Review
Toxicology
Amy L. Schofield, Joseph P. Brown, Jack Brown, Ania Wilczynska, Catherine Bell, Warren E. Glaab, Matthias Hackl, Lawrence Howell, Stephen Lee, James W. Dear, Mika Remes, Paul Reeves, Eunice Zhang, Jens Allmer, Alan Norris, Francesco Falciani, Louise Y. Takeshita, Shiva Seyed Forootan, Robert Sutton, B. Kevin Park, Chris Goldring
Summary: miRNAs are short non-coding RNA molecules that have been shown to be dysregulated and released in different organ systems. Circulating miRs are proposed as useful biomarkers for various disease states, potentially replacing existing traditional biomarkers. However, pre-analytical and analytical challenges need to be addressed before their clinical use can be realized.
ARCHIVES OF TOXICOLOGY
(2021)
Article
Genetics & Heredity
Mengfeng Liu, Xiran Yu, Jianlong Bu, Qifan Xiao, Sitong Ma, Naozhong Chen, Changfa Qu
Summary: This study found that miRNAs in salivary exosomes may serve as biomarkers for the prediction and diagnosis of lung cancer. By miRNA sequencing and qPCR validation, differentially expressed miRNAs between lung cancer and non-lung cancer groups were identified, which were associated with pathways related to cancer.
FRONTIERS IN GENETICS
(2023)
Review
Biochemistry & Molecular Biology
Esperanza Salcedo Lobera, Macarena Arroyo Varela, Rafael Larrosa Jimenez, Rocio Bautista Moreno
Summary: Lung cancer, with its late diagnosis and limited treatment, is a disease with high prevalence and mortality. Finding biomarkers that allow a faster diagnosis and improve the survival of patients is essential. miRNAs, small RNA sequences, have shown considerable advancements as diagnostic, therapeutic, and prognostic biomarkers. Obtaining miRNA biomarkers from liquid biopsies provides better accessibility, safety, and repeatability for both diagnosis and monitoring of patients.
MOLECULAR BIOLOGY REPORTS
(2023)
Review
Biochemistry & Molecular Biology
Monu Pandey, Abhirup Mukhopadhyay, Surender K. Sharawat, Sachin Kumar
Summary: SCLC, a smoking-related aggressive cancer, shows universal loss of TP53 and RB1 tumor suppressor genes, with miRNAs playing a key role in regulating cell processes and potential clinical applications in monitoring chemotherapy responses and predicting survival outcomes.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2021)
Article
Medicine, General & Internal
Minhan Yi, Zexi Liao, Langmei Deng, Li Xu, Yun Tan, Kun Liu, Ziliang Chen, Yuan Zhang
Summary: This study conducted a meta-analysis of 80 studies and identified several single miRNAs and combined groups with high diagnostic power for non-small cell lung carcinoma (NSCLC), indicating specific miRNAs as good biomarker candidates for NSCLC, further researches are needed.
ANNALS OF MEDICINE
(2021)
Article
Health Care Sciences & Services
Arafat Rahman Oany, Mamun Mia, Tahmina Pervin, Salem Ali Alyami, Mohammad Ali Moni
Summary: This study used systems biology approaches to identify potential biomarkers and pathways for cervical cancer (CC). It found 12 hub genes crucial for CC, including newly reported genes LILRB2 and CYBB, as well as potentially vital gene CXCR4 for patient survival. These findings suggest CXCR4 could serve as a prognostic and/or diagnostic biomarker and a drug target for CC.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Medicine, Research & Experimental
Soudeh Ghafouri-Fard, Bashdar Mahmud Hussen, Elham Badrlou, Atefe Abak, Mohammad Taheri
Summary: miRNAs play a significant role in CRC by influencing the expression and activity of CRC-related pathways and interacting with long non-coding RNAs. Levels of miRNAs can be used to distinguish CRC patients from healthy controls. Despite evaluation of therapeutic application of miRNAs in CRC in animal models, it has not been verified in clinical settings.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
Article
Biology
Yining Liu, Min Zhao, Hong Qu
Summary: We developed a lung cancer-specific database that contains genetic and literature data from over 10,000 separate studies. The database includes meticulously curated and quality controlled cancer subtype information, allowing for novel exploration of subtype-specific genetics. Additionally, we created the Lung Cancer Gene (LCGene) database, an open-access web interface for researchers and clinicians to explore this data and conduct large-scale integrative analyses. On LCGene, users can perform gene list-based data integration to understand the shared and unique characteristics of different subtypes of lung cancer. The data from subtype-based survival analysis, comparative analysis, and CRISPR knockout provide valuable information for genome-wide gene/biomarker screening in lung cancer subtypes.
Review
Biochemistry & Molecular Biology
Jacek Kabzinski, Monika Maczynska, Ireneusz Majsterek
Summary: This article discusses the potential use of microRNAs in the diagnosis of head and neck squamous cell carcinoma, highlighting their application in radiotherapy and immunotherapy, as well as addressing the challenges and future research directions in developing this promising technology.
Review
Cell Biology
Boya Peng, Poh Ying Theng, Minh T. N. Le
Summary: miR-125b, a key miRNA in cancer pathogenesis, is deregulated in various types of cancer and plays important roles in tumourigenesis and cancer progression. Its potential as a diagnostic and prognostic biomarker, as well as a therapeutic tool against cancer, is supported by emerging evidence on its essential functions.
CELL PROLIFERATION
(2021)
Article
Medicine, Research & Experimental
Jinbao Zhou, Hongshu Wang, Qiangling Sun, Xiaomin Liu, Zong Wu, Xianyi Wang, Wentao Fang, Zhongliang Ma
Summary: NSCLC is a common form of cancer, and exosomes enriched with miR-224-5p promote tumor growth and metastasis. miR-224-5p affects NSCLC tumor growth by inhibiting AR and mediating EMT.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2021)
Article
Oncology
He-Guo Jiang, Chun-Hua Dai, Ya-Ping Xu, Qian Jiang, Xian-Bin Xia, Yang Shu, Jian Li
Summary: This study investigated the diagnostic and prognostic value of four plasma miRNAs in non-small cell lung cancer (NSCLC), confirming that miR-210, miR-1290, miR-150, and miR-21-5p were highly expressed in NSCLC patients. The four-miRNA panel showed high accuracy in distinguishing NSCLC patients from healthy controls and those with benign lung disease, suggesting their potential as useful biomarkers for early diagnosis and prognosis of NSCLC.
Review
Oncology
Zihan Ran, Shaobo Wu, Zijng Ma, Xiuwen Chen, Jing Liu, Jingcheng Yang
Summary: Cervical cancer is one of the most common malignancies in females globally. Exosomes, a type of extracellular vesicles released by various cells, play a crucial role in biological processes through carrying proteins and genetic material from their parent cells. This review article focuses on the investigation of exosomes in cervical cancer, particularly their components. The findings suggest that exosomes in cervical cancer regulate the behavior of cancer cells by affecting various biological pathways. Additionally, exosomal RNAs and proteins show potential as biomarkers for cervical cancer. Furthermore, cancer-derived exosomes are found to play a critical role in the metastasis and progression of cervical cancer.
Article
Oncology
Mariusz Rogucki, Iwona Sidorkiewicz, Magdalena Niemira, Janusz Bogdan Dzieciol, Angelika Buczynska, Agnieszka Adamska, Katarzyna Siewko, Maria Kosciuszko, Katarzyna Maliszewska, Anna Wojcicka, Jakub Supronik, Malgorzata Szelachowska, Joanna Reszec, Adam Jacek Kretowski, Anna Poplawska-Kita
Summary: In this study, the microRNA profile of papillary thyroid cancer (PTC) tissue was investigated to identify important pathways and propose a diagnostic biomarker. Four microRNAs (miR-152-3p, miR-221-3p, miR-551b-3p, and miR-7-5p) were identified as potential diagnostic tools for PTC. This study highlights the potential of microRNAs as diagnostic biomarkers for PTC.
Review
Cell Biology
Dean Rao, Chengpeng Yu, Jiaqi Sheng, Enjun Lv, Wenjie Huang
Summary: Circular RNAs (circRNAs) are a class of stable and resistant non-coding RNAs widely expressed in eukaryotic cells, playing important roles in various diseases. CircRNA Foxhead box O3 (circFOXO3) has been studied extensively in cancers as a molecular sponge. Understanding the roles of circFOXO3 can enrich our knowledge of circRNA functions in cancer.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Mohammad Farhadian, Seyed Aabbas Rafat, Bahman Panahi, Esmaeil Ebrahimie
Summary: The gene expression and regulation during lactation in Ghezel sheep breed were studied, revealing 75 differentially expressed genes between the before and after peak stages of lactation. DEGs were mainly involved in metabolic processes and oxidative phosphorylation. PPI network analysis highlighted the contributions of PPAR signaling and other pathways in the lactation process.
ANIMAL BIOTECHNOLOGY
(2022)
Article
Neurosciences
Elham Ghasemi, Mansour Ebrahimi, Esmaeil Ebrahimie
Summary: Accurate diagnosis of ADHD is challenging, but automatic diagnosis using machine learning analysis of brain signals is receiving increased attention. This study developed a model to accurately discriminate between ADHD patients and healthy controls by pattern discovery and feature combination. The results showed that complementary features can significantly improve the performance of predictive models.
COGNITIVE NEURODYNAMICS
(2022)
Article
Agriculture, Dairy & Animal Science
Somayeh Sharifi, Maryam Lotfi Shahreza, Abbas Pakdel, James M. Reecy, Nasser Ghadiri, Hadi Atashi, Mahmood Motamedi, Esmaeil Ebrahimie
Summary: This study aimed to predict candidate drugs for the control and management of E. coli mastitis by integrating different levels of systems biology data. The use of a novel semi-supervised heterogeneous label propagation algorithm identified potential therapeutic avenues for the treatment of E. coli mastitis, including novel drugs such as Glibenclamide, Ipratropium, Salbutamol, and Carbidopa.
Article
Pharmacology & Pharmacy
Zahra Shakoori, Roghiyeh Pashaei-Asl, Maryam Pashaiasl, Soodabeh Davaran, Hossein Ghanbari, Esmaeil Ebrahimie, Seyed Mahdi Rezayat
Summary: This study evaluated the biocompatibility and cytotoxicity of a magnetic nanocomposite as a drug delivery system. The results showed that the nanocomposite had good hemocompatibility and cytocompatibility, and exhibited significant cytotoxicity against cervical cancer cells.
JOURNAL OF DRUG DELIVERY SCIENCE AND TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Roohollah Shamloo-Dashtpagerdi, Hooman Razi, Abbas Alemzadeh, Esmaeil Ebrahimie
Summary: This study analyzed the transcriptomes of Brassica rapa to understand the molecular basis of drought and salinity stress responses and identified a hub regulatory gene. The results suggest that BnABI1 may contribute to the regulation of response and tolerance to drought and salinity stresses.
JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ibrahim O. Alanazi, Salman F. Alamery, Esmaeil Ebrahimie, Manijeh Mohammadi-Dehcheshmeh
Summary: This study profiles splice-disrupt genomic variants and their target genes in different types of prostate cancer, revealing important cancer-associated functions. The findings suggest that these variants could serve as potential diagnostic and prognostic markers for prostate cancer progression and metastasis.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Agriculture, Dairy & Animal Science
Zahra Pezeshkian, Seyed Ziaeddin Mirhoseini, Shahrokh Ghovvati, Esmaeil Ebrahimie
Summary: This study aimed to investigate the transcriptome of breast muscle tissue in male turkeys with high and low feed efficiency. The results showed that high feed efficiency turkeys increased the expression of genes related to amino acid biosynthesis, while low feed efficiency turkeys increased the expression of genes related to the immune response. Furthermore, key genes associated with feed efficiency may serve as potential biomarkers for genetic selection in turkeys.
Article
Biology
Muhammad Mujammami, Mohamed Rafiullah, Assim A. Alfadda, Khalid Akkour, Ibrahim O. Alanazi, Afshan Masood, Mohthash Musambil, Hani Alhalal, Maria Arafah, Anas M. Abdel Rahman, Hicham Benabdelkamel
Summary: This study investigated the role of diabetes in endometrial cancer using a proteomic approach and identified differentially expressed proteins that may be related to cancer metastasis.
Article
Biochemical Research Methods
Raktim Kumar Mondol, Nhan Duy Truong, Mohammad Reza, Samuel Ippolito, Esmaeil Ebrahimie, Omid Kavehei
Summary: In this paper, the authors propose a dual-stage neural network architecture named AFExNet, based on adversarial auto-encoder (AAE), to extract features from high-dimensional genetic data. The performance of AFExNet is evaluated using twelve different supervised classifiers, demonstrating consistent results across all performance metrics and classifier independence.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2022)
Article
Cell Biology
Khalid Akkour, Ibrahim O. Alanazi, Assim A. Alfadda, Hani Alhalal, Afshan Masood, Mohthash Musambil, Anas M. Abdel Rahman, Moudi A. Alwehaibi, Maria Arafah, Ali Bassi, Hicham Benabdelkamel
Summary: This study identified potential protein markers for distinguishing between endometrial cancer and hyperplasia, as well as for early diagnosis and progression prediction of endometrial cancer. The differential expression of proteins between endometrial cancer and hyperplasia patients were linked to AKT, ACTA2, and other signaling pathways.
Article
Nutrition & Dietetics
Antonina Govic, Helen Nasser, Elizabeth A. Levay, Matt Zelko, Esmaeil Ebrahimie, Manijeh Mohammadi Dehcheshmeh, Stephen Kent, Jim Penman, Agnes Hazi
Summary: The study found that long-term calorie restriction can reduce anxiety-like behavior at different stages and identified a transcriptome signature of long-term calorie restriction.
Article
Oncology
Nezar H. Khdary, Abdulaziz A. Alangari, Khadijah M. Katubi, Mohammad Alanazi, Ahmed Alhassan, Sami D. Alzahrani, Zahid Khan, Ibrahim O. Alanazi
Summary: Herbs are valuable medicinal sources and have been extensively studied for their health effects. In this study, gingerol-metal complexes were synthesized and their anticancer activity was investigated, showing promising results and suggesting further research opportunities.
CANCER MANAGEMENT AND RESEARCH
(2023)
Article
Chemistry, Medicinal
Mandana Shariatzadeh, Akbar Karami, Ali Moghadam, Mahbobeh Lotfi, Filippo Maggi, Esmaeil Ebrahimie
Summary: Oliveria decumbens Vent. is a traditional aromatic and medicinal plant used in Iran for various ailments including infections, gastrointestinal diseases, cancer, and inflammation. This study investigated the pharmacological potential of its essential oil (OEO) and its main compounds, particularly in relation to its cytotoxic effects on MCF-7 breast cancer cells. The results showed that OEO could inhibit cell growth, activate apoptosis, and enhance tumor suppression through the activation of specific genes. Molecular docking studies also revealed the potential of OEO's main compounds to target specific proteins involved in cancer growth. These findings suggest that OEO has promising potential as a cancer therapy agent in the pharmaceutical industry.
Article
Multidisciplinary Sciences
Abdullah Othman Alawad, Faisal Sultan Alagrafi, Ahmed Jaman Alfahad, Hala Abdulrahman Alamari, Fatimah Othman Alghamdi, Hussam Mokhtar Fallatah, Alhassan Hamood Aodah, Sultan Suleiman Alyousef, Muhammed Adnan Bakhrebah, Ibrahim Oqla Alanazi, Mohannad Mokhtar Fallatah
Summary: This study investigated the effects of organic extracts from different parts of Rhazya Stricta plant on human pluripotent stem cells-derived neural stem cells. The methanolic extract from the stem was found to significantly increase the growth of neural stem cells. The potential bioactive compounds in the extract can be further studied for research and medical purposes.
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.
