Phylogenetic relationships of the Mangrove Hummingbird, "Amazilia" boucardi (Apodiformes: Trochilidae) of Costa Rica / Relaciones filogenéticas del Colibrí manglero "Amazilia" boucardi (Apodiformes: Trochilidae) de Costa Rica

Abstract Introduction: A recent revision of the generic classification of the Trochilidae based on DNA sequences revealed many inconsistencies with the current generic classification, largely based on plumage characters subject to homoplasy, especially in the Trochilini, the largest tribe. A thorough generic reorganization brought the classification into accord with the phylogeny, but due to lack of genetic data, two species remained unclassified. One of these was the Mangrove Hummingbird, "Amazilia" boucardi, endemic to Costa Rica and included in the IUCN red list of threatened species. Objective: To obtain molecular evidence to clarify the generic relationships of "A." boucardi. Methods: We isolated DNA from tissues of this species and amplified 4 nuclear and 4 mitochondrial fragments and compared these with homologous fragments from 56 species in the Trochilini, constructing phylogenetic trees with maximum likelihood and Bayesian methods. Results: Our phylogenetic analyses confirmed the placement of boucardi in the Trochilini and definitely excluded it from Amazilia but placed it with high confidence in the genus Chrysuronia Bonaparte, 1850, within which its closest relative is C. coeruleogularis, which also inhabits mangroves. Conclusions: Our genetic data based on nuclear and mitochondrial regions clearly indicate the relationship of A. boucardi and L. coeruleogularis. Moreover, it is also supported by their habitat distribution in the mangroves of the Pacific coast of Costa Rica and Western Panama. Therefore, we suggested to exclude A. boucardi as "incertae sedis".

Resumen Introducción: Una revisión reciente de la clasificación de la familia Trochilidae con base en secuencias de ADN demostró muchas incongruencias con la clasificación genérica previa, que había sido hecho con base en caracteres del plumaje muy sujetos a homoplasia, especialmente en la tribu más grande, Trochillini. Una reorganización de los géneros logró llevar su clasificación genérica a la concordancia con la filogenia, pero debido a la ausencia de datos genéticos, dos especies permanecieron sin clasificar. Una de estas fue el colibrí de manglar Amazilia boucardi, una especie endémica de Costa Rica, considerada como amenazada en la lista roja de la UICN. Objetivo: Obtener evidencia molecular para esclarecer las relaciones genéricas de A. boucardi. Métodos: Se aisló ADN de tejidos de esta especie y se amplificaron 4 fragmentos de ADN del núcleo y 5 de la mitocondria, y se compararon con fragmentos homólogos de 56 especies en la tribu Trochillini, generando árboles filogenéticos con métodos de máxima verosimilitud y bayesiano. Resultados: Los análisis filogénticos obtenidos confirmaron la ubicación de boucardi en Trochilini y definitivamente la excluyó del género Amazilia, pero la ubicó con un alto grado de confianza en el género Chrysuronia Bonaparte, 1850, dentro los cuales su pariente más cercano es C. coeruleogularis, que también habita manglares. Conclusiones: Nuestros datos genéticos basados en regiones nucleares y mitocondriales indican claramente la relación entre A. boucardi and L. coeruleogularis. Es más, lo anterior se sustenta por su distribución en los manglares de la costa Pacífica de Costa Rica y oeste de Panamá. Por lo tanto, sugerimos excluir a A. boucardi como "incertae sedis".

Homologous recombination deficiency gene panel analysis results in synchronous endometrial and ovarian cancers

SUMMARY OBJECTIVE: The objective of this study was to analyze the genetic alterations of tumors within the scope of the homologous recombination deficiency gene panel in patients diagnosed with synchronous endometrial ovarian cancer who have been followed for over 5 years using next-generation sequencing. METHODS: DNA was isolated from the patient's formalin-fixed, paraffin-embedded tissue blocks. Next-generation sequencing was performed using the Illumina capture-based sequencing method. Samples were sequenced using the Sophia HR Solution DNA Kit. RESULTS: Seven patients were included in this study. The ratios of likely pathogenic (LP)/pathogenic (P) somatic mutations in ATM (serine/threonine kinase or Ataxia-telangiectasia mutated gene), BRCA2 (breast cancer type 2 susceptibility gene), BARD1 (BRCA1 associated RING domain 1), TP53 (tumor protein p53), BIRP1 (BRCA1-interacting helicase 1 gene), PALB2 (partner and localizer of BRCA2), and CHECK2 were 21 (48.8%), 8 (18.6%), 5 (11.6%), 3 (6.9%), 2 (4.6%), 2 (4.6%), and 2 (4.6%), respectively, in endometrium, and the ratios of somatic mutations in ATM, BRCA2, TP53, BARD1, RAD54L (DNA repair/recombination protein like), BIRP1, and RAD51D (RAD51 recombinase paralog D) were 24 (60%), 6 (15%), 5 (12.5%), 2 (5%), 2 (5%), 1 (2.5%), and 1 (2.5%), respectively, in ovary. In endometrioid-synchronous endometrial ovarian cancer cases, P/LP mutations were observed in ATM and CHECK2 genes in endometrium and ATM, BRCA2, and TP53 genes in ovary. In two non-endometrioid-synchronous endometrial ovarian cancer cases, CHEK2 (checkpoint kinase 2) mutations were observed in endometrium and ATM and TP53 mutations in ovary, whereas in one case, P/LP mutations in ATM and TP53 genes were common in both tissues. CONCLUSION: Pathogenic variations confirming the diagnosis of synchronous endometrial ovarian cancer with genetic alterations were identified in all but one case. ATM gene mutation emerged as the most common alteration and has a potential association with a favorable prognosis.

Atrofia Muscular Espinal: A Propósito de un Caso Clínico / Spinal Muscular Atrophy: A Case Report

La atrofia muscular espinal (AME) se engloba dentro de las enfermedades motoneuronales. Su herencia es autosómica recesiva y se la considera una enfermedad rara. Su fisiopatología radica en el conocimiento de los genes SMN1 y SMN2. Clínicamente se presenta con elementos de motoneurona inferior tanto a nivel craneal como espinal. Existen varias formas de clasificación y presenta un curso clínico variable. Su diagnóstico es clínico con confirmación genética. La importancia de esta entidad es que presenta tratamiento modificador de la enfermedad con diferentes targets terapéuticos. Palabras clave: Atrofia muscular espinal (AME), genes SMN1 y SMN2, tratamiento modificador de la enfermedad.

Abstract. Spinal muscular atrophy (SMA) is classified within motor neuron diseases. It is inherited in an autosomal recessive manner and is considered a rare disease. Its pathophysiology involves understanding the SMN1 and SMN2 genes. Clinically, it presents with lower motor neuron elements at both cranial and spinal levels. There are various classification forms, and it presents a variable clinical course. Diagnosis is clinical with genetic confirmation. The importance of this entity lies in the fact that it has disease-modifying treatments with different therapeutic targets. Keywords: Spinal muscular atrophy (SMA), SMN1 and SMN2 genes, disease-modifying treatment.

Inborn errors of immunity and its clinical significance in children with lymphoma in China: a single-center study

Abstract Objective: To investigate the incidence, clinical and genetic characteristics of pediatric lymphoma patients of China with inborn errors of immunity (IEI)-related gene mutations, which have not been fully studied. Method: From Jan. 2020 to Mar. 2023, IEI-related genetic mutations were retrospectively explored in 108 children with lymphomas admitted to Beijing Children's Hospital by NGS. Genetic rule and clinical characteristics as well as treatment outcomes were compared between patients with or without IEI-related gene mutations. Results: A total of 17 patients (15.7 %) harbored IEI-associated mutations, including 4 cases with X-linked lymphoproliferative syndrome (XLP), 3 cases had mutations in tumor necrosis factor receptor superfamily 13B (TNFRSF13B), 2 cases with Activated p110 syndrome (APDS). Patients with IEI all had alteration of immunocompetence with decreased levels of immunoglobulin and lymphocyte subsets. Recurrent infection existed in 41.2 % of patients. The 18-month event-free survival (EFS) and the overall response rate (ORR) of patients with IEI are significantly lower than those without IEI (33.86% vs. 73.26 %, p = 0.011; 52.94% vs. 87.91 %, p = 0.002, respectively). In addition, patients with IEI had a higher progression disease (PD) rate of 23.5 % than those without IEI of 4.4% (p = 0.006). Conclusion: The present study demonstrated that IEI-associated lymphomas were much more common than originally appreciated in pediatric lymphomas, and those were insensitive to treatment and more likely to progress or relapse. The genomic analysis and a thorough review of the medical history of IEI can be used to distinguish them from pediatric lymphomas without IEI, which are beneficial for the early diagnosis and direct intervention.

Características de la Diabetes del adulto de inicio juvenil y su diagnóstico en el laboratorio / Characteristics of Maturity Onset Diabetes of the Young and its diagnosis in the laboratory / Características do diabetes adulto de início juvenil e seu diagnóstico laboratorial

La Diabetes del adulto de inicio juvenil, es un subtipo hereditario poco común que se manifiesta a una edad temprana, relacionado con mutaciones en genes específicos que principalmente afectan la función de las células beta pancreática. Un diagnóstico preciso es fundamental para un tratamiento efectivo, aunque puede ser desafiante debido a la variabilidad en sus características clínicas y moleculares. Esta revisión analiza la evidencia disponible sobre estas características y los métodos de diagnóstico utilizados en laboratorio. Se realizó una búsqueda exhaustiva en bases de datos científicas, seleccionando estudios relevantes según criterios específicos. Se analizaron características clínicas, hallazgos moleculares y métodos de diagnóstico, utilizando tablas, gráficos y síntesis narrativas. Se identificaron mutaciones genéticas asociadas con MODY, así como biomarcadores útiles en el laboratorio clínico. Además, se describieron métodos de diagnóstico molecular, incluyendo la secuenciación de próxima generación (NGS). Esta revisión resalta la importancia del diagnóstico preciso de MODY, subrayando la diversidad de sus características biológicas y moleculares, y la necesidad de una investigación más profunda para mejorar su identificación y manejo clínico

Maturity Onset Diabetes of the Young is a rare hereditary subtype that manifests at an early age, related to mutations in specific genes that primarily affect the function of pancreatic beta cells. An accurate diagnosis is crucial for effective treatment, though it can be challenging due to variability in clinical and molecular characteristics. This review examines available evidence on these characteristics and laboratory diagnostic methods. A comprehensive search was conducted in scientific databases, selecting relevant studies based on specific criteria. Clinical features, molecular findings, and diagnostic methods were analyzed using tables, graphs, and narrative synthesis. Genetic mutations associated with MODY were identified, as well as useful biomarkers in clinical laboratory settings. Additionally, molecular diagnostic methods were described, including next-generation sequencing (NGS). This review emphasizes the importance of precise MODY diagnosis, highlighting the diversity of its biological and molecular characteristics, and the need for further research to enhance its identification and clinical management

A diabetes adulto de início juvenil é um subtipo hereditário raro que se manifesta em uma idade precoce, relacionado a mutações em genes específicos que afetam principalmente a função das células beta do pâncreas. Um diagnóstico preciso é fundamental para um tratamento eficaz, embora possa ser desafiador devido à variabilidade em suas características clínicas e moleculares. Esta revisão analisa a evidência disponível sobre essas características e os métodos de diagnóstico utilizados em laboratório. Foi realizada uma busca abrangente em bases de dados científicas, selecionando estudos relevantes com base em critérios específicos. Características clínicas, descobertas moleculares e métodos de diagnóstico foram analisados utilizando tabelas, gráficos e síntese narrativa. Foram identificadas mutações genéticas associadas ao MODY, assim como biomarcadores úteis em laboratório clínico. Além disso, foram descritos métodos de diagnóstico molecular, incluindo a sequenciação de próxima geração (NGS). Esta revisão enfatiza a importância do diagnóstico preciso do MODY, destacando a diversidade de suas características biológicas e moleculares e a necessidade de uma pesquisa mais aprofundada para melhorar sua identificação e manejo clínico

Análisis bibliométrico de la investigación en genética y la ruptura de ligamento cruzado anterior en deporte: una revisión / Bibliometric analysis of research in genetic and anterior cruciate ligament rupture in sport: a review / Análise bibliométrica da pesquisa em genética e ruptura do ligamento cruzado anterior no esporte: uma revisão

Resumen: Introducción: El componente genético se ha establecido como un factor de riesgo considerable para la ruptura del ligamento cruzado anterior (RLCA). La investigación actual se ha centrado en conocer los genes candidatos que pueden influir y predisponer a un sujeto a padecer esta lesión. Objetivo: Se llevó a cabo un análisis bibliométrico para rastrear los resultados de la indagación e identificar las tendencias globales, así como las brechas en el conocimiento sobre la relación entre el componente genético y la RLCA. Metodología: Los datos fueron extraídos de las bases Pubmed y Scopus, igual que analizados en el paquete Bibliometrix del software R. Se identificó un total de 63 estudios publicados a partir del 2007. Resultados: La mayoría de las publicaciones identificadas fueron artículos de investigación (85.71 %). Los autores con mayor número de aquellas se encuentran en Polonia y Sudáfrica. El análisis a través del mapa de coocurrencias reveló que hay una línea principal de investigación basada en el estudio de polimorfismos genéticos, especialmente en los genes de las familias del colágeno (COL1A1, COL5A1, COL12A1, en mayor frecuencia). Un total de 54 genes candidatos fueron identificados en los estudios. Conclusión: Esperamos que este estudio pueda contribuir a encontrar puntos claves y vacíos de investigación, al proporcionar análisis integrales e información estructurada sobre este tema.

Abstract: Introduction: Genetic component has been established as a significant risk factor for anterior cruciate ligament rupture (ACLR). Current research has focused on knowing the candidate genes that can influence and predispose a subject to this injury. Objective: A bibliometric analysis was carried out to trace the results of the research and identify global trends and gaps in knowledge about the relationship between the genetic component and ACLR. Methodology: Data were extracted from the Pubmed and Scopus databases and analyzed in the Bibliometrix package of the R software. A total of 63 studies published since 2007 were identified. Results: Most of the publications recovered were research articles (85.71%). The authors with the highest number of those are in Poland and South Africa. The analysis through the co-occurrence map reveals that there is a mainline of research based on the study of genetic polymorphisms, especially in the genes of the collagen families (COL1A1, COL5A1, COL12A1, in greater frequency). A total of 54 candidate genes were identified within the studies. Conclusion: We hope that this study can help to find key points and research gaps by providing a comprehensive analysis and structured information on this topic.

Resumo: Introdução: O componente genético foi estabelecido como um fator de risco significativo para a ruptura do ligamento cruzado anterior (RLCA). As pesquisas atuais têm se concentrado em identificar os genes candidatos que podem influenciar e predispor um indivíduo a essa lesão. Objetivo: Foi realizada uma análise bibliométrica para rastrear os resultados das pesquisas e identificar tendências globais e lacunas no conhecimento sobre a relação entre o componente genético e a RLCA. Metodologia: Os dados foram extraídos das bases de dados Pubmed e Scopus e analisados no pacote Bibliometrix do software R. Um total de 63 estudos publicados desde 2007 foram identificados. Resultados: A maioria das publicações recuperadas foram artigos de pesquisa (85,71%). Os autores com o maior número dessas publicações estão na Polônia e na África do Sul. A análise por meio do mapa de coocorrência revela que há uma linha principal de pesquisa baseada no estudo de polimorfismos genéticos, especialmente nos genes das famílias de colágeno (COL1A1, COL5A1, COL12A1, com maior frequência). Um total de 54 genes candidatos foram identificados nos estudos. Conclusão: Esperamos que este estudo possa ajudar a encontrar pontos-chave e lacunas de pesquisa, fornecendo uma análise abrangente e informações estruturadas sobre este tema.

Perfil molecular de cáncer de endometrio en mujeres de Bogotá DC, Colombia / Molecular profile of endometrial cancer in women from Bogota DC, Colombia

Introducción: El cáncer de endometrio ocupa el sexto lugar en incidencia del cáncer en mujeres. La caracterización molecular de este cáncer permite optimizar la estratificación de riesgo para mejorar el tratamiento de las pacientes. Objetivo: Determinar el perfil molecular TCGA de pacientes con cáncer de endometrio en Bogotá, D.C., Colombia. Método: Estudio descriptivo en una cohorte de pacientes con cáncer de endometrio. Las mutaciones en los exones 9 a 14 del gen POLE fueron identificadas mediante amplificación por reacción en cadena de la polimerasa, seguida de secuenciación Sanger y análisis bioinformático. La expresión de las proteínas MMR y p53 se identificó mediante inmunohistoquímica. Resultados: Se incluyeron 40 pacientes con una mediana de edad de 66 años. El 15% presentaron mutaciones en el dominio exonucleasa de POLE. El 32% de las pacientes que no presentaron mutaciones manifestaron deficiencia en el sistema MMR. El 43,47% de las pacientes sin mutaciones en POLE ni alteración del sistema MMR presentaron alteración de la proteína p53. Conclusiones: La población de cáncer de endometrio analizada presenta un perfil molecular TCGA similar a lo reportado para otras poblaciones.

Introduction: Endometrial cancer ranks sixth in cancer incidence among women. Its molecular characterization allows for a more precise risk stratification with the aim of improving patient treatment. Objective: To determine the TCGA molecular profile of patients with endometrial cancer in Bogota, Colombia. Method: A descriptive study of a cohort of patients with endometrial cancer. The expression of MMR proteins and p53 was identified through immunohistochemistry. Mutations in exons 9 to 14 of the POLE gene were identified through polymerase chain reaction amplification, followed by Sanger sequencing and bioinformatic analysis. Results: Forty patients were included in the study, with a median age of 66 years, 15% of them exhibited mutations in the exonuclease domain of POLE, while 32% of patients without mutations showed deficiency in the MMR system. Forty three percent of patients without mutations in POLE or MMR alterations showed aberrant p53 protein expression. Conclusions: The analyzed population of endometrial cancer presents a TCGA molecular profile similar to that reported for other populations.

Mining of Gene Modules and Identification of Key Genes for Early Diagnosis of Gastric Cancer

Gastric cancer (GC) is one of the most common malignant tumors with high incidence and mortality rates. Most patients with GC are not diagnosed until the advanced stage of cancer or during tumor screening, resulting in missing the best treatment time. This study identified key modules and hub genes associated with GC by weighted gene co-expression network analysis (WGCNA). The "limma" package in R was used to identify differentially expressed genes (DEGs) in GC samples from TCGA, and a total of 4892 DEGs were identified. GO enrichment and KEGG pathway enrichment analyses were conducted to detect the related pathways and functions of DEGs. These DEGs were primarily associated with extracellular matrix organization, DNA replication, cell cycle, and p53 signaling pathway. Gene modules associated with clinical characteristics were identified with WGCNA in tumor and normal samples. Six gene modules were obtained in the WGCNA network, of which two modules were significantly correlated with GC. Hub genes of key modules were identified using survival analysis and expression analysis. Finally, one-way ANOVA was used to explore the relationship between hub gene expression in normal tissues and different pathological stages of GC. Through survival and expression analysis, a total of 19 genes with good prognosis and significantly differential expressed were identified. The hub genes were significantly differential expressed in normal tissues and different pathological stages of GC, indicating that these genes have important diagnostic value for early GC and can be used as auxiliary indicators in the diagnosis of early GC.

Asociación del resultado auditivo final, en pacientes con hipoacusia súbita, a la respuesta a glucocorticoides in vitro / Association of the final hearing result, in patients with sudden hearing loss, to the response to glucocorticoids in vitro

Introducción: La hipoacusia súbita (HS) es poco frecuente y su etiopatogenia no está definida. La terapia con corticoides es de elección en base a recomendaciones de expertos por sus efectos teóricos y no en base a utilidad clínica demostrada. Objetivo: Evaluar si existe correlación entre el resultado auditivo final, de pacientes con HS tratados con corticoides, y la respuesta in vitro de sus leucocitos a corticoides, medida como diferencias en la expresión relativa de genes blanco del receptor de glucocorticoides. Material y Método: Estudio de casos (recuperación total) y controles (no recuperados) de pacientes con HS tratados con corticoides en el Hospital Clínico de la Universidad de Chile, durante 2017-2019. Se obtuvo DNA que fue almacenado en el Biobanco de Tejidos y Fluidos de la Universidad de Chile (BTUCH). Se purificaron y cultivaron leucocitos mononucleares de sangre periférica, expuestos in vitro a hidrocortisona. Se determinó la diferencia en la expresión relativa de genes blanco (IGFBP1, CAT, HSD17B12, APOA2), por Q-RTPCR, entre ambos grupos. Resultados: Se reclutaron 35 pacientes; se incluyeron para análisis 23: 11 casos y 12 controles, con edad promedio de 54,9 y 50,8 años respectivamente, distribución homogénea de sexo. No hubo diferencia estadísticamente significativa en la expresión relativa de los genes blanco, a la exposición in vitro a corticoides, entre ambos grupos. Conclusión: En nuestro estudio, modelo, y sistema de evaluación no se evidenciaron efectos de los corticoides. No podemos descartar que, con un número mayor de pacientes, otros genes blanco u otros protocolos de estudio podrían detectarse diferencias.

Introduction: Sudden hearing loss (SHL) is rare and its etiopathogenesis is still not clear. Corticosteroid therapy is of choice based on expert recommendations due to its theoretical effects and no based on proved clinical efficacy. Objectives: To assess whether there is a correlation between the final auditory outcome of patients with SHL treated with corticosteroids and the in vitro response of their leukocytes to corticosteroids, measured as differences in the relative expression of glucocorticoid receptor target genes. Material and Method: Case-control (total recovery and not recovered respectively) study of patients with SHL treated with corticosteroids at Clinical Hospital Universidad de Chile between 2017 and 2019. DNA was obtained and stored in the Biobanco de Tejidos y Fluidos de la Universidad de Chile (BTUCH). Peripheral blood mononuclear leukocytes were purified and cultured and then exposed to hydrocortisone. The difference in the relative expression of target genes (GFBP1, CAT, HSD17B12, APOA2), by Q-RTPCR was determined. Results: Thirty-five patients were recruited, 24 were included for the analysis: 11 cases and 12 controls, with and average age of 54.9 and 50.,8 years respectively, homogeneous sex distribution. There was no statistically significant difference in the relative expression of the target genes, upon in vitro exposure to corticosteroids, between both groups. Conclusion: In our study, model and evaluation system, no effects of corticosteroids were evidenced. With a larger number of patients, other target genes or other study protocols, we cannot rule out that differences could be detected.

Detección de hemoglobinopatías en gestantes cubanas del programa: Anemias por Hematíes Falciformes en Cuba

Fundamento: La detección prenatal de hemoglobinopatías en Cuba se realiza a todas las gestantes en la atención Primaria de Salud, a través de la electroforesis de hemoglobina para identificar parejas de alto riesgo. El programa brinda asesoramiento genético, diagnóstico prenatal molecular e interrupciones selectivas de fetos afectados, a solicitud de las parejas. Objetivo: Determinar el tipo y frecuencia de hemoglobinopatías en gestantes cubanas. Método: Se realizó un estudio descriptivo, retrospectivo y de corte transversal para determinar el tipo de hemoglobinopatías en 1 342 917 gestantes captadas en un periodo de diez años. El método de pesquisa fue la electroforesis de hemoglobina en geles de agarosa a pH alcalino. La confirmación por electroforesis de hemoglobina en gel de agarosa a pH ácido, ambos métodos mediante el equipo Hydrasys 2. Resultados: La frecuencia global de gestantes con hemoglobinopatías fue de 3,5 %. Se detectó hemoglobinopatías en 47 465 mujeres; 38 698 con variante S heterocigoto, 8 706 variantes de hemoglobina C y 158 de otras variantes. Se detectaron 44 283 esposos con hemoglobinopatías, 3 099 parejas de alto riesgo y se realizaron 2 689 diagnósticos prenatales moleculares. Se confirmaron 522 fetos afectados y 382 parejas solicitaron la interrupción del embarazo. El programa alcanzó 99,24 % de cobertura en el país. Conclusiones: La detección de las hemoglobinopatías en gestantes residentes en Cuba, permitió conocer el tipo de hemoglobinopatía y la frecuencia de hemoglobinas anormales y nuevas variantes, de ahí el interés de continuar el programa de pesquisa para prevenir la aparición de formas graves de la enfermedad.

Foundation: Prenatal detection of hemoglobinopathies in Cuba is performed on all pregnant women in Primary Health Care, through hemoglobin electrophoresis to identify high-risk couples. The program provides genetic counseling, molecular prenatal diagnosis and selective interruptions of affected fetuses, at the request of couples. Objective: Determine the type and frequency of hemoglobinopathies in Cuban pregnant women. Method: A descriptive, retrospective and cross-sectional study was carried out to determine the type of hemoglobinopathies in 1,342,917 pregnant women recruited over a period of ten years. The research method was hemoglobin electrophoresis in agarose gels at alkaline pH. Confirmation by electrophoresis of hemoglobin in agarose gel at acidic pH, both methods using the Hydrasys 2 equipment. Results: The overall frequency of pregnant women with hemoglobinopathies was 3.5%. Hemoglobinopathies were detected in 47,465 women; 38,698 with heterozygous S variant, 8,706 hemoglobin C variants and 158 other variants. 44,283 husbands with hemoglobinopathies were detected, 3,099 high-risk couples were detected, and 2,689 molecular prenatal diagnoses were performed. 522 affected fetuses were confirmed and 382 couples requested termination of pregnancy. The program reached 99.24% coverage in the country. Conclusions: The detection of hemoglobinopathies in pregnant women residing in Cuba allowed us to know the type of hemoglobinopathy and the frequency of abnormal hemoglobins and new variants, hence the interest in continuing the research program to prevent the appearance of severe forms of the disease.

COMMON HUB GENES AND DRUG CANDIDATES FOR DIABETIC KIDNEY DISEASE AND NON-ALCOHOLIC FATTY LIVER DISEASE: A COMPREHENSIVE BIOINFORMATIC STUDY

Diabetes mellitus (DM) is one of the most prevalent diseases responsible for worldwide morbidity and mortality. The kidney and liver are the most commonly affected organs resulting in diabetic kidney disease (DKD) and non-alcoholic fatty liver disease (NAFLD). However, pathophysiological mechanisms that may be common to both DKD and NAFLD have not been elaborated despite having a common underlying cause. This study aimed to identify the hub genes that are common to both DKD and NAFLD and explore the potential drugs for their treatment. Gene expression datasets for DKD and NAFLD from the gene expression omnibus database were analyzed to identify differentially expressed genes (DEGs). A functional enrichment analysis of the DEGs was done to reveal pathways important in the etiology of DKD and NAFLD. Protein-protein interaction (PPI) network was constructed and hub genes were identified. The hub genes were further analyzed to identify potentially viable drug candidates after screening. A total of 89 DEGs were found to be common between DKD and NAFLD. Functional enrichment of said DEGs found Ppar, FoxO signaling and hepatocellular carcinoma pathways to be most prevalent in DKD and NAFLD. From the PPI network, 32 common hub genes were identified. The hub genes were analyzed for interacting drugs. Finally, 9 drugs were identified as potential candidates for the treatment of both diseases. The hub genes identified can provide new insights into the common etiology of DKD and NAFLD. The potentially viable drugs may be repurposed for the treatment of both DKD and NAFLD.

Analysis of the differences in immune-related genes and immune cell subtypes in acute myocardial infarction

Acute myocardial infarction (AMI) continues to be a leading cause of death globally, with distinct immune cell dynamics in ST-segment elevation myocardial infarction (STEMI) and non-ST-segment elevation myocardial infarction (NSTEMI) playing a critical role in disease progression and patient outcomes. Sample data for STEMI and NSTEMI were downloaded from the Sequence Read Archive (SRA) database (https://www.ncbi.nlm.nih.gov/sra). Differences and correlations of immune infiltrating cells were assessed by CIBERSORT. Differentially expressed genes (DEGs) were identified between STEMI and NSTEMI, followed by functional analysis. Immune-related DEGs were further identified. Some immune-related DEGs were selected to perform expression verification using real-time PCR. There was a significant difference in immune cells between STEMI and NSTEMI, including activated dendritic cells, memory CD4 T cells, mast cells, and CD8 T cells. A total of 229 DEGs were identified, with functions related to inflammatory regulation and drug metabolism. A total of 21 immune-related DEGs, which may play important roles in STEMI and NSTEMI, were identified. Among the 21 immune-related DEGs, genes like CCL18, NRP2, CXCR2, CXCL9, KIR2DL4, BPIFB1, and IL33 were significantly correlated with immune cells and had a tendency for differential expression between STEMI and NSTEMI patients. Our study reveals differences in the distribution of immune cell subsets between STEMI and NSTEMI, highlighting key immune-related genes and their association with immune cells, which may provide new insights into the treatment of AMI.

Research progress in the mechanism of stimulator of interferon genes in type 2 diabetes mellitus and its microvascular complication / 中国糖尿病杂志

Type 2 diabetes mellitus(T2DM)is a chronic metabolic disease that can lead to the damage of multiple tissues and organs throughout the body.Stimulator of interferon genes(STING)is an endoplasmic reticulum membrane protein that acts as an indirect cytoplasmic DNA sensor.The activation of the STING signaling pathway may be involved in T2DM and its microvascular complications through various mechanisms.This article reviews the research progress in the mechanism of STING in T2DM and its microvascular complications.

Pyroptosis-related genes defines the progression and im-mune tolerance microenvironment of hepatocellular carcino-ma / 中国现代普通外科进展

Objective:To explore the expression pattern of pyroptosis-related genes(PRGs)in hepatocellular carcinoma(HCC),and analyze the relationship between its expression and tumor prog-nosis and immune microenvironment.Methods:TCGA database was used to analyze the genetic changes and expression patterns of PRGs in primary HCC cells,and cluster analysis was used to i-dentify the pyrogenic subtypes of HCC.To compare the difference of prognosis and immune mi-croenvironment among HCC pyrodeath subtypes.Scorch death score quantified the comprehensive expression of PRGs in each sample,and analyzed the correlation between scorch death score and each immune score.Results:Two pyroptosis-associated subtypes of primary HCC were identi-fied,and the expression pattern of PRGs is closely related to the prognosis of cancer patients and the tumor microenvironment.The subtype with high expression of PRGs had a poor prognosis,and functional enrichment analysis found that some tumor-promoting pathways and PD-1 checkpoint pathways were significantly enriched in this subtype.And various cells and immune checkpoints re-lated to immunosuppression were also enriched in this subtype.By constructing PYROPTO-SIS_score to quantify the comprehensive expression of pyroptosis-related genes in each sample,it was found that PYROPTOSIS_score was significantly positively correlated with tumor-infiltrating macrophages,myeloid-derived suppressor cells,and Treg cells.Conclusion:These results sug-gest that pyroptosis may play a tumor-promoting as well as immunosuppressive role in HCC,pro-viding new insights into the assessment of tumor patient prognosis and the immune microenviron-ment.

Antibody-based gene expression profiling of peripheral blood from patients with idiopathic inflammatory myopathy / 中华风湿病学杂志

Objective:To elucidate the pathophysiological mechanisms of idiopathic inflammatory myopathy subtypes by analyzing the gene expression profiles of peripheral blood mononuclear cells (PBMCs) from anti-MDA5 antibody-positive and anti-Jo-1 antibody-positive myositis patients.Methods:Gene expression profiling screening and analysis of PBMCs from 12 anti-MDA5 positive, 16 anti-Jo-1 positive myositis patients and 43 healthy controls were performed using Illumina HT-12 v4 expression profiling microarrays. Applying the unpaired t test with Benjamini-Hochberg correction, the genes with the absolute value of fold change (FC) in gene expression signal ≥2 and adjusted P<0.05 were selected as differentially expressed genes. Differential gene sets were subjected to Gene Ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, with P<0.05 as the threshold for being significantly enriched. Validation of differentially expressed genes by real time-PCR. The Kolmogorov-Smirnov test was used to test the normality of continuous variables. If the distribution was normal and the variance was homogeneous, analysis of variance (one-way ANOVA) was used.If the distribution was not normal, Kruskal-Wallis test was used, and P<0.05 was regarded as statistically significant difference. Results:Analysis of gene expression profiles of PBMCs from patients with positive anti-MDA5 and anti-Jo-1 antibody revealed significant differences in gene expression of PBMCs from patients with the two myositis subtypes. The number of differentially expressed genes that specifically up-regulated in anti-MDA5 antibody positive patients was 407, and the GO functional enrichment analysis was mainly enriched in biological processes such as innate immune response ( P<0.001), response to virus ( P<0.001) and type Ⅰ interferon signaling pathway ( P<0.001), and the KEGG pathway enrichment analysis was mainly enriched in the viral infection-associated pathway ( P<0.001), RIG-Ⅰ like receptor signaling pathway ( P<0.001) and Toll-like receptor signaling pathway ( P=0.002), etc. The 259 differential genes specifically down-regulated in the anti-MDA5 antibody positive group were mainly enriched in biological processes such as immune response ( P=0.006), TGF-β receptor signaling pathway ( P=0.010) and natural killer cell mediated immunity ( P=0.015) in GO functional enrichment analysis. There were 162 differentially expressed genes up-regulated specifically in anti-Jo-1 antibody positive patients, and GO functional enrichment analysis was mainly enriched in biological processes such as nucleosome assembly ( P<0.001), negative regulation of cell growth ( P=0.001), negative regulation of apoptotic process P=0.004), and innate immune response in mucosa ( P=0.012), and the KEGG pathway enrichment analysis mainly enriched in metabolic-related signaling pathways ( P<0.001) and immune-related pathways ( P<0.001), etc. Real-time PCR confirmed that IFIH1 ( P=0.037), ISG15 ( P=0.003), and DDX58 ( P=0.032) in the RIG-Ⅰ-like receptor pathway as well as chemokines MCP-1 ( P=0.003), MCP-2 ( P<0.001), and transcription factor BATF2 ( P=0.002), and inflammatory signaling pathway-associated MYD88 ( P<0.001) were highly expressed in PBMCs from anti-MDA5 antibody-positive myositis patients. Conclusion:The gene expression profile of PBMCs in anti-MDA5 antibody-positive patients suggests that the pathogenesis of patients with anti-MDA 5 antibody positive is closely related to biological processes such as innate immune response, viral infection, and interferon response.

Study on the role of NR1H4 in chronic atrophic gastritis and drug prediction based on bioinformatics / 中国现代医生

Objective To explore the differential gene expression profile and small molecule drugs for chronic atrophic gastritis(CAG)by bioinformatics technology.Methods Two gene expression samples of CAG chips(GSE27411,GSE116312)were obtained through the Gene Expression Synthesis(GEO)database,screen the differentially expressed genes(DEGs)of CAG by R language,and CAG immune-related genes were obtained for gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis.Protein-protein interaction(PPI)network was constructed using STRING database to screen out core genes,further study on immune invasion of core genes based on GSE27411 dataset,small molecular compounds interacting with core genes were predicted,molecular docking was carried out by MOE2022,and survival analysis was carried out by GEPIA2 website.Results A total of 517 DEGs were screened out based on GEO database.GO function enrichment analysis found that it mainly involved in granulocyte chemotaxis、leukocyte chemotaxis and neutrophil chemotaxis biological processes.KEGG pathway enrichment analysis showed that it mainly involved in cytokine-cytokine receptor interaction、nuclear factor kappa B signaling pathway、interleukin-17 signaling pathway.Six key genes of NR1H4、CCK、CCL20、CXCL1、LCN2、SAA1 were obtained by PPI network,through relevant verification,NR1H4 was regarded as the core gene.Immune cell infiltration analysis showed that central memory CD8 T cell、effector memeory CD4 T cell、gamma delta T cell、natural killer T cell、neutrophil and other immune cells may be involved in the development of CAG,and the neutrophil was positively correlated with NR1H4.It was predicted that six small molecular drugs,corilagin,stigmasterol,geniposide,tangeretin,chenodeoxycholic acid and epigallocatechin 3-gallate,have good binding force with NR1H4.Conclusion The potential mechanism of CAG is preliminarily explored in this study,the key gene of NR1H4 and neutrophil may play an important role in the"inflammatory cancer transformation"process of CAG,which can provide a certain reference for the study of the"inflammatory cancer transformation"mechanism of CAG.

Prediction of prognosis and identification of potential therapeutic agents for liver cancer patients based on acetyl-coa carboxylase 1-associated dendritic cell / 中国现代医生

@#Objective To investigate the expression,prognostic value of acetyl-coa carboxylase 1(ACACA)gene in liver cancer,its correlation with immune cells,and to construct a prognostic model.Methods Integrating genotype-tissue expression(GTEx)and the cancer genome atlas(TCGA)data to analyze ACACA expression in cancers and adjacent tissues,and perform prognosis analysis.Examine the correlation between ACACA and immune cells.Use GSE156625 cell RNA seq(scRNA-seq)data to study ACACA expression in dendritic cells(DCs).Construct an hepatocellular carcinoma(HCC)prognosis model based on apolipoprotein c-Ⅰ(APOC1)and apolipoprotein c-Ⅲ(APOC3),using Kaplan-Meier survival curves and time-dependent receiver operator characteristic(ROC)curves to evaluate prognostic capability,and analyze the effect of traditional Chinese medicine components on APOC1 and APOC3 through molecular docking.Results ACACA shows significant differential expression in various cancers and is associated with the prognosis of liver cancer.High expression of ACACA reduces the content of dendritic cells.APOC1 and APOC3,the major DCs marker genes,were positively correlated with ACACA expression.Using Kaplan-Meier curves,we predicted the 1-year,3-year,and 5-year overall survival(OS)probabilities for HCC patients in the TCGA cohort,and confirmed the reliability through calibration curve analysis.Salvianolic acid B,Asiaticoside,and Neohesperidin may have potential effects on APOC1 and APOC3.Conclusion ACACA is closely related to HCC prognosis,and the prognostic model based on APOC1 and APOC3 can serve as a predictive indicator.Some traditional Chinese medicine components may hold therapeutic potential for HCC treatment.

Distribution of virulence genes in clinical isolates of hospital-associated and community-associated methicillin-susceptible Staphylococcus aureus from Terengganu, Malaysia

@#Staphylococcus aureus is a common bacterial pathogen known to cause various kinds of infections due to its repertoire of virulence factors. This study aimed to investigate the distribution of 19 types of virulence genes among clinical isolates of methicillin-susceptible S. aureus (MSSA) using the polymerase chain reaction. A total of 109 MSSA isolates, i.e., 63 hospital-associated (HA) and 46 community-associated (CA) were collected from Hospital Sultanah Nur Zahirah, the main tertiary hospital in Terengganu, Malaysia, from July 2016 to June 2017. The most frequent virulence genes detected were hla (78.9%, n=86) and hld (78.0%, n=85) encoding hemolysins, lukED (56.9%, n=62) encoding leukotoxin ED, followed by seb (26.6%, n=29) and sea (24.8%, n=27) encoding enterotoxins. Among 34 (31.2%) isolates carrying six or more virulence genes, only five were multidrug resistant (MDR) while the remaining isolates were susceptible. Significant associations were discovered between the hld gene with CA-MSSA (p=0.016) and the seo gene with HA-MSSA (p=0.023). However, there is no significant association between virulence genes among the different types of infection. The clinical MSSA isolates in Terengganu showed high prevalence and high diversity of virulence gene carriage.

A Multiplex Network Control Method for Identifying Personalized Cancer Driver Genes / 生物化学与生物物理进展

ObjectiveInferring cancer driver genes, especially rare or sample-specific cancer driver genes, is crucial for precision oncology. Considering the high inter-tumor heterogeneity, a few recent methods attempt to reveal cancer driver genes at the individual level. However, most of these methods generally integrate multi-omics data into a single biomolecular network (e.g., gene regulatory network or protein-protein interaction network) to identify cancer driver genes, which results in missing important interactions highlighted in different networks. Thus, the development of a multiplex network method is imperative in order to integrate the interactions of different biomolecular networks and facilitate the identification of cancer driver genes. MethodsA multiplex network control method called Personalized cancer Driver Genes with Multiplex biomolecular Networks (PDGMN) was proposed. Firstly, the sample-specific multiplex network, which contains protein-protein interaction layer and gene-gene association layer, was constructed based on gene expression data. Subsequently, somatic mutation data was integrated to weight the nodes in the sample-specific multiplex network. Finally, a weighted minimum vertex cover set identification algorithm was designed to find the optimal set of driver nodes, facilitating the identification of personalized cancer driver genes. ResultsThe results derived from three TCGA cancer datasets indicate that PDGMN outperforms other existing methods in identifying personalized cancer driver genes, and it can effectively identify the rare driver genes in individual patients. Particularly, the experimental results indicate that PDGMN can capture the unique characteristics of different biomolecular networks to improve cancer driver gene identification. ConclusionPDGMN can effectively identify personalized cancer driver genes and broaden our understanding of cancer driver gene identification from a multiplex network perspective. The source code and datasets used in this work are available at https://github.com/NWPU-903PR/PDGMN.

Profiles of antibiotic resistance genes in the Lhasa River / 公共卫生与预防医学

Objective To investigate the pollution of antibiotic resistance genes (ARGs) in the Lhasa River and provide a scientific basis for the safety of drinking water for the regional population and the prevention and control of water environment pollution. Methods A total of five water samples were collected in the Lhasa River in July 2022. Using quantitative real-time polymerase chain reaction (qPCR) assay, 19 types of ARGs, including eight “last-resort” ARGs (LARGs) were detected and analyzed. Statistical analysis was conducted using the SPSS 22.0 software, and Student's t-test was used to compare data between two groups. Results All the 19 ARGs were detected with high frequencies, with the aminoglycoside resistance gene aadA having the highest concentration, followed by the sulfonamide resistance gene sul1 and the macrolide resistance gene ermB. Among the eight LARGs, the carbapenem resistance gene blaOXA-48 had the highest concentration. The absolute and relative concentrations of LARGs were lower than those of common ARGs. There was a statistically significant difference in the absolute concentrations between them, but no significant difference was observed in the relative concentrations. Conclusion Both “conventional” ARGs and LAGRs have been detected in the Lhasa River. Although they are at a relatively low level compared to other domestic waters, in view of the serious adverse effects that ARGs, especially LARGs, may cause, the pollution of ARGs in the Lhasa River should be taken seriously.