{"title":"Free-fatty acid receptor-4 gene polymorphism (rs61866610) and colorectal cancer risk.","authors":"Ramin Shekarriz, Maryam Hasanian, Mohadeseh Ahmadi, Versa Omrani-Nava, Reza Alizadeh-Navaei","doi":"10.1080/15257770.2024.2406242","DOIUrl":"https://doi.org/10.1080/15257770.2024.2406242","url":null,"abstract":"<p><p>This study aimed to investigate the impact of Free-fatty acid receptor-4 (FFAR4) rs61866610 polymorphism on colorectal cancer (CRC) risk. Herein, ninety-two histopathologically confirmed CRC patients and 95 healthy individuals were evaluated for FFAR4 polymorphism by RFLP-PCR. Gender, age, body mass index (BMI), underlying disease, and smoking status were recorded for all subjects. Clinical and histopathologic findings including tumor grade and TNM stage were also prepared in the patient group. Except for type 2 diabetes which was more prevalent in the control group, there were no differences between the two groups regarding underlying diseases (<i>p</i> > 0.05). The frequency of genotypes was as follows: in the CRC group 75% wild type, 23.9% heterozygous, and 1.1% homozygous mutant. In the control group 85.3% wild type, 12.6% heterozygous, and 2.1% homozygous mutant. Mutant allele carriers were more frequent in CRC subjects (25%) than in the normal group (14.7%) but it did not reach a significant level. The frequency of mutant genotypes in colon cancer and rectal cancer was 27.5% and 8.3% respectively (<i>p</i> = 0.282). The mutant genotypes were found more in patients with high-grade tumors (<i>p</i> = 0.154). Subjects with stage III/IV had a higher frequency of mutant genotypes than low-stage cases (<i>p</i> = 0.011). No association was found regarding rs61866610 and obesity or type 2 diabetes (<i>p</i> > 0.05). In conclusion, FFAR4 (rs61866610) has no significant association with the risk of CRC, but the higher frequency of mutant genotypes in subjects with advanced cancer stages (III/IV) suggests further studies to determine the role of FFAR4 in colorectal tumorigenesis.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-10"},"PeriodicalIF":1.1,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142292317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Interrelationships among MTHFR gene polymorphisms, MTRR gene polymorphisms, and HBV gene BCP 1762/1764 mutations with disease progression in Chronic hepatitis B virus infection patients.","authors":"Qiu Shunhua, Jin Lifen, Yang Dan, Zhang Dewen","doi":"10.1080/15257770.2024.2406223","DOIUrl":"https://doi.org/10.1080/15257770.2024.2406223","url":null,"abstract":"<p><strong>Objective: </strong>Chronic hepatitis B virus (HBV) infection is a major disease that seriously affects the health of patients. In this paper, the relationship among MTHFR gene polymorphism, MTRR gene polymorphism and 1762/1764 mutation in the BCP region of HBV gene with disease progression in chronic HBV patients was studied.</p><p><strong>Methods: </strong>A total of 144 chronic HBV infection patients from January 2021 to June 2022 in the Third People's Hospital of Zigong City, were included as the study subjects. These patients were divided into hepatitis B primary liver cancer patients group (PLC) in 51 cases, Non-primary liver cancer patients group (Non-PLC) in 93 cases, Non-PLC is also divided into chronic hepatitis B virus carriers (CHC) in 49 cases, hepatitis B Live cirrhosis(LC) in 44 cases. MTHFR (C677T), MTRR (A66G) and MTHFR (A1298C) genes polymorphisms were detected by PCR-dissolution curve. The level of HBV-DNA was quantified by real-time PCR, and the 1762/1764 mutation site in the BCP region of the HBV gene were detected by ARMS-PCR. Data were statistically analyzed using the SPSS statistical software.</p><p><strong>Results: </strong>The proportion of HBV mutations in BCP region 1762/1764 in PLC group was 82.4%, which was higher than that in LC group (63.6%) and CHC group (51.0%), and the differences were statistically significant (<i>p</i> < 0.05). There were no significant differences in the distribution of MTHFR C677T, MTHFR A1298C and MTRR A66G polymorphisms among CHC, LC and PLC (<i>p</i> > 0.05). The polymorphism distribution of MTHFR C677T, MTRR A66G and MTHFR A1298C genes in patients with chronic hepatitis B virus infection at different stages (CHC, LC and PLC) showed no gender or age differences between and within groups (<i>p</i> > 0.05). Among the patients with MTHFR 677CT + TT, MTRR 66AG + GG and MTHFR 1298AA genotype, the proportion of HBV mutation in BCP region 1762/1764 in PLC group was higher than that in CHC group and LC group, and the differences were statistically significant (<i>p</i> < 0.05). Folate levels in the PLC group were lower than those in the non-PLC group (CHC and LC patients), and the difference was statistically significant compared with the CHC group (<i>p</i> < 0.05). In different MTHFR C677T and MTRR A66G genotypes, the serum GGT activity were statistically significant between mutant PLC and mutant Non-PLC (<i>p</i> < 0.05).</p><p><strong>Conclusion: </strong>MTHFR C677T, MTRR A66G and MTHFR A1298C gene polymorphisms distribution have no gender and age differences in chronic hepatitis B virus infection patients. The mutation of HBV gene BCP region 1762/1764 may be associated with the occurrence and development of liver cancer in patients with chronic HBV infection. Single difference of MTHFR C677T, MTHFR A1298C and MTRR A66G gene polymorphisms may have little effect on the disease progression in patients with chronic HBV infection. MTHFR 677CT + TT, MTRR 66AG + GG and MTHFR 1298AA geno","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-19"},"PeriodicalIF":1.1,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142292318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Optimization of microRNA extraction from the plasma of the common carp.","authors":"Yiwen Wan, Xiaoling Li, Xiangyi Chen, Yong He, Wenwen Suo, Xiao Yang, Zhonggui Xie","doi":"10.1080/15257770.2024.2400200","DOIUrl":"https://doi.org/10.1080/15257770.2024.2400200","url":null,"abstract":"<p><p>Efficient and safe extraction of microRNAs (miRNAs) from biological samples is pivotal for genetic regulation studies and biotechnological applications. This study focuses on optimizing the microRNA extraction process from the plasma of common carp, a significant species in aquaculture. Recognizing the limitations and hazards of commercial extraction kits, which often employ toxic chemicals like phenol and chloroform, we sought to develop a safer and more effective alternative. Our optimized protocol utilizes guanidinium isothiocyanate (GITC) and sarkosyl, omitting hazardous substances. We explored several parameters including GITC concentration, the addition of sarkosyl, and the role of sodium chloride in enhancing miRNA yield. Our findings demonstrate that optimal conditions involve a GITC concentration of 4.2 M, a 3% sarkosyl concentration, and the use of sodium chloride at 0.5 M. We also investigated the utility of glycogen as a nucleic acid carrier, finding 160 µg to be the optimal concentration. Comparative analysis with commercial kits indicated our method provides higher miRNA yields with reduced cycle threshold values, underscoring the effectiveness of our custom protocol. This optimized approach not only enhances miRNA recovery but also emphasizes safety and cost-effectiveness, making it a valuable method for both research and practical applications in aquaculture.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-19"},"PeriodicalIF":1.1,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142133281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The genetic variants of miR-1206 and miR-125b in breast cancer patients: <i>in vitro</i> and <i>in silico</i> analysis.","authors":"Hamideh Amini Mostafaabadi, Reza Mohammadzadeh, Somayeh Reiisi","doi":"10.1080/15257770.2024.2398548","DOIUrl":"https://doi.org/10.1080/15257770.2024.2398548","url":null,"abstract":"<p><strong>Background: </strong>This study aimed to investigate the association of rs12976445 polymorphism in the promoter region of miR-125a and rs2114358 in the precursor region of miR-1206 to breast cancer susceptibility.</p><p><strong>Method: </strong>A total of 230 participants (110 breast cancer and 120 controls) enrolled in this study and extracted genomic DNA. The genotypes were determined by the Tetra-ARMS method. The allele and genotype frequencies were determined.</p><p><strong>Results: </strong>Allele variation in the rs12976445 (miR-125a) sequence increased the risk of breast cancer; a significant relationship was observed between breast cancer and allele change in individuals with the C allele (<i>p</i> = 0.01). However, allele variation in the rs2114358 (miR-1206) decreased the risk of breast cancer in individuals with allele A (<i>p</i> = 0.01). In silico study showed that allele change was associated with a reduction in structural stability.</p><p><strong>Conclusion: </strong>Therefore, the rs12976445 variant can be considered a risk factor for breast cancer, and the rs2114358 variant is a protective factor against it.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-14"},"PeriodicalIF":1.1,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142109978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"miR-146a rs2910164 (G/C) variant may predict morbid obesity risk in adults.","authors":"Zeki Ozsoy, Ayse Feyda Nursal, Seyma Ozsoy, Akin Tekcan, Serbulent Yigit","doi":"10.1080/15257770.2024.2393323","DOIUrl":"https://doi.org/10.1080/15257770.2024.2393323","url":null,"abstract":"<p><p>Obesity is a common public health problem associated with serious, life-threatening complications. MicroRNAs (miRs) have modulating roles in the immune and inflammatory systems. Therefore, this study aimed to analyze the relationship between <i>miR-146a</i> and morbid obesity <b>(</b>MO) in a Turkish population. In this study, a total of 258 subjects (110 patients with MO and 148 controls) were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method to analyze <i>miR-146a</i> rs2910164. Then, we examined the patients as males and females separately. The results of the analyses were evaluated for statistical significance. There was a significant difference in genotype and allele frequencies of <i>miR-146a</i> rs2910164 between patients with MO and control individuals. <i>miR-146a</i> rs2910164 CC genotype and C allele were shown to increase in the MO patients' group compared to the control group (<i>p</i> = 0.000, <i>p</i> = 0.000, respectively). Also, the C allele was higher in both female and male patients compared to controls (<i>p</i> = 0.000, <i>p</i> = 0.000, respectively). High differences were also observed when the patients and the controls were compared according to CC versus GG + GC and GG versus GC + CC (<i>p</i> = 0.000, <i>p</i> = 0.000, respectively). A significant difference was found between the female/male patients and the female/male controls in terms of GG + GC versus CC (<i>p</i> = 0.000, <i>p</i> = 0.000, respectively). To the best of our knowledge, this is the first study to investigate the relationship between this variant and MO in Turkey. Our results showed that <i>miR-146a</i> rs2910164 is a valuable biomarker that can be used to distinguish between patients with MO and the healthy population. The findings can be extended by increasing the sample sizes with diverse ethnicities.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-11"},"PeriodicalIF":1.1,"publicationDate":"2024-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142004890","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Clinical significance of <i>LIN28A</i> gene polymorphisms and expression in pan-cancer: a meta-analysis and bioinformatic analysis.","authors":"Surui Zhou, Jinyin Xue, Qijun Yang, Wenjing Zang, Yi Chen, Yining Zhao, Xueren Gao","doi":"10.1080/15257770.2024.2393316","DOIUrl":"https://doi.org/10.1080/15257770.2024.2393316","url":null,"abstract":"<p><p>Several studies have reported the relationship between <i>LIN28A</i> gene polymorphisms (rs3811463 T > C and rs34787247 G > A) and cancer susceptibility, but the results are inconsistent and need further clarification. The current study aimed to evaluate their relationship and also to explore the relationship between <i>LIN28A</i> gene expression and immune infiltration, tumor stage, survival prognosis, and drug sensitivity in pan-cancer. The meta-analysis and data mining were completed by STATA software and the GSCA platform, respectively. The meta-analysis showed that the rs3811463 polymorphism was not associated with cancer susceptibility, while the rs34787247 polymorphism was associated with cancer susceptibility in the Chinese population [AA vs. GG: Odd Ratio (OR)=1.98, 95% Confidence Interval (CI)=1.35-2.89, P<sub>Z</sub><0.001; GA vs. GG: OR = 1.17, 95%CI= 1.01-1.36, P<sub>Z</sub>=0.04; (AA + GA) vs. GG: OR = 1.24, 95%CI = 1.07-1.43, P<sub>Z</sub>=0.004; AA vs. (GA + GG): OR = 1.90, 95%CI = 1.30- 2.78, P<sub>Z</sub>=0.001; A vs. G: OR = 1.27, 95%CI = 1.12-1.44, P<sub>Z</sub><0.001]. <i>LIN28A</i> gene expression was associated not only with immune infiltration, pathological stage, and survival prognosis of certain cancers, but also with sensitivity to multiple anticancer drugs, such as cisplatin, pazopanib, olaparib, and selumetinib. In conclusion, the current study suggested that the rs34787247 G > A polymorphism might be used as a cancer risk marker in the Chinese population, and LIN28A might serve as a prognostic marker and therapeutic target for certain cancers.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-10"},"PeriodicalIF":1.1,"publicationDate":"2024-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141996168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Tissue distribution of renadirsen sodium, a dystrophin exon-skipping antisense oligonucleotide, in heart and diaphragm after subcutaneous administration to cynomolgus monkeys.","authors":"Naotoshi Yamamura, Hideo Takakusa, Daigo Asano, Kyoko Watanabe, Yukari Shibaya, Ryo Yamanaka, Keiichi Fusegawa, Akira Kanda, Hiroyuki Nagase, Kiyosumi Takaishi, Makoto Koizumi, Yasuhiro Takeshima, Masafumi Matsuo","doi":"10.1080/15257770.2024.2389545","DOIUrl":"https://doi.org/10.1080/15257770.2024.2389545","url":null,"abstract":"<p><p>The pharmacokinetics and tissue distribution of renadirsen sodium, a dystrophin exon-skipping phosphorothioate-modified antisense oligonucleotide with 2'-<i>O</i>,4'-<i>C</i>-ethylene-bridged nucleic acid (ENA), after subcutaneous or intravenous administration to cynomolgus monkeys were investigated. The plasma concentration of renadirsen after subcutaneous administration at 1, 3, and 10 mg/kg increased with the dose. The absolute bioavailability at 3 mg/kg after subcutaneous administration was calculated as 88.6%, and the time to reach maximum plasma concentration of renadirsen was within 4 h, indicating the efficient and rapid absorption following subcutaneous administration. The exposure of muscle tissues to renadirsen was found to increase with repeated dosing at 6 mg/kg, and higher exposure was observed in the diaphragm and heart than in the quadriceps femoris and anterior tibialis muscles. Renadirsen achieved more exon 45-skipped dystrophin mRNA in the diaphragm and heart than in the quadriceps femoris and anterior tibialis muscles. Renadirsen also showed a cumulative skipping effect in a repeated-dose study. The findings on exon 45-skipped dystrophin mRNA in these muscle tissues were consistent with the concentration of renadirsen in these tissues. Because it is not feasible to directly evaluate drug concentration and exon skipping in the heart and diaphragm in humans, the pharmacokinetics and pharmacodynamics of renadirsen in these tissues in monkeys are crucial for the design and interpretation of clinical settings.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-17"},"PeriodicalIF":1.1,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141913463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"An expanded framework toward improving the detritylation reaction in solid-phase oligonucleotide syntheses - filling the gap.","authors":"Quanjian Li, Yogesh S Sanghvi, Hongbin Yan","doi":"10.1080/15257770.2024.2388789","DOIUrl":"https://doi.org/10.1080/15257770.2024.2388789","url":null,"abstract":"<p><p>A few interactions should be considered during the detritylation reaction of solid-phase oligonucleotide synthesis (SPOS): (i) interaction of solvent with acid; (ii) interaction (or reaction) of solvent with trityl cation, and (iii) interaction of scavenger with acid, with the last one as the focus of this work. Using a stopped-flow setup, commonly used trityl cation scavengers (methanol, thioanisole, 1-dodecanethiol, triisopropylsilane, triethylsilane, and trihexylsilane) were evaluated for their reactivity toward tritylium hexafluorophosphate. Among the scavengers screened, methanol and thioanisole were found to be the most and least reactive, respectively; however, methanol does interact and react with trichloroacetic acid, thus it should not be pre-mixed and stored with acid as deblock solutions. Overall, all aspects of interactions must be taken into consideration while optimizing the detritylation reaction, especially for large scale SPOS.</p>","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":" ","pages":"1-9"},"PeriodicalIF":1.1,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141907291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marika A. Frańczak, Claudine van der Sande, Elisa Giovannetti, Godefridus J. Peters
{"title":"Effects of nucleoside analogues, lipophilic prodrugs and elaidic acids on core signaling pathways in cancer cells","authors":"Marika A. Frańczak, Claudine van der Sande, Elisa Giovannetti, Godefridus J. Peters","doi":"10.1080/15257770.2024.2339952","DOIUrl":"https://doi.org/10.1080/15257770.2024.2339952","url":null,"abstract":"Nucleoside analogs such as gemcitabine (GEM; dFdC) and cytarabine (Ara-C) require nucleoside transporters to enter cells, and deficiency in equilibrative nucleoside transporter 1 (ENT1) can lead to...","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":"50 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140592357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Aylar Nazari, Tayyebeh Ghasemi, Mohammad Khalaj-Kondori, Ramin Fathi
{"title":"Promoter of lncRNA MORT is aberrantly methylated in colorectal cancer","authors":"Aylar Nazari, Tayyebeh Ghasemi, Mohammad Khalaj-Kondori, Ramin Fathi","doi":"10.1080/15257770.2024.2328732","DOIUrl":"https://doi.org/10.1080/15257770.2024.2328732","url":null,"abstract":"Aberrant DNA methylation plays essential roles in the colorectal cancer (CRC) carcinogenesis and has been demonstrated as a promising marker for cancer early detection. In this project, methylation...","PeriodicalId":19343,"journal":{"name":"Nucleosides, Nucleotides & Nucleic Acids","volume":"41 1","pages":""},"PeriodicalIF":1.3,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140592565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}