Review
Oncology
Judy S. Crabtree
Summary: Gastroenteropancreatic neuroendocrine neoplasms are rare and diverse tumors associated with genetic disorders and epigenetic regulation. Epigenetic signatures can be used as biomarkers for diagnosis and as targets for the development of new treatment approaches.
FRONTIERS IN ONCOLOGY
(2022)
Article
Agriculture, Multidisciplinary
Bowen Chen, Yaojing Yue, Jianye Li, Chao Yuan, Tingting Guo, Dan Zhang, Jianbin Liu, Bohui Yang, Zengkui Lu
Summary: This study investigated the methylation patterns and differences in miRNA and mRNA expression in the F1 sheep longissimus dorsi muscle tissue using RNA sequencing, bisulfite sequencing, and small-RNA sequencing. The results identified differentially expressed genes, differentially methylated regions, and differentially expressed miRNAs that are significantly enriched in AMPK signaling, fatty acid degradation, metabolism, and other related pathways. Furthermore, a DNA methylation-mRNA and miRNA-mRNA coexpression network was constructed. The study provides valuable information and evidence for understanding the regulation of muscle growth and fat metabolism in hybrid sheep populations.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Immunology
Wu Tong, Gu Wenze, Hong Libing, Cao Yuchen, Zhao Hejia, Guo Xi, Yang Xiongyi, Yi Guoguo, Fu Min
Summary: This study identified shared differentially expressed RNAs in type 2 diabetes mellitus (T2DM) and breast cancer (BC) and constructed critical networks to understand the shared mechanisms. The study found that certain mRNAs and miRNAs were shared between T2DM and BC and were enriched in cytochrome pathways. Further analysis revealed the correlation of certain RNAs with the survival and prognosis of BC patients. These findings provide potential gene candidates and immune features for immunotherapy in BC patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Chemistry, Medicinal
Carmen Nunez-Carro, Margarita Blanco-Blanco, Karla Mariuxi Villagran-Andrade, Francisco J. Blanco, Maria C. de Andres
Summary: In this study, we reviewed the current understanding of epigenetic mechanisms in relation to the pathogenesis of OA, particularly in articular cartilage. Evidence suggests that dysregulation of crucial cartilage molecules is a result of aberrant epigenetic regulatory mechanisms, which contribute to the development and progression of OA. This provides an opportunity to explore new therapeutic targets and novel biomarkers for the disease.
Article
Immunology
Lu Han, Shiyun Chen, Zhe Luan, Mengjiao Fan, Yanrong Wang, Gang Sun, Guanghai Dai
Summary: Colon cancer is a complex disease involving interactions between cancer cells and the immune microenvironment. Recent studies have shown that microRNAs (miRNAs) play a critical role in gene regulation in colon cancer, particularly in modulating the immune microenvironment. Identifying miRNAs associated with colon cancer and their regulation of immune function-related genes could provide insights into prognosis and guide personalized treatment strategies.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Plant Sciences
Yuling Lin, Yan Chen, Youjing Zeng, Shuting Zhang, Zihao Zhang, YuKun Chen, Jiawei Gong, Zhongxiong Lai
Summary: A genome-wide analysis of longan miRNA genes was conducted, and 80 miRNA precursors (pre-miRNA) were predicted. Full-length cDNA sequences of 13 longan primary miRNAs (pri-miRNAs) were amplified by RLM-RACE and SMART-RACE, revealing multiple transcription start sites (TSSs) and polymorphic downstream pre-miRNAs. Analysis of the longan miRNA gene promoter elements indicated the presence of light-responsive, stress-responsive, and hormone-responsive elements. Quantitative real-time PCR assay elucidated potential spatial and temporal expression patterns of longan pre-miRNAs during somatic embryogenesis and in different longan organs/tissues.
Article
Oncology
Nitin Patil, Mohammed L. Abba, Chan Zhou, Shujian Chang, Timo Gaiser, Joerg H. Leupold, Heike Allgayer
Summary: Changes in methylation patterns can significantly impact the expression of miRs involved in cancer progression and metastasis, highlighting alternative mechanisms of gene regulation. Genome-wide methylation analysis in colorectal cancer revealed differential methylation of several miR genes, with implications for important cancer-related pathways. These findings suggest the importance of considering epigenetic changes in addition to genetic and transcriptional regulation of miRs in cancer.
Article
Biochemistry & Molecular Biology
Vitaly I. Loginov, Irina V. Pronina, Elena A. Filippova, Alexey M. Burdennyy, Svetlana S. Lukina, Tatiana P. Kazubskaya, Leonid A. Uroshlev, Marina V. Fridman, Olga I. Brovkina, Natalya V. Apanovich, Alexander V. Karpukhin, Ivan S. Stilidi, Nikolay E. Kushlinskii, Alexey A. Dmitriev, Eleonora A. Braga
Summary: This study aimed to differentiate aberrantly methylated miRNA genes involved in different stages of ovarian carcinoma (OvCa) development and metastasis using methylation-specific qPCR. The results revealed distinct patterns of methylation and expression levels of miRNA genes during the progression and metastasis of OvCa, with some miRNA genes showing a significant association with poor overall survival of patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Qi Tang, Haozhe Lv, Qimeng Li, Xiaoyue Zhang, Le Li, Jie Xu, Fengkai Wu, Qingjun Wang, Xuanjun Feng, Yanli Lu
Summary: This study found that miRNAs play important roles in response to drought stress in maize roots. By analyzing miRNAs in the roots of 16 inbred lines, it was found that the expression patterns of miRNAs differed between parental lines and their derived recombinant inbred lines (RILs). The expression of miRNAs changed significantly under water stress, and miRNAs in drought-tolerant lines exhibited marked changes. The study also investigated the relationship between miRNAs and drought through analysis of histone modifications, miRNA target prediction, and correlation analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Harshita Makkar, Sakshi Arora, Aniruddhabhai K. Khuman, Bhupendra Chaudhary
Summary: The study highlights the significant role of miR167 diminution in enhancing plant organogenesis under salt-stress conditions, potentially through upregulated auxin signaling pathways. The synergistic effect of salt-stress and miR167 diminution on auxin transporter genes lead to increased callus formation and decreased organogenesis. Moreover, the study suggests a regulatory shift in cellular metabolism may contribute to salt-stress tolerance in plants, offering new avenues for future crop research.
JOURNAL OF PLANT GROWTH REGULATION
(2022)
Article
Biochemistry & Molecular Biology
Xingchen Fan, Xuan Zou, Cheng Liu, Jiawen Liu, Shuang Peng, Shiyu Zhang, Xin Zhou, Tongshan Wang, Xiangnan Geng, Guoxin Song, Wei Zhu
Summary: The study aimed to identify potential miRNA-mRNA regulatory networks contributing to the pathogenesis of LUSC. Four pairs of miRNA-mRNA regulatory networks were screened, with miR-205-5p and PTPRM being validated in LUSC tissues. The research provided new insights into the genesis and development of LUSC.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Food Science & Technology
Pauline Mosca, Aurelie Robert, Jean-Marc Alberto, Marie Meyer, Urbi Kundu, Sebastien Hergalant, Remy Umoret, David Coelho, Jean-Louis Gueant, Bruno Leheup, Natacha Dreumont
Summary: This study found that Vitamin B-12 deficiency leads to reduced m6A methylation levels in mRNA, potentially mediated by overexpression of FTO. Additionally, m6A hypermethylation of Prkca mRNA and increased expression of PKC alpha were observed in two cellular models, suggesting a link between mRNA m6A methylation and neurological manifestations caused by Vitamin B-12 deficiency.
MOLECULAR NUTRITION & FOOD RESEARCH
(2021)
Article
Oncology
Shuang Peng, Cheng Liu, Xingchen Fan, Jingfeng Zhu, Shiyu Zhang, Xin Zhou, Tongshan Wang, Feng Gao, Wei Zhu
Summary: This study identified negatively regulatory miRNA-mRNA pairs in PRAD by analyzing TCGA RNA-Seq data and GEO mRNA/miRNA expression profiles, and established a diagnostic model that can distinguish PRADs from normal controls.
Article
Agriculture, Dairy & Animal Science
Kai Xing, Yu Chen, Liang Wang, Xueze Lv, Zheng Li, Xiaolong Qi, Xiangguo Wang, Longfei Xiao, Hemin Ni, Yong Guo, Xihui Sheng
Summary: In this study, the molecular mechanisms underlying sperm motility in the epididymis of roosters were investigated. The researchers identified candidate genes and miRNAs that affect sperm motility and shed light on the regulatory mechanisms of fertility. The findings provide valuable information for understanding and improving chicken production.
Article
Multidisciplinary Sciences
Haining Zhou, Chad B. Stein, Tiasha A. Shafiq, Gergana Shipkovenska, Marian Kalocsay, Joao A. Paulo, Jiuchun Zhang, Zhenhua Luo, Steven P. Gygi, Karen Adelman, Danesh Moazed
Summary: Polycomb repressive complexes (PRCs) and the RIX1 complex work together to silence Polycomb target genes in human cells, with the recruitment of the RIX1 complex to chromatin being essential for silencing.
Article
Biochemistry & Molecular Biology
Vitaly I. Loginov, Irina V. Pronina, Elena A. Filippova, Alexey M. Burdennyy, Svetlana S. Lukina, Tatiana P. Kazubskaya, Leonid A. Uroshlev, Marina V. Fridman, Olga I. Brovkina, Natalya V. Apanovich, Alexander V. Karpukhin, Ivan S. Stilidi, Nikolay E. Kushlinskii, Alexey A. Dmitriev, Eleonora A. Braga
Summary: This study aimed to differentiate aberrantly methylated miRNA genes involved in different stages of ovarian carcinoma (OvCa) development and metastasis using methylation-specific qPCR. The results revealed distinct patterns of methylation and expression levels of miRNA genes during the progression and metastasis of OvCa, with some miRNA genes showing a significant association with poor overall survival of patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Medicine, Research & Experimental
O. Brovkina, I. Pronina, A. M. Burdennyy, L. A. Uroshlev, E. A. Filippova, M. Fridman, T. P. Kazubskaya, K. Zhordania, V. Loginov, N. E. Kushlinskii, E. A. Braga
Summary: Late diagnosis of ovarian cancer is a significant issue in its treatment, and long non-coding RNA (lncRNA) may serve as promising diagnostic biomarkers. By studying the lncRNA interactome, two lncRNAs (CCAT1 and SNHG14) were identified as potential biomarkers for molecular diagnostics of ovarian cancer. Real-time PCR confirmed the high expression levels of CCAT1 and SNHG14 in ovarian cancer samples, and they showed a positive correlation with the mRNA expression of five genes associated with the epithelial-mesenchymal transition. The activating effect of CCAT1 and SNHG14 on gene expression may be mediated by miR-203 and miR-124.
BULLETIN OF EXPERIMENTAL BIOLOGY AND MEDICINE
(2022)
Article
Medicine, Research & Experimental
S. S. Lukina, A. M. Burdennyy, E. A. Filippova, I. Pronina, N. A. Ivanova, T. P. Kazubskaya, D. N. Kushlinskii, D. O. Utkin, V. Loginov, E. A. Braga, N. E. Kushlinskii
Summary: The study found correlations between the methylation levels of 21 microRNA genes in primary tumors and metastases of ovarian cancer, suggesting involvement in common processes and pathways of gene regulation and interaction. This highlights the potential for these microRNA gene pairs to serve as new markers for the diagnosis and prognosis of ovarian cancer metastasis.
BULLETIN OF EXPERIMENTAL BIOLOGY AND MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Irina V. Pronina, Leonid A. Uroshlev, Alexey A. Moskovtsev, Danila M. Zaichenko, Elena A. Filippova, Marina V. Fridman, Alexey M. Burdennyy, Vitaly I. Loginov, Tatiana P. Kazubskaya, Nikolay E. Kushlinskii, Alexey A. Dmitriev, Eleonora A. Braga, Olga I. Brovkina
Summary: This study aimed to identify lncRNA-miRNA-mRNA competing triplets that promote ovarian tumorigenesis. Through analysis of tumor samples and experimental validation, multiple RNA triplets related to ovarian cancer were identified. Some triplets showed direct binding sites between lncRNA, mRNA, and miRNA. Transfection of miRNA into cells confirmed novel connections between miRNA and OC-related genes. These findings provide potential biomarkers for early detection of metastasis.
Article
Medicine, Research & Experimental
A. D. Selezneva, E. A. Filippova, S. S. Lukina, I. Pronina, N. A. Ivanova, T. P. Kazubskaya, A. M. Burdennyy, E. A. Braga, V. Loginov
Summary: This study analyzed the changes in methylation of CpG islands in four lncRNA genes as potential markers for breast cancer. The study found significantly increased methylation in three of the four genes and significant correlations between the methylation levels of these genes with cancer stage and lymphogenic metastasis. New potential markers for the diagnosis and prognosis of breast cancer can be proposed based on these findings.
BULLETIN OF EXPERIMENTAL BIOLOGY AND MEDICINE
(2022)
Review
Agronomy
Meisam Zargar, Tatiana Zavarykina, Sergey Voronov, Irina Pronina, Maryam Bayat
Summary: Doubled haploid (DH) plants, with a doubled set of chromosomes, speed up the selection process by fixing genetic traits in a homozygous state in each locus within one generation. Recent research focuses on the production of doubled haploids in vivo and their fundamental bases, exploring mechanisms such as parthenogenesis induction, genome elimination during interspecific hybridization, and centromeric histone 3 (CENH3) modification.
Review
Biochemistry & Molecular Biology
Eleonora A. Braga, Marina Fridman, Alexey M. Burdennyy, Elena A. Filippova, Vitaly Loginov, Irina Pronina, Alexey A. Dmitriev, Nikolay E. Kushlinskii
Summary: A decrease in miR-124 expression has been observed in epithelial cancers, and it functions as a suppressor by inhibiting the translation of oncogenic proteins. Epigenetic mechanisms and the effects of long non-coding RNAs and circular RNAs play a significant role in regulating miR-124 expression. The interaction between miR-124 and its partners may be promising targets for cancer therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Medicine, Research & Experimental
N. A. Ivanova, A. M. Burdennyi, S. S. Lukina, E. A. Braga, I. V. Pronina, A. V. Karpukhin, V. B. Matveev, T. P. Kazubskaya, V. I. Loginov, E. A. Braga, N. E. Kushlinskii
Summary: The role of methylation of 9 miRNA genes in the pathogenesis of metastatic clear cell renal cell carcinoma was investigated using quantitative methylation-specific PCR (MS-PCR). Certain miRNA genes were found to be significantly correlated with later stages, larger tumor size, and lymph node or distant organ metastasis. Other genes showed significant correlation with loss of differentiation in the tumor. These findings suggest potential biomarkers for the early diagnosis and prognosis of metastatic clear cell renal cell carcinoma.
BULLETIN OF EXPERIMENTAL BIOLOGY AND MEDICINE
(2023)
Review
Biochemistry & Molecular Biology
Eleonora A. Braga, Marina V. Fridman, Alexey M. Burdennyy, Vitaly I. Loginov, Alexey A. Dmitriev, Irina V. Pronina, Sergey G. Morozov
Summary: Long non-coding RNAs (lncRNAs) play a crucial role in the pathogenesis of non-small-cell lung cancer (NSCLC), primarily through competing binding with microRNAs (miRNAs). However, other mechanisms involving RNA-binding proteins (RBPs) that increase the stability of target mRNAs, and potential involvement of lncRNAs in m6A modification, have also been reported. Analysis of target proteins using the DAVID database and protein interactions using the STRING website revealed that JAK-STAT and Hippo signaling pathways, cytokine pathways, VEGFA-VEGFR2 pathway, cell cycle regulation, and neovascularization are the most relevant pathways affected by lncRNAs in NSCLC.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, General & Internal
Natalya Apanovich, Alexey Matveev, Natalia Ivanova, Alexey Burdennyy, Pavel Apanovich, Irina Pronina, Elena Filippova, Tatiana Kazubskaya, Vitaly Loginov, Eleonora Braga, Andrei Alimov
Summary: Clear cell renal cell carcinoma (ccRCC) is a common and aggressive type of cancer with high metastatic potential. This study analyzed gene expression and methylation levels in tumor and normal kidney tissue samples from patients with metastatic and non-metastatic ccRCC. A panel of genes was identified that can accurately predict the probability of metastasis with up to 92% accuracy.