Genetics and Molecular Biology最新文献_第9页

Structure-based prediction of protein-protein interaction network in rice. 基于结构的水稻蛋白质相互作用网络预测

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2024-02-02 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0068

Fangnan Sun, Yaxin Deng, Xiaosong Ma, Yuan Liu, Lingxia Zhao, Shunwu Yu, Lida Zhang

{"title":"Structure-based prediction of protein-protein interaction network in rice.","authors":"Fangnan Sun, Yaxin Deng, Xiaosong Ma, Yuan Liu, Lingxia Zhao, Shunwu Yu, Lida Zhang","doi":"10.1590/1678-4685-GMB-2023-0068","DOIUrl":"10.1590/1678-4685-GMB-2023-0068","url":null,"abstract":"Comprehensive protein-protein interaction (PPI) maps are critical for understanding the functional organization of the proteome, but challenging to produce experimentally. Here, we developed a computational method for predicting PPIs based on protein docking. Evaluation of performance on benchmark sets demonstrated the ability of the docking-based method to accurately identify PPIs using predicted protein structures. By employing the docking-based method, we constructed a structurally resolved PPI network consisting of 24,653 interactions between 2,131 proteins, which greatly extends the current knowledge on the rice protein-protein interactome. Moreover, we mapped the trait-associated single nucleotide polymorphisms (SNPs) to the structural interactome, and computationally identified 14 SNPs that had significant consequences on PPI network. The protein structural interactome map provided a resource to facilitate functional investigation of PPI-perturbing alleles associated with agronomically important traits in rice.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 1","pages":"e20230068"},"PeriodicalIF":2.1,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10849033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Brazilian women in Bioinformatics: Challenges and opportunities. 生物信息学领域的巴西妇女：挑战与机遇。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-22 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0134

Thayne Woycinck Kowalski, Giovanna Câmara Giudicelli, Maria Clara de Freitas Pinho, Marília Körbes Rockenbach, Miriãn Ferrão Maciel-Fiuza, Mariana Recamonde-Mendoza, Fernanda Sales Luiz Vianna

{"title":"Brazilian women in Bioinformatics: Challenges and opportunities.","authors":"Thayne Woycinck Kowalski, Giovanna Câmara Giudicelli, Maria Clara de Freitas Pinho, Marília Körbes Rockenbach, Miriãn Ferrão Maciel-Fiuza, Mariana Recamonde-Mendoza, Fernanda Sales Luiz Vianna","doi":"10.1590/1678-4685-GMB-2023-0134","DOIUrl":"10.1590/1678-4685-GMB-2023-0134","url":null,"abstract":"Bioinformatics is a growing research field that received great notoriety in the years of the COVID-19 pandemic. It is a very integrative area, comprising professionals from science, technology, engineering, and mathematics (STEM). In agreement with the other STEM areas, several women have greatly contributed to bioinformatics ascension; however, they had to surpass prejudice and stereotypes to achieve recognition and leadership positions, a path that studies have demonstrated to be more comfortable to their male colleagues. In this review, we discuss the several difficulties that women in STEM, including bioinformatics, surpass during their careers. First, we present a historical context on bioinformatics and the main applications for this area. Then, we discuss gender disparity in STEM and present the challenges that still contribute to women's inequality in STEM compared to their male colleagues. We also present the opportunities and the transformation that we can start, acting in academia, inside the family and school environments, and as a society, hence contributing to gender equality in STEM. Finally, we discuss specific challenges in the bioinformatics field and how we can act to overcome them, especially in low and middle-income countries, such as Brazil.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230134"},"PeriodicalIF":1.7,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10829893/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139520511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Oral microbiota, co-evolution, and implications for health and disease: The case of indigenous peoples. 口腔微生物群、共同进化以及对健康和疾病的影响：原住民的案例。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-22 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0129

Mariana Marcano-Ruiz, Thaynara Lima, Gustavo Medina Tavares, Maria Thereza Schmitt Mesquita, Luana da Silva Kaingang, Lavínia Schüler-Faccini, Maria Cátira Bortolini

{"title":"Oral microbiota, co-evolution, and implications for health and disease: The case of indigenous peoples.","authors":"Mariana Marcano-Ruiz, Thaynara Lima, Gustavo Medina Tavares, Maria Thereza Schmitt Mesquita, Luana da Silva Kaingang, Lavínia Schüler-Faccini, Maria Cátira Bortolini","doi":"10.1590/1678-4685-GMB-2023-0129","DOIUrl":"10.1590/1678-4685-GMB-2023-0129","url":null,"abstract":"Evidence indicates that oral microbiota plays a crucial role in human health and disease. For instance, diseases with multifactorial etiology, such as periodontitis and caries, which cause a detrimental impact on human well-being and health, can be caused by alterations in the host-microbiota interactions, where non-pathogenic bacteria give way to pathogenic orange/red-complex bacterial species (a change from a eubiotic to dysbiotic state). In this scenario, where thousands of oral microorganisms, including fungi, archaea, and phage species, and their host are co-evolving, a set of phenomena, such as the arms race and Red or Black Queen dynamics, are expected to operate. We review concepts on the subject and revisit the nature of bacterial complexes linked to oral health and diseases, as well as the problem of the bacterial resistome in the face of the use of antibiotics and what is the impact of this on the evolutionary trajectory of the members of this symbiotic ecosystem. We constructed a 16SrRNA tree to show that adaptive consortia of oral bacterial complexes do not necessarily rescue phylogenetic relationships. Finally, we remember that oral health is not exempt from health disparity trends in some populations, such as Native Americans, when compared with non-Indigenous people.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230129"},"PeriodicalIF":1.7,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10829892/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139520517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Broken silence: 22,841 predicted deleterious synonymous variants identified in the human exome through computational analysis. 打破沉默：通过计算分析在人类外显子组中发现 22,841 个预测的有害同义变异。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-22 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0125

Ana Carolina Mello, Delva Leao, Luis Dias, Felipe Colombelli, Mariana Recamonde-Mendoza, Andreia Carina Turchetto-Zolet, Ursula Matte

{"title":"Broken silence: 22,841 predicted deleterious synonymous variants identified in the human exome through computational analysis.","authors":"Ana Carolina Mello, Delva Leao, Luis Dias, Felipe Colombelli, Mariana Recamonde-Mendoza, Andreia Carina Turchetto-Zolet, Ursula Matte","doi":"10.1590/1678-4685-GMB-2023-0125","DOIUrl":"10.1590/1678-4685-GMB-2023-0125","url":null,"abstract":"Synonymous single nucleotide variants (sSNVs) do not alter the primary structure of a protein, thus it was previously accepted that they were neutral. Recently, several studies demonstrated their significance to a range of diseases. Still, variant prioritization strategies lack focus on sSNVs. Here, we identified 22,841 deleterious synonymous variants in 125,748 human exomes using two in silico predictors (SilVA and CADD). While 98.2% of synonymous variants are classified as neutral, 1.8% are predicted to be deleterious, yielding an average of 9.82 neutral and 0.18 deleterious sSNVs per exome. Further investigation of prediction features via Heterogeneous Ensemble Feature Selection revealed that impact on amino acid sequence and conservation carry the most weight for a deleterious prediction. Thirty nine detrimental sSNVs are not rare and are located on disease associated genes. Ten distinct putatively non-deleterious sSNVs are likely to be under positive selection in the North-Western European and East Asian populations. Taken together our analysis gives voice to the so-called silent mutations as we propose a robust framework for evaluating the deleteriousness of sSNVs in variant prioritization studies.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230125"},"PeriodicalIF":1.7,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10804382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139520515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Tailed bacteriophages (Caudoviricetes) dominate the microbiome of a diseased stingless bee. 尾部噬菌体（Caudoviricetes）在患病无刺蜂的微生物组中占主导地位。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0120

Lilian Caesar, Karen Luisa Haag

{"title":"Tailed bacteriophages (Caudoviricetes) dominate the microbiome of a diseased stingless bee.","authors":"Lilian Caesar, Karen Luisa Haag","doi":"10.1590/1678-4685-GMB-2023-0120","DOIUrl":"10.1590/1678-4685-GMB-2023-0120","url":null,"abstract":"Bacteriophages, viruses that infect bacterial hosts, are known to rule the dynamics and diversity of bacterial populations in a number of ecosystems. Bacterial communities residing in the gut of animals, known as the gut microbiome, have revolutionized our understanding of many diseases. However, the gut phageome, while of apparent importance in this context, remains an underexplored area of research. Here we identify for the first time genomic sequences from tailed viruses (Caudoviricetes) that are associated with the microbiome of stingless bees (Melipona quadrifasciata). Both DNA and RNA were extracted from virus particles isolated from healthy and diseased forager bees, the latter showing symptoms from an annual syndrome that only affects M. quadrifasciata. Viral contigs from previously sequenced metagenomes of healthy and diseased forager bees were used for the analyses. Using conserved proteins deduced from their genomes, we found that Caudoviricetes were only present in the worker bee gut microbiome from diseased stingless bees. The most abundant phages are phylogenetically related to phages that infect Gram-positive bacteria from the order Lactobacillales and Gram-negative bacteria from the genus Gilliamella and Bartonella, that are common honey bee symbionts. The potential implication of these viruses in the M. quadrifasciata syndrome is discussed.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230120"},"PeriodicalIF":1.7,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139512370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Position Weight Matrix or Acyclic Probabilistic Finite Automaton: Which model to use? A decision rule inferred for the prediction of transcription factor binding sites. 位置权重矩阵或循环概率有限自动机：使用哪种模型？用于预测转录因子结合位点的决策规则推论。

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0048

Guilherme Miura Lavezzo, Marcelo de Souza Lauretto, Luiz Paulo Moura Andrioli, Ariane Machado-Lima

{"title":"Position Weight Matrix or Acyclic Probabilistic Finite Automaton: Which model to use? A decision rule inferred for the prediction of transcription factor binding sites.","authors":"Guilherme Miura Lavezzo, Marcelo de Souza Lauretto, Luiz Paulo Moura Andrioli, Ariane Machado-Lima","doi":"10.1590/1678-4685-GMB-2023-0048","DOIUrl":"10.1590/1678-4685-GMB-2023-0048","url":null,"abstract":"Prediction of transcription factor binding sites (TFBS) is an example of application of Bioinformatics where DNA molecules are represented as sequences of A, C, G and T symbols. The most used model in this problem is Position Weight Matrix (PWM). Notwithstanding the advantage of being simple, PWMs cannot capture dependency between nucleotide positions, which may affect prediction performance. Acyclic Probabilistic Finite Automata (APFA) is an alternative model able to accommodate position dependencies. However, APFA is a more complex model, which means more parameters have to be learned. In this paper, we propose an innovative method to identify when position dependencies influence preference for PWMs or APFAs. This implied using position dependency features extracted from 1106 sets of TFBS to infer a decision tree able to predict which is the best model - PWM or APFA - for a given set of TFBSs. According to our results, as few as three pinpointed features are able to choose the best model, providing a balance of performance (average precision) and model simplicity.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 4","pages":"e20230048"},"PeriodicalIF":2.1,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10945726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139570329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Adaptive strategies of aquatic mammals: Exploring the role of the HIF pathway and hypoxia tolerance. 水生哺乳动物的适应策略：探索 HIF 通路和耐缺氧性的作用。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0140

Yuri Yépez, Mariana Marcano-Ruiz, Maria Cátira Bortolini

{"title":"Adaptive strategies of aquatic mammals: Exploring the role of the HIF pathway and hypoxia tolerance.","authors":"Yuri Yépez, Mariana Marcano-Ruiz, Maria Cátira Bortolini","doi":"10.1590/1678-4685-GMB-2023-0140","DOIUrl":"10.1590/1678-4685-GMB-2023-0140","url":null,"abstract":"Aquatic mammals (marine and freshwater species) share significant and similar adaptations, enabling them to tolerate hypoxia during regular breath-hold diving. Despite the established importance of HIF1A, a master regulator in the molecular mechanism of hypoxia response, and other associated genes, their role in the evolutionary adaptation of aquatic mammals is not fully understood. In this study, we investigated this topic by employing a candidate gene approach to analyze 11 critical genes involved in the HIF1A signaling pathway in aquatic mammals. Our gene analyses included evaluating positive and negative selection, relaxation or constriction of selection, and molecular convergence compared to other terrestrial mammals, including subterranean mammals. Evidence of selection suggested a significant role of negative selection, as well as relaxation of the selective regime in cetaceans for most of these genes. We found that the glutamine 68 variant in the HIF3α protein is unique to cetaceans and initial evaluations indicated a destabilizing effect on protein structure. However, further analyses are necessary to evaluate its functional impact and adaptive relevance in this taxon.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230140"},"PeriodicalIF":1.7,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802827/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139512324","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Gene-environment interactions and preterm birth predictors: A Bayesian network approach. 基因-环境相互作用与早产预测因素：贝叶斯网络方法

IF 2.1 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0090

Dario E Elias, Maria R Santos, Hebe Campaña, Fernando A Poletta, Silvina L Heisecke, Juan A Gili, Julia Ratowiecki, Viviana R Cosentino, Rocio Uranga, Diana Rojas Málaga, Alice Brinckmann Oliveira Netto, Ana Carolina Brusius-Facchin, César Saleme, Mónica Rittler, Hugo B Krupitzki, Jorge S Lopez Camelo, Lucas G Gimenez

{"title":"Gene-environment interactions and preterm birth predictors: A Bayesian network approach.","authors":"Dario E Elias, Maria R Santos, Hebe Campaña, Fernando A Poletta, Silvina L Heisecke, Juan A Gili, Julia Ratowiecki, Viviana R Cosentino, Rocio Uranga, Diana Rojas Málaga, Alice Brinckmann Oliveira Netto, Ana Carolina Brusius-Facchin, César Saleme, Mónica Rittler, Hugo B Krupitzki, Jorge S Lopez Camelo, Lucas G Gimenez","doi":"10.1590/1678-4685-GMB-2023-0090","DOIUrl":"10.1590/1678-4685-GMB-2023-0090","url":null,"abstract":"Preterm birth (PTB) is the main condition related to perinatal morbimortality worldwide. The aim of this study was to identify gene-environment interactions associated with spontaneous PTB or its predictors. We carried out a retrospective case-control study including parental sociodemographic and obstetric data as well as newborn genetic variants of 69 preterm and 61 at term newborns born at a maternity hospital from Tucumán, Argentina, between 2005 and 2010. A data-driven Bayesian network including the main PTB predictors was created where we identified gene-environment interactions. We used logistic regressions to calculate the odds ratios and confidence intervals of the interactions. From the main PTB predictors (nine exposures and six genetic variants) we identified an interaction between low neighbourhood socioeconomic status and rs2074351 (PON1, genotype GG) variant that was associated with an increased risk of toxoplasmosis (odds ratio 12.51, confidence interval 95%: 1.71 - 91.36). The results of this exploratory study suggest that structural social disparities could influence the PTB risk by increasing the frequency of exposures that potentiate the risk associated with individual characteristics such as genetic traits. Future studies with larger sample sizes are necessary to confirm these findings.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 4","pages":"e20230090"},"PeriodicalIF":2.1,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10804443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139570318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring the frequency of a TP53 polyadenylation signal variant in tumor DNA from patients diagnosed with lung adenocarcinomas, sarcomas and uterine leiomyomas. 探索肺腺癌、肉瘤和子宫肌瘤患者肿瘤 DNA 中 TP53 多腺苷酸化信号变异的频率。

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0133

Igor Araujo Vieira, Guilherme Danielski Viola, Eduarda Heidrich Pezzi, Thayne Woycinck Kowalski, Bruna Vieira Fernandes, Tiago Finger Andreis, Natascha Bom, Giulianna Sonnenstrahl, Yasminne Marinho de Araújo Rocha, Bruno da Silveira Corrêa, Luiza Mezzomo Donatti, Gabriela Dos Santos Sant'Anna, Helena von Eye Corleta, Ilma Simoni Brum, Clévia Rosset, Fernanda Sales Luiz Vianna, Gabriel S Macedo, Edenir Inez Palmero, Patricia Ashton-Prolla

{"title":"Exploring the frequency of a TP53 polyadenylation signal variant in tumor DNA from patients diagnosed with lung adenocarcinomas, sarcomas and uterine leiomyomas.","authors":"Igor Araujo Vieira, Guilherme Danielski Viola, Eduarda Heidrich Pezzi, Thayne Woycinck Kowalski, Bruna Vieira Fernandes, Tiago Finger Andreis, Natascha Bom, Giulianna Sonnenstrahl, Yasminne Marinho de Araújo Rocha, Bruno da Silveira Corrêa, Luiza Mezzomo Donatti, Gabriela Dos Santos Sant'Anna, Helena von Eye Corleta, Ilma Simoni Brum, Clévia Rosset, Fernanda Sales Luiz Vianna, Gabriel S Macedo, Edenir Inez Palmero, Patricia Ashton-Prolla","doi":"10.1590/1678-4685-GMB-2023-0133","DOIUrl":"10.1590/1678-4685-GMB-2023-0133","url":null,"abstract":"The TP53 3'UTR variant rs78378222 A>C has been detected in different tumor types as a somatic alteration that reduces p53 expression through modification of polyadenylation and miRNA regulation. Its prevalence is not yet known in all tumors. Herein, we examine tumor tissue prevalence of rs7837822 in Brazilian cohorts of patients from south and southeast regions diagnosed with lung adenocarcinoma (LUAD, n=586), sarcoma (SARC, n=188) and uterine leiomyoma (ULM, n=41). The minor allele (C) was identified in heterozygosity in 6/586 LUAD tumors (prevalence = 1.02 %) and none of the SARC and ULM samples. Additionally, next generation sequencing analysis revealed that all variant-positive tumors (n=4) with sample availability had additional pathogenic or likely pathogenic somatic variants in the TP53 coding regions. Among them, 3/4 (75 %) had the same pathogenic or likely pathogenic sequence variant (allele frequency <0.05 in tumor DNA) namely c.751A>C (p.Ile251Leu). Our results indicate a low somatic prevalence of rs78378222 in LUAD, ULM and SARC tumors from Brazilian patients, which suggests that no further analysis of this variant in the specific studied regions of Brazil is warranted. However, these findings should not exclude tumor molecular testing of this TP53 3'UTR functional variant for different populations.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230133"},"PeriodicalIF":1.7,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802224/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139512326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Microcephaly in South Brazil: Are cases of Congenital Zika Syndrome increasing in recent years? 南巴西的小头畸形：先天性寨卡综合征病例近年来是否有所增加？

IF 1.7 4区生物学

Genetics and Molecular Biology Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0191

Anna Pires Terra, Ricardo Rohweder, Silvani Herber, Luciana Friedrich, Maria Teresa Vieira Sanseverino, Catia Favreto, Fernanda Santa Maria, Emilly de Jesus Athayde, Laércio Moreira Cardoso-Júnior, Andrea Cristina Pereira Marinho, Allanamara Pereira Marinho, Tailine Zarpelon, Lavínia Schuler-Faccini

{"title":"Microcephaly in South Brazil: Are cases of Congenital Zika Syndrome increasing in recent years?","authors":"Anna Pires Terra, Ricardo Rohweder, Silvani Herber, Luciana Friedrich, Maria Teresa Vieira Sanseverino, Catia Favreto, Fernanda Santa Maria, Emilly de Jesus Athayde, Laércio Moreira Cardoso-Júnior, Andrea Cristina Pereira Marinho, Allanamara Pereira Marinho, Tailine Zarpelon, Lavínia Schuler-Faccini","doi":"10.1590/1678-4685-GMB-2023-0191","DOIUrl":"10.1590/1678-4685-GMB-2023-0191","url":null,"abstract":"Northeast Brazil was the first region to detect a significant increase in babies born with microcephaly associated with prenatal zika virus infection in 2015. Rio Grande do Sul (RS) state was less impacted due to the temperate climate preventing the spread of the vector. This study investigated the prevalence and etiology of congenital microcephaly in RS in two different periods. This cross-sectional descriptive study included all live births with congenital microcephaly in RS from 2015 to 2022. Cases were divided into two groups: P1 \"outbreak\" (2015-16); and P2 \"endemic\" (2017-22). There were 58 cases of microcephaly (3.8/10,000) in P1 and 148 (1.97/10,000) in P2. Congenital Zika Virus infection was the etiology in 5.2% (n=3) in P1 and 6.7% (n=10) in P2. In conclusion, although the ZIKV outbreak in Brazil has receded, RS remains an area of concern, with a possible slight increase of live births with microcephaly secondary to ZIKV prenatal infection relative to the number of cases due to congenital infections. The broader distribution of the vector Aedes aegypti with warmer temperatures in our state might be linked to the increase in recent years. This study can be an alert to other regions of temperate or subtropical climates.","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230191"},"PeriodicalIF":1.7,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139512369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0