Molecular Genetics and Genomics最新文献

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Exome sequencing in four families with neurodevelopmental disorders: genotype-phenotype correlation and identification of novel disease-causing variants in VPS13B and RELN. 四个神经发育障碍家族的外显子组测序:基因型与表型的相关性以及 VPS13B 和 RELN 中新型致病变异的鉴定。
IF 2.3 3区 生物学
Molecular Genetics and Genomics Pub Date : 2024-05-21 DOI: 10.1007/s00438-024-02149-y
Tehseen Ullah Khan Afridi, Ambrin Fatima, Humayoon Shafique Satti, Zaineb Akram, Imran Khan Yousafzai, Wajahat Bin Naeem, Nasreen Fatima, Asmat Ali, Zafar Iqbal, Ayaz Khan, Muhammad Shahzad, Chunyu Liu, Mathias Toft, Feng Zhang, Muhammad Tariq, Erica E Davis, Tahir N Khan
{"title":"Exome sequencing in four families with neurodevelopmental disorders: genotype-phenotype correlation and identification of novel disease-causing variants in VPS13B and RELN.","authors":"Tehseen Ullah Khan Afridi, Ambrin Fatima, Humayoon Shafique Satti, Zaineb Akram, Imran Khan Yousafzai, Wajahat Bin Naeem, Nasreen Fatima, Asmat Ali, Zafar Iqbal, Ayaz Khan, Muhammad Shahzad, Chunyu Liu, Mathias Toft, Feng Zhang, Muhammad Tariq, Erica E Davis, Tahir N Khan","doi":"10.1007/s00438-024-02149-y","DOIUrl":"10.1007/s00438-024-02149-y","url":null,"abstract":"<p><p>Neurodevelopmental disorders (NDDs) are a clinically and genetically heterogeneous group of early-onset pediatric disorders that affect the structure and/or function of the central or peripheral nervous system. Achieving a precise molecular diagnosis for NDDs may be challenging due to the diverse genetic underpinnings and clinical variability. In the current study, we investigated the underlying genetic cause(s) of NDDs in four unrelated Pakistani families. Using exome sequencing (ES) as a diagnostic approach, we identified disease-causing variants in established NDD-associated genes in all families, including one hitherto unreported variant in RELN and three recurrent variants in VPS13B, DEGS1, and SPG11. Overall, our study highlights the potential of ES as a tool for clinical diagnosis.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141071498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of soybean mosaic virus strain SC7 resistance loci and candidate genes in soybean [Glycine max (L.) Merr.]. 大豆[Glycine max (L.) Merr.]中大豆花叶病毒株 SC7 抗性基因座和候选基因的鉴定。
IF 3.1 3区 生物学
Molecular Genetics and Genomics Pub Date : 2024-05-17 DOI: 10.1007/s00438-024-02151-4
Yixiang Pu, Rujuan Yan, Dongbing Jia, Zhijun Che, Rufei Yang, Changyun Yang, Hui Wang, Hao Cheng, Deyue Yu
{"title":"Identification of soybean mosaic virus strain SC7 resistance loci and candidate genes in soybean [Glycine max (L.) Merr.].","authors":"Yixiang Pu, Rujuan Yan, Dongbing Jia, Zhijun Che, Rufei Yang, Changyun Yang, Hui Wang, Hao Cheng, Deyue Yu","doi":"10.1007/s00438-024-02151-4","DOIUrl":"https://doi.org/10.1007/s00438-024-02151-4","url":null,"abstract":"<p><p>Soybean [Glycine max (L.) Merr.] is an important legume crop worldwide, which provides abundant plant protein and oil for human beings. Soybean mosaic virus (SMV) can cause serious damage to the yield and quality of soybean, but it is difficult to control SMV with chemicals, breeding SMV-resistant varieties has become the most effective way to control the disease. Therefore, it is important to identify SMV resistance genes from soybean resources and apply them to soybean breeding. In this study, the disease rates (DRs) of 219 soybean accessions to SMV strain SC7 in two environments were investigated. A high-density NJAU 355 K SoySNP array was used for genome-wide association study (GWAS) of DR. A 274 kb region on chromosome 15 (1,110,567 bp to 1,384,173 bp) was repeatedly detected in two environments. Six new significant single nucleotide polymorphisms (SNPs) on chromosome 15 were identified. Four of these six SNPs were located within two candidate genes, Glyma.15G015700 and Glyma.15G015800. The elite haplotype Glyma.15G015700<sup>Hap I</sup> with low DR exhibited strong resistance to SC7. The expression of Glyma.15G015700 in the SMV-resistant accession increased significantly after inoculation with SC7. Furthermore, most of the proteins predicted to interact with Glyma.15G015700 are heat shock proteins, which have been shown to be related to disease resistance. In summary, new SMV resistance loci and a new candidate gene, Glyma.15G015700, were identified and might be utilized in further soybean disease resistance breeding.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140958186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
SoxB family genes delay regeneration and cause abnormal movement in Dugesia japonica. SoxB 家族基因会延迟再生,并导致日本杉属植物的异常运动。
IF 3.1 3区 生物学
Molecular Genetics and Genomics Pub Date : 2024-05-16 DOI: 10.1007/s00438-024-02142-5
Yibo Yang, Ziyi Lin, Nannan Li, Ning Li, Dezeng Liu, Zimei Dong, Guangwen Chen
{"title":"SoxB family genes delay regeneration and cause abnormal movement in Dugesia japonica.","authors":"Yibo Yang, Ziyi Lin, Nannan Li, Ning Li, Dezeng Liu, Zimei Dong, Guangwen Chen","doi":"10.1007/s00438-024-02142-5","DOIUrl":"https://doi.org/10.1007/s00438-024-02142-5","url":null,"abstract":"<p><p>SoxB subfamily is an important branch of Sox family and plays a key role in animal physiological process, but little is known about their function in planarian regeneration. This study aims to evaluate the function of DjSoxB family genes in intact and regenerating planarians Dugesia japonica. Here, we amplify the full-length cDNA of DjSoxB1 and DjSoxB2 in D. japonica by rapid amplification of the cDNA ends (RACE), detect the expression of DjSoxB family genes in planarian. The results show that DjSoxBs are expressed in parenchymal tissue and the hybridization signals partially disappear after irradiation indicates DjSoxB family genes are expressed in neoblasts. After the RNA interference (RNAi) of DjSoxB1, DjSoxB2 and DjSoxB3 separately, the numbers of proliferative cells are all reduced that causes planarians show slower growth of blastema in the early stage of regeneration, and nerves of planarians are affected that the movement speed of planarians decreases in varying degrees. Specially, planarians in the DjSoxB3 RNAi group show shrinkage and twisting. Overall, this study reveals that DjSoxB family genes play a role in cell proliferation during regeneration. They also play an important role in the maintenance of normal nerve function and nerve regeneration. These results provide directions for the functional study of SoxB family genes and provide an important foundation for planarian regeneration.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140945505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
EMP1 correlated with cancer progression and immune characteristics in pan-cancer and ovarian cancer. EMP1与泛癌症和卵巢癌的癌症进展和免疫特征相关。
IF 2.3 3区 生物学
Molecular Genetics and Genomics Pub Date : 2024-05-14 DOI: 10.1007/s00438-024-02146-1
Jun Zhang, Jing Yang, Xing Li, Lin Mao, Yan Zhang, Yi Liu, Yindi Bao
{"title":"EMP1 correlated with cancer progression and immune characteristics in pan-cancer and ovarian cancer.","authors":"Jun Zhang, Jing Yang, Xing Li, Lin Mao, Yan Zhang, Yi Liu, Yindi Bao","doi":"10.1007/s00438-024-02146-1","DOIUrl":"10.1007/s00438-024-02146-1","url":null,"abstract":"<p><p>This study examines the prognostic role and immunological relevance of EMP1 (epithelial membrane protein-1) in a pan-cancer analysis, with a focus on ovarian cancer. Utilizing data from TCGA, CCLE, and GTEx databases, we assessed EMP1 mRNA expression and its correlation with tumor progression, prognosis, and immune microenvironment across various cancers. Our results indicate that EMP1 expression is significantly associated with poor prognosis in multiple cancer types, including ovarian, bladder, testicular, pancreatic, breast, brain, and uveal melanoma. Immune-related analyses reveal a positive correlation between EMP1 and immune cell infiltration, particularly neutrophils, macrophages, and dendritic cells, as well as high expression of immune checkpoint such as CD274, HAVCR2, IL10, PDCD1LG2, and TGFB1 in most tumors. In vivo experiments confirm that EMP1 promotes ovarian cancer cell proliferation, metastasis, and invasion. In conclusion, EMP1 emerges as a potential prognostic biomarker and therapeutic target in various cancers, particularly ovarian cancer, due to its influence on tumor progression and immune cell dynamics. Further research is warranted to elucidate the precise mechanisms of EMP1 in cancer biology and to translate these findings into clinical applications.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140922283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Distribution of pathogenic variants in the CFTR gene in a representative cohort of people with cystic fibrosis in the Kingdom of Bahrain. 巴林王国具有代表性的囊性纤维化患者队列中 CFTR 基因致病变体的分布情况。
IF 2.3 3区 生物学
Molecular Genetics and Genomics Pub Date : 2024-05-14 DOI: 10.1007/s00438-024-02119-4
Osama A Karim Majed, Fatema Osama Majed, Nabeel Jasim Almoamen, Husain Baqer Alsatrawi, Salma Dawood Shehabi, Jana Hrbková, Malgorzata Libik, Milan Macek
{"title":"Distribution of pathogenic variants in the CFTR gene in a representative cohort of people with cystic fibrosis in the Kingdom of Bahrain.","authors":"Osama A Karim Majed, Fatema Osama Majed, Nabeel Jasim Almoamen, Husain Baqer Alsatrawi, Salma Dawood Shehabi, Jana Hrbková, Malgorzata Libik, Milan Macek","doi":"10.1007/s00438-024-02119-4","DOIUrl":"10.1007/s00438-024-02119-4","url":null,"abstract":"<p><strong>Background: </strong>Cystic fibrosis (CF) is a rare multi-systemic recessive disorder. The spectrum and the frequencies of CFTR mutations causing CF vary amongst different populations in Europe and the Middle East. In this study, we characterised the distribution of CF-causing mutations (i.e. pathogenic variants in the  CFTR gene) in a representative CF cohort from the Kingdom of Bahrain based on a three-decade-long analysis at a single tertiary centre. We aim to improve CF genetic diagnostics, introduce of CF neonatal screening and provide CFTR modulator therapy (CFTRm).</p><p><strong>Methods: </strong>CFTR genotyping  and associated clinical information were drawn from a longitudinal cohort. We sequenced 56 people with CF (pwCF) that had one or both CFTR mutations unidentified and carried out comprehensive bioinformatic- and family-based segregation analyses of detected variants, including genotype-phenotype correlations and disease incidence estimates. The study methodology could serve as a basis for other non-European CF populations with a high degree of consanguinity.</p><p><strong>Results: </strong>Altogether 18 CF-causing mutations  were identified, 15 of which were not previously detected in Bahrain, accounting for close to 100% of all population-specific alleles. The most common alleles comprise c.1911delG [2043delG; 22.8%], c.2988+1G > A [3120+1G>A; 16.3%], c.2989-1G>A [3121-1G>A; 14.1%], c.3909C>G [N1303K; 13.0%], and c.1521_1523delCTT [p.PheF508del; 7.6%]. Although the proportion of 1st cousin marriages has decreased to 50%, the frequency of homozygosity in our pwCF is 67.4%, thereby indicating that CF still occurs in large, often related, families. pwCF in Bahrain present with faltering growth, pancreatic insufficiency and classical sino-pulmonary manifestations. Interestingly, two pwCF also suffer from sickle cell disease. The estimated incidence of CF in Bahrain based on data from the last three decades is 1 in 9,880 live births.</p><p><strong>Conclusion: </strong>The most commonCF-causing  mutations in Bahraini pwCF were identified, enabling more precise diagnosis, introduction of two-tier neonatal screening and fostering administration of CFTRm.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11093839/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140922213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Signature and function of plasma exosome-derived circular RNAs in patients with hypertensive intracerebral hemorrhage. 高血压脑出血患者血浆外泌体衍生环状 RNA 的特征和功能
IF 3.1 3区 生物学
Molecular Genetics and Genomics Pub Date : 2024-05-11 DOI: 10.1007/s00438-024-02144-3
Kejie Chen, Xiaoyuan Cheng, Shanshan Yuan, Yang Sun, Junli Hao, Quandan Tan, Yapeng Lin, Shuping Li, Jie Yang
{"title":"Signature and function of plasma exosome-derived circular RNAs in patients with hypertensive intracerebral hemorrhage.","authors":"Kejie Chen, Xiaoyuan Cheng, Shanshan Yuan, Yang Sun, Junli Hao, Quandan Tan, Yapeng Lin, Shuping Li, Jie Yang","doi":"10.1007/s00438-024-02144-3","DOIUrl":"https://doi.org/10.1007/s00438-024-02144-3","url":null,"abstract":"<p><p>Intracerebral hemorrhage (ICH) is one of the major causes of death and disability, and hypertensive ICH (HICH) is the most common type of ICH. Currently, the outcomes of HICH patients remain poor after treatment, and early prognosis prediction of HICH is important. However, there are limited effective clinical treatments and biomarkers for HICH patients. Although circRNA has been widely studied in diseases, the role of plasma exosomal circRNAs in HICH remains unknown. The present study was conducted to investigate the characteristics and function of plasma exosomal circRNAs in six HICH patients using circRNA microarray and bioinformatics analysis. The results showed that there were 499 differentially expressed exosomal circRNAs between the HICH patients and control subjects. According to GO annotation and KEGG pathway analyses, the targets regulated by differentially expressed exosomal circRNAs were tightly related to the development of HICH via nerve/neuronal growth, neuroinflammation and endothelial homeostasis. And the differentially expressed exosomal circRNAs could mainly bind to four RNA-binding proteins (EIF4A3, FMRP, AGO2 and HUR). Moreover, of differentially expressed exosomal circRNAs, hsa_circ_00054843, hsa_circ_0010493 and hsa_circ_00090516 were significantly associated with bleeding volume and Glasgow Coma Scale score of the subjects. Our findings firstly revealed that the plasma exosomal circRNAs are significantly involved in the progression of HICH, and could be potent biomarkers for HICH. This provides the basis for further research to pinpoint the best biomarkers and illustrate the mechanism of exosomal circRNAs in HICH.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140909603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Chromosome-Y haplogroups in Asturias (Northern Spain) and their association with severe COVID-19. 阿斯图里亚斯(西班牙北部)的染色体 Y 单倍群及其与严重 COVID-19 的关系。
IF 3.1 3区 生物学
Molecular Genetics and Genomics Pub Date : 2024-05-04 DOI: 10.1007/s00438-024-02143-4
Mar González-Fernández, Daniel Vázquez-Coto, Guillermo M Albaiceta, Laura Amado-Rodríguez, Marta G Clemente, Lucinda Velázquez-Cuervo, Claudia García-Lago, Juan Gómez, Eliecer Coto
{"title":"Chromosome-Y haplogroups in Asturias (Northern Spain) and their association with severe COVID-19.","authors":"Mar González-Fernández, Daniel Vázquez-Coto, Guillermo M Albaiceta, Laura Amado-Rodríguez, Marta G Clemente, Lucinda Velázquez-Cuervo, Claudia García-Lago, Juan Gómez, Eliecer Coto","doi":"10.1007/s00438-024-02143-4","DOIUrl":"https://doi.org/10.1007/s00438-024-02143-4","url":null,"abstract":"<p><p>The main objective of this study was to determine whether the common Y-haplogroups were be associated with the risk of developing severe COVID-19 in Spanish male. We studied 479 patients who required hospitalization due to COVID-19 and 285 population controls from the region of Asturias (northern Spain), They were genotyped for several polymorphisms that define the common European Y-haplogroups. We compared the frequencies between patients and controls aged ≤ 65 and >65 years. There were no different haplogroup frequencies between the two age groups of controls. Haplogroup R1b was less common in patients aged ≤65 years. Haplogroup I was more common in the two patient´s groups compared to controls (p = 0.02). Haplogroup R1b was significantly more frequent among hypertensive patients, without difference between the hypertensive and normotensive controls. This suggested that R1b could increase the risk for severe COVID-19 among male with pre-existing hypertension. In conclusion, we described the Y-haplogroup structure among Asturians. We found an increased risk of severe COVID-19 among haplogroup I carriers, and a significantly higher frequency of R1b among hypertensive patients. These results indicate that Y-chromosome variants could serve as markers to define the risk of developing a severe form of COVID-19.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11069473/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140869131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
CircSSBP2 acts as a MiR-2400 sponge to promote intramuscular preadipocyte proliferation by regulating NDRG1. CircSSBP2 作为 MiR-2400 的海绵,通过调节 NDRG1 促进肌肉内前脂肪细胞增殖。
IF 3.1 3区 生物学
Molecular Genetics and Genomics Pub Date : 2024-05-03 DOI: 10.1007/s00438-024-02138-1
Yanqing Zhao, Wenzhen Zhang, Sayed Haidar Abbas Raza, Xiaopeng Qu, Zhimei Yang, Jiahan Deng, Jing Ma, Bandar Hamad Aloufi, Juze Wang, Linsen Zan
{"title":"CircSSBP2 acts as a MiR-2400 sponge to promote intramuscular preadipocyte proliferation by regulating NDRG1.","authors":"Yanqing Zhao, Wenzhen Zhang, Sayed Haidar Abbas Raza, Xiaopeng Qu, Zhimei Yang, Jiahan Deng, Jing Ma, Bandar Hamad Aloufi, Juze Wang, Linsen Zan","doi":"10.1007/s00438-024-02138-1","DOIUrl":"10.1007/s00438-024-02138-1","url":null,"abstract":"<p><p>Intramuscular fat (IMF) is a critical factor in beef quality. IMF is mainly distributed between muscle fibres and its accumulation can affect the marbling and meat quality of beef. IMF formation and deposition is a complex process and in recent years a group of non-coding RNAs (ncRNAs), known as circRNAs, have been discovered to play an important role in regulating intramuscular fat deposition. CircRNAs form a covalent loop structure after reverse splicing of precursor mRNAs. They can act by adsorbing miRNAs, thereby reducing their repressive effects on downstream target genes. Based on high-throughput sequencing of circRNAs in intramuscular fat of Qinchuan and Japanese black cattle, we identified a novel circSSBP2 that is differentially expressed between the two species and associated with adipogenesis. We show that circSSBP2 knockdown promotes bovine intramuscular preadipocyte proliferation, whereas overexpression inhibits bovine intramuscular preadipocyte proliferation. We also show that circSSBP2 can act as a molecular sponge for miR-2400 and that miR-2400 overexpression promotes bovine intramuscular preadipocyte proliferation. Furthermore, N-myc downstream-regulated gene 1 (NDRG1) was identified as a direct target gene of miR-2400, and NDRG1 interference promoted the proliferation of bovine intramuscular preadipocytes. In conclusion, our results suggest that circSSBP2 inhibits the proliferation of bovine intramuscular preadipocytes by regulating the miR-2400/NDRG1 axis.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140863557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Construction of immune-related gene pairs signature to predict the overall survival of multiple myeloma patients based on whole bone marrow gene expression profiling 基于全骨髓基因表达谱构建免疫相关基因对特征以预测多发性骨髓瘤患者的总生存率
IF 3.1 3区 生物学
Molecular Genetics and Genomics Pub Date : 2024-04-22 DOI: 10.1007/s00438-024-02140-7
Farideh Jafari-Raddani, Zeinab Davoodi-Moghaddam, Davood Bashash
{"title":"Construction of immune-related gene pairs signature to predict the overall survival of multiple myeloma patients based on whole bone marrow gene expression profiling","authors":"Farideh Jafari-Raddani, Zeinab Davoodi-Moghaddam, Davood Bashash","doi":"10.1007/s00438-024-02140-7","DOIUrl":"https://doi.org/10.1007/s00438-024-02140-7","url":null,"abstract":"<p>Multiple myeloma (MM) is a plasma cell dyscrasia that is characterized by the uncontrolled proliferation of malignant PCs in the bone marrow. Due to immunotherapy, attention has returned to the immune system in MM, and it appears necessary to identify biomarkers in this area. In this study, we created a prognostic model for MM using immune-related gene pairs (IRGPs), with the advantage that it is not affected by technical bias. After retrieving microarray data of MM patients, bioinformatics analyses like COX regression and least absolute shrinkage and selection operator (LASSO) were used to construct the signature. Then its prognostic value is assessed via time-dependent receiver operating characteristic (ROC) and the Kaplan–Meier (KM) analysis. We also used XCELL to examine the status of immune cell infiltration among MM patients. 6-IRGP signatures were developed and proved to predict MM prognosis with a P-value of 0.001 in the KM analysis. Moreover, the risk score was significantly associated with clinicopathological characteristics and was an independent prognostic factor. Of note, the combination of age and β2-microglobulin with risk score could improve the accuracy of determining patients’ prognosis with the values of the area under the curve (AUC) of 0.73 in 5 years ROC curves. Our model was also associated with the distribution of immune cells. This novel signature, either alone or in combination with age and β2-microglobulin, showed a good prognostic predictive value and might be used to guide the management of MM patients in clinical practice.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140802702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
New comparative genomic evidence supporting the proteomic diversification role of A-to-I RNA editing in insects 支持昆虫 A 到 I RNA 编辑的蛋白质组多样化作用的新比较基因组证据
IF 3.1 3区 生物学
Molecular Genetics and Genomics Pub Date : 2024-04-20 DOI: 10.1007/s00438-024-02141-6
Jiyao Liu, Caiqing Zheng, Yuange Duan
{"title":"New comparative genomic evidence supporting the proteomic diversification role of A-to-I RNA editing in insects","authors":"Jiyao Liu, Caiqing Zheng, Yuange Duan","doi":"10.1007/s00438-024-02141-6","DOIUrl":"https://doi.org/10.1007/s00438-024-02141-6","url":null,"abstract":"<p>Adenosine-to-inosine (A-to-I) RNA editing, resembling A-to-G mutation, confers adaptiveness by increasing proteomic diversity in a temporal-spatial manner. This evolutionary theory named “proteomic diversifying hypothesis” has only partially been tested in very few organisms like <i>Drosophila melanogaster</i>, mainly by observing the positive selection on nonsynonymous editing events. To find additional genome-wide evidences supporting this interesting assumption, we retrieved the genomes of four <i>Drosophila</i> species and collected 20 deep-sequenced transcriptomes of different developmental stages and neuron populations of <i>D. melanogaster</i>. We systematically profiled the RNA editomes in these samples and performed meticulous comparative genomic analyses. Further evidences were found to support the diversifying hypothesis. (1) None of the nonsynonymous editing sites in <i>D. melanogaster</i> had ancestral G-alleles, while the silent editing sites had an unignorable fraction of ancestral G-alleles; (2) Only very few nonsynonymous editing sites in <i>D. melanogaster</i> had corresponding G-alleles derived in the genomes of sibling species, and the fraction of such situation was significantly lower than that of silent editing sites; (3) The few nonsynonymous editing with corresponding G-alleles had significantly more variable editing levels (across samples) than other nonsynonymous editing sites in <i>D. melanogaster</i>. The proteomic diversifying nature of RNA editing in <i>Drosophila</i> excludes the restorative role which favors an ancestral G-allele. The few fixed G-alleles in sibling species might facilitate the adaptation to particular environment and the corresponding nonsynonymous editing in <i>D. melanogaster</i> would introduce stronger advantage of flexible proteomic diversification. With multi-Omics data, our study consolidates the nature of evolutionary significance of A-to-I RNA editing sites in model insects.</p>","PeriodicalId":18816,"journal":{"name":"Molecular Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140624845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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