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Perfil molecular dos genes ACE2 e TMPRSS2 na população açoriana : estudo da variabilidade genética nos principais genes associados à infeção por SARS-CoV-2
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Abstract(s)
A doença COVID-19 (Coronavirus Disease 2019), causada pelo agente infecioso SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2), é a principal responsável pela atual crise de saúde pública a nível mundial. Sabe-se que a doença resulta da interação entre fatores de risco ambientais, fisio-patológicos e genéticos. ACE2 (Angiotensin Converting Enzyme 2) e TMPRSS2 (Transmembrane Protease Serine 2) são os principais genes envolvidos na interação de SARS-CoV-2 com o Homem; variação nestes genes pode contribuir, por isso, para a virulência da infeção e determinar uma resposta diferencial à COVID-19. Este estudo tem como principal objetivo caracterizar o perfil molecular dos genes ACE2 e TMPRSS2 numa amostra representativa da população do arquipélago dos Açores e compará-lo com os perfis estabelecidos para as populações europeia e mundial. Como tal, inicialmente procedeu-se à compilação e caracterização de variantes em ACE2 e TMPRSS2, descritas em bases de dados genómicas e na literatura científica, com base nas suas frequências alélicas (FA) nas populações europeia e mundial e nos seus efeitos funcionais previstos. Adicionalmente, num estudo piloto, identificaram-se variantes nestes genes, a partir de dados de Whole Exome Sequencing (WES), pertencentes a uma amostra de 20 indivíduos da população açoriana. As variantes genéticas (SNVs ou INDELs) de maior interesse, potencialmente relacionadas com alterações na quantidade do transcrito ou na qualidade da proteína produzida, foram selecionadas para posterior genotipagem. Foram genotipadas 20 variantes genéticas (11 em ACE2 e 9 em TMPRSS2), pela tecnologia “iPlex for SNPs and INDELs Genotyping” (AgenaBioscience), numa amostra de 180 indivíduos da população geral açoriana para as quais se calcularam e compararam as frequências alélicas e genotípicas em 3 populações (açoriana, europeia e mundial) usando testes de diferenciação populacional. Avaliaram-se, ainda, outros parâmetros de genética de populações, como o equilíbrio de Hardy-Weinberg e o linkage disequilibrium (LD). No estudo piloto realizado, a partir dos dados WES, foi detetada uma nova variante (ENST00000332149.5: c.727+114G>A) em TMPRSS2, não descrita nas bases de dados genómicas, que carece de validação por Sequenciação de Sanger, e que poderá ser relevante para esta população. Para as 20 variantes genotipadas, não foram detetadas diferenças estatisticamente significativas entre as frequências obtidas na população de estudo e as estabelecidas para a população europeia, realçando a semelhança genética entre ambas as populações, sugestiva de uma idêntica suscetibilidade genética à COVID-19, no que concerne aos genes ACE2 e TMPRSS2. Para as variantes rs12329760, rs8126497 e rs9985159, todavia, a frequência de homozigotia diferiu entre as duas populações, podendo influenciar a suscetibilidade populacional a SARS-CoV-2. De salientar que, no presente estudo, não foi detetada a SNV rs4646116 em ACE2, classificada como potenciadora da infeção por SARS-CoV-2, e foi possível identificar uma variante protetora da infeção, rs12329760, em TMPRSS2 (FA = 17,2%), o que poderá contribuir para uma menor suscetibilidade genética à COVID-19 por parte da população açoriana, no que se refere a ambos os loci estudados. Apesar da baixa frequência alélica obtida para a variante missense rs41303171 em ACE2 (FA = 0,6%), estima-se que cerca de 2 143 açorianos possam ser portadores desta variante de risco, capaz de facilitar o processo de internalização viral. Os resultados obtidos no presente trabalho permitiram a identificação, na população açoriana, de variantes cujo efeito funcional e impacto na doença deverá continuar a ser investigado.
ABSTRACT: COVID-19 (Coronavirus Disease 2019), caused by the infectious agent SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2), is the main cause of the current public health crisis worldwide. It is known that the disease results from the interaction between environmental, pathophysiological and genetic risk factors. ACE2 (Angiotensin Converting Enzyme 2) and TMPRSS2 (Transmembrane Protease Serine 2) are the main genes involved in the interaction of SARS-CoV-2 with humans; variation in these genes may contribute to the virulence of the infection and determine a differential response to COVID-19. The main objective of this study was to characterize the molecular profile of the ACE2 and TMPRSS2 genes in a representative sample of the Azorean population and compare it with the profiles established for the European and worldwide populations. Therefore, we initially compiled and characterized genetic variants in ACE2 and TMPRSS2, described in genomic databases and in the scientific literature, based on their allelic frequencies (FA) in European and worldwide populations and in their predicted functional effects. Additionally, in a pilot study, variants in these genes were identified from Whole Exome Sequencing (WES) data belonging to a sample of 20 Azorean individuals. The most promising genetic variants (SNVs or INDELs), potentially related to alterations in the quantity of transcript or in the quality of the protein produced, were selected for further genotyping. Twenty variants were genotyped (11 in ACE2 and 9 in TMPRSS2), by the technology "iPlex for SNPs and INDELs Genotyping" (AgenaBioscience), in a sample of 180 individuals from Azorean population for which allelic and genotypic frequencies were calculated and compared in 3 populations (Azorean, European and worldwide) using population differentiation tests. Other population genetics parameters were also determined, such as the Hardy-Weinberg equilibrium and the linkage disequilibrium (LD). A new variant (ENST00000332149.5: c.727+114G>A) in TMPRSS2, which was not described in the genomic databases, was detected from the pilot study based on WES; however, the validation of this variant by Sanger Sequencing should be performed, as it might be relevant to this population. Frequencies of the 20 genotyped variants were not significantly different between Azorean and European populations, highlighting the genetic similarity between both populations, and therefore suggesting an identical genetic susceptibility to COVID-19, concerning the ACE2 and TMPRSS2 genes. Importantly, homozygosity frequencies of the rs12329760, rs8126497 and rs9985159 variants, located at TMPRSS2, were different between Azorean and European populations, which may influence the population's susceptibility to SARS-CoV-2. In the present study, the SNV rs4646116, a variant related with a highest potential of SARS-CoV-2 infection, was not detected in ACE2, and a protective variant, rs12329760, was detected in TMPRSS2 (FA = 17.2%), which may contribute to a lower genetic susceptibility to COVID-19 by the Azorean population, regarding both loci studied. Despite the missense variant rs41303171 in ACE2 had low frequency in the Azorean population (FA = 0.6%), we were able to estimate that about 2 143 Azoreans may be carriers of this risk variant, that promote the process of viral internalization. The results obtained in this study allowed the identification, in the Azorean population, of variants whose functional effect and impact on the disease should continue to be investigated.
ABSTRACT: COVID-19 (Coronavirus Disease 2019), caused by the infectious agent SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2), is the main cause of the current public health crisis worldwide. It is known that the disease results from the interaction between environmental, pathophysiological and genetic risk factors. ACE2 (Angiotensin Converting Enzyme 2) and TMPRSS2 (Transmembrane Protease Serine 2) are the main genes involved in the interaction of SARS-CoV-2 with humans; variation in these genes may contribute to the virulence of the infection and determine a differential response to COVID-19. The main objective of this study was to characterize the molecular profile of the ACE2 and TMPRSS2 genes in a representative sample of the Azorean population and compare it with the profiles established for the European and worldwide populations. Therefore, we initially compiled and characterized genetic variants in ACE2 and TMPRSS2, described in genomic databases and in the scientific literature, based on their allelic frequencies (FA) in European and worldwide populations and in their predicted functional effects. Additionally, in a pilot study, variants in these genes were identified from Whole Exome Sequencing (WES) data belonging to a sample of 20 Azorean individuals. The most promising genetic variants (SNVs or INDELs), potentially related to alterations in the quantity of transcript or in the quality of the protein produced, were selected for further genotyping. Twenty variants were genotyped (11 in ACE2 and 9 in TMPRSS2), by the technology "iPlex for SNPs and INDELs Genotyping" (AgenaBioscience), in a sample of 180 individuals from Azorean population for which allelic and genotypic frequencies were calculated and compared in 3 populations (Azorean, European and worldwide) using population differentiation tests. Other population genetics parameters were also determined, such as the Hardy-Weinberg equilibrium and the linkage disequilibrium (LD). A new variant (ENST00000332149.5: c.727+114G>A) in TMPRSS2, which was not described in the genomic databases, was detected from the pilot study based on WES; however, the validation of this variant by Sanger Sequencing should be performed, as it might be relevant to this population. Frequencies of the 20 genotyped variants were not significantly different between Azorean and European populations, highlighting the genetic similarity between both populations, and therefore suggesting an identical genetic susceptibility to COVID-19, concerning the ACE2 and TMPRSS2 genes. Importantly, homozygosity frequencies of the rs12329760, rs8126497 and rs9985159 variants, located at TMPRSS2, were different between Azorean and European populations, which may influence the population's susceptibility to SARS-CoV-2. In the present study, the SNV rs4646116, a variant related with a highest potential of SARS-CoV-2 infection, was not detected in ACE2, and a protective variant, rs12329760, was detected in TMPRSS2 (FA = 17.2%), which may contribute to a lower genetic susceptibility to COVID-19 by the Azorean population, regarding both loci studied. Despite the missense variant rs41303171 in ACE2 had low frequency in the Azorean population (FA = 0.6%), we were able to estimate that about 2 143 Azoreans may be carriers of this risk variant, that promote the process of viral internalization. The results obtained in this study allowed the identification, in the Azorean population, of variants whose functional effect and impact on the disease should continue to be investigated.
Description
Mestrado em Ciências Biomédicas, 21 de abril de 2022, Universidade dos Açores.
Keywords
COVID-19 Doenças Infecciosas Genética Molecular Humana INDELs População Açoriana Genetic Susceptibility Predicted Functional Impact Single Nucleotide Variants (SNVs)
Citation
Rocha, Tânia de Fátima Soares (2022). "Perfil molecular dos genes ACE2 e TMPRSS2 na população açoriana: estudo da variabilidade genética nos principais genes associados à infeção por SARS-CoV-2", 138 p.. Mestrado em Ciências Biomédicas. Ponta Delgada: Universidade dos Açores. [Consult. Dia Mês Ano]. Disponível em www:<http://hdl.handle.net/10400.3/6362>