago Tavares de Abreu
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte (CHLN), Lisbon, Portugal
| | - Cristina Bárbara
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte (CHLN), Lisbon, Portugal.,Instituto de Saúde Ambiental, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Júlio Semedo
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte (CHLN), Lisbon, Portugal
| | - Leonor Mota
- Unidade de Técnicas Invasivas Pneumológicas, Pneumologia II, Hospital Pulido Valente, Centro Hospitalar Lisboa Norte (CHLN), Lisbon, Portugal
| | - Ana Sofia Carvalho
- Computational and Experimental Biology Group, CEDOC, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Rune Matthiesen
- Computational and Experimental Biology Group, CEDOC, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Luísa Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.,Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Susana Seixas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal. .,Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
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Marques PI, Gonçalves JC, Monteiro C, Cavadas B, Nagirnaja L, Barros N, Barros A, Carvalho F, Lopes AM, Seixas S. Semen quality is affected by HLA class I alleles together with sexually transmitted diseases. Andrology 2019; 7:867-877. [PMID: 31002754 DOI: 10.1111/andr.12625] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/28/2019] [Accepted: 03/14/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND The human leukocyte antigen (HLA) locus includes several genes with key roles in antigen presentation and immune response, some of them inclusively found to be associated with non-obstructive azoospermia. Still, HLA connections to other infertility phenotypes such as semen hyperviscosity (SHV), asthenozoospermia (AST), and oligozoospermia (OLI) have been often neglected. OBJECTIVES In this work, we aimed to evaluate the association of HLA class I and II genes with SHV, AST, and OLI phenotypes while exploring a possible role in an adaptive immune response to sexually transmitted diseases (STD). MATERIALS AND METHODS Whole-exome sequencing was performed in a Portuguese cohort of 71 infertility cases and 68 controls, followed by HLA typing using a specific software-HLA*PRG:LA tool. Molecular screenings of seven STD were carried out in a subset of 72 samples (30 cases and 42 controls). RESULTS Statistical tests uncovered three protective alleles: HLA-A*11:01, associated with all forms of male infertility (p = 0.0006); HLA-DQB1*03:02 with SHV and OLI (PSHV = 0.0303, POLI = 0.0153); and HLA-A*29:02 with OLI (p = 0.0355), which was found to interfere in sperm number together with HPV (p = 0.0313). Five risk alleles were also identified: two linked with SHV (HLA-B*50:01, p = 0.0278; and HLA-C*06:02, p = 0.0461), another one with both SHV and OLI (HLA-DQA1*05:01, PSHV = 0.0444 and POLI =0.0265), and two with OLI (HLA-C*03:03, p = 0.0480; and HLA-DQB1*03:01, p = 0.0499). Here, HLA-C*03:03 carriers tend to be HPV infected. CONCLUSIONS The application of HLA*PRG:LA tool to the study of male infertility provided novel insights for an HLA correlation with semen quality, namely among SHV and OLI phenotypes. The discovery of an HLA-A*29:02/HPV crosstalk, together with former reports of HLA alleles conferring resistance-susceptibility to diverse human pathogens, raises the hypothesis of a mechanistic link between male infertility, HLA polymorphism, and host response to STD.
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Affiliation(s)
- P I Marques
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal
| | - J C Gonçalves
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal
| | - C Monteiro
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal
| | - B Cavadas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - L Nagirnaja
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - N Barros
- Center for Reproductive Genetics Alberto Barros, Porto, Portugal
| | - A Barros
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S), Porto, Portugal.,Center for Reproductive Genetics Alberto Barros, Porto, Portugal.,Genetics, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - F Carvalho
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S), Porto, Portugal.,Genetics, Department of Pathology, Faculty of Medicine, University of Porto, Porto, Portugal
| | - A M Lopes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal
| | - S Seixas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (i3S), Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Porto, Portugal
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5
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Valente C, Alvarez L, Marques PI, Gusmão L, Amorim A, Seixas S, João Prata M. Genes from the TAS1R and TAS2R Families of Taste Receptors: Looking for Signatures of Their Adaptive Role in Human Evolution. Genome Biol Evol 2018; 10:1139-1152. [PMID: 29635333 PMCID: PMC5905477 DOI: 10.1093/gbe/evy071] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2018] [Indexed: 02/06/2023] Open
Abstract
Taste perception is crucial in monitoring food intake and, hence, is thought to play a significant role in human evolution. To gain insights into possible adaptive signatures in genes encoding bitter, sweet, and umami taste receptors, we surveyed the available sequence variation data from the 1000 Genomes Project Phase 3 for TAS1R (TAS1R1-3) and TAS2R (TAS2R16 and TAS2R38) families. Our study demonstrated that genes from these two families have experienced contrasting evolutionary histories: While TAS1R1 and TAS1R3 showed worldwide evidence of positive selection, probably correlated with improved umami and sweet perception, the patterns of variation displayed by TAS2R16 and TAS2R38 were more consistent with scenarios of balancing selection that possibly conferred a heterozygous advantage associated with better capacity to perceive a wide range of bitter compounds. In TAS2R16, such adaptive events appear to have occurred restrictively in mainland Africa, whereas the strongest evidence in TAS2R38 was detected in Europe. Despite plausible associations between taste perception and the TAS1R and TAS2R selective signatures, we cannot discount other biological mechanisms as driving the evolutionary trajectories of those TAS1R and TAS2R members, especially given recent findings of taste receptors behaving as the products of pleiotropic genes involved in many functions outside the gustatory system.
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Affiliation(s)
- Cristina Valente
- I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Portugal
- Faculty of Sciences, University of Porto, Portugal
| | - Luis Alvarez
- I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Portugal
| | - Patrícia Isabel Marques
- I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Portugal
| | - Leonor Gusmão
- DNA Diagnostic Laboratory (LDD), State University of Rio de Janeiro (UERJ), Brazil
| | - António Amorim
- I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Portugal
- Faculty of Sciences, University of Porto, Portugal
| | - Susana Seixas
- I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Portugal
| | - Maria João Prata
- I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Portugal
- Faculty of Sciences, University of Porto, Portugal
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6
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Marques PI, Fernandes S, Carvalho F, Barros A, Sousa M, Marques CJ. DNA methylation imprinting errors in spermatogenic cells from maturation arrest azoospermic patients. Andrology 2017; 5:451-459. [PMID: 28296202 DOI: 10.1111/andr.12329] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/12/2016] [Accepted: 12/16/2016] [Indexed: 11/30/2022]
Abstract
Imprinting errors have been described in spermatozoa from infertile patients with oligozoospermia and azoospermia. However, little is known about methylation of imprinted genes in other spermatogenic cells from azoospermic patients. Therefore, we aimed to evaluate the methylation status of single CpGs located in the differentially methylated regions (DMRs) of two imprinted genes, one paternally (H19) and one maternally (MEST) methylated, in primary spermatocytes of azoospermic patients presenting complete (MAc, n = 7) and incomplete (MAi, n = 8) maturation arrest, as well as in other spermatogenic cells from MAi patients that presented focus of complete spermatogenesis in some seminiferous tubules. We observed H19 imprinting errors in primary spermatocytes from one MAi patient and MEST imprinting errors in one MAi and two MAc patients. Additionally, H19 imprinting errors were observed in elongated spermatids/spermatozoa from one MAi patient. Nevertheless, no statistical differences were found for H19 and MEST global methylation levels (percentage of methylated and unmethylated CpGs, respectively) between patients with complete and incomplete MA and also between MA groups and a control group. These results provide further evidence that imprinting errors occur in spermatogenic cells from patients presenting impaired spermatogenesis, as we and others have previously described in ejaculated and testicular spermatozoa. As paternal imprinting errors can be transmitted to the embryo by the sperm cell, they can provide a possible explanation for poor embryo development and/or low pregnancy rates as correct expression of imprinted genes is crucial for embryo and placental development and function. Therefore, in cases with male factor infertility where unsuccessful in vitro fertilization (IVF) treatments are recurrent, analysis of imprinting marks in spermatozoa might be a useful diagnostic tool.
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Affiliation(s)
- P I Marques
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal.,I3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - S Fernandes
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal.,I3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - F Carvalho
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal.,I3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - A Barros
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal.,I3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Centre for Reproductive Genetics A Barros, Porto, Portugal
| | - M Sousa
- Centre for Reproductive Genetics A Barros, Porto, Portugal.,Department of Microscopy, Laboratory of Cell Biology, Multidisciplinary Unit for Biomedical Research-UMIB, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - C J Marques
- Department of Genetics, Faculty of Medicine, University of Porto, Porto, Portugal.,I3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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Marques PI, Fonseca F, Carvalho AS, Puente DA, Damião I, Almeida V, Barros N, Barros A, Carvalho F, Azkargorta M, Elortza F, Osório H, Matthiesen R, Quesada V, Seixas S. Sequence variation atKLKandWFDCclusters and its association to semen hyperviscosity and other male infertility phenotypes. Hum Reprod 2016; 31:2881-2891. [DOI: 10.1093/humrep/dew267] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 09/15/2016] [Accepted: 10/17/2016] [Indexed: 12/22/2022] Open
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Marques PI, Fonseca F, Sousa T, Santos P, Camilo V, Ferreira Z, Quesada V, Seixas S. Adaptive Evolution Favoring KLK4 Downregulation in East Asians. Mol Biol Evol 2015; 33:93-108. [PMID: 26420451 DOI: 10.1093/molbev/msv199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The human kallikrein (KLK) cluster, located at chromosome 19q13.3-13.4, encodes 15 serine proteases, including neighboring genes (KLK3, KLK2, KLK4, and KLK5) with key roles in the cascades of semen liquefaction, tooth enamel maturation, and skin desquamation. KLK2 and KLK3 were previously identified as targets of adaptive evolution in primates through different mechanisms linked to reproductive biology and, in humans, genome-wide scans of positive selection captured, a yet unexplored, evidence for KLK neutrality departure in East Asians. We perform a detailed evaluation of KLK3-KLK5 variability in the 1000 Genomes samples from East Asia, Europe, and Africa, which was sustained by our own sequencing. In East Asians, we singled out a 70-kb region surrounding KLK4 that combined unusual low levels of diversity, high frequency variants with significant levels of population differentiation (FST > 0.5) and fairly homogenous haplotypes given the large local recombination rates. Among these variants, rs1654556_G, rs198968_T, and rs17800874_A stand out for their location on putative regulatory regions and predicted functional effects, namely the introduction of several microRNA binding sites and a repressor motif. Our functional assays carried out in different cellular models showed that rs198968_T and rs17800874_A operate synergistically to reduce KLK4 expression and could be further assisted by rs1654556_G. Considering the previous findings that KLK4 inactivation causes enamel malformations in humans and mice, and that this gene is coexpressed in epidermal layers along with several substrates involved in either cell adhesion or keratinocyte differentiation, we propose KLK4 as another target of selection in East Asians correlated to tooth and epidermal morphological traits.
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Affiliation(s)
- Patrícia Isabel Marques
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal Department of Biochemistry and Molecular Biology-IUOPA, University of Oviedo, Oviedo, Spain Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Filipa Fonseca
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Tânia Sousa
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Paulo Santos
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Vânia Camilo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Zélia Ferreira
- Department of Computational and Systems Biology, University of Pittsburgh
| | - Victor Quesada
- Department of Biochemistry and Molecular Biology-IUOPA, University of Oviedo, Oviedo, Spain
| | - Susana Seixas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto (I3S), Porto, Portugal Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
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Lima AC, Carvalho F, Gonçalves J, Fernandes S, Marques PI, Sousa M, Barros A, Seixas S, Amorim A, Conrad DF, Lopes AM. Rare double sex and mab-3-related transcription factor 1 regulatory variants in severe spermatogenic failure. Andrology 2015; 3:825-33. [PMID: 26139570 PMCID: PMC4802187 DOI: 10.1111/andr.12063] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 05/09/2015] [Accepted: 05/11/2015] [Indexed: 02/03/2023]
Abstract
The double sex and mab-3-related transcription factor 1 (DMRT1) gene has long been linked to sex-determining pathways across vertebrates and is known to play an essential role in gonadal development and maintenance of spermatogenesis in mice. In humans, the genomic region harboring the DMRT gene cluster has been implicated in disorders of sex development and recently DMRT1 deletions were shown to be associated with non-obstructive azoospermia (NOA). In this work, we have employed different methods to screen a cohort of Portuguese NOA patients for DMRT1 exonic insertions and deletions [by multiplex ligation probe assay (MLPA); n = 68] and point mutations (by Sanger sequencing; n = 155). We have found three novel patient-specific non-coding variants in heterozygosity that were absent from 357 geographically matched controls. One of these is a complex variant with a putative regulatory role (c.-223_-219CGAAA>T), located in the promoter region within a conserved sequence involved in Dmrt1 repression. Moreover, while DMRT1 domains are highly conserved across vertebrates and show reduced levels of diversity in human populations, two rare synonymous substitutions (rs376518776 and rs34946058) and two rare non-coding variants that potentially affect DMRT1 expression and splicing (rs144122237 and rs200423545) were overrepresented in patients when compared with 376 Portuguese controls (301 fertile and 75 normozoospermic). Overall our previous and present results suggest a role of changes in DMRT1 dosage in NOA potentially also through a process of gene misregulation, even though DMRT1 deleterious variants seem to be rare.
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Affiliation(s)
- Ana Cristina Lima
- Graduate Program in Areas of Basic and Applied Biology (GABBA), Abel Salazar Institute of Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal – I3S
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal – IPATIMUP, 4200-465 Porto, Portugal
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Filipa Carvalho
- Department of Genetics, Faculty of Medicine of the University of Porto, 4200-319 Porto, Portugal
| | - João Gonçalves
- Department of Human Genetics - National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisboa, Portugal
| | - Susana Fernandes
- Department of Genetics, Faculty of Medicine of the University of Porto, 4200-319 Porto, Portugal
| | - Patrícia Isabel Marques
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal – I3S
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal – IPATIMUP, 4200-465 Porto, Portugal
- Abel Salazar Institute of Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal
| | - Mário Sousa
- Laboratory of Cell Biology, UMIB, ICBAS, University of Porto, 4050-313 Porto, Portugal
| | - Alberto Barros
- Department of Genetics, Faculty of Medicine of the University of Porto, 4200-319 Porto, Portugal
| | - Susana Seixas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal – I3S
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal – IPATIMUP, 4200-465 Porto, Portugal
| | - António Amorim
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal – I3S
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal – IPATIMUP, 4200-465 Porto, Portugal
- Faculty of Sciences of the University of Porto, 4169 - 007 Porto, Portugal
| | - Donald Franklin Conrad
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alexandra Manuel Lopes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal – I3S
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal – IPATIMUP, 4200-465 Porto, Portugal
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Marques PI, Ferreira Z, Martins M, Figueiredo J, Silva DI, Castro P, Morales-Hojas R, Simões-Correia J, Seixas S. SERPINA2 is a novel gene with a divergent function from SERPINA1. PLoS One 2013; 8:e66889. [PMID: 23826168 PMCID: PMC3691238 DOI: 10.1371/journal.pone.0066889] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 05/11/2013] [Indexed: 11/23/2022] Open
Abstract
Serine protease inhibitors (SERPINs) are a superfamily of highly conserved proteins that play a key role in controlling the activity of proteases in diverse biological processes. The SERPIN cluster located at the 14q32.1 region includes the gene coding for SERPINA1, and a highly homologous sequence, SERPINA2, which was originally thought to be a pseudogene. We have previously shown that SERPINA2 is expressed in different tissues, namely leukocytes and testes, suggesting that it is a functional SERPIN. To investigate the function of SERPINA2, we used HeLa cells stably transduced with the different variants of SERPINA2 and SERPINA1 (M1, S and Z) and leukocytes as the in vivo model. We identified SERPINA2 as a 52 kDa intracellular glycoprotein, which is localized at the endoplasmic reticulum (ER), independently of the variant analyzed. SERPINA2 is not significantly regulated by proteasome, proposing that ER localization is not due to misfolding. Specific features of SERPINA2 include the absence of insoluble aggregates and the insignificant response to cell stress, suggesting that it is a non-polymerogenic protein with divergent activity of SERPINA1. Using phylogenetic analysis, we propose an origin of SERPINA2 in the crown of primates, and we unveiled the overall conservation of SERPINA2 and A1. Nonetheless, few SERPINA2 residues seem to have evolved faster, contributing to the emergence of a new advantageous function, possibly as a chymotrypsin-like SERPIN. Herein, we present evidences that SERPINA2 is an active gene, coding for an ER-resident protein, which may act as substrate or adjuvant of ER-chaperones.
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Affiliation(s)
- Patrícia Isabel Marques
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Zélia Ferreira
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Manuella Martins
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Joana Figueiredo
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Medical Faculty, University of Porto, Porto, Portugal
| | - Diana Isabel Silva
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Patrícia Castro
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Ramiro Morales-Hojas
- Molecular Evolution, Institute of Molecular and Cell Biology, University of Porto, Porto, Portugal
| | - Joana Simões-Correia
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Institute of Biomedical Research on Light and Image, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Susana Seixas
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- * E-mail: (SS)
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Marques PI, Bernardino R, Fernandes T, Green ED, Hurle B, Quesada V, Seixas S. Birth-and-death of KLK3 and KLK2 in primates: evolution driven by reproductive biology. Genome Biol Evol 2013. [PMID: 23204305 PMCID: PMC3542562 DOI: 10.1093/gbe/evs111] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The kallikrein (KLK) gene family comprises the largest uninterrupted locus of serine proteases in the human genome and represents a notable case for studying the evolutionary fate of duplicated genes. In primates, a recent duplication event gave rise to KLK2 and KLK3, both encoding essential proteins for the cascade of seminal plasma liquefaction. We reconstructed the evolutionary history of KLK2 and KLK3 by comparative analysis of the orthologous sequences from 22 primate species, calculated d(N)/d(S) ratios, and addressed the hypothesis of coevolution with their substrates, the semenogelins (SEMG1 and SEMG2). Our findings support the placement of the KLK2-KLK3 duplication in the Catarrhini ancestor and unveil the frequent loss of KLK2 throughout primate evolution by different genomic mechanisms, including unequal crossing-over, deletions, and pseudogenization. We provide evidences for an adaptive evolution of KLK3 toward an expanded enzymatic spectrum, with an effect on the hydrolysis of semen coagulum. Furthermore, we found associations between mating system, the number of SEMG repeat units, and the number of functional KLK2 and KLK3, suggesting complex evolutionary dynamics shaped by reproductive biology.
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Affiliation(s)
- Patrícia Isabel Marques
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Department of Biochemistry and Molecular Biology-IUOPA, University of Oviedo, Oviedo, Spain
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | | | | | - NISC Comparative Sequencing Program
- National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, Maryland
- NIH Intramural Sequencing Center (NISC), National Human Genome Research Institute, National Institutes of Health, Rockville, Maryland
| | - Eric D. Green
- National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, Maryland
| | - Belen Hurle
- National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, Maryland
| | - Victor Quesada
- Department of Biochemistry and Molecular Biology-IUOPA, University of Oviedo, Oviedo, Spain
- *Corresponding author: E-mail: ;
| | - Susana Seixas
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- *Corresponding author: E-mail: ;
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