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Unravelling the transcriptomic characteristics of bronchoalveolar lavage in post-covid pulmonary fibrosis.
IF 2.1 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2025-03-17 DOI: 10.1186/s12920-025-02110-x
Mohammad Shadab Ali, Vijay Hadda, Sonia Verma, Anita Chopra, Saurabh Mittal, Karan Madan, Pawan Tiwari, Tejas Menon Suri, Anant Mohan

Background: Post-Covid Pulmonary Fibrosis (PCPF) has emerged as a significant global issue associated with a poor quality of life and significant morbidity. Currently, our understanding of the molecular pathways of PCPF is limited. Hence, in this study, we performed whole transcriptome sequencing of the RNA isolated from the bronchoalveolar lavage (BAL) samples of PCPF and compared it with idiopathic pulmonary fibrosis (IPF) and non-ILD (Interstitial Lung Disease) control to understand the gene expression profile and associated pathways.

Methods: BAL samples from PCPF (n = 3), IPF (n = 3), and non-ILD Control (n = 3) (individuals with apparent healthy lung without interstitial lung disease) groups were obtained and RNA were isolated for whole transcriptomic sequencing. Differentially Expressed Genes (DEGs) were determined followed by functional enrichment analysis and qPCR validation.

Results: A panel of differentially expressed genes were identified in bronchoalveolar lavage fluid cells (BALF) of PCPF as compare to control and IPF. Our analysis revealed dysregulated pathways associated with cell cycle regulation, immune responses, and neuroinflammatory processes. Real-time validation further supported these findings. The PPI network and module analysis shed light on potential biomarkers and underscore the complex interplay of molecular mechanisms in PCPF. The comparison of PCPF and IPF identified a significant downregulation of pathways that were more prominent in IPF.

Conclusion: This investigation provides crucial insights into the molecular mechanism of PCPF and also outlines avenues for prospective research and the development of therapeutic approaches.

{"title":"Unravelling the transcriptomic characteristics of bronchoalveolar lavage in post-covid pulmonary fibrosis.","authors":"Mohammad Shadab Ali, Vijay Hadda, Sonia Verma, Anita Chopra, Saurabh Mittal, Karan Madan, Pawan Tiwari, Tejas Menon Suri, Anant Mohan","doi":"10.1186/s12920-025-02110-x","DOIUrl":"10.1186/s12920-025-02110-x","url":null,"abstract":"<p><strong>Background: </strong>Post-Covid Pulmonary Fibrosis (PCPF) has emerged as a significant global issue associated with a poor quality of life and significant morbidity. Currently, our understanding of the molecular pathways of PCPF is limited. Hence, in this study, we performed whole transcriptome sequencing of the RNA isolated from the bronchoalveolar lavage (BAL) samples of PCPF and compared it with idiopathic pulmonary fibrosis (IPF) and non-ILD (Interstitial Lung Disease) control to understand the gene expression profile and associated pathways.</p><p><strong>Methods: </strong>BAL samples from PCPF (n = 3), IPF (n = 3), and non-ILD Control (n = 3) (individuals with apparent healthy lung without interstitial lung disease) groups were obtained and RNA were isolated for whole transcriptomic sequencing. Differentially Expressed Genes (DEGs) were determined followed by functional enrichment analysis and qPCR validation.</p><p><strong>Results: </strong>A panel of differentially expressed genes were identified in bronchoalveolar lavage fluid cells (BALF) of PCPF as compare to control and IPF. Our analysis revealed dysregulated pathways associated with cell cycle regulation, immune responses, and neuroinflammatory processes. Real-time validation further supported these findings. The PPI network and module analysis shed light on potential biomarkers and underscore the complex interplay of molecular mechanisms in PCPF. The comparison of PCPF and IPF identified a significant downregulation of pathways that were more prominent in IPF.</p><p><strong>Conclusion: </strong>This investigation provides crucial insights into the molecular mechanism of PCPF and also outlines avenues for prospective research and the development of therapeutic approaches.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"54"},"PeriodicalIF":2.1,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bioinformatics identification and validation of pyroptosis-related gene for ischemic stroke.
IF 2.1 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2025-03-16 DOI: 10.1186/s12920-025-02119-2
Xinying Shang, Rui Wei, Di Yang, Bawei Yu, Wei Zhang

Background: Ischemic stroke (IS) is one of the common and frequent diseases with extremely high lethality and disability in the world, and there is no effective treatment at present. This study aimed to screen hub genes involved in cerebral ischemia/reperfusion injury (CIRI) and pyroptosis, and explore promising intervention targets.

Methods: CIRI-related genes (GSE202659 and GSE131193) and pyroptosis-related genes (PRGs) in mice were obtained from the Gene Expression Omnibus (GEO) and GeneCards database. We screened for LASSO regression to construct a prognostic model of GSE131193 and PRGs and examined by GSE137482. The functional enrichment analysis of Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) were performed on pyroptosis-related differentially expressed genes (PRDEGs) of GSE202659.The key modules for CIRI and pyroptosis were identified by Weight Gene Co-expression Network Analysis (WGCNA). Subsequently, Protein-protein Interaction (PPI) network and the Cytoscape was constructed to screen out hub genes. Used the starBase to predict miRNA interacting with hub genes and constructed mRNA-miRNA-lncRNA interaction networks. CIRI-related Molecular Subtypes were constructed for hub genes. The relationship between immune cells and hub genes was verified via CIBERSORT. Finally, we selected C57BL/6 mice to construct models to confirm hub genes by enzyme linked immunosorbent assay (ELISA), reverse transcription-polymerase chain reaction (RT-PCR), western blot, and Immunofluorescence.

Results: A total of 272 PRGs and 35 PRDEGs were screened. An eight-gene risk prediction models were established (AUC = 0.868). GO, KEGG, GSEA and GSVA analyses revealed that PRDEGs were mainly involved in positive regulation of cytokine production, and NOD-like receptor signaling pathway. And then, seven hub genes (Irf1, Icam1, Tlr2, Tnf, Cebpb, Il1rn, and Casp8) were identified by PPI. Icam1, Tnf, Cebpb, Il1rn, and Casp8 had high expression profiles in Cluster2 by hierarchical clustering. The immune infiltration analysis results showed that among the hub genes, Cebpb, Il1rn, and Casp8, showed a significant positive correlation with the degree of NK.Actived, and Icam1 showed a significant negative correlation with B.Cells.Memory. The results of animal experiments significantly demonstrated an upregulation of Irf1, Icam1, Tlr2, Cebpb, and Il1rn.

Conclusion: Our finding indicated that Irf1, Icam1, Tlr2, Cebpb, and Il1rn are hub genes associated with pyroptosis, and these genes are all associated with different immune cells, so as to provide new targets for the prevention and treatment of IS from the perspective of pyroptosis.

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引用次数: 0
Inherited rare epidermal growth factor receptor mutation and somatic mutations in patients with non-small cell lung cancer: a case report.
IF 2.1 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2025-03-14 DOI: 10.1186/s12920-025-02113-8
Zacharenia Saridaki, Elena Fountzilas, Athanasios Alexopoulos, Niki Karachaliou

Background: Recent advances in molecular oncology have increasingly illuminated the role of germline EGFR mutations in non-small cell lung cancer (NSCLC). This case report presents the presence of a unique familial occurrence of EGFR mutations in patients with NSCLC.

Case description: A mother and son, both never-smokers of Caucasian ethnicity, were diagnosed with advanced metastatic lung adenocarcinoma. In one patient, tumor molecular analysis by next generation sequencing (NGS) identified two EGFR mutations: the activating mutation c.2573T > G; p.Leu858Arg (p.L858R) in exon 21 of the EGFR gene, and the somatic non-pathogenic mutation c.2612 C > A; p.Ala871Glu (p.A871E) in exon 21 of the EGFR gene. The second patient also harbored the same two EGFR mutations. The patient underwent genetic testing which revealed the germline origin of the A871E mutation. Whether the presence of this mutations was associated with increased predisposition to cancer has yet to be determined. Our case report highlights the need for further exploration of the role of germline mutations, including the A871E mutation, in tumorigenesis and its implications for treatment response and inheritance patterns.

Conclusions: The investigation and comprehension of the significance of each individual EGFR mutation hold the promise for potential in cancer prevention or early diagnosis within family cohorts and understanding the mechanisms of tumorigenesis in sporadic cases.

背景:分子肿瘤学的最新进展日益揭示了种系表皮生长因子受体突变在非小细胞肺癌(NSCLC)中的作用。本病例报告介绍了非小细胞肺癌患者中出现的一种独特的家族性表皮生长因子受体突变:一对从未吸烟的白种人母子被诊断出患有晚期转移性肺腺癌。其中一名患者通过新一代测序(NGS)进行了肿瘤分子分析,发现了两个表皮生长因子受体突变:表皮生长因子受体基因第 21 外显子中的激活突变 c.2573T > G; p.Leu858Arg (p.L858R),以及表皮生长因子受体基因第 21 外显子中的体细胞非致病突变 c.2612 C > A; p.Ala871Glu (p.A871E)。第二名患者也携带同样的两个表皮生长因子受体突变。该患者接受了基因检测,结果显示A871E突变来源于种系。这种突变的存在是否与癌症易感性的增加有关尚待确定。我们的病例报告强调了进一步探索种系突变(包括 A871E 突变)在肿瘤发生中的作用及其对治疗反应和遗传模式的影响的必要性:调查和了解每种表皮生长因子受体突变的意义,有望在家族队列中预防或早期诊断癌症,并了解散发性病例的肿瘤发生机制。
{"title":"Inherited rare epidermal growth factor receptor mutation and somatic mutations in patients with non-small cell lung cancer: a case report.","authors":"Zacharenia Saridaki, Elena Fountzilas, Athanasios Alexopoulos, Niki Karachaliou","doi":"10.1186/s12920-025-02113-8","DOIUrl":"10.1186/s12920-025-02113-8","url":null,"abstract":"<p><strong>Background: </strong>Recent advances in molecular oncology have increasingly illuminated the role of germline EGFR mutations in non-small cell lung cancer (NSCLC). This case report presents the presence of a unique familial occurrence of EGFR mutations in patients with NSCLC.</p><p><strong>Case description: </strong>A mother and son, both never-smokers of Caucasian ethnicity, were diagnosed with advanced metastatic lung adenocarcinoma. In one patient, tumor molecular analysis by next generation sequencing (NGS) identified two EGFR mutations: the activating mutation c.2573T > G; p.Leu858Arg (p.L858R) in exon 21 of the EGFR gene, and the somatic non-pathogenic mutation c.2612 C > A; p.Ala871Glu (p.A871E) in exon 21 of the EGFR gene. The second patient also harbored the same two EGFR mutations. The patient underwent genetic testing which revealed the germline origin of the A871E mutation. Whether the presence of this mutations was associated with increased predisposition to cancer has yet to be determined. Our case report highlights the need for further exploration of the role of germline mutations, including the A871E mutation, in tumorigenesis and its implications for treatment response and inheritance patterns.</p><p><strong>Conclusions: </strong>The investigation and comprehension of the significance of each individual EGFR mutation hold the promise for potential in cancer prevention or early diagnosis within family cohorts and understanding the mechanisms of tumorigenesis in sporadic cases.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"51"},"PeriodicalIF":2.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11909994/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genomic characteristics and prognostic correlations in Chinese multiple myeloma patients.
IF 2.1 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2025-03-14 DOI: 10.1186/s12920-025-02116-5
Xi Chen, Tianchen Luo, Wenhui Zhang, Sheng Wang, Mengxuan Zhu, Haiyan He, Jin Liu, Jing Lu, Wanting Qiang, Yanchun Jia, Nan Hou, Xuenan Zhao, Shan Zhang, Jing Li, Juan Du

Background: Multiple myeloma (MM) is a hematologic malignancy characterized by the proliferation of abnormal clonal plasma cells in the bone marrow. The heterogeneity in Chinese MM populations remains underexplored.

Methods: We conducted whole-exome sequencing (WES) on 241 tumor samples, complemented by RNA sequencing (RNA-seq) on 131 samples from 212 Chinese MM patients.

Results: We identified a novel mutational signature and analyzed molecular differences between newly diagnosed MM (NDMM) and relapsed/refractory MM (RRMM) patients. NFKBIA mutations were notably more frequent in NDMM patients compared to the MMRF-COMMPASS cohort (4/50 vs 22/937, p = 0.048), with additional recurrent mutations in several genes like TTN, IGLL5 and SYNE1. In RRMM patients, UBR5 mutations were more prevalent (4/24 vs 0/50, p = 0.01), alongside frequent mutations in OBSCN, CACNA1H, and HSPG2. Clonal evolution was assessed through multiple time points and locations, identifying genes potentially linked to circulating plasma cell formation. Cox regression analysis revealed that age and mutations in OBSCN and RB1 were significant predictors of progression-free survival (PFS) in NDMM patients. Additionally, albumin, β2-microglobulin, and RB1 mutations were correlated with overall survival (OS).

Conclusions: In summary, we characterized the genomic landscape of MM in diverse Chinese populations, confirmed clonal evolution, and identified prognostic genes.

{"title":"Genomic characteristics and prognostic correlations in Chinese multiple myeloma patients.","authors":"Xi Chen, Tianchen Luo, Wenhui Zhang, Sheng Wang, Mengxuan Zhu, Haiyan He, Jin Liu, Jing Lu, Wanting Qiang, Yanchun Jia, Nan Hou, Xuenan Zhao, Shan Zhang, Jing Li, Juan Du","doi":"10.1186/s12920-025-02116-5","DOIUrl":"10.1186/s12920-025-02116-5","url":null,"abstract":"<p><strong>Background: </strong>Multiple myeloma (MM) is a hematologic malignancy characterized by the proliferation of abnormal clonal plasma cells in the bone marrow. The heterogeneity in Chinese MM populations remains underexplored.</p><p><strong>Methods: </strong>We conducted whole-exome sequencing (WES) on 241 tumor samples, complemented by RNA sequencing (RNA-seq) on 131 samples from 212 Chinese MM patients.</p><p><strong>Results: </strong>We identified a novel mutational signature and analyzed molecular differences between newly diagnosed MM (NDMM) and relapsed/refractory MM (RRMM) patients. NFKBIA mutations were notably more frequent in NDMM patients compared to the MMRF-COMMPASS cohort (4/50 vs 22/937, p = 0.048), with additional recurrent mutations in several genes like TTN, IGLL5 and SYNE1. In RRMM patients, UBR5 mutations were more prevalent (4/24 vs 0/50, p = 0.01), alongside frequent mutations in OBSCN, CACNA1H, and HSPG2. Clonal evolution was assessed through multiple time points and locations, identifying genes potentially linked to circulating plasma cell formation. Cox regression analysis revealed that age and mutations in OBSCN and RB1 were significant predictors of progression-free survival (PFS) in NDMM patients. Additionally, albumin, β2-microglobulin, and RB1 mutations were correlated with overall survival (OS).</p><p><strong>Conclusions: </strong>In summary, we characterized the genomic landscape of MM in diverse Chinese populations, confirmed clonal evolution, and identified prognostic genes.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"50"},"PeriodicalIF":2.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11907858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comprehensive clinical and genetic characterization of hyperprogressive biliary tract cancer during PD-1 blockade monotherapy: case report and literature review. PD-1阻断剂单药治疗期间胆道癌过度进展的综合临床和遗传特征:病例报告和文献综述。
IF 2.1 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2025-03-14 DOI: 10.1186/s12920-025-02097-5
Kang-Xin Wang, Xu-Dong Yang, Fen Guo, Hui Sun, Yue-Yu Fang, Nan-Yuan Jiang, Xiao-Feng Chen

Background: Some genetically characterized patients show the rapid disease progression during immune checkpoint inhibitors (ICIs) monotherapy, a phenomenon known as hyperprogressive disease (HPD).

Case presentation: Herein we report a relevant case of biliary tract cancer (BTC) that initially responded to gemcitabine plus oxaliplatin (GEMOX) and PD-1 blockade but subsequently developed HPD in the process of PD-1 blockade maintenance therapy, leading to death within two weeks. Genomic analysis revealed mutations in CDKN2A, PIK3CA, KRAS and EPHA2 in both baseline and hyperprogressive plasma and tumor samples. Notably, higher KRAS mutation abundance was observed in plasma and ascites after disease progression.

Conclusions: These findings suggest a potential association between these negative genes especially KRAS mutation and HPD. Therefore, administration of PD-1 blockade monotherapy in this subgroup of patients harboring KRAS mutation should be performed with caution. Further studies are warranted to confirm these results and explore the correlation between genomic mutations and HPD.

{"title":"Comprehensive clinical and genetic characterization of hyperprogressive biliary tract cancer during PD-1 blockade monotherapy: case report and literature review.","authors":"Kang-Xin Wang, Xu-Dong Yang, Fen Guo, Hui Sun, Yue-Yu Fang, Nan-Yuan Jiang, Xiao-Feng Chen","doi":"10.1186/s12920-025-02097-5","DOIUrl":"10.1186/s12920-025-02097-5","url":null,"abstract":"<p><strong>Background: </strong>Some genetically characterized patients show the rapid disease progression during immune checkpoint inhibitors (ICIs) monotherapy, a phenomenon known as hyperprogressive disease (HPD).</p><p><strong>Case presentation: </strong>Herein we report a relevant case of biliary tract cancer (BTC) that initially responded to gemcitabine plus oxaliplatin (GEMOX) and PD-1 blockade but subsequently developed HPD in the process of PD-1 blockade maintenance therapy, leading to death within two weeks. Genomic analysis revealed mutations in CDKN2A, PIK3CA, KRAS and EPHA2 in both baseline and hyperprogressive plasma and tumor samples. Notably, higher KRAS mutation abundance was observed in plasma and ascites after disease progression.</p><p><strong>Conclusions: </strong>These findings suggest a potential association between these negative genes especially KRAS mutation and HPD. Therefore, administration of PD-1 blockade monotherapy in this subgroup of patients harboring KRAS mutation should be performed with caution. Further studies are warranted to confirm these results and explore the correlation between genomic mutations and HPD.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"52"},"PeriodicalIF":2.1,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11909846/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Spectrum of genetic variants associated with maple syrup urine disease in the Middle East, North Africa, and Türkiye (MENAT): a systematic review.
IF 2.1 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2025-03-13 DOI: 10.1186/s12920-025-02083-x
Salma Younes, Razan Elkahlout, Houda Kilani, Sarah Okashah, Hussain Al Sharshani, Zoulikha Rezoug, Hatem Zayed, Nader Al-Dewik

Background: Maple syrup urine disease (MSUD) is a hereditary metabolic disorder caused by a deficiency in the branched-chain α-keto acid dehydrogenase (BCKD) enzymatic complex. The Middle East and North Africa, and Türkiye (MENAT) region has witnessed a significant rise in the prevalence of MSUD due to high rates of consanguinity. Despite numerous genetic association studies, the complex relationships between genotype and phenotype in MSUD remain elusive.

Aim: This study aimed to systematically review the variants significantly associated with MSUD in the MENAT region.

Methods: We systematically searched four literature databases (PubMed, Scopus, Web of Science, and Science Direct) from inception until December 2023 to gather all reported genetic data pertaining to MSUD in the MENAT region. Quality assessment and data extraction were diligently performed by a team of six investigators.

Results: A total of 16 studies, involving patients, were included in this systematic review. Among them, 211 patients presented with 105 variants located within genes known to be associated with MSUD. The majority of the identified MSUD variants were found in BCKDHA (38%), followed by BCKDHB (38%), DBT (23%), and PPM1K (1%). Notably, 77% of the captured variants were unique to the MENAT region.

Conclusion: Our systematic review reveals a distinctive genetic and clinical susceptibility profile of MSUD among individuals from the MENAT region. These findings highlight the importance of understanding the specific genetic landscape of MSUD in this population. Further research is warranted to elucidate the complex genotype-phenotype relationships in MSUD in the MENAT region.

背景:枫糖尿病(MSUD)是一种遗传性代谢疾病,由支链α-酮酸脱氢酶(BCKD)酶复合物缺乏引起。由于近亲结婚率高,中东、北非和土耳其(MENAT)地区的 MSUD 患病率显著上升。尽管开展了大量遗传关联研究,但 MSUD 基因型与表型之间的复杂关系仍然难以捉摸:我们系统地检索了四个文献数据库(PubMed、Scopus、Web of Science 和 Science Direct),收集了中东北非地区所有与 MSUD 相关的遗传数据。由六名研究人员组成的团队认真进行了质量评估和数据提取:本系统综述共纳入 16 项涉及患者的研究。其中,211 名患者的 105 个变异位于已知与 MSUD 相关的基因中。大多数已确定的 MSUD 变异存在于 BCKDHA(38%),其次是 BCKDHB(38%)、DBT(23%)和 PPM1K(1%)。值得注意的是,所发现的变异中有 77% 是中东和北非地区特有的:我们的系统综述揭示了中东和北非地区个体对 MSUD 独特的遗传和临床易感性特征。这些发现凸显了了解该人群中 MSUD 特殊遗传情况的重要性。有必要开展进一步研究,以阐明中东和北非地区 MSUD 基因型与表型之间的复杂关系。
{"title":"Spectrum of genetic variants associated with maple syrup urine disease in the Middle East, North Africa, and Türkiye (MENAT): a systematic review.","authors":"Salma Younes, Razan Elkahlout, Houda Kilani, Sarah Okashah, Hussain Al Sharshani, Zoulikha Rezoug, Hatem Zayed, Nader Al-Dewik","doi":"10.1186/s12920-025-02083-x","DOIUrl":"10.1186/s12920-025-02083-x","url":null,"abstract":"<p><strong>Background: </strong>Maple syrup urine disease (MSUD) is a hereditary metabolic disorder caused by a deficiency in the branched-chain α-keto acid dehydrogenase (BCKD) enzymatic complex. The Middle East and North Africa, and Türkiye (MENAT) region has witnessed a significant rise in the prevalence of MSUD due to high rates of consanguinity. Despite numerous genetic association studies, the complex relationships between genotype and phenotype in MSUD remain elusive.</p><p><strong>Aim: </strong>This study aimed to systematically review the variants significantly associated with MSUD in the MENAT region.</p><p><strong>Methods: </strong>We systematically searched four literature databases (PubMed, Scopus, Web of Science, and Science Direct) from inception until December 2023 to gather all reported genetic data pertaining to MSUD in the MENAT region. Quality assessment and data extraction were diligently performed by a team of six investigators.</p><p><strong>Results: </strong>A total of 16 studies, involving patients, were included in this systematic review. Among them, 211 patients presented with 105 variants located within genes known to be associated with MSUD. The majority of the identified MSUD variants were found in BCKDHA (38%), followed by BCKDHB (38%), DBT (23%), and PPM1K (1%). Notably, 77% of the captured variants were unique to the MENAT region.</p><p><strong>Conclusion: </strong>Our systematic review reveals a distinctive genetic and clinical susceptibility profile of MSUD among individuals from the MENAT region. These findings highlight the importance of understanding the specific genetic landscape of MSUD in this population. Further research is warranted to elucidate the complex genotype-phenotype relationships in MSUD in the MENAT region.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"49"},"PeriodicalIF":2.1,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Association of metabolic dysregulation with treatment response in rectal cancer patients undergoing chemoradiotherapy.
IF 2.1 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2025-03-12 DOI: 10.1186/s12920-025-02114-7
Qiliang Peng, Yi Shen, Yingying Xu, Zhengyang Feng, Yao Xu, Yong Wang, Li Zou, Yaqun Zhu, Yuntian Shen

Background: This study aimed to explore the metabolic changes during neoadjuvant chemoradiotherapy (NCRT) in patients with locally advanced rectal cancer (LARC) by serum metabolomics analysis, and to provide new biomarkers for individualized treatment and efficacy prediction.

Methods: Serum samples from 20 patients with LARC before, during and after NCRT were collected for metabolomic analysis. The metabolites in the serum samples were analyzed qualitatively and quantitatively using gas chromatography-mass spectrometry (GC-MS). Meanwhile, the differences in metabolic profiles at different time points were compared and significantly changed metabolites were screened.

Results: The metabolic profiles of patients were significantly altered at different time points of NCRT. Through metabolomic analysis, we identified metabolites that were significantly altered during NCRT and revealed alterations in the associated metabolic pathways. The predictive power of pre-radiotherapy isocitric acid and pro-radiotherapy 3-hydroxy-3-(4'-hydroxy-3'-methoxyphenyl) propionic acid in distinguishing patients sensitive and non-sensitive to NCRT was markedly high, with AUC values of 0.875 and 0.75, respectively. Additional analysis indicated that a combined panel of serum metabolites yielded even higher AUC values, thereby enhancing the accuracy of predicting the efficacy of neoadjuvant NCRT.

Conclusion: This study revealed metabolic changes and corresponding alterations in metabolic pathways during NCRT in patients with LARC by serum metabolomic analysis. The metabolic disorders may be associated with poor outcomes in patients treated with NCRT for rectal cancer, providing new biomarkers for individualized treatment and prognostic assessment. Further studies and validation will help to gain insight into the mechanism of these metabolic changes and provide more basis for clinical application.

{"title":"Association of metabolic dysregulation with treatment response in rectal cancer patients undergoing chemoradiotherapy.","authors":"Qiliang Peng, Yi Shen, Yingying Xu, Zhengyang Feng, Yao Xu, Yong Wang, Li Zou, Yaqun Zhu, Yuntian Shen","doi":"10.1186/s12920-025-02114-7","DOIUrl":"10.1186/s12920-025-02114-7","url":null,"abstract":"<p><strong>Background: </strong>This study aimed to explore the metabolic changes during neoadjuvant chemoradiotherapy (NCRT) in patients with locally advanced rectal cancer (LARC) by serum metabolomics analysis, and to provide new biomarkers for individualized treatment and efficacy prediction.</p><p><strong>Methods: </strong>Serum samples from 20 patients with LARC before, during and after NCRT were collected for metabolomic analysis. The metabolites in the serum samples were analyzed qualitatively and quantitatively using gas chromatography-mass spectrometry (GC-MS). Meanwhile, the differences in metabolic profiles at different time points were compared and significantly changed metabolites were screened.</p><p><strong>Results: </strong>The metabolic profiles of patients were significantly altered at different time points of NCRT. Through metabolomic analysis, we identified metabolites that were significantly altered during NCRT and revealed alterations in the associated metabolic pathways. The predictive power of pre-radiotherapy isocitric acid and pro-radiotherapy 3-hydroxy-3-(4'-hydroxy-3'-methoxyphenyl) propionic acid in distinguishing patients sensitive and non-sensitive to NCRT was markedly high, with AUC values of 0.875 and 0.75, respectively. Additional analysis indicated that a combined panel of serum metabolites yielded even higher AUC values, thereby enhancing the accuracy of predicting the efficacy of neoadjuvant NCRT.</p><p><strong>Conclusion: </strong>This study revealed metabolic changes and corresponding alterations in metabolic pathways during NCRT in patients with LARC by serum metabolomic analysis. The metabolic disorders may be associated with poor outcomes in patients treated with NCRT for rectal cancer, providing new biomarkers for individualized treatment and prognostic assessment. Further studies and validation will help to gain insight into the mechanism of these metabolic changes and provide more basis for clinical application.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"48"},"PeriodicalIF":2.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905535/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143613265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A systematic review and meta-analysis on antibiotic resistance genes in Ghana.
IF 2.1 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2025-03-12 DOI: 10.1186/s12920-024-02050-y
Eric S Donkor, Alex Odoom, Abdul-Halim Osman, Samuel Darkwah, Fleischer C N Kotey

Background: Addressing antimicrobial resistance (AMR) poses a complex challenge, primarily because of the limited understanding of bacterial antibiotic resistance genes (ARGs) and the spread of these genes across different domains. To bridge this knowledge gap in Ghana, we undertook a comprehensive systematic review and meta-analysis to quantify and estimate the prevalence of circulating ARGs in bacteria isolated from human, animal, and environmental sources.

Methods: A thorough literature search was conducted across three major databases-Web of Science, PubMed, and Scopus-to retrieve all relevant articles related to ARGs in Ghana from the inception of the databases to February 25, 2024. A risk-of-bias evaluation was performed using the Newcastle-Ottawa Scale (NOS), and the data analysis involved descriptive statistics and proportional meta-analysis.

Results: Of the 371 articles initially obtained, 38 met the inclusion criteria. These studies adequately covered Ghana geographically. The most prevalent ESBL gene identified was blaCTX-M, with a prevalence of 31.6% (95% CI: 17.6-45.7), followed by blaTEM (19.5% [95% CI: 9.7-29.3]), and blaSHV (3.5% [95% CI: 0.3-6.6]). The pooled prevalence of carbapenemase genes ranged from 17.2% (95% CI: 6.9-27.6) for blaNDM to 10.3% (95% CI: 1.9-18.7) for blaOXA. Additionally, other ARGs, including sul1, qnrS, gyrA, erm(B), and mecA, were detected, with prevalence ranging from 3.9% (95% CI: 0.0-8.5) to 16.4% (95% CI: 3.1-29.8). Several ARGs were shared across human, animal, and environmental sources.

Conclusion: This review revealed that bacteria obtained from human, animal, and environmental samples in Ghana shared genes associated with AMR. This finding provides evidence on the interconnection of AMR across these three domains. Horizontal gene transfer, which enables the dissemination of ARGs between genetically diverse bacteria, can occur, necessitating a multidisciplinary approach to addressing antimicrobial resistance in Ghana.

{"title":"A systematic review and meta-analysis on antibiotic resistance genes in Ghana.","authors":"Eric S Donkor, Alex Odoom, Abdul-Halim Osman, Samuel Darkwah, Fleischer C N Kotey","doi":"10.1186/s12920-024-02050-y","DOIUrl":"10.1186/s12920-024-02050-y","url":null,"abstract":"<p><strong>Background: </strong>Addressing antimicrobial resistance (AMR) poses a complex challenge, primarily because of the limited understanding of bacterial antibiotic resistance genes (ARGs) and the spread of these genes across different domains. To bridge this knowledge gap in Ghana, we undertook a comprehensive systematic review and meta-analysis to quantify and estimate the prevalence of circulating ARGs in bacteria isolated from human, animal, and environmental sources.</p><p><strong>Methods: </strong>A thorough literature search was conducted across three major databases-Web of Science, PubMed, and Scopus-to retrieve all relevant articles related to ARGs in Ghana from the inception of the databases to February 25, 2024. A risk-of-bias evaluation was performed using the Newcastle-Ottawa Scale (NOS), and the data analysis involved descriptive statistics and proportional meta-analysis.</p><p><strong>Results: </strong>Of the 371 articles initially obtained, 38 met the inclusion criteria. These studies adequately covered Ghana geographically. The most prevalent ESBL gene identified was bla<sub>CTX-M</sub>, with a prevalence of 31.6% (95% CI: 17.6-45.7), followed by bla<sub>TEM</sub> (19.5% [95% CI: 9.7-29.3]), and bla<sub>SHV</sub> (3.5% [95% CI: 0.3-6.6]). The pooled prevalence of carbapenemase genes ranged from 17.2% (95% CI: 6.9-27.6) for bla<sub>NDM</sub> to 10.3% (95% CI: 1.9-18.7) for bla<sub>OXA</sub>. Additionally, other ARGs, including sul1, qnrS, gyrA, erm(B), and mecA, were detected, with prevalence ranging from 3.9% (95% CI: 0.0-8.5) to 16.4% (95% CI: 3.1-29.8). Several ARGs were shared across human, animal, and environmental sources.</p><p><strong>Conclusion: </strong>This review revealed that bacteria obtained from human, animal, and environmental samples in Ghana shared genes associated with AMR. This finding provides evidence on the interconnection of AMR across these three domains. Horizontal gene transfer, which enables the dissemination of ARGs between genetically diverse bacteria, can occur, necessitating a multidisciplinary approach to addressing antimicrobial resistance in Ghana.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"47"},"PeriodicalIF":2.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11899156/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143613255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A genome-wide association study of methamphetamine use among people with HIV.
IF 2.1 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2025-03-11 DOI: 10.1186/s12920-025-02105-8
A Venkataraman, T Jia, S A Ruderman, C B Haas, R M Nance, L S Mixson, K H Mayer, M S Saag, G Chander, R D Moore, J Jacobson, S Napravnik, K Christopolous, W J Lee, B M Whitney, I Peter, H M Crane, J A C Delaney, S Lindström

Background: Amphetamine-like stimulants are the most used psychostimulants in the world; methamphetamine use is the most prevalent in people with HIV. Prolonged methamphetamine use can cause lasting damage to the heart, gut, and brain, as well as auditory hallucinations and paranoid thinking. However, relatively little is known about methamphetamine use and its genetic contributors.

Methods: Using genetic information from the Centers for AIDS Research Network of Integrated Clinical Systems (CNICS) cohort, we conducted a multi-ancestry genome-wide association study (GWAS) of methamphetamine use among people with HIV (n = 1,196 reported ever use, n = 4,750 reported never use).

Results: No single nucleotide polymorphism was statistically associated with methamphetamine use at the genome-wide level (p < 5 * 10-8) in our study. Further, we did not replicate previously suggested genetic variants from other studies (all p > 0.05 in our analysis).

Discussion: Our study suggests that there is no single strong genetic contributor to lifetime use of methamphetamine in people with HIV enrolled in CNICS. Larger studies with more refined outcome assessment are warranted to further understand the contribution of genetics to methamphetamine use and use disorder. Investigation into social and environmental contributors to methamphetamine use are similarly necessary.

{"title":"A genome-wide association study of methamphetamine use among people with HIV.","authors":"A Venkataraman, T Jia, S A Ruderman, C B Haas, R M Nance, L S Mixson, K H Mayer, M S Saag, G Chander, R D Moore, J Jacobson, S Napravnik, K Christopolous, W J Lee, B M Whitney, I Peter, H M Crane, J A C Delaney, S Lindström","doi":"10.1186/s12920-025-02105-8","DOIUrl":"10.1186/s12920-025-02105-8","url":null,"abstract":"<p><strong>Background: </strong>Amphetamine-like stimulants are the most used psychostimulants in the world; methamphetamine use is the most prevalent in people with HIV. Prolonged methamphetamine use can cause lasting damage to the heart, gut, and brain, as well as auditory hallucinations and paranoid thinking. However, relatively little is known about methamphetamine use and its genetic contributors.</p><p><strong>Methods: </strong>Using genetic information from the Centers for AIDS Research Network of Integrated Clinical Systems (CNICS) cohort, we conducted a multi-ancestry genome-wide association study (GWAS) of methamphetamine use among people with HIV (n = 1,196 reported ever use, n = 4,750 reported never use).</p><p><strong>Results: </strong>No single nucleotide polymorphism was statistically associated with methamphetamine use at the genome-wide level (p < 5 * 10<sup>-8</sup>) in our study. Further, we did not replicate previously suggested genetic variants from other studies (all p > 0.05 in our analysis).</p><p><strong>Discussion: </strong>Our study suggests that there is no single strong genetic contributor to lifetime use of methamphetamine in people with HIV enrolled in CNICS. Larger studies with more refined outcome assessment are warranted to further understand the contribution of genetics to methamphetamine use and use disorder. Investigation into social and environmental contributors to methamphetamine use are similarly necessary.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"46"},"PeriodicalIF":2.1,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11895338/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143596043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ARMC5 mutations in primary bilateral macronodular adrenal hyperplasia: a family case report.
IF 2.1 4区 医学 Q3 GENETICS & HEREDITY Pub Date : 2025-03-10 DOI: 10.1186/s12920-025-02112-9
Yikai Wang, Weibing Shuang

Background: Primary bilateral macronodular adrenal hyperplasia (PBMAH) is a rare cause of overt Cushing's syndrome (CS), which usually manifests as bilateral macronodular adrenal nodules and varying levels of cortisol secretion. Previous studies have shown that ARMC5 play a huge role in the occurrence of PBMAH, which may be inherited to family members and lead to more severe clinical symptoms. ARMC5 variants may be associated with meningiomas, which is also illustrated by our report.

Case presentation: This is a 41-year-old male patient with high blood pressure for 10 years and multiple adrenal nodules on both sides. In addition, the patient also suffered from pituitary microadenoma and meningioma. According to the patient's clinical manifestations, laboratory tests, imaging examinations, and the results of whole exon gene testing, we diagnosed the patient with PBMAH. The patient underwent a posterior laparoscopic nephrectomy of the left adrenal gland. Pathology reported a left macronodular adrenal hyperplasia, multifocal, 2 cm to 3 cm in diameter. Molecular analysis of DNA extracted from the patient's peripheral blood revealed an ARMC5 heterozygous mutation, which was classified as likely pathogenic.

Conclusion: Screening of family members of PBMAH patients with ARMC5 germline mutations and active monitoring of family members carrying ARMC5 variants are recommended.

{"title":"ARMC5 mutations in primary bilateral macronodular adrenal hyperplasia: a family case report.","authors":"Yikai Wang, Weibing Shuang","doi":"10.1186/s12920-025-02112-9","DOIUrl":"10.1186/s12920-025-02112-9","url":null,"abstract":"<p><strong>Background: </strong>Primary bilateral macronodular adrenal hyperplasia (PBMAH) is a rare cause of overt Cushing's syndrome (CS), which usually manifests as bilateral macronodular adrenal nodules and varying levels of cortisol secretion. Previous studies have shown that ARMC5 play a huge role in the occurrence of PBMAH, which may be inherited to family members and lead to more severe clinical symptoms. ARMC5 variants may be associated with meningiomas, which is also illustrated by our report.</p><p><strong>Case presentation: </strong>This is a 41-year-old male patient with high blood pressure for 10 years and multiple adrenal nodules on both sides. In addition, the patient also suffered from pituitary microadenoma and meningioma. According to the patient's clinical manifestations, laboratory tests, imaging examinations, and the results of whole exon gene testing, we diagnosed the patient with PBMAH. The patient underwent a posterior laparoscopic nephrectomy of the left adrenal gland. Pathology reported a left macronodular adrenal hyperplasia, multifocal, 2 cm to 3 cm in diameter. Molecular analysis of DNA extracted from the patient's peripheral blood revealed an ARMC5 heterozygous mutation, which was classified as likely pathogenic.</p><p><strong>Conclusion: </strong>Screening of family members of PBMAH patients with ARMC5 germline mutations and active monitoring of family members carrying ARMC5 variants are recommended.</p>","PeriodicalId":8915,"journal":{"name":"BMC Medical Genomics","volume":"18 1","pages":"44"},"PeriodicalIF":2.1,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11895384/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143595962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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BMC Medical Genomics
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