Pub Date : 2024-11-02DOI: 10.1016/j.bbrep.2024.101862
Sofi Imran Ul Umar , Sushil Prasad , Soumen Naskar , Pooja Chowdhury , Anju Rana , Pranab Jyoti Das
Achieving the optimum extraction of RNA from spermatozoal cells is crucial for carrying out effective high-throughput analysis regarding its role in fertility and other reproduction processes in Bos indicus. Nevertheless, semen comprises spermatozoa and several other secretions from the male reproductive system, which as well consist of diverse somatic cell types. Therefore, the elimination of somatic cells guarantees the purity of the sperm RNA. In the present study, we tested five different RNA isolation protocols and evaluated them for their yield and purity using spectrophotometer and polymerase chain reaction. Among the five RNA isolation protocols, the Triazol + RNAeasy plus Kit + TCEP method revealed optimum performance. We successfully achieved isolation of spermatozoal RNA without any spermatozoal DNA contamination from Bos indicus spermatozoa that contains approx. 1000 to 10,000 times less RNA as compared to other mammalian somatic cells. RNA quality was assessed using primers Protamine1 (spermatozoal RNA and spermatozoal DNA), CDH1 (epithelial cell), KIT (germ cell) and PTPRC (leukocytes) designed using primer BLAST where there was no product amplified except Prm1 whose product size was specific for spermatozoal RNA. The results of our investigation on RNA isolation procedures indicate that the inclusion of a disulphide reducing agent (TCEP) is crucial for the process of sperm cell lysis.
{"title":"Development and optimization of an efficient RNA isolation protocol from bovine (Bos indicus) spermatozoa","authors":"Sofi Imran Ul Umar , Sushil Prasad , Soumen Naskar , Pooja Chowdhury , Anju Rana , Pranab Jyoti Das","doi":"10.1016/j.bbrep.2024.101862","DOIUrl":"10.1016/j.bbrep.2024.101862","url":null,"abstract":"<div><div>Achieving the optimum extraction of RNA from spermatozoal cells is crucial for carrying out effective high-throughput analysis regarding its role in fertility and other reproduction processes in <em>Bos indicus</em>. Nevertheless, semen comprises spermatozoa and several other secretions from the male reproductive system, which as well consist of diverse somatic cell types. Therefore, the elimination of somatic cells guarantees the purity of the sperm RNA. In the present study, we tested five different RNA isolation protocols and evaluated them for their yield and purity using spectrophotometer and polymerase chain reaction. Among the five RNA isolation protocols, the Triazol + RNAeasy plus Kit + TCEP method revealed optimum performance. We successfully achieved isolation of spermatozoal RNA without any spermatozoal DNA contamination from <em>Bos indicus</em> spermatozoa that contains approx. 1000 to 10,000 times less RNA as compared to other mammalian somatic cells. RNA quality was assessed using primers <em>Protamine1</em> (spermatozoal RNA and spermatozoal DNA), <em>CDH1</em> (epithelial cell), <em>KIT</em> (germ cell) and <em>PTPRC</em> (leukocytes) designed using primer BLAST where there was no product amplified except <em>Prm1</em> whose product size was specific for spermatozoal RNA. The results of our investigation on RNA isolation procedures indicate that the inclusion of a disulphide reducing agent (TCEP) is crucial for the process of sperm cell lysis.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"40 ","pages":"Article 101862"},"PeriodicalIF":2.3,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142573066","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}
Uterine corpus endometrial carcinoma (UCEC), derived from the endometrium, is the most common type of endometrial malignasis. This gynecological malignancy is very common all over the world, especially in developed countries and shows a potentially rising trend correlated with the increase in obese women.
Methods
Differentially Expressed Genes (DEGs) analysis was conducted on GSE7305 and GSE25628 datasets from the Gene Expression Omnibus (GEO). DEGs were identified using GEO2R (adjusted p-value <0.05, |logFC| > 1). Pathway analysis employed KEGG and Gene Ontology databases, while protein-protein interactions were analyzed using Cytoscape and Gephi. GEPIA was used for target gene validation.
Results
We have identified 304 common DEGs and 78 hub genes using GEO and PPI analysis, respectively. The GO and KEGG pathways analysis revealed enrichment of DEGs in extracellular matrix structural constituent, extracellular space, cell adhesion, and ECM-receptor interaction. GEPIA analysis identified three genes, ENG, GNG4, and ECT2, whose expression significantly differed between normal and tumor samples.
Conclusion
This analysis study identified the hub genes and associated pathways involved in the pathogenesis of UCEC. The identified hub genes exhibit remarkable potential as diagnostic biomarkers, providing a significant opportunity for early diagnosis and more effective therapeutic approaches for UCEC.
{"title":"Identification of hub genes and pathways in Uterine corpus endometrial carcinoma (UCEC): A comprehensive in silico study","authors":"Mahsa Ejlalidiz , Ameneh Mehri-Ghahfarrokhi , Mohammadreza Saberiyan","doi":"10.1016/j.bbrep.2024.101860","DOIUrl":"10.1016/j.bbrep.2024.101860","url":null,"abstract":"<div><h3>Background</h3><div>Uterine corpus endometrial carcinoma (UCEC), derived from the endometrium, is the most common type of endometrial malignasis. This gynecological malignancy is very common all over the world, especially in developed countries and shows a potentially rising trend correlated with the increase in obese women.</div></div><div><h3>Methods</h3><div>Differentially Expressed Genes (DEGs) analysis was conducted on GSE7305 and GSE25628 datasets from the Gene Expression Omnibus (GEO). DEGs were identified using GEO2R (adjusted p-value <0.05, |logFC| > 1). Pathway analysis employed KEGG and Gene Ontology databases, while protein-protein interactions were analyzed using Cytoscape and Gephi. GEPIA was used for target gene validation.</div></div><div><h3>Results</h3><div>We have identified 304 common DEGs and 78 hub genes using GEO and PPI analysis, respectively. The GO and KEGG pathways analysis revealed enrichment of DEGs in extracellular matrix structural constituent, extracellular space, cell adhesion, and ECM-receptor interaction. GEPIA analysis identified three genes, ENG, GNG4, and ECT2, whose expression significantly differed between normal and tumor samples.</div></div><div><h3>Conclusion</h3><div>This analysis study identified the hub genes and associated pathways involved in the pathogenesis of UCEC. The identified hub genes exhibit remarkable potential as diagnostic biomarkers, providing a significant opportunity for early diagnosis and more effective therapeutic approaches for UCEC.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"40 ","pages":"Article 101860"},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142573054","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}
Breast cancer (BC) presents as a worldwide challenge, known as the most frequently diagnosed cancer in women. In 2022, BC was diagnosed in 2.3 million women with 670,000 deaths globally. In this research, our objective was to examine the CST7 and has-miR-4793-5p gene expression in BC tumor tissues and adjacent normal tissues.
Using GSE57897 gene expression data from 422 BC samples and 31 breast samples from healthy controls which was based on the Platform GPL18722 (spotted oligonucleotide Homo sapiens microRNA (miRNA) array) in the Gene Expression Omnibus (GEO) and compare with miRNAs with a conserved target location on CST7 mRNA were found using databases. The study population included 60 fresh BC tissue samples and adjacent normal tissues as control. The Quantitative Real-Time PCR was used to evaluate the expression levels of CST7 and has-miR-4793-5p in the breast tissues.
The present study, found that CST7 and hsa-miR-4793-5p were significantly increased in tumoral tissues in compare to normal tissues. Further analysis revealed a remarkable association between CST7 and hsa-miR-4793-5p gene expression alteration. ROC curve analysis demonstrated high accuracy for CST7 expression in BC tumors. Comparison of gene expression between different stages and patient family history showed significant findings. Due to the high sensitivity and specificity of the expression changes of these two genes, they are suitable candidates for further investigations to be considered as part of a diagnosis and prognosis panel.
{"title":"Investigation of CST7 and hsa-miR-4793-5p gene expression in breast cancer","authors":"Niloufar Sadat Kalaki , Mozhgan Ahmadzadeh , Mandana Dehghan , Venus Shahabi Rabori , Sima Davoudi , Hamed Afkhami","doi":"10.1016/j.bbrep.2024.101863","DOIUrl":"10.1016/j.bbrep.2024.101863","url":null,"abstract":"<div><div>Breast cancer (BC) presents as a worldwide challenge, known as the most frequently diagnosed cancer in women. In 2022, BC was diagnosed in 2.3 million women with 670,000 deaths globally. In this research, our objective was to examine the CST7 and has-miR-4793-5p gene expression in BC tumor tissues and adjacent normal tissues.</div><div>Using GSE57897 gene expression data from 422 BC samples and 31 breast samples from healthy controls which was based on the Platform GPL18722 (spotted oligonucleotide Homo sapiens microRNA (miRNA) array) in the Gene Expression Omnibus (GEO) and compare with miRNAs with a conserved target location on CST7 mRNA were found using databases. The study population included 60 fresh BC tissue samples and adjacent normal tissues as control. The Quantitative Real-Time PCR was used to evaluate the expression levels of CST7 and has-miR-4793-5p in the breast tissues.</div><div>The present study, found that CST7 and hsa-miR-4793-5p were significantly increased in tumoral tissues in compare to normal tissues. Further analysis revealed a remarkable association between CST7 and hsa-miR-4793-5p gene expression alteration. ROC curve analysis demonstrated high accuracy for CST7 expression in BC tumors. Comparison of gene expression between different stages and patient family history showed significant findings. Due to the high sensitivity and specificity of the expression changes of these two genes, they are suitable candidates for further investigations to be considered as part of a diagnosis and prognosis panel.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"40 ","pages":"Article 101863"},"PeriodicalIF":2.3,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142573065","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}
Studies have shown various effects of CCN5/WISP2 on metabolic pathways, yet no prior investigation has established a link between its serum levels and CAD and/or T2DM. Therefore, this study seeks to explore the relation between CCN5 and the risk factor of CAD and/or diabetes, in comparison to individuals with good health, marking a pioneering endeavor in this field.
Methods
This case-control study investigates serum levels of CCN5, TNF-α, IL-6, adiponectin, and fasting insulin in a population of 160 individuals recruited into four equal groups (T2DM, CAD, CAD-T2DM, and healthy controls). Statistical tests comprise Chi-square tests, ANOVA, Spearman correlation, and logistic regression. ROC curves were used to represent the diagnostic potential of CCN5. Disease states are predicted by machine learning algorithms: Decision Tree, Gradient Boosted Trees, Random Forest, Naïve Bayes, and KNN. These models' performance was evaluated by various metrics, all of which were ensured to be robust by applying 10-fold cross-validation. Analyses were done in SPSS and GraphPad Prism and RapidMiner software.
Results
The CAD, T2DM, and CAD-T2DM groups had significantly higher CCN5 concentrations compared to the healthy control group (CAD: 336.87 ± 107.36 ng/mL, T2DM: 367.46 ± 102.15 ng/mL, CAD-T2DM: 404.68 ± 108.15 ng/mL, control: 205.62 ± 63.34 ng/mL; P < 0.001). A positive and significant correlation was observed between CCN5 and cytokines (IL-6 and TNF-α) in all patient groups (P < 0.05). Multinomial logistic regression analysis indicated a significant association between CCN5 and T2DM-CAD, T2DM, and CAD conditions (P < 0.001) even after adjusting for gender, BMI, and age (P < 0.001). Regarding the machine learning models, the Naïve Bayes model showed the best performance for classifying cases of T2DM, achieving an AUC value of 0.938±0.066. For predicting CAD, the Random Forest classifier achieved the highest AUC value of 0.994±0.020. In the case of CAD-T2DM prediction, the Naïve Bayes model demonstrated the highest AUC of 0.981±0.059, along with an Accuracy of 97.50 % ± 7.91 % and an F-measure of 96.67 % ± 10.54 %.
Conclusion
Our study has revealed, for the first time, a positive connection between CCN5 serum levels and the risk of developing T2DM and CAD. Nonetheless, more research is needed to ascertain whether CCN5 can serve as a predictive marker.
{"title":"CCN5/WISP2 serum levels in patients with coronary artery disease and type 2 diabetes and its correlation with inflammation and insulin resistance; a machine learning approach","authors":"Reza Afrisham , Vida Farrokhi , Seyed Mohammad Ayyoubzadeh , Akram Vatannejad , Reza Fadaei , Nariman Moradi , Yasaman Jadidi , Shaban Alizadeh","doi":"10.1016/j.bbrep.2024.101857","DOIUrl":"10.1016/j.bbrep.2024.101857","url":null,"abstract":"<div><h3>Introduction</h3><div>Studies have shown various effects of CCN5/WISP2 on metabolic pathways, yet no prior investigation has established a link between its serum levels and CAD and/or T2DM. Therefore, this study seeks to explore the relation between CCN5 and the risk factor of CAD and/or diabetes, in comparison to individuals with good health, marking a pioneering endeavor in this field.</div></div><div><h3>Methods</h3><div>This case-control study investigates serum levels of CCN5, TNF-α, IL-6, adiponectin, and fasting insulin in a population of 160 individuals recruited into four equal groups (T2DM, CAD, CAD-T2DM, and healthy controls). Statistical tests comprise Chi-square tests, ANOVA, Spearman correlation, and logistic regression. ROC curves were used to represent the diagnostic potential of CCN5. Disease states are predicted by machine learning algorithms: Decision Tree, Gradient Boosted Trees, Random Forest, Naïve Bayes, and KNN. These models' performance was evaluated by various metrics, all of which were ensured to be robust by applying 10-fold cross-validation. Analyses were done in SPSS and GraphPad Prism and RapidMiner software.</div></div><div><h3>Results</h3><div>The CAD, T2DM, and CAD-T2DM groups had significantly higher CCN5 concentrations compared to the healthy control group (CAD: 336.87 ± 107.36 ng/mL, T2DM: 367.46 ± 102.15 ng/mL, CAD-T2DM: 404.68 ± 108.15 ng/mL, control: 205.62 ± 63.34 ng/mL; P < 0.001). A positive and significant correlation was observed between CCN5 and cytokines (IL-6 and TNF-α) in all patient groups (P < 0.05). Multinomial logistic regression analysis indicated a significant association between CCN5 and T2DM-CAD, T2DM, and CAD conditions (P < 0.001) even after adjusting for gender, BMI, and age (P < 0.001). Regarding the machine learning models, the Naïve Bayes model showed the best performance for classifying cases of T2DM, achieving an AUC value of 0.938±0.066. For predicting CAD, the Random Forest classifier achieved the highest AUC value of 0.994±0.020. In the case of CAD-T2DM prediction, the Naïve Bayes model demonstrated the highest AUC of 0.981±0.059, along with an Accuracy of 97.50 % ± 7.91 % and an F-measure of 96.67 % ± 10.54 %.</div></div><div><h3>Conclusion</h3><div>Our study has revealed, for the first time, a positive connection between CCN5 serum levels and the risk of developing T2DM and CAD. Nonetheless, more research is needed to ascertain whether CCN5 can serve as a predictive marker.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"40 ","pages":"Article 101857"},"PeriodicalIF":2.3,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142551976","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 : 2024-10-30DOI: 10.1016/j.bbrep.2024.101855
Tetsuya Okuda
Isoglobotrihexosylceramide (iGb3), a well-characterized natural killer T cell ligand found in mammalian tissues, is also known as a glycosphingolipid that contains the human IgE epitope α-Gal (Galα1,3Gal) structure. Here, we analyzed the reactivity of several mice and human serum immunoglobulins against iGb3. Additionally, we isolated and characterized the variable region sequences of a monoclonal antibody that specifically recognizes iGb3. No IgE reactive with iGb3 was detected in sera from MRL/lpr mice, which are known to produce autoreactive antibodies, or in sera from healthy human donors. Furthermore, no induction of IgE and IgG was observed in the sera of mice immunized with iGb3; only IgM reactivity to iGb3 was detected. Further analysis of an anti-iGb3 monoclonal antibody generated from the splenocytes of an iGb3-immunized mouse revealed that the nucleotide sequences of the variable regions exhibited high homology to those of antibodies recognizing glycoconjugates containing Galα1,3 or Galα1,4 structures. These results indicate that the mouse genome harbors genes capable of encoding antibodies that recognize α-linked galactose-containing glycans, including iGb3, but that iGb3 is not sufficiently immunogenic to induce IgE in mammalian lymphocytes.
{"title":"Characterization of antibodies induced by immunization of mice with isoglobotrihexosylceramide (iGb3)","authors":"Tetsuya Okuda","doi":"10.1016/j.bbrep.2024.101855","DOIUrl":"10.1016/j.bbrep.2024.101855","url":null,"abstract":"<div><div>Isoglobotrihexosylceramide (iGb3), a well-characterized natural killer T cell ligand found in mammalian tissues, is also known as a glycosphingolipid that contains the human IgE epitope α-Gal (Galα1,3Gal) structure. Here, we analyzed the reactivity of several mice and human serum immunoglobulins against iGb3. Additionally, we isolated and characterized the variable region sequences of a monoclonal antibody that specifically recognizes iGb3. No IgE reactive with iGb3 was detected in sera from MRL/lpr mice, which are known to produce autoreactive antibodies, or in sera from healthy human donors. Furthermore, no induction of IgE and IgG was observed in the sera of mice immunized with iGb3; only IgM reactivity to iGb3 was detected. Further analysis of an anti-iGb3 monoclonal antibody generated from the splenocytes of an iGb3-immunized mouse revealed that the nucleotide sequences of the variable regions exhibited high homology to those of antibodies recognizing glycoconjugates containing Galα1,3 or Galα1,4 structures. These results indicate that the mouse genome harbors genes capable of encoding antibodies that recognize α-linked galactose-containing glycans, including iGb3, but that iGb3 is not sufficiently immunogenic to induce IgE in mammalian lymphocytes.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"40 ","pages":"Article 101855"},"PeriodicalIF":2.3,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142551978","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 : 2024-10-30DOI: 10.1016/j.bbrep.2024.101858
Qingyuan Tao , Xiaojin Li , Yanyan Xia , Bin Zheng , Yijun Yan , Songrun Wang , Li Jia
Background
Long-chain non-coding RNA (LINC00261) in the treatment of papillary thyroid carcinoma (PTC) with 131I is still unknown despite its proven anti-tumour effect in thyroid cancer (TC) and other types of cancer.
Methods
The database and RT-qPCR were used to analyze the expression level of LINC00261 in PTC and cell lines. PTC cells resistant to 131I (TPC-1/R) were created through ongoing exposure to a lethal dose of 131I, and a subcutaneous xenotransplantation model was developed using PTC mice. Bioinformatics analysis and dual-luciferase assays demonstrated the interaction between LINC00261, miR-23a-3p, and CELF2. RT-qPCR and Western blot were used to detect the expression of LINC00261, miR-23a-3p, and CELF2. Additionally, CCK-8, flow cytometry, immunofluorescence (IF), Western blot, and comet assay were employed to measure cell viability level and DNA damage.
Results
PTC cell lines exhibited a decrease in the expression of LINC00261. The growth and progression through the S-phase of TPC-1/R cells were suppressed by LINC00261, leading to increased apoptosis and DNA damage. The objective of LINC00261 was to regulate the axis of miR-23a-3p/CELF2. Downregulating LINC00261 enhances the growth and advancement of 131I-resistant cells in the S-phase by activating the miR-23a-3p/CELF2 pathway while suppressing cell death and DNA harm. The miR-23a-3p/CELF2 axis activates DNA damage in 131I-resistant PTC cells by LINC00261.
Conclusions
LINC00261 activates DNA damage in 131I-resistant PTC cells caused by miR-23a-3p/CELF2 axis, improving the progression of cancer cells of PTC.
背景长链非编码RNA（LINC00261）在甲状腺乳头状癌（PTC）131I治疗中的作用尚不清楚，尽管它在甲状腺癌（TC）和其他类型癌症中的抗肿瘤作用已得到证实。方法利用数据库和RT-qPCR分析LINC00261在PTC和细胞系中的表达水平。通过持续暴露于致死剂量的 131I 建立了对 131I 耐药的 PTC 细胞（TPC-1/R），并利用 PTC 小鼠建立了皮下异种移植模型。生物信息学分析和双荧光素酶测定证明了LINC00261、miR-23a-3p和CELF2之间的相互作用。RT-qPCR 和 Western 印迹被用来检测 LINC00261、miR-23a-3p 和 CELF2 的表达。此外，还采用了 CCK-8、流式细胞术、免疫荧光（IF）、Western 印迹和彗星试验来检测细胞活力水平和 DNA 损伤。LINC00261抑制了TPC-1/R细胞的生长和S期进展，导致细胞凋亡和DNA损伤增加。LINC00261 的目的是调节 miR-23a-3p/CELF2 轴。通过激活 miR-23a-3p/CELF2 通路，下调 LINC00261 可增强 131I 抗性细胞在 S 期的生长和进展，同时抑制细胞死亡和 DNA 损伤。结论LINC00261能激活miR-23a-3p/CELF2轴引起的131I耐药PTC细胞的DNA损伤，改善PTC癌细胞的进展。
{"title":"LINC00261 triggers DNA damage via the miR-23a-3p/CELF2 axis to mitigate the malignant characteristics of 131I-resistant papillary thyroid carcinoma cells","authors":"Qingyuan Tao , Xiaojin Li , Yanyan Xia , Bin Zheng , Yijun Yan , Songrun Wang , Li Jia","doi":"10.1016/j.bbrep.2024.101858","DOIUrl":"10.1016/j.bbrep.2024.101858","url":null,"abstract":"<div><h3>Background</h3><div>Long-chain non-coding RNA (LINC00261) in the treatment of papillary thyroid carcinoma (PTC) with <sup>131</sup>I is still unknown despite its proven anti-tumour effect in thyroid cancer (TC) and other types of cancer.</div></div><div><h3>Methods</h3><div>The database and RT-qPCR were used to analyze the expression level of LINC00261 in PTC and cell lines. PTC cells resistant to <sup>131</sup>I (TPC-1/R) were created through ongoing exposure to a lethal dose of <sup>131</sup>I, and a subcutaneous xenotransplantation model was developed using PTC mice. Bioinformatics analysis and dual-luciferase assays demonstrated the interaction between LINC00261, miR-23a-3p, and CELF2. RT-qPCR and Western blot were used to detect the expression of LINC00261, miR-23a-3p, and CELF2. Additionally, CCK-8, flow cytometry, immunofluorescence (IF), Western blot, and comet assay were employed to measure cell viability level and DNA damage.</div></div><div><h3>Results</h3><div>PTC cell lines exhibited a decrease in the expression of LINC00261. The growth and progression through the S-phase of TPC-1/R cells were suppressed by LINC00261, leading to increased apoptosis and DNA damage. The objective of LINC00261 was to regulate the axis of miR-23a-3p/CELF2. Downregulating LINC00261 enhances the growth and advancement of <sup>131</sup>I-resistant cells in the S-phase by activating the miR-23a-3p/CELF2 pathway while suppressing cell death and DNA harm. The miR-23a-3p/CELF2 axis activates DNA damage in <sup>131</sup>I-resistant PTC cells by LINC00261.</div></div><div><h3>Conclusions</h3><div>LINC00261 activates DNA damage in <sup>131</sup>I-resistant PTC cells caused by miR-23a-3p/CELF2 axis, improving the progression of cancer cells of PTC.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"40 ","pages":"Article 101858"},"PeriodicalIF":2.3,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142551977","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 : 2024-10-28DOI: 10.1016/j.bbrep.2024.101832
Yinqiang Liu , Hongjv Yang , Guoli Lv, Jin Duan, Wei Zhao, Yunfei Shi, Youming Lei
Background
Long non-coding RNAs (lncRNAs) are importantly involved in the initiation and progression of non-small cell lung cancer (NSCLC). However, the classification and mechanisms of lncRNAs remain largely elusive.
Aim
Hence, we addressed this through bioinformatics analysis.
Methods and results
We utilized microarray technology to analyze lncRNAs and mRNAs in twenty paired NSCLC tumor tissues and adjacent normal tissues. Gene set enrichment analysis, Kyoto Encyclopedia of Genes and Genomes, and Gene Ontology were conducted to discern the biological functions of identified differentially expressed transcripts. Additionally, networks of lncRNA-mRNA co-expression, including cis-regulation, lncRNA-transcription factor (TF)-mRNA, trans-regulation, and lncRNA-miRNA-mRNA interactions were explored. Furthermore, the study examined differentially expressed transcripts and their prognostic values in a large RNA-seq dataset of 1016 NSCLC tumors and normal tissues extracted from the Cancer Genome Atlas (TCGA). The analysis revealed 391 lncRNAs and 344 mRNAs with differential expression in NSCLC tumor tissues compared to adjacent normal tissues. Subsequently, 43,557 co-expressed lncRNA-mRNA pairs were identified, including 27 lncRNA-mRNA pairs in cis, 9 lncRNA-TF-mRNA networks, 34 lncRNA-mRNA pairs in trans, and 8701 lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) networks. Notably, these lncRNAs were found to be involved in immune-related pathways. Six significant transcripts, including NTF4, PTPRD-AS, ITGA11, HID1-AS1, RASGRF2-AS1, and TBX2-AS1, were identified within the ceRNA network and trans-regulation.
Conclusion
This study brings important insights into the regulatory roles of lncRNAs in NSCLC, providing a fresh perspective on lncRNA research in tumor biology.
{"title":"Integration analysis of cis- and trans-regulatory long non-coding RNAs associated with immune-related pathways in non-small cell lung cancer","authors":"Yinqiang Liu , Hongjv Yang , Guoli Lv, Jin Duan, Wei Zhao, Yunfei Shi, Youming Lei","doi":"10.1016/j.bbrep.2024.101832","DOIUrl":"10.1016/j.bbrep.2024.101832","url":null,"abstract":"<div><h3>Background</h3><div>Long non-coding RNAs (lncRNAs) are importantly involved in the initiation and progression of non-small cell lung cancer (NSCLC). However, the classification and mechanisms of lncRNAs remain largely elusive.</div></div><div><h3>Aim</h3><div>Hence, we addressed this through bioinformatics analysis.</div></div><div><h3>Methods and results</h3><div>We utilized microarray technology to analyze lncRNAs and mRNAs in twenty paired NSCLC tumor tissues and adjacent normal tissues. Gene set enrichment analysis, Kyoto Encyclopedia of Genes and Genomes, and Gene Ontology were conducted to discern the biological functions of identified differentially expressed transcripts. Additionally, networks of lncRNA-mRNA co-expression, including <em>cis</em>-regulation, lncRNA-transcription factor (TF)-mRNA, <em>trans</em>-regulation, and lncRNA-miRNA-mRNA interactions were explored. Furthermore, the study examined differentially expressed transcripts and their prognostic values in a large RNA-seq dataset of 1016 NSCLC tumors and normal tissues extracted from the Cancer Genome Atlas (TCGA). The analysis revealed 391 lncRNAs and 344 mRNAs with differential expression in NSCLC tumor tissues compared to adjacent normal tissues. Subsequently, 43,557 co-expressed lncRNA-mRNA pairs were identified, including 27 lncRNA-mRNA pairs in cis, 9 lncRNA-TF-mRNA networks, 34 lncRNA-mRNA pairs in trans, and 8701 lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) networks. Notably, these lncRNAs were found to be involved in immune-related pathways. Six significant transcripts, including NTF4, PTPRD-AS, ITGA11, HID1-AS1, RASGRF2-AS1, and TBX2-AS1, were identified within the ceRNA network and <em>trans</em>-regulation.</div></div><div><h3>Conclusion</h3><div>This study brings important insights into the regulatory roles of lncRNAs in NSCLC, providing a fresh perspective on lncRNA research in tumor biology.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"40 ","pages":"Article 101832"},"PeriodicalIF":2.3,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142535144","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 : 2024-10-26DOI: 10.1016/j.bbrep.2024.101856
Dewi Lidya Ichwana Nasution , Sri Tjahajawati , Ratna Indriyanti , Amaliya Amaliya
Background
Periodontitis, marked by deep periodontal pocket depth (PPD), facilitates bacterial colonization and inflammation, necessitating adjunctive therapies. Although 0.2 % chlorhexidine (CHX) mouthwash is effective, its side effects have led to the search for alternative treatments. Peperomia pellucida (L.) Kunth, known as Pepper Elder, is a traditional medicinal plant with potential as an adjunctive herbal therapy for periodontitis.
Objective
This study aimed to investigate the anti-inflammatory efficacy of Peperomia pellucida extract in rats with induced periodontitis.
Methods
A post-test control group design was used in this laboratory experimental study. Four groups of Wistar strain Rattus norvegicus rats were utilized: a Pristine group (without periodontitis), a negative control group (induced periodontitis only), a positive control group (induced periodontitis and administered 0.2 % CHX), and an experimental group (induced periodontitis and administered 2.5 μL of Pepper Elder extract). Each treatment group received daily administration for one week. PPD measurements were taken on days 0, 3, 5, and 7. Blood serum was collected on day 7 for ELISA to measure IL-1β, TNF-α, IL-10, and IL-13 levels. Statistical analysis was performed using the Kruskal-Wallis test with a post hoc LSD and Mann-Whitney test.
Results
The extract-treated rats showed a decrease in PPD, with significant differences between the extract group and the negative control group (p < 0.05). TNF-α levels in the extract group differed significantly from the negative control group (p < 0.05) but not from the Pristine and positive control groups. IL-1β levels differed significantly only from the negative control group. IL-10 levels were significantly different from both the Pristine and negative control groups, while IL-13 levels differed significantly only from the negative control group.
Conclusion
Peperomia pellucida (L.) Kunth extract exhibits anti-inflammatory effects in rats with induced periodontitis.
{"title":"Anti-inflammatory effectiveness of Peperomia pellucida (L.) Kunth in rats induced with periodontitis","authors":"Dewi Lidya Ichwana Nasution , Sri Tjahajawati , Ratna Indriyanti , Amaliya Amaliya","doi":"10.1016/j.bbrep.2024.101856","DOIUrl":"10.1016/j.bbrep.2024.101856","url":null,"abstract":"<div><h3>Background</h3><div>Periodontitis, marked by deep periodontal pocket depth (PPD), facilitates bacterial colonization and inflammation, necessitating adjunctive therapies. Although 0.2 % chlorhexidine (CHX) mouthwash is effective, its side effects have led to the search for alternative treatments. Peperomia pellucida (L.) Kunth, known as Pepper Elder, is a traditional medicinal plant with potential as an adjunctive herbal therapy for periodontitis.</div></div><div><h3>Objective</h3><div>This study aimed to investigate the anti-inflammatory efficacy of Peperomia pellucida extract in rats with induced periodontitis.</div></div><div><h3>Methods</h3><div>A post-test control group design was used in this laboratory experimental study. Four groups of Wistar strain <em>Rattus norvegicus</em> rats were utilized: a Pristine group (without periodontitis), a negative control group (induced periodontitis only), a positive control group (induced periodontitis and administered 0.2 % CHX), and an experimental group (induced periodontitis and administered 2.5 μL of Pepper Elder extract). Each treatment group received daily administration for one week. PPD measurements were taken on days 0, 3, 5, and 7. Blood serum was collected on day 7 for ELISA to measure IL-1β, TNF-α, IL-10, and IL-13 levels. Statistical analysis was performed using the Kruskal-Wallis test with a post hoc LSD and Mann-Whitney test.</div></div><div><h3>Results</h3><div>The extract-treated rats showed a decrease in PPD, with significant differences between the extract group and the negative control group (p < 0.05). TNF-α levels in the extract group differed significantly from the negative control group (p < 0.05) but not from the Pristine and positive control groups. IL-1β levels differed significantly only from the negative control group. IL-10 levels were significantly different from both the Pristine and negative control groups, while IL-13 levels differed significantly only from the negative control group.</div></div><div><h3>Conclusion</h3><div>Peperomia pellucida (L.) Kunth extract exhibits anti-inflammatory effects in rats with induced periodontitis.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"40 ","pages":"Article 101856"},"PeriodicalIF":2.3,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142535652","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 : 2024-10-24DOI: 10.1016/j.bbrep.2024.101852
Arezoo Fallah , Abbas Ali Imani Fooladi , Seyed Asghar Havaei , Mahdieh Mahboobi , Hamid Sedighian
Aptamers are nucleic acid (Ribonucleic acid (RNA) and single strand deoxyribonucleic acid (ssDNA)) with a length of approximately 25–80 bases that can bind to particular target molecules, similar to monoclonal antibodies. Due to their many benefits, which include a long shelf life, minimal batch-to-batch variations, extremely low immunogenicity, the possibility of chemical modifications for improved stability, an extended serum half-life, and targeted delivery, they are receiving a lot of attention in a variety of clinical applications. The development of high-affinity modification approaches has attracted significant attention in aptamer applications. Stable three-dimensional aptamers that have undergone chemical modification can engage firmly with target proteins through improved non-covalent binding, potentially leading to hundreds of affinity improvements. This review demonstrates how cutting-edge methodologies for aptamer discovery are being developed to consistently and effectively construct high-performing aptamers that need less money and resources yet have a high chance of success. Also, High-affinity aptamer modification techniques were discussed.
{"title":"Recent advances in aptamer discovery, modification and improving performance","authors":"Arezoo Fallah , Abbas Ali Imani Fooladi , Seyed Asghar Havaei , Mahdieh Mahboobi , Hamid Sedighian","doi":"10.1016/j.bbrep.2024.101852","DOIUrl":"10.1016/j.bbrep.2024.101852","url":null,"abstract":"<div><div>Aptamers are nucleic acid (Ribonucleic acid (RNA) and single strand deoxyribonucleic acid (ssDNA)) with a length of approximately 25–80 bases that can bind to particular target molecules, similar to monoclonal antibodies. Due to their many benefits, which include a long shelf life, minimal batch-to-batch variations, extremely low immunogenicity, the possibility of chemical modifications for improved stability, an extended serum half-life, and targeted delivery, they are receiving a lot of attention in a variety of clinical applications. The development of high-affinity modification approaches has attracted significant attention in aptamer applications. Stable three-dimensional aptamers that have undergone chemical modification can engage firmly with target proteins through improved non-covalent binding, potentially leading to hundreds of affinity improvements. This review demonstrates how cutting-edge methodologies for aptamer discovery are being developed to consistently and effectively construct high-performing aptamers that need less money and resources yet have a high chance of success. Also, High-affinity aptamer modification techniques were discussed.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"40 ","pages":"Article 101852"},"PeriodicalIF":2.3,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142535145","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 : 2024-10-23DOI: 10.1016/j.bbrep.2024.101853
Pawel Krawczyk, Dagmara Klopotowska, Janusz Matuszyk
TrkB and TrkC are quite common neurotrophin receptors found on the same cells in CNS. In the C-terminal tail, TrkB and TrkC differ only in two amino acid residues at positions immediately preceding the tyrosine residue, which, upon phosphorylation, becomes the docking site for phospholipase Cγ1 (PLCγ1). The question arose whether such a difference near the PLCγ1 docking site might contribute to differential response to neurotrophin. PC12 clones with the following receptors were obtained: wild-type TrkC, TrkC-Y820F with a defective PLCγ1 binding site, TrkC-T817S–I819V with two amino acid residues replaced with those in the TrkB tail. The outgrowth of neurite-like processes from TrkC-Y820F-containing cells appeared to be impaired, while the TrkC-T817S–I819V variant appeared more effective than wild-type TrkC in promoting the outgrowth of neurite-like processes after neurotrophin stimulation, at least in the compared PC12 cell clones. Taken together, both the tyrosine residue at the PLCγ1 docking site and the amino acid residues immediately preceding it appear important for TrkC-supported outgrowth of neurite-like processes.
{"title":"Modifications in the C-terminal tail of TrkC significantly alter neurotrophin-3-promoted outgrowth of neurite-like processes from PC12 cells","authors":"Pawel Krawczyk, Dagmara Klopotowska, Janusz Matuszyk","doi":"10.1016/j.bbrep.2024.101853","DOIUrl":"10.1016/j.bbrep.2024.101853","url":null,"abstract":"<div><div>TrkB and TrkC are quite common neurotrophin receptors found on the same cells in CNS. In the C-terminal tail, TrkB and TrkC differ only in two amino acid residues at positions immediately preceding the tyrosine residue, which, upon phosphorylation, becomes the docking site for phospholipase Cγ1 (PLCγ1). The question arose whether such a difference near the PLCγ1 docking site might contribute to differential response to neurotrophin. PC12 clones with the following receptors were obtained: wild-type TrkC, TrkC-Y820F with a defective PLCγ1 binding site, TrkC-T817S–I819V with two amino acid residues replaced with those in the TrkB tail. The outgrowth of neurite-like processes from TrkC-Y820F-containing cells appeared to be impaired, while the TrkC-T817S–I819V variant appeared more effective than wild-type TrkC in promoting the outgrowth of neurite-like processes after neurotrophin stimulation, at least in the compared PC12 cell clones. Taken together, both the tyrosine residue at the PLCγ1 docking site and the amino acid residues immediately preceding it appear important for TrkC-supported outgrowth of neurite-like processes.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"40 ","pages":"Article 101853"},"PeriodicalIF":2.3,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142535143","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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