Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide. This study aimed to explore the role of hsa-miR-101-3p in HCC pathogenesis by identifying key genes and pathways. A comprehensive bioinformatics analysis revealed twelve hub genes (ETNK1, BICRA, IL1R1, KDM3A, ARID2, GSK3β, EZH2, NOTCH1, SMARCA4, FOS, CREB1, and CASP3) and highlighted their involvement in crucial oncogenic pathways, including PI3K/Akt, mTOR, MAPK, and TGF-β. Gene expression analysis showed significant overexpression of ETNK1, KDM3A, EZH2, SMARCA4, and CASP3 in HCC tissues, correlating with poorer survival outcomes. Drug screening identified therapeutic candidates, including Tazemetostat for EZH2 and lithium compounds for GSK3β, underscoring their potential for targeted treatment. These findings provide novel insights into the complexity of HCC pathogenesis, suggesting that the identified hub genes could serve as diagnostic or prognostic biomarkers and therapeutic targets. While bioinformatics-driven, this study offers a strong basis for future clinical validation to advance precision medicine in HCC.
{"title":"Comprehensive system biology analysis of microRNA-101-3p regulatory network identifies crucial genes and pathways in hepatocellular carcinoma","authors":"Nasim Rahimi-Farsi , Abozar Ghorbani , Negar Mottaghi-Dastjerdi , Taha Shahbazi , Fatemeh Bostanian , Parvin Mohseni , Fateme Yazdani","doi":"10.1016/j.jgeb.2025.100471","DOIUrl":"10.1016/j.jgeb.2025.100471","url":null,"abstract":"<div><div>Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide. This study aimed to explore the role of hsa-miR-101-3p in HCC pathogenesis by identifying key genes and pathways. A comprehensive bioinformatics analysis revealed twelve hub genes (ETNK1, BICRA, IL1R1, KDM3A, ARID2, GSK3β, EZH2, NOTCH1, SMARCA4, FOS, CREB1, and CASP3) and highlighted their involvement in crucial oncogenic pathways, including PI3K/Akt, mTOR, MAPK, and TGF-β. Gene expression analysis showed significant overexpression of ETNK1, KDM3A, EZH2, SMARCA4, and CASP3 in HCC tissues, correlating with poorer survival outcomes. Drug screening identified therapeutic candidates, including Tazemetostat for EZH2 and lithium compounds for GSK3β, underscoring their potential for targeted treatment. These findings provide novel insights into the complexity of HCC pathogenesis, suggesting that the identified hub genes could serve as diagnostic or prognostic biomarkers and therapeutic targets. While bioinformatics-driven, this study offers a strong basis for future clinical validation to advance precision medicine in HCC.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 1","pages":"Article 100471"},"PeriodicalIF":3.5,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143429475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-17DOI: 10.1016/j.jgeb.2025.100472
Jan Clyden B. Tenorio , Muhammad Fikri Heikal , Alok Kafle , Mark Andrian B. Macalalad , Fredmoore L. Orosco , Prasert Saichua , Sutas Suttiprapa
Background
Benzimidazole resistance is an emerging challenge among parasitic helminths. It is caused by single nucleotide polymorphisms (SNPs) in specific loci in helminths’ β-tubulin genes. Field studies and laboratory investigations reported resistance-associated SNPs in 4 codon locations with 7 allelic variations among hookworms. This study aimed to determine the effects of these mutations on the binding efficiency and behavior of the β-tubulin protein in four hookworm species against four benzimidazole drugs.
Methods
β-tubulin gene coding sequences of Ancylostoma caninum, A. duodenale, A. ceylanicum, and Necator americanus were retrieved, assessed phylogenetically, and used to construct the 3D structure models of the proteins. The modeled protein structures were verified and edited to contain the reported SNPs: Q134H, F167Y, E198A, E198K, E198V, F200L, and F200Y. Benzimidazole drugs such as albendazole (ABZ), fenbendazole (FBZ), mebendazole (MBZ) and oxfendazole (OBZ) were used as ligands. Molecular docking experiments were performed with the wild-type and mutated proteins. Molecular dynamics simulation assessed the dynamic behavior of the β-tubulin-benzimidazole complex.
Results
In silico docking assessments showed that various amino acid substitutions due to resistance-associated SNPs cause alterations in binding affinities and positions. E198K and Q134H in hookworm β-tubulins substantially weakened the binding affinities and altered the binding positions of benzimidazole drugs. Molecular dynamics analysis revealed that these mutations also caused marked reductions in the binding free energies owing to diminished hydrogen bond contacts with the benzimidazole ligands.
Conclusion
The evidence shown herein indicates that mutations at positions 198 and 134 are detrimental to conferring benzimidazole resistance among hookworms. The presence of these mutations may alter the efficacy of pharmacological interventions. Hence, further studies should be conducted to assess their emergence among hookworms in endemic areas with histories of chemotherapy.
{"title":"Unraveling the mechanisms of benzimidazole resistance in hookworms: A molecular docking and dynamics study","authors":"Jan Clyden B. Tenorio , Muhammad Fikri Heikal , Alok Kafle , Mark Andrian B. Macalalad , Fredmoore L. Orosco , Prasert Saichua , Sutas Suttiprapa","doi":"10.1016/j.jgeb.2025.100472","DOIUrl":"10.1016/j.jgeb.2025.100472","url":null,"abstract":"<div><h3>Background</h3><div>Benzimidazole resistance is an emerging challenge among parasitic helminths. It is caused by single nucleotide polymorphisms (SNPs) in specific loci in helminths’ β-tubulin genes. Field studies and laboratory investigations reported resistance-associated SNPs in 4 codon locations with 7 allelic variations among hookworms. This study aimed to determine the effects of these mutations on the binding efficiency and behavior of the β-tubulin protein in four hookworm species against four benzimidazole drugs.</div></div><div><h3>Methods</h3><div>β-tubulin gene coding sequences of <em>Ancylostoma caninum, A. duodenale, A. ceylanicum,</em> and <em>Necator americanus</em> were retrieved, assessed phylogenetically, and used to construct the 3D structure models of the proteins. The modeled protein structures were verified and edited to contain the reported SNPs: Q134H, F167Y, E198A, E198K, E198V, F200L, and F200Y. Benzimidazole drugs such as albendazole (ABZ), fenbendazole (FBZ), mebendazole (MBZ) and oxfendazole (OBZ) were used as ligands. Molecular docking experiments were performed with the wild-type and mutated proteins. Molecular dynamics simulation assessed the dynamic behavior of the β-tubulin-benzimidazole complex.</div></div><div><h3>Results</h3><div><em>In silico</em> docking assessments showed that various amino acid substitutions due to resistance-associated SNPs cause alterations in binding affinities and positions. E198K and Q134H in hookworm β-tubulins substantially weakened the binding affinities and altered the binding positions of benzimidazole drugs. Molecular dynamics analysis revealed that these mutations also caused marked reductions in the binding free energies owing to diminished hydrogen bond contacts with the benzimidazole ligands.</div></div><div><h3>Conclusion</h3><div>The evidence shown herein indicates that mutations at positions 198 and 134 are detrimental to conferring benzimidazole resistance among hookworms. The presence of these mutations may alter the efficacy of pharmacological interventions. Hence, further studies should be conducted to assess their emergence among hookworms in endemic areas with histories of chemotherapy.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 1","pages":"Article 100472"},"PeriodicalIF":3.5,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143429156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-17DOI: 10.1016/j.jgeb.2025.100469
Aariz Hussain, Areeba Fareed
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer with a five-year survival rate of just 7%. Its late diagnosis and limited treatment options contribute to poor outcomes. Immunotherapy has had little success due to PDAC’s dense and immunosuppressive tumor environment. Emerging mRNA vaccines, such as autogene cevumeran (BNT122), show promise in enhancing treatment. Preliminary trials have reported prolonged survival with minimal side effects. Despite this progress, the complexity of PDAC remains a significant challenge. Continued research is essential to fully realize the potential of mRNA-based therapies in combating this deadly cancer.
{"title":"Personalized medicine in pancreatic cancer: Harnessing the potential of mRNA vaccines","authors":"Aariz Hussain, Areeba Fareed","doi":"10.1016/j.jgeb.2025.100469","DOIUrl":"10.1016/j.jgeb.2025.100469","url":null,"abstract":"<div><div>Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer with a five-year survival rate of just 7%. Its late diagnosis and limited treatment options contribute to poor outcomes. Immunotherapy has had little success due to PDAC’s dense and immunosuppressive tumor environment. Emerging mRNA vaccines, such as autogene cevumeran (BNT122), show promise in enhancing treatment. Preliminary trials have reported prolonged survival with minimal side effects. Despite this progress, the complexity of PDAC remains a significant challenge. Continued research is essential to fully realize the potential of mRNA-based therapies in combating this deadly cancer.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 1","pages":"Article 100469"},"PeriodicalIF":3.5,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143429157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Thymus satureioides is an endemic and medicinal plant of Morocco, widely distributed in the arid and semiarid habitats. Communally used in traditional medicine. In the current study, twelve Inter-Simple Sequence Repeats (ISSR) primers combined with 11 agro-morphological traits were applied to evaluate 60 accessions of T. satureioides collected from 10 spontaneous sites covering most geographical area. These accessions were cultivated in two experimental stations Khémisset and Rabat. Variation coefficient of Phenotypic studied traits (CV) varied from 2.99 (inflorescence/stems) to 47.37 % (secondary branches/stem number). ANOVA showed very highly significant differences between accessions for of of all the studied traits (p < 0.0001). The experimental station of Khémisset recorded the highest values compared to Rabat. PCA plot showed that 90.39 % were the most six variable morphological characters. At 80 %, Cluster analysis grouped the accessions into two major clusters based on their morphological resemblance. AMOVA revealed that the molecular variation within and between accessions was demonstrated to 82 % and 18 %, respectively. The number of bands is ranged from 12 for primer UBC825 to 28 for primer ISSR-4, those amplified 119 band and generating 739 amplicons. The UPGMA dendrogram, established through dissimilarity index, exhibited three groups. PCoA plot revealed three major groups of populations and consistent with genetic relationships derived from Cluster analysis. Tamssount region recorded high values of genetic diversity (He = 0.182), percentage polymorphic loci (PPL = 63.03 %) and Shannon information index (I = 0.283). These results highlighted a variability that will be useful for the breeding program aiming at improving the productivity, conservation and domestication of Thymus satureioides.
{"title":"Morphological and genetic diversity assessment of cultivated Thymus satureioides (endemic species) of Morocco","authors":"Zoubida Belmahi , Khadija Bakhy , Fatima Gaboun , Rabha Abdelwahd , Karim Saghir , Soumiya Ouedrhiri , Hamid Khamar , Hanaa Abdelmoumen , Majid Mounir , Ghizlane Diria","doi":"10.1016/j.jgeb.2025.100467","DOIUrl":"10.1016/j.jgeb.2025.100467","url":null,"abstract":"<div><div><em>Thymus satureioides</em> is an endemic and medicinal plant of Morocco, widely distributed in the arid and semiarid habitats. Communally used in traditional medicine. In the current study, twelve Inter-Simple Sequence Repeats (ISSR) primers combined with 11 agro-morphological traits were applied to evaluate 60 accessions of <em>T. satureioides</em> collected from 10 spontaneous sites covering most geographical area. These accessions were cultivated in two experimental stations Khémisset and Rabat. Variation coefficient of Phenotypic studied traits (CV) varied from 2.99 (inflorescence/stems) to 47.37 % (secondary branches/stem number). ANOVA showed very highly significant differences between accessions for of of all the studied traits (p < 0.0001). The experimental station of Khémisset recorded the highest values compared to Rabat. PCA plot showed that 90.39 % were the most six variable morphological characters. At 80 %, Cluster analysis grouped the accessions into two major clusters based on their morphological resemblance. AMOVA revealed that the molecular variation within and between accessions was demonstrated to 82 % and 18 %, respectively. The number of bands is ranged from 12 for primer UBC825 to 28 for primer ISSR-4, those amplified 119 band and generating 739 amplicons. The UPGMA dendrogram, established through dissimilarity index, exhibited three groups. PCoA plot revealed three major groups of populations and consistent with genetic relationships derived from Cluster analysis. Tamssount region recorded high values of genetic diversity (He = 0.182), percentage polymorphic loci (PPL = 63.03 %) and Shannon information index (I = 0.283). These results highlighted a variability that will be useful for the breeding program aiming at improving the productivity, conservation and domestication of <em>Thymus satureioides</em>.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 1","pages":"Article 100467"},"PeriodicalIF":3.5,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143394852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-13DOI: 10.1016/j.jgeb.2025.100468
Ajay Kumar , Kanhaiya Singh , Amit Kumar Singh , Jai Prakash , Amit Kumar Goswami , Gyan Prakash Mishra , Vishaw Bandhu Patel , Suman Lata , Anshuman Singh
Indian blackberry (Syzygium cumini L.) also known as jamun is a very important underutilized fruit crop with notable medicinal and economic value. However, its genetic improvement has been constrained by limited knowledge of the genetic diversity within existing collections. Therefore, a comprehensive characterization of genetic diversity in this species, using molecular tools, is essential to support effective germplasm management and application in breeding programs. In this investigation, a total of 32 jamun genotypes consisting of 30 seedling-origin genotypes, one improved cultivar CISH J-37 and one wild genotype (Syzygium fruitecosum) were analysed using the two gene-targeted markers, CBDP and SCoT. In total, 29 primers (22 CBDP and 7 SCoT primers) detected genetic polymorphism across the genotypes. The CBDP markers amplified a higher polymorphism percentage, 94.85% across 291 bands, than the SCoT markers, 92.75% across 69 bands. The mean PIC values for CBDP and SCoT were 0.28 and 0.31, respectively. MI values were higher for CBDP (3.21) than for SCoT (2.88). Cluster analysis using UPGMA identified six clades, which grouped genotypes into seedling-origin, improved and wild categories. The PCoA based on molecular profiling data of CBDP, SCoT and both together explained 26.65%, 38.39% and 23.22% of the variation respectively. AMOVA results revealed that 85–90% of genetic variation existed within populations. Bayesian STRUCTURE analysis grouped genotypes into two major populations confirming genetic divergence between seedling-origin, improved and wild genotypes. This study is the first to integrate CBDP and SCoT markers for genetic diversity analysis of the Indian blackberry. The results highlight the utility of these markers in genetic variation assessment and would help design germplasm conservation and breeding strategies in this crop.
{"title":"Genetic diversity and population structure analysis of Indian blackberry (Syzygium cumini L.) using CAAT box‑derived polymorphism (CBDP) and start codon targeted polymorphism (SCoT) markers","authors":"Ajay Kumar , Kanhaiya Singh , Amit Kumar Singh , Jai Prakash , Amit Kumar Goswami , Gyan Prakash Mishra , Vishaw Bandhu Patel , Suman Lata , Anshuman Singh","doi":"10.1016/j.jgeb.2025.100468","DOIUrl":"10.1016/j.jgeb.2025.100468","url":null,"abstract":"<div><div>Indian blackberry (<em>Syzygium cumini</em> L.) also known as jamun is a very important underutilized fruit crop with notable medicinal and economic value. However, its genetic improvement has been constrained by limited knowledge of the genetic diversity within existing collections. Therefore, a comprehensive characterization of genetic diversity in this species, using molecular tools, is essential to support effective germplasm management and application in breeding programs. In this investigation, a total of 32 jamun genotypes consisting of 30 seedling-origin genotypes, one improved cultivar CISH J-37 and one wild genotype (<em>Syzygium fruitecosum</em>) were analysed using the two gene-targeted markers, CBDP and SCoT. In total, 29 primers (22 CBDP and 7 SCoT primers) detected genetic polymorphism across the genotypes. The CBDP markers amplified a higher polymorphism percentage, 94.85% across 291 bands, than the SCoT markers, 92.75% across 69 bands. The mean PIC values for CBDP and SCoT were 0.28 and 0.31, respectively. MI values were higher for CBDP (3.21) than for SCoT (2.88). Cluster analysis using UPGMA identified six clades, which grouped genotypes into seedling-origin, improved and wild categories. The PCoA based on molecular profiling data of CBDP, SCoT and both together explained 26.65%, 38.39% and 23.22% of the variation respectively. AMOVA results revealed that 85–90% of genetic variation existed within populations. Bayesian STRUCTURE analysis grouped genotypes into two major populations confirming genetic divergence between seedling-origin, improved and wild genotypes. This study is the first to integrate CBDP and SCoT markers for genetic diversity analysis of the Indian blackberry. The results highlight the utility of these markers in genetic variation assessment and would help design germplasm conservation and breeding strategies in this crop.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 1","pages":"Article 100468"},"PeriodicalIF":3.5,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143403648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-11DOI: 10.1016/j.jgeb.2025.100464
Eman M. Ragab, Abeer A. Khamis, Tarek M. Mohamed, Doaa M. El Gamal
Background
Cancer cells display oxidative metabolic dysregulation to fulfill their bioenergy requirements. Specifically, efforts were made to regulate the metabolite succinate and its negative effects as an inducer for neoplasm invasion and metastasis.
Methods
Binding affinity of naringenin (NAR) to mitochondria complex II (CΙΙ) subunits, sirtuin3 (SIRT3), tumor necrosis factor associate protein 1(TRAP1), and succinate receptor (SUCNR1) was studied by molecular docking. NAR nanoparticles (NARNPs) were synthesized and characterized by IR, X-ray, UV, drug release, zeta potential, TEM, and SEM. The IC50 was evaluated in normal mice, normal fibroblast, and A549 cells by using the MTT technique. Moreover, the impact of NAR and NARNPs against 5-FLU on CΙΙ activity, SOD activity, and mitochondrial swelling was assessed. Apoptosis was also assessed using the flow cytometry method. While the expression of relevant genes such as SDHC, D, SIRT-3, TRAP1, SUCNR1, and ERK1/2 genes was determined by using RT-qPCR analysis. Western blot evaluated PI3K, NF-κB against β-actin.
Results
Theoretically, the binding affinity between NAR & SDHC, D, SIRT-3, TRAP1, and SUCNR1 proteins was stronger. Cytotoxic effects of NAR and NARNPs were evaluated. Also, the activity of SDH C, and D was inhibited more than SDH A, and B activity in the A549 than normal cell lines (NARNPs < NAR < 5-FLU), This was accompanied by downregulation of SDH C, D, TRAP1, SUCNR1, and ERK1/2 genes expression, and upregulation of SIRT-3 gene expression. Additionally, NF-κB and PI3K protein expression declined. On the other hand, there was a significant increase in apoptotic effects with mitochondria enlargement (NARNPs > NAR > 5-FLU) in A549 compared with normal cells.
In conclusion
Controlling succinate by SDH parallel with SUCNR1 signal regulation by NARNPs will be a novel understanding mechanism and candidate for therapeutic target in lung cancer.
{"title":"Management succinate release through SDHA by G protein-coupled receptor 91 signal, TRAP1, and SIRT3 regulation in lung cancer cells by NAR nanoparticles","authors":"Eman M. Ragab, Abeer A. Khamis, Tarek M. Mohamed, Doaa M. El Gamal","doi":"10.1016/j.jgeb.2025.100464","DOIUrl":"10.1016/j.jgeb.2025.100464","url":null,"abstract":"<div><h3>Background</h3><div>Cancer cells display oxidative metabolic dysregulation to fulfill their bioenergy requirements. Specifically, efforts were made to regulate the metabolite succinate and its negative effects as an inducer for neoplasm invasion and metastasis.</div></div><div><h3>Methods</h3><div>Binding affinity of naringenin (NAR) to mitochondria complex II (CΙΙ) subunits, sirtuin3 (SIRT3), tumor necrosis factor associate protein 1(TRAP1), and succinate receptor (SUCNR1) was studied by molecular docking. NAR nanoparticles (NARNPs) were synthesized and characterized by IR, X-ray, UV, drug release, zeta potential, TEM, and SEM. The IC<sub>50</sub> was evaluated in normal mice, normal fibroblast, and A549 cells by using the MTT technique. Moreover, the impact of NAR and NARNPs against 5-FLU on CΙΙ activity, SOD activity, and mitochondrial swelling was assessed. Apoptosis was also assessed using the flow cytometry method. While the expression of relevant genes such as SDHC, D, SIRT-3, TRAP1, SUCNR1, and ERK1/2 genes was determined by using RT-qPCR analysis. Western blot evaluated PI3K, NF-κB against β-actin.</div></div><div><h3>Results</h3><div>Theoretically, the binding affinity between NAR & SDHC, D, SIRT-3, TRAP1, and SUCNR1 proteins was stronger. Cytotoxic effects of NAR and NARNPs were evaluated. Also, the activity of SDH C, and D was inhibited more than SDH A, and B activity in the A549 than normal cell lines (NARNPs < NAR < 5-FLU), This was accompanied by downregulation of SDH C, D, TRAP1, SUCNR1, and ERK1/2 genes expression, and upregulation of SIRT-3 gene expression. Additionally, NF-κB and PI3K protein expression declined. On the other hand, there was a significant increase in apoptotic effects with mitochondria enlargement (NARNPs > NAR > 5-FLU) in A549 compared with normal cells.</div></div><div><h3>In conclusion</h3><div>Controlling succinate by SDH parallel with SUCNR1 signal regulation by NARNPs will be a novel understanding mechanism and candidate for therapeutic target in lung cancer.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 1","pages":"Article 100464"},"PeriodicalIF":3.5,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143386442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pigeonpea is an important legume valued for its high nutritional, agricultural, and economic significance in the Asian subcontinent. Despite its potential for high yield, productivity remains stagnant due to several abiotic and biotic stresses. To mitigate these challenges, biotechnological interventions like genome editing offer promising solutions. Towards this, developing a species-specific editing toolkit is crucial for recalcitrant species like pigeonpea. In this study, we established a CRISPR/Cas9 genome editing system targeting the phytoene desaturase (PDS) gene. We developed pigeonpea-compatible vector components, including the CcU6_7.1 promoter and an amenable Cas9 gene driven by the potato ubiquitin promoter, creating a pigeonpea-specific CRISPR/Cas9 binary vector (PP_CRISPR_pCAMBIA2301). The system was validated by Agrobacterium tumefaciens-mediated apical meristem-targeted in planta and in vitro embryonic axis explant transformations, with gene knockout confirmed by albino/bleached phenotypes. Editing efficiencies were 8.80% and 9.16% in the in planta and in vitro transformations respectively. While PCR analysis confirmed T-DNA integration, sequence analysis identified PDS gene mutations. Stability of the phenotype was demonstrated in T1 generation plants of in planta transformation-developed mutants. This system may support functional genomics studies and trait improvement in pigeonpea and other legumes.
{"title":"Establishing a CRISPR/Cas9 genome editing framework in pigeonpea (Cajanus cajan L.) by targeting phytoene desaturase (PDS) gene disruption","authors":"Kameshwaran Senthil, Maniraj Rathinam, Manisha Parashar , Narasimham Dokka , Shaily Tyagi, Vandana Mathur, Sandhya Sharma, Kishor Gaikwad, Ramcharan Bhattacharya, Rohini Sreevathsa","doi":"10.1016/j.jgeb.2025.100465","DOIUrl":"10.1016/j.jgeb.2025.100465","url":null,"abstract":"<div><div>Pigeonpea is an important legume valued for its high nutritional, agricultural, and economic significance in the Asian subcontinent. Despite its potential for high yield, productivity remains stagnant due to several abiotic and biotic stresses. To mitigate these challenges, biotechnological interventions like genome editing offer promising solutions. Towards this, developing a species-specific editing toolkit is crucial for recalcitrant species like pigeonpea. In this study, we established a CRISPR/Cas9 genome editing system targeting the <em>phytoene desaturase</em> (<em>PDS</em>) gene. We developed pigeonpea-compatible vector components, including the <em>Cc</em>U6_7.1 promoter and an amenable Cas9 gene driven by the potato ubiquitin promoter, creating a pigeonpea-specific CRISPR/Cas9 binary vector (PP_CRISPR_pCAMBIA2301). The system was validated by <em>Agrobacterium tumefaciens</em>-mediated apical meristem-targeted <em>in planta</em> and <em>in vitro</em> embryonic axis explant transformations, with gene knockout confirmed by albino/bleached phenotypes. Editing efficiencies were 8.80% and 9.16% in the <em>in planta</em> and <em>in vitro</em> transformations respectively. While PCR analysis confirmed T-DNA integration, sequence analysis identified <em>PDS</em> gene mutations. Stability of the phenotype was demonstrated in T<sub>1</sub> generation plants of <em>in planta</em> transformation-developed mutants. This system may support functional genomics studies and trait improvement in pigeonpea and other legumes.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 1","pages":"Article 100465"},"PeriodicalIF":3.5,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143326023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.jgeb.2025.100462
Noor A. Mohammed , Ghassan M. Sulaiman , Hazima M. Alabassi , Khalil A.A. Khalil , Elsadig M. Ahmed
The study aims to evaluate the significant role of interleukin 15 (IL-15), IL-22, IL-37, and Caspase 9 gene expression in polycystic ovary syndrome (PCOS), focusing on the underlying mechanisms and potential diagnostic or therapeutic implications. Peripheral blood has been collected, and serum was separated for the evaluation of the serum IL-15, IL-22, and IL-37. The ELISA technique has been carried out to determine the serum levels of understudied factors mentioned above in Iraqi women patients diagnosed with PCOS (No. = 90) via a specialized gynecologist and healthy fertile women (No. = 48) as a control group. In addition, a genetic study on the expression of the caspase 9 gene in these patients had been performed. The data reveals statistically significant differences in interleukin levels in PCOS patients versus the control group. Specifically, the PCOS group exhibits significantly higher levels of IL-15 and IL-22 as compared to the control group. Conversely, the PCOS group shows significantly lower levels of IL-37 compared to the control group. The results showed no statistically significant difference in the mean expression of the Caspase 9 gene when comparing these fold graduations. However, it’s worth noting that a higher fold frequency was observed in both the PCOS and control groups, with 57.1 % and 60 %, respectively, having folds less than 1. The distribution of folds varied across other categories was also addressed. Additionally, there was a notable difference in the frequency of 11.4 % in the PCOS group compared to 2 % in the control group for folds greater than 9. The findings suggest that interleukins, particularly IL-22 and IL-37, hold promise as diagnostic markers for distinguishing PCOS from healthy conditions. However, the potential diagnostic utility of the Caspase 9 gene expression was not confirmed in this study.
{"title":"The significant role of IL-15, IL-22, IL-37, and caspase 9 in polycystic ovary syndrome: A case-control study in a sample of Iraqi women","authors":"Noor A. Mohammed , Ghassan M. Sulaiman , Hazima M. Alabassi , Khalil A.A. Khalil , Elsadig M. Ahmed","doi":"10.1016/j.jgeb.2025.100462","DOIUrl":"10.1016/j.jgeb.2025.100462","url":null,"abstract":"<div><div>The study aims to evaluate the significant role of interleukin 15 (IL-15), IL-22, IL-37, and Caspase 9 gene expression in polycystic ovary syndrome (PCOS), focusing on the underlying mechanisms and potential diagnostic or therapeutic implications. Peripheral blood has been collected, and serum was separated for the evaluation of the serum IL-15, IL-22, and IL-37. The ELISA technique has been carried out to determine the serum levels of understudied factors mentioned above in Iraqi women patients diagnosed with PCOS (No. = 90) via a specialized gynecologist and healthy fertile women (No. = 48) as a control group. In addition, a genetic study on the expression of the caspase 9 gene in these patients had been performed. The data reveals statistically significant differences in interleukin levels in PCOS patients versus the control group. Specifically, the PCOS group exhibits significantly higher levels of IL-15 and IL-22 as compared to the control group<em>.</em> Conversely, the PCOS group shows significantly lower levels of IL-37 compared to the control group. The results showed no statistically significant difference in the mean expression of the Caspase 9 gene when comparing these fold graduations. However, it’s worth noting that a higher fold frequency was observed in both the PCOS and control groups, with 57.1 % and 60 %, respectively, having folds less than 1. The distribution of folds varied across other categories was also addressed. Additionally, there was a notable difference in the frequency of 11.4 % in the PCOS group compared to 2 % in the control group for folds greater than 9. The findings suggest that interleukins, particularly IL-22 and IL-37, hold promise as diagnostic markers for distinguishing PCOS from healthy conditions. However, the potential diagnostic utility of the Caspase 9 gene expression was not confirmed in this study.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 1","pages":"Article 100462"},"PeriodicalIF":3.5,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143128826","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-27DOI: 10.1016/j.jgeb.2025.100460
Aman D. Moudgil, Anil K. Nehra
The hard tick Hyalomma dromedarii, a vector for numerous animal and human pathogens, was investigated for genetic diversity using the mitochondrial cytochrome C oxidase subunit I (cox I) and 16S ribosomal RNA (16S rRNA) genes. Hyalomma dromedarii sequences (n = 11 cox I; n = 7 16S rRNA) were deposited in GenBank (LC761179-89, LC761173-78, LC654692), showing 99.52–100 % (cox I) and 98.15–100 % (16S rRNA) similarity to existing GenBank sequences. Phylogenetic analysis revealed monophyletic clades for H. dromedarii sequences from this study and GenBank. Haplotype network analysis identified 34 and 11 haplotypes for the cox I and 16S rRNA genes, respectively, displaying stellate configurations. The overall cox I dataset showed very low nucleotide diversity (0.0019 ± 0.0002) and high haplotype diversity (0.535 ± 0.052). In contrast, the 16S rRNA gene dataset displayed low nucleotide (0.00211 ± 0.00071) and haplotype (0.351 ± 0.079) diversities. Neutrality tests showed significant negative values (Tajima’s D, Fu and Li’s D, and Fu and Li’s F), indicating recent population expansion or selective sweep. Pairwise FST values (−0.00942 to 0.02007 for cox I; −0.04878 to 0 for 16S rRNA) suggested non-significant genetic differentiation between populations, supported by high gene flow (Nm) values. This study provided novel insights into H. dromedarii population genetics, revealing recent expansion, weak population differentiation, and high gene flow. These findings have implications for understanding the tick’s evolutionary history and epidemiological significance.
{"title":"Mitochondrial genetic markers based phylogenetic analyses of Hyalomma dromedarii Koch, 1844 (Acari: Ixodidae)","authors":"Aman D. Moudgil, Anil K. Nehra","doi":"10.1016/j.jgeb.2025.100460","DOIUrl":"10.1016/j.jgeb.2025.100460","url":null,"abstract":"<div><div>The hard tick <em>Hyalomma dromedarii</em>, a vector for numerous animal and human pathogens, was investigated for genetic diversity using the mitochondrial cytochrome <em>C</em> oxidase subunit I (<em>cox I</em>) and 16S ribosomal RNA (<em>16S rRNA</em>) genes. <em>Hyalomma dromedarii</em> sequences (n = 11 <em>cox I</em>; n = 7 <em>16S rRNA</em>) were deposited in GenBank (LC761179-89, LC761173-78, LC654692), showing 99.52–100 % (<em>cox I</em>) and 98.15–100 % (<em>16S rRNA</em>) similarity to existing GenBank sequences. Phylogenetic analysis revealed monophyletic clades for <em>H. dromedarii</em> sequences from this study and GenBank. Haplotype network analysis identified 34 and 11 haplotypes for the <em>cox I</em> and <em>16S rRNA</em> genes, respectively, displaying stellate configurations. The overall <em>cox I</em> dataset showed very low nucleotide diversity (0.0019 ± 0.0002) and high haplotype diversity (0.535 ± 0.052). In contrast, the <em>16S rRNA</em> gene dataset displayed low nucleotide (0.00211 ± 0.00071) and haplotype (0.351 ± 0.079) diversities. Neutrality tests showed significant negative values (Tajima’s D, Fu and Li’s D, and Fu and Li’s F), indicating recent population expansion or selective sweep. Pairwise F<sub><em>ST</em></sub> values (−0.00942 to 0.02007 for <em>cox I</em>; −0.04878 to 0 for <em>16S rRNA</em>) suggested non-significant genetic differentiation between populations, supported by high gene flow (Nm) values. This study provided novel insights into <em>H. dromedarii</em> population genetics, revealing recent expansion, weak population differentiation, and high gene flow. These findings have implications for understanding the tick’s evolutionary history and epidemiological significance.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 1","pages":"Article 100460"},"PeriodicalIF":3.5,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143128822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-25DOI: 10.1016/j.jgeb.2025.100463
Raúl Vargas , Carmen N. Vigo , Lily Juarez-Contreras , Manuel Oliva-Cruz
The genetic improvement of Physalis peruviana L. faces important challenges because it is a recalcitrant species, which limits its use in breeding and conservation programs. In the present research, the objective was to develop an effective regeneration protocol using cotyledon cultures. For this purpose, the effects of zeatin (ZT) and meta-topoline (mT) at concentrations of 0, 0.5, 1.0 and 2.0 mg/L and the effects of several auxins, including indolbutyric acid (IBA), indolacetic acid (IAA), naphthaleneacetic acid (NAA) and 2.4-dichlorophenoxyacetic acid (2.4-D), on morphogenetic responses were evaluated. A maximum regeneration of 62.5 % was achieved with the combination of 2 mg/L ZT, 2 mg/L mT, and 0.5–1 mg/L IBA. For root formation, the best results were obtained with the combination of 2 mg/L ZT, 2 mg/L mT, and 1 mg/L NAA, reaching a maximum rate of 87.5 %. In conclusion, specific combinations of cytokinins and auxins can overcome the resistance of P. peruviana to regeneration and provide a solid basis for biotechnological applications such as genetic transformation and germplasm conservation.
{"title":"Development and optimization of in vitro shoot regeneration in Physalis peruviana using cotyledon explants","authors":"Raúl Vargas , Carmen N. Vigo , Lily Juarez-Contreras , Manuel Oliva-Cruz","doi":"10.1016/j.jgeb.2025.100463","DOIUrl":"10.1016/j.jgeb.2025.100463","url":null,"abstract":"<div><div>The genetic improvement of <em>Physalis peruviana</em> L. faces important challenges because it is a recalcitrant species, which limits its use in breeding and conservation programs. In the present research, the objective was to develop an effective regeneration protocol using cotyledon cultures. For this purpose, the effects of zeatin (ZT) and <em>meta</em>-topoline (mT) at concentrations of 0, 0.5, 1.0 and 2.0 mg/L and the effects of several auxins, including indolbutyric acid (IBA), indolacetic acid (IAA), naphthaleneacetic acid (NAA) and 2.4-dichlorophenoxyacetic acid (2.4-D), on morphogenetic responses were evaluated. A maximum regeneration of 62.5 % was achieved with the combination of 2 mg/L ZT, 2 mg/L mT, and 0.5–1 mg/L IBA. For root formation, the best results were obtained with the combination of 2 mg/L ZT, 2 mg/L mT, and 1 mg/L NAA, reaching a maximum rate of 87.5 %. In conclusion, specific combinations of cytokinins and auxins can overcome the resistance of <em>P. peruviana</em> to regeneration and provide a solid basis for biotechnological applications such as genetic transformation and germplasm conservation.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 1","pages":"Article 100463"},"PeriodicalIF":3.5,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143128886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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