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".

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.

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 D.C., 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.

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.

Asociación del resultado auditivo final, en pacientes con hipoacusia súbita, a la respuesta a glucocorticoides 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.

Research progress on the association between biorhythm disorders and cardiovascular metabolic risk in adolescents and possible mechanisms / 中国学校卫生

Abstract@#Adolescence is a unique transitional period from childhood to adulthood, during which behavioral habits and physiological cycles undergo significant changes, and biorhythms are vulnerable to be disrupted. Meanwhile, due to increased rates of overweight and obesity, cardiovascular metabolic risk significantly increases during adolescence. The article reviews the prevalence, correlation, and potential epigenetic regulatory mechanisms of biorhythm disorders and adolescent cardiovascular metabolic health, providing a theoretical basis for regulating biorhythm to promote adolescent cardiovascular metabolic health.

Bioinformatics analysis based on pelvic organ prolapse related aging genes of GEO Database and LASSO regression algorithm / 吉林大学学报(医学版)

Objective:To screen the aging genes closely associated with pelvic organ prolapse(POP)by bioinformatics techniques,and to clarify the potential clinical significance and value of key genes.Methods:Gene Expression Omnibus(GEO)Database was used to download the datasets GSE53868 and GSE151188 for POP-related genes with the keyword"pelvic organ prolapse".The aging-related genes were obtained from Aging Atlas,CellAge,and the Human Ageing Genomic Resources(HAGR)Databases;the intersection of genes related with POP in two groups provided a list of differentially expressed genes(DEGs)associated with aging in POP;gene Set Enrichment Analysis(GSEA)was conducted with R software version 4.2.1;Gene Ontology(GO)functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)signaling pathway enrichment analysis of DEGs were conducted by the Database for Annotation,Visualization and Integrated Discovery(DAVID);the protein-protein interaction(PPI)network was constructed with Cytoscape 3.9.1 software;the top 10 Hub genes were selected by cytoHubba plugin;the infiltration of 22 types of immune cells in the patients in POP group and control group was analyzed by CIBERSORT deconvolution method using R software;the key genes were further screened by LASSO regression algorithm;the correlation and diagnostic efficacy between key genes and immune cell infiltration were analyzed.Results:From the Aging Atlas,CellAge,and HAGR Databases,724 aging-related genes were identified.Intersection with the POP expression profile yielded an aging gene expression matrix related to POP containing 624 genes,and 29 POP-related DEGs were identified after differential analysis,including 2 upregulated genes and 27 downregulated genes.The GSEA results showed that the upregulated pathways were mainly related to diabetes and cellular senescence,whereas the downregulated pathways included Alzheimer's disease and hypoxia-inducible factor-1(HIF-1)signaling pathways.The GO functional enrichment analysis mainly enriched in the biological processes such as the response of the cells to lipopolysaccharide,inflammatory response,and negative regulation of cell proliferation.The KEGG signaling pathway enrichment analysis mainly enriched in interleukin-17(IL-17),tumor necrosis factor(TNF),and nuclear factor-kappa B(NF-κB)signaling pathways.The PPI network analysis got 10 Hub genes including interleukin-6(IL-6),interleukin-1B(IL-1B),prostaglandin-endoperoxide synthase 2(PTGS2),and NF-kappa-B inhibitor alpha(NFKBIA).The CIBERSORT deconvolution method results showed a relatively higher infiltration proportion of neutrophils and activated mast cells in the patients in POP group,the activated mast cells had a positive correlation with most of the DEGs(r>0.5)and the macrophages had a significant positive correlation with IL-1B(r>0.6).The key genes Jun D proto-oncogene(JUND),Snail homolog 1(SNAI1),amphiregulin(AREG),Lamin A/C(LMNA),and superoxide dismutase 2(SOD2)selected by LASSO regression analysis had high diagnostic efficacies,and the area under receiver operating characteristic curve(ROC)(AUC)were all greater than 0.75.Conclusion:During the aging process,the genes such as JUND,SNAI1,AREG,LMNA,and SOD2 may participate in the pathophysiology of POP through various pathways,including inflammation-related pathways,transcription regulation,and affecting collagen secretion and metabolism,thereby influence the connective tissue support function and promote the occurrence and development of POP.

Clinical features of CpG island methylation in colon cancer and its prognostic significance in dMMR colon cancer / 国际外科学杂志

Objective:To investigate the clinical characteristics and prognosis of CpG island methylator phenotype (CIMP+ ) colon cancer, and the significance of CIMP status in the diagnosis and prognosis prediction in defective mismatch repair (dMMR) colon cancer.Methods:The keywords "colorectal cancer" "patient" and "CpG Island Methylator Phenotype" were used to search the Gene Expression Omnibus (GEO) database, and the GSE39582 was obtained, which included the clinical data of 585 patients with colorectal cancer and the sequencing data of the whole transcriptome of the tumor tissues. After excluding 72 cases with missing CIMP values, 513 cases were included for further analysis, including 278 males and 235 females, with a mean age of (67±13) years. According to the CIMP status, they were divided into CIMP+ group ( n=93) and CIMP-group ( n=420), then compare the differences in clinical characteristics, the Kaplan-Meier survival curves were plotted to compare the overall survival and disease-free survival; 71 dMMR cases were divided into CIMP+ group ( n=43) and CIMP-group ( n=28), and the K-M curves were plotted to analyze the differences in overall survival (OS) and disease free survival (DFS). Comparisons between groups were performed by t-test, χ2 test or Mann-Whitney U nonparametric test, and the difference in survival curves was tested by Long-rank test. Results:Patients in the CIMP+ group were significantly older than those in the CIMP-group [(70.84±12.60) years vs (66.21±13.08) years, t=3.18, P=0.002]. Right colon tumors originating from the CIMP+ molecular pathway were 9.3 times more likely to be CIMP+ than those of the left colon cancers ( OR=9.3, 95% CI: 5.2-17.9). BRAF mutant colon cancer originating from CIMP+ was 215.2 times more common than BRAF wild-type colon cancer originating with CIMP+ ( OR=215.2, 95% CI: 53.2-1906.7); and patients with dMMR colon cancer originated 12.8 times more common than patients with pMMR ( OR=12.8, 95% CI: 7.0-23.9). The difference between the CIMP+ and CIMP-groups was not statistically significant in terms of overall survival and disease-free survival ( P=0.590, 0.220). In the dMMR colon cancer subgroup, CIMP status did not correlate with patients′ overall survival and disease-free survival ( P>0.05). Conclusions:CIMP+ colon cancer patients were mostly of advanced age, with tumors originating from the right colon, mostly combined with BRAF gene mutations, and manifested as mismatch repair-deficient colon cancers. CIMP status had no correlation with TNM stage and survival of colon cancers patients. There was no significant difference in the survival between dMMR colon cancers caused by CIMP+ and those caused by MMR gene mutations.

Study on the Difference of Gene Expression Between Left and Right Colon Cancer and the Mechanism of Sophorae Flavescentis Radix-Sargentodoxae Caulis-Scutellariae Barbatae Herba Based on TCGA / 广州中医药大学学报

Abstact:Objective To investigate the gene expression differences between left-sided colon cancer and right-sided colon cancer and the mechanism differences between the colorectal cancer core drug pairs of Sophorae Flavescentis Radix-Sargentodoxae Caulis-Scutellariae Barbatae Herba acting on left-sided and right-sided colon cancer.Methods The transcriptome data of 134 patients with left-sided colon cancer and 194 patients with right-sided colon cancer from The Cancer Genome Atlas(TCGA)were downloaded,and the R software was applied to realize the differential gene analysis of the two groups and the enrichment analysis of Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway;the BATMAN-TCM database was used to obtain the active ingredients and targets of the drug pair of Sophorae Flavescentis Radix-Sargentodoxae Caulis-Scutellariae Barbatae Herba,and based on the different genes of the left-and right-sided colon cancers,KEGG enrichment analysis of the drug pair-left/right-sided colon cancers was performed respectively,and the protein-protein-interaction(PPI)network was constructed to compare the differences of the biosignaling pathways enriched by the drug pairs for the treatment of left-and right-sided colon cancers,as well as the differences of the key target points.Results There were 6 051 differentially expressed genes common to left-and right-sided colon cancers relative to normal paracancerous tissues,1958 differentially expressed genes specific to left-sided colon cancer,and 1739 differentially expressed genes specific to right-sided colon cancer;14 KEGG-enriched pathways specific to left-sided colon cancer,and 23 KEGG-enriched pathways specific to right-sided colon cancer.There were 85 active compounds in the drug-pair of Sophorae Flavescentis Radix-Sargentodoxae Caulis-Scutellariae Barbatae Herba,corresponding to a total of 469 targets.The drug-pair-left-sided colon cancer targets were enriched in 10 KEGG signaling pathways,with the key targets being DRD2,CACNA1C,HTR3A,COMT,and TH;and the drug-pair-right-sided colon cancer targets were enriched in 1 KEGG signaling pathway,with the core targets being HTR3A,DRD2 TH,AGT,GRIN2B.Conclusion There are gene expression differences between left-and right-sided colon cancers:left-sided colon cancer is associated with abnormal immune function,abnormal AMPK signaling pathway and other mechanisms,and right-sided colon cancer is associated with neutrophil extracellular trap formation,alcoholism,abnormal Hippo signaling pathway and other mechanisms.In addition to regulating cell cycle and essential amino acid metabolism and other mechanisms,Sophorae Flavescentis Radix-Sargentodoxae Caulis-Scutellariae Barbatae Herba drug pairs have specific effects on regulating the intestinal endocrine function of the left-sided colon cancer,inhibiting inflammatory response of the right-sided colon cancer,and may also have mood-regulating effects on patients with colon cancer.

Mechanism of cGAS/STING Signaling Pathway in Regulating Lung Cancer and Traditional Chinese Medicine Treatment： A Review / 中国实验方剂学杂志

According to the latest global cancer statistics， the incidence and mortality of lung cancer rank first in China. Classical therapies remain the most common cancer treatment options， such as surgical resection， radiotherapy， and chemotherapy， but not all cancer patients respond to classical therapies， which require new lung cancer treatment strategies. After decades of research and development， cancer immunotherapy has achieved certain curative effect， which provides new possibilities for cancer treatment. Cyclic guanosine monophosphate-adenosine monophosphate synthase （cGAS） is a cytosolic DNA sensor. It can induce protective immune defense responses against various DNA-containing pathogens and provide anti-tumor immunity by activating the interferon （IFN） gene stimulator （STING） protein. At present， relevant researchers in China and abroad have done a lot of research on the occurrence and development of lung cancer and the pathophysiological mechanism of drug intervention in the treatment of lung cancer. The results show that cGAS/STING signaling pathway plays an important role in the development of the disease， and traditional Chinese medicine monomers or compounds can intervene in lung cancer cells by regulating the cGAS/STING signaling pathway， induce their autophagy and death， regulate their cycle operation， promote senescence， inhibit their proliferation and tumor angiogenesis， promote their invasion and metastasis， and promote the immune activation of anti-lung cancer cells， so as to inhibit or delay the occurrence and development of lung cancer. In recent years， the related research results have been updated rapidly， and the previous literature has not included the latest research results in time， which causes a lot of inconvenience for many scholars to search the literature. Based on this， this paper mainly summarized the mechanism of cGAS/STING signaling pathway intervention in lung cancer in China and abroad in recent years， as well as the research progress of related traditional Chinese medicine intervention， so as to provide new ideas for the development of lung cancer in molecular biology， drug treatment research， and clinical new drug research and provide a reference for further mechanism research.

Clinical value of genetic polymorphism analysis of hypertension drugs for individualized treatment of hypertension patients in the southern Anhui region / 中国临床药理学与治疗学

AIM: To analyze the distribution frequency of gene polymorphisms of β receptor blockers, angiotensin receptor antagonists, angiotensin converting enzyme inhibitors, calcium antagonists, and diuretics in hypertensive patients from southern Anhui province, and provide a theoretical basis for gene detection of hypertension drugs and personalized medication. METHODS: Drug gene testing information from 839 hospitalized patients with hypertension at Yijishan Hospital of Wannan Medical College from July 2021 to April 2023 were collected, and the distribution frequency of each gene locus were analyzed. RESULTS: The genotype frequencies of ACE (I/D) I/I, I/D, and D/D were 42.1%, 46.0%, and 11.9%, respectively. the genotype frequencies of ADRB1 (1165G>C) G/G, G/C, and C/C were 8.3%, 40.0%, and 51.6%, respectively. The genotype frequencies of AGTR1 (1166A>C) A/A, A/C, and C/C were 90.2%, 9.8%, and 0.0%. The genotype frequencies of CYP2C9*3 (1075A>C) *1/*1, *1/*3, and *3/*3 were 91.3%, 8.7%, and 0.0%, respectively; the genotype frequencies of CYP2D6* 10 (100C > T) *1/*1, *1/*10, and *10/*10 were 25.0%, 36.6%, and 38.4%, respectively. The genotype frequencies of CYP3A5*3 (6986A>G) *1/*1, *1/*3, and *3/*3 were 7.0%, 39.0%, and 54.0%, respectively. The frequencies of NPPA (2238T>C) T/T, T / C, and C / C genotypes were 97.9%, 2.1%, and 0.0%, respectively. In addition, there was a significant difference in the genotype distribution frequency of multiple drug related gene loci in southern Anhui compared to other regions in China (P< 0.05). CONCLUSION: The genotype distribution frequency of hypertensive drug related gene loci had certain bias in southern Anhui, and were significant different from other regions in China, indicating that conducting genetic polymorphism testing of hypertensive drugs had certain guiding significance for the individualized application of hypertensive drugs in southern Anhui.

Construction of m6A modification related prognostic model in older patients with FLT3 mutated acute myeloid leukemia / 中华老年医学杂志

Objective:To screen m6A modification-related genes, and to establish a prognostic model in patients with FLT3 mutated acute myeloid leukemia(AML), especially in older patients and to evaluate the prognostic efficiency of the model.Methods:Gene expression omnibus(GEO)datasets were used to analyze abnormally expressed m6A enzymes and reading proteins in FLT3 mutated AML; Correlation analysis was used to screen m6A modified-related genes in expression profiles.By integrating TCGA and BEAT data, 83 FLT3 mutated AML patients were included, and 32 of them were older than 60 years.Univariate Cox analysis and Lasso regression were conducted to construct the risk model.Kaplan-Meier curve and time-dependent receiver operating characteristic curve(tROC)were used to evaluate the prognostic efficiency of the model; subgroup analysis was conducted in the older patients.The concordance index(C-index)and calibration curve were used to evaluate the discrimination and accuracy of the model.Results:14 m6A modification enzymes or reading proteins were abnormally expressed in patients with FLT3 mutated AML.Correlation analysis filtered out 2 476 m6A related genes in expression profile.In TCGA and BEAT integrated data, univariate Cox analysis identified 132 prognostic genes.Lasso regression selected seven candidate genes to establish the prognostic risk model, including AKAP9, AVEN, DMCA1, DPYD, FAR2, GPHN and SPECC1L.Kaplan-Meier curve showed that high-risk group of the model had significantly shorter overall survival with a hazard ratio( HR)of 5.08(95% CI: 2.54-10.14, P<0.001).The area under the curve(AUC)in tROC for 1-year survival was 0.83; the C-index of risk model was 0.737.In older patients, the hazard ratio( HR)of the risk model for 1-year overall survival was 3.40(95% CI: 1.25-9.24, P=0.017)with an AUC of 0.79. Conclusions:The risk model based on m6A modified-related genes has some predictive value in assessing the prognosis of patients with FLT3 mutated AML, especially indicative to prognosis prediction in the elderly.

Identification of overlay differentially expressed genes in both rats and goats with blast lung injury through comparative transcriptomics / 中华创伤杂志(英文版)

PURPOSE@#To identify the potential target genes of blast lung injury (BLI) for the diagnosis and treatment.@*METHODS@#This is an experimental study. The BLI models in rats and goats were established by conducting a fuel-air explosive power test in an unobstructed environment, which was subsequently validated through hematoxylin-eosin staining. Transcriptome sequencing was performed on lung tissues from both goats and rats. Differentially expressed genes were identified using the criteria of q ≤ 0.05 and |log2 fold change| ≥ 1. Following that, enrichment analyses were conducted for gene ontology and the Kyoto Encyclopedia of Genes and Genomes pathways. The potential target genes were further confirmed through quantitative real-time polymerase chain reaction and enzyme linked immunosorbent assay.@*RESULTS@#Observations through microscopy unveiled the presence of reddish edema fluid, erythrocytes, and instances of focal or patchy bleeding within the alveolar cavity. Transcriptome sequencing analysis identified a total of 83 differentially expressed genes in both rats and goats. Notably, 49 genes exhibited a consistent expression pattern, with 38 genes displaying up-regulation and 11 genes demonstrating down-regulation. Enrichment analysis highlighted the potential involvement of the interleukin-17 signaling pathway and vascular smooth muscle contraction pathway in the underlying mechanism of BLI. Furthermore, the experimental findings in both goats and rats demonstrated a strong association between BLI and several key genes, including anterior gradient 2, ankyrin repeat domain 65, bactericidal/permeability-increasing fold containing family A member 1, bactericidal/permeability-increasing fold containing family B member 1, and keratin 4, which exhibited up-regulation.@*CONCLUSIONS@#Anterior gradient 2, ankyrin repeat domain 65, bactericidal/permeability-increasing fold containing family A member 1, bactericidal/permeability-increasing fold containing family B member 1, and keratin 4 hold potential as target genes for the prognosis, diagnosis, and treatment of BLI.

Cell-to-Cell Communications of cGAS-STING Pathway in Tumor Immune Microenvironment / 浙江大学学报·医学版

Targeting cGAS-STING pathway is a promising strategy in tumor treatment. The pattern recognition receptor cGAS identifies dsDNA and catalyzes the formation of the second messenger 2'3'-cGAMP, activating the downstream interferons and pro-inflammatory cytokines through the adaptor protein STING. Notably, in tumor immune microenvironment, key components of cGAS-STING pathway are transferred among neighboring cells. The intercellular transmission under these contexts serves to sustain and amplify innate immune responses while facilitating the emergence of adaptive immunity. The membrane-based system, including extracellular vesicles transport, phagocytosis and membrane fusion transmit dsDNA, cGAMP and activated STING, enhancing the immune surveillance and inflammatory. The membrane proteins, including specific protein channel and intercellular gap junctions, transfer cGAMP and dsDNA, which are crucial to regulate immune responses. And the ligand-receptor interactions for interferons transmission amplifies the anti-tumor response. This review elaborates on the regulatory mechanisms of cell-to-cell communications of cGAS-STING pathway in tumor immune microenvironment. We further explore how these mechanisms modulate immunological processes and discuss potential interventions and immunotherapeutic strategies targeting these signaling cascades.

Role of micronucleus-activated cGAS-STING signaling in antitumor immunity / 浙江大学学报·医学版

cGAS-STING signaling is a significant component of the innate immune system and functions as a vital sentinel mechanism to monitor cellular and tissue aberrations in microbial invasion and organ injury. cGAS, a cytosolic DNA sensor, is specialized in recognizing abnormally localized cytoplasmic double-stranded DNA (dsDNA) and catalytically synthesizes the second messenger cyclic-GMP-AMP (cGAMP), which initiates a cascade of type I interferon and inflammatory responses mediated by STING. Micronucleus, a byproduct of chromosomal missegregation during anaphase, are also significant contributors to cytoplasmic dsDNA. These unstable subcellular structures are susceptible to irreversible nuclear envelope rupture, exposing genomic dsDNA to the cytoplasm, which potently recruits cGAS and activates STING-mediated innate immune signaling and its downstream activities, including type I interferon and classical nuclear factor-κB (NF-κB) signaling pathways lead to senescence, apoptosis, autophagy activating anti-cancer immunity or directly killing tumor cells. However, sustained STING activation-induced endoplasmic reticulum stress, activated chronic type I interferon and nonclassical NF-κB signaling pathways remodel immunosuppressive tumor microenvironment, leading to immune evasion and facilitating tumor metastasis. Therefore, activated cGAS-STING signaling plays a dual role of suppressing or facilitating tumor growth in tumorigenesis and therapy. This review elaborates on research advances in mechanisms of micronucleus inducing activation of cGAS-STING signaling and its implications in tumorigenesis and therapeutic strategies of malignant tumors.

Mapping of QTL associated with rice cooking quality and candidate gene analysis / 生物工程学报

Excavating the quantitative trait locus (QTL) associated with rice cooking quality, analyzing candidate genes, and improving cooking quality-associated traits of rice varieties by genetic breeding can effectively improve the taste of rice. In this study, we used the indica rice HZ, the japonica rice Nekken2 and 120 recombinant inbred lines (RILs) populations constructed from them as experimental materials to measure the gelatinization temperature (GT), gel consistency (GC) and amylose content (AC) of rice at the maturity stage. We combined the high-density genetic map for QTL mapping. A total of 26 QTLs associated with rice cooking quality (1 QTL associated with GT, 13 QTLs associated with GC, and 12 QTLs associated with AC) were detected, among which the highest likelihood of odd (LOD) value reached 30.24. The expression levels of candidate genes in the localization interval were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR), and it was found that the expression levels of six genes were significantly different from that in parents. It was speculated that the high expression of LOC_Os04g20270 and LOC_Os11g40100 may greatly increase the GC of rice, while the high expression of LOC_Os01g04920 and LOC_Os02g17500 and the low expression of LOC_Os03g02650 and LOC_Os05g25840 may reduce the AC. The results lay a molecular foundation for the cultivation of new high-quality rice varieties, and provide important genetic resources for revealing the molecular regulation mechanism of rice cooking quality.

Qizhi Zhoufei Granule Alleviate Chronic Obstructive Pulmonary Disease by Regulating Th1/Th2 Immunologic Balance Through Notch Signaling Pathway / 世界科学技术-中医药现代化

Objective To investigate the role of homologous genes absent from the wings of drosophila melanogaster(Notch)signaling pathway in the imbalance of helper T cells 1(Th1)and helper T cells 2(Th2)and the intervention mechanism of Qizhi Zhoufei Granule in chronic obstructive pulmonary disease(COPD).Methods Ten of seventy Wistar rats were selected as the blank control group,and the other rats were established by cigarette smoking combined(CS)with tracheal infusion of lipopolysaccharide(LPS).The COPD model was established by randomly selecting 3 rats in the control group and the model group to verify the success of the model.At the end of modeling,gavage administration was performed.The rats in the model group were randomly divided into model control group,positive control group(67.5 μg·kg-1)and Qizhi Zhoufei Granule high,medium and low treatment group(3.24,1.62,0.81 g·kg-1).Each group was treated with normal saline,dexamethasone acetate suspension and Qizhi Zhoufei Granule suspension at high,medium and low doses.The rats in the blank control group were given the same volume of normal saline as the model control group.After modeling with 28 days and treatment with 28 days,peak inspiratory flow(PIF)and peak expiratory flow(PEF)were detected by the animal lung function test system.Rats were killed to extract lungs,spleen,serum and bronchoalveolar lavage fluid(BALF),hematoxylin-eosin(HE)staining was used to evaluate the pathological changes of lung tissues.The level of tumor necrosis factor-α(TNF-α)in serum and BALF was determined by enzyme-linked immunosorbent assay(ELISA).Flow cytometry was used to detect Th1/Th2 cells in spleen.Immunohistochemistry(IHC)and western blot were used to detect Notch1,Hes1 and Hey1 protein levels in lung tissues.Real-time fluorescence quantitative polymerase chain reaction(Real-Time PCR)was used to detect Notch1,Hes1 and Hey1 gene expression levels in lung tissues.Result Compared with the blank control group,the lung function of the model control group was significantly decreased(P<0.05),inflammatory cell infiltration and bronchial structure destruction occurred in the lung tissue,TNF-α content in serum and BALF increased significantly(P<0.05),the percentage of spleen Th1 cells was significantly decreased(P<0.05),and the percentage of Th2 cells was significantly increased(P<0.05),the protein and mRNA expressions of Notch1,Hes1 and Hey1 in lung tissues were significantly increased(P<0.05),the differences were statistically significant;Compared with the model control group,the lung function of rats in each administration group was significantly increased(P<0.05),the pathological injury of lung tissue was alleviated,TNF-α content in serum and BALF decreased significantly(P<0.05),the percentage of spleen Th1 cells was significantly increased(P<0.05),the percentage of Th2 cells was significantly decreased(P<0.05),the lung tissue of Notch1,Hes1,Hey1 protein and mRNA expression were significantly decreased(P<0.05),the differences were statistically significant.Conclusion Qizhi Zhoufei Granule regulate Th1/Th2 balance by inhibiting Notch signaling pathway,thereby improving pulmonary function and pathological injury,and affecting immune function in COPD rats.

Screening of IL-3 and IL-3+SCF Induce Differentially Expressed Genes and Signaling Pathways in Bone Marrow-derived Mast Cells Based on Bioinformatics / 现代检验医学杂志

Objective To identify the differentially expressed genes and pathways of bone marrow-derived mast cells(BMMCs)of mice induced by IL-3 and IL-3+stem cell factor(SCF)using bioinformatics analysis,which may provide a foundation for in vitro culture and functional study of mast cells(MC).Methods The matrix data of GSE35332 dataset in IL-3 and IL-3+SCF induced BMMCs was downloaded from the GEO database,and the R software was applied to screen differentially expressed genes(DEGs).The gene ontology(GO)and Kyoto encyclopedia of genes and genomes(KEGG)pathway enrichment analysis of EDGs were performed based on the online tool DAVID database.The protein interaction network was constructed by STRING database and hub genes were screened through MCODE plugin of the Cytoscape software.Results The GSE35332 data set was analyzed by R software,and 1 339 DEGs were screened,including 723 up-regulated genes and 616 down-regulated genes.A total of 6 hub genes were screened through the MCODE plugin of Cytoscape software,namely Psmd8,Psmd6,Psmd14,Psmc4,Psma6 and Psma3.GO and KEGG analysis showed that the hub genes were concentrated in proteolysis,antigen processing and presentation of exogenous peptide antigen via MHC class I,proteasome-mediated ubiquitin-dependent protein catabolism process,and Epstein-Barr virus infection.Conclusion This study found that there were significant differences in BMMCs gene expression profiles in mice induced by two modes and 6 hub genes participated in ubiquitin-dependent protein decomposition process through bioinformatics based on the GEO database,providing help for further research on MC vitro culture and function.

Construction and Evaluation of the Disulfidptosis-Related Genes(DRGs)Prognostic Risk Model for Hepatocellular Carcinoma Based on TCGA Database / 现代检验医学杂志

Objective To construct and evaluate a disulfidptosis-related genes(DRGs)prognostic risk model for hepatocellular carcinoma(HCC)based on the cancer genome atlas(TCGA)database.Methods The expression of 15 DRGs in 371 HCC samples and 50 adjacent cancer samples in the TCGA database was analyzed using bioinformatics methods,and then gene ontology(GO)functional annotation,Kyoto encyclopedia of genes and genomes(KEGG)enrichment analysis and Kaplan-Meier(KM)survival analysis were performed.Statistical significant DRGs were screened through univariate COX regression analysis,and key DRGs were selected through LASSO regression analysis and multivariate COX regression analysis to construct a prognostic risk model.HCC patients were divided into high-risk and low-risk groups based on risk scores,and the KM survival curves and time-dependent receiver operator characteristic(ROC)curves were created to validate and evaluate prognostic risk models.Results Compared with the adjacent cancer samples,FLNA,MYH9,TLN1,ACTB,MYL6,CAPZB,DSTN,ACTN4,SLC7A11,INF2,CD2AP,PDLIM1,and FLNB were all upregulated in the 15 DRGs of HCC samples,and the differences were significant(t=1 793～6 310,all P<0.001).According to GO functional annotation and KEGG enrichment analysis,DRGs were closely related to biological processes or pathways related to actin cytoskeleton and cell adhesion.The results of KM survival analysis showed that the survival rate of the high expression group of SLC7A11,INF2,CD2AP,MYL6,and ACTB were lower than that of the low expression group[HR=1.46(1.03～2.07)～1.93(1.36～2.75),all P<0.05].Univariate COX regression analysis,LASSO analysis,and multivariate COX regression analysis were used to construct a prognostic risk model,with risk score=(0.247×SLC7A11)+(0.289×INF2)+(0.076×CD2AP)+(0.06×MYL6).The risk score of the sample in this model was calculated,and the higher the risk score,the more HCC patients with poor prognosis.KM survival analysis showed that the overall survival rate of the high-risk group was lower than that of the low-risk group.The AUC values for 1,3,and 5 years were 0.709,0.661,and 0.648,respectively.Multivariate COX regression analysis showed that SLC7A11[HR=1.832(1.274～2.636),P=0.001]was an independent prognostic risk factor.Conclusion The prognostic risk model was constructed by four DRGs,which has a certain role in predicting the prognosis of HCC patients.