Article
Immunology
Fengge Ma, Yating Zhan, Rocio Bartolome-Cabrero, Wei Ying, Masahide Asano, Zhe Huang, Changchun Xiao, Alicia Gonzalez-Martin
Summary: miRNAs often exert their biological functions through regulating a small number of key target genes, rather than through small changes in the expression of hundreds of target genes. This study provides evidence for the role of key target genes in mediating the function of miR-148a.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biology
Erik Waskiewicz, Michalis Vasiliou, Isaac Corcoles-Saez, Rita S. Cha
Summary: Through data mining and functional genetic analysis, the study identified functionally important and evolutionarily conserved residues in ATM/ATR, shedding light on their diverse roles in enzyme functions. The findings suggest that loss of intrinsic kinase activity in ATM/ATR is infrequent in carcinogenesis.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sarah Janati-Idrissi, Mariana Roza de Abreu, Cervin Guyomar, Fernanda de Mello, Thaovi Nguyen, Nazim Mechkouri, Stephanie Gay, Jerome Montfort, Anne Alicia Gonzalez, Marzieh Abbasi, Jerome Bugeon, Violette Thermes, Herve Seitz, Julien Bobe
Summary: This study provides a proof of concept for the successful identification of miRNA phenotypic targets from RNA-seq data. The researchers identified tead3b as a target of miR-202-5p, which is involved in ovarian function and egg production. This study highlights the importance of understanding miRNA functions and their targets in order to better understand biological processes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Endocrinology & Metabolism
Wenjing Xu, Liwei Xie, Yingying Yang, Jiayu Xu, Shang Cai, Ye Tian
Summary: This study found that highly expressed KAT5 is associated with poor prognosis in ATC patients. The KAT5 inhibitor NU9056 can inhibit ATC cells while having no impact on normal thyroid cells. This inhibitory effect may be achieved by regulating microRNA related to NU9056.
INTERNATIONAL JOURNAL OF ENDOCRINOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Du Tian-zhao, Yang Yang, Wang Xing-xua, Che Yu-xin, Wang Xue-lia
Summary: This study identified a large number of differentially expressed circular RNAs in cervical cancer samples, with circTPCN and circFAM185A significantly upregulated and potentially serving as biomarkers. Knockdown of circTPCN inhibited proliferation, migration, and invasion, while promoting apoptosis in cervical cancer cells. The study suggests that circTPCN could be a potential therapeutic target in cervical cancer through its regulatory pathway involving miR-634 and mTOR.
Article
Agriculture, Dairy & Animal Science
Bushra T. Mohammed, F. Xavier Donadeu
Summary: miR-202 is localized in Sertoli cells and germ cells at different stages of development in bovine testicular tissue. It is involved in regulating proliferation and viability of testicular cells through protein modification, phosphorylation processes, and the longevity regulating pathway.
REPRODUCTION IN DOMESTIC ANIMALS
(2022)
Article
Genetics & Heredity
Kevin Chun Hei Wu, Qian He, Adam N. N. Bennett, Jie Li, Kei Hang Katie Chan
Summary: Recent studies have shown that patients with type 2 diabetes (T2D) who are infected with COVID-19 are more likely to experience severe complications and mortality. A genetic correlation analysis revealed shared genetic variants and pathways between T2D and COVID-19, particularly those related to metabolic pathways and chemokines. These findings suggest that certain chemokines and receptors may contribute to the hyperinflammatory response in T2D patients infected with COVID-19.
FRONTIERS IN GENETICS
(2022)
Review
Biochemical Research Methods
Joel Defo, Denis Awany, Raj Ramesar
Summary: Genome-wide association studies (GWAS) have been greatly improved by high-throughput technology and GWAS meta-analysis has gained popularity in understanding the genetic architecture of complex traits. Different approaches, from SNP to pathway based meta-analysis, have been developed to perform GWAS meta-analysis at different levels. This article provides a comprehensive review of these methods, discussing their strengths, weaknesses, and suggesting recommendations.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Pharmacology & Pharmacy
Fernanda Daniela Dornelas Nunes, Leticia Perticarrara Ferezin, Sherliane Carla Pereira, Fernanda Viana Figaro-Drumond, Lucas Cezar Pinheiro, Itiana Castro Menezes, Cristiane von Werne Baes, Fernanda Borchers Coeli-Lacchini, Jose Eduardo Tanus-Santos, Mario Francisco Juruena, Riccardo Lacchini
Summary: The study found that genetic polymorphisms in the VEGF pathway are associated with the number of suicide attempts and the severity of depressive symptoms.
Article
Biochemistry & Molecular Biology
Wonuola A. Akingbuwa, Anke R. Hammerschlag, Meike Bartels, Michel G. Nivard, Christel M. Middeldorp
Summary: This study integrates single-cell gene expression data with GWAS and exome sequenced data, and finds that both common and ultra-rare genetic variants associated with schizophrenia are overrepresented in specific gene-sets. These gene-sets include protein-truncating variant (PTV)-intolerant (PI) genes, genes expressed in specific brain cell types and neurons, genes defined by synaptic function and location, and genes expressed in both human and mouse brain cell gene-sets. The findings suggest that genes under stringent selection and those expressed in particular brain cell types play important roles in the biological pathways influencing the risk for schizophrenia.
MOLECULAR PSYCHIATRY
(2022)
Article
Genetics & Heredity
Seyed Mehdi Esmaeili-Fard, Mohsen Gholizadeh, Seyed Hasan Hafezian, Rostam Abdollahi-Arpanahi
Summary: In this study, alternative genome-wide association study (GWAS) approaches were used on the genome of Baluchi sheep to identify genes affecting pregnancy outcomes and lamb growth. The results revealed that calcium ion transport during pregnancy and feeding lambs by milk after parturition have the greatest impact on weight gain.
FRONTIERS IN GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
Asha M. Miles, Christian J. Posbergh, Heather J. Huson
Summary: New genetic markers associated with udder and teat conformation in cows were identified, and a composite risk index was proposed to determine potential genes related to mastitis. Integrating genetic information into breeding programs can efficiently reduce economic losses caused by mastitis.
Article
Biochemistry & Molecular Biology
Hairul-Islam Mohamed Ibrahim, Mohammad Bani Ismail, Rebai Ben Ammar, Emad A. Ahmed
Summary: The study revealed that Thidiazuron (TDZ) can suppress the metastasis of drug-resistant breast cancer cells by targeting miRNA-132, the miR-202-5p-PTEN axis, and the PI3K-Akt signaling pathway downstream.
BIOCHEMISTRY AND CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Danyang Wang, Qingmin Liu, Yanjun Ren, Yan Zhang, Xin Wang, Bing Liu
Summary: The study reveals abnormal expression of miR-143/145 and KRAS in colorectal cancer and suggests that genetic polymorphisms related to miRNA may have an impact on CRC development and progression. Certain genetic variations are associated with susceptibility to CRC and patient survival.
BIOSCIENCE REPORTS
(2021)
Article
Pharmacology & Pharmacy
Xiaoling Wei, Lingjun Dong, Xiubing Lei
Summary: This study investigated the potential modulatory mechanisms of NORAD in hepatoma through in vitro experiments. The results showed that NORAD interacted with miR-202-5p and regulated cell viability, apoptosis, and cell cycle arrest by modulating miR-202-5p expression.
TROPICAL JOURNAL OF PHARMACEUTICAL RESEARCH
(2023)
Article
Biochemical Research Methods
Jonathan D. Lee, Joao A. Paulo, Ryan R. Posey, Vera Mugoni, Nikki R. Kong, Giulia Cheloni, Yu-Ru Lee, Frank J. Slack, Daniel G. Tenen, John G. Clohessy, Steven P. Gygi, Pier Paolo Pandolfi
Summary: The iDAPT method allows for detection and inference of transcription factor gene regulatory networks, protein interactors, and chromatin accessibility regulation. It serves as a platform for studying dynamic epigenomic landscapes and the transcription factor components associated with biological phenomena and disease.
Review
Oncology
Paula Milan-Rois, Anan Quan, Frank J. Slack, Alvaro Somoza
Summary: Uveal melanoma is a rare and deadly cancer that requires novel treatment and diagnostic approaches. Long non-coding RNAs (lncRNAs) are crucial in cancer and other diseases, offering potential as therapeutic targets and diagnostic markers. Understanding lncRNAs related to uveal melanoma could inspire the development of new treatments and diagnostics, with their interaction with other non-coding RNAs playing a significant role in cancer development.
Review
Oncology
Vida Karimnia, Frank J. Slack, Jonathan P. Celli
Summary: Pancreatic ductal adenocarcinoma (PDAC) is a deadly cancer with current clinical trials showing limited improvements in patient survival. Photodynamic therapy (PDT) has emerged as a potential approach for treating pancreatic tumors based on studies indicating its effectiveness in activating photosensitizing agents in target tissues.
Article
Multidisciplinary Sciences
Jeffrey R. Haswell, Kaia Mattioli, Chiara Gerhardinger, Philipp G. Maass, Daniel J. Foster, Paola Peinado, Xiaofeng Wang, Pedro P. Medina, John L. Rinn, Frank J. Slack
Summary: This study describes a method to modulate lncRNA expression during human embryonic stem cell differentiation and identifies key lncRNA loci involved in differentiation. A clustering approach was developed to infer mechanisms of action of lncRNA hits, leading to the validation of FOXD3-AS1 as a functional lncRNA essential for pluripotency and differentiation. The cell lines and methodology presented in this study can be adapted to discover and characterize novel regulators of differentiation into any lineage.
Article
Multidisciplinary Sciences
Soo Mi Lee, Kenneth M. Kaye, Frank J. Slack
Summary: The study identified miR-127-3p as a potential tumor suppressor in Kaposi's sarcoma, inhibiting KSHV-driven cellular transformation and proliferation by directly targeting the oncogene SKP2. This led to G(1) cell cycle arrest, activation of the RB protein tumor suppressor pathway, and down-regulation of key oncoprotein transcription factors crucial for KSHV tumorigenesis. Restoring miR-127-3p may serve as a viable therapeutic strategy for Kaposi's sarcoma.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Oncology
Allison R. Baker, Christos Miliotis, Julia Ramirez-Moya, Talia Marc, Ioannis S. Vlachos, Pilar Santisteban, Frank J. Slack
Summary: ADAR1 plays a critical role in triple-negative breast cancer, and its loss leads to reduced cell growth, invasion, and mammosphere formation. ADAR1 regulates both coding and noncoding targets by altering gene expression level, A-to-I editing, and splicing. The study also reveals that several tumor suppressor miRNAs are upregulated upon ADAR1 loss, suppressing cell-cycle progression and invasion.
MOLECULAR CANCER RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Wen Cai Zhang, Nicholas Skiados, Fareesa Aftab, Cerena Moreno, Luis Silva, Paul Joshua Anthony Corbilla, John M. Asara, Aaron N. Hata, Frank J. Slack
Summary: In EGFR-mutant lung cancer, drug-tolerant persister cells (DTPCs) show prolonged survival when receiving EGFR tyrosine kinase inhibitor (TKI) treatments. They are a likely source of drug resistance. This study found that upregulation of miR-21-5p and miR-21-3p tune purine metabolism leading to increased drug tolerance.
CANCER GENE THERAPY
(2022)
Correction
Biotechnology & Applied Microbiology
Wen Cai Zhang, Nicholas Skiados, Fareesa Aftab, Cerena Moreno, Luis Silva, Paul Joshua Anthony Corbilla, John M. Asara, Aaron N. Hata, Frank J. Slack
CANCER GENE THERAPY
(2022)
Editorial Material
Biochemistry & Molecular Biology
Sai Pallavi Pradeep, Shipra Malik, Frank J. Slack, Raman Bahal
Summary: RNA therapeutics have become the next-generation therapy for many diseases, using Watson-Crick base-pairing rules to recognize and modulate target RNA. Antisense oligonucleotides (ASOs) are a powerful approach to treat genetic disorders by altering gene expression. PNAs, with their synthetic DNA mimic structure, have been explored as an effective and safe RNA-targeting platform, demonstrating advances in coding and noncoding RNA targeting for therapeutic applications.
Article
Biochemistry & Molecular Biology
Adrienne Vancura, Alejandro H. Gutierrez, Thorben Hennig, Carlos Pulido-Quetglas, Frank J. Slack, Rory Johnson, Simon Haefliger
Summary: This study has found a bias in the evaluation of evolutionary conservation for cancer-related lncRNAs, raising doubts about its relevance in cancer research.
Article
Cell Biology
Latika Matai, Thalyana Stathis, Jonathan D. Lee, Christine Parsons, Tanvi Saxena, Kovi Shlomchik, Frank J. Slack
Summary: Several microRNAs, such as miR-228 and miR-229-66, have been identified as regulators of aging pathways in C. elegans. These microRNAs interact with transcription factors and are required for normal lifespan and longevity. miR-229-66 is specifically involved in lifespan extension through dietary restriction, reduced insulin signaling, and SKN-1 activation.
Article
Oncology
Urmila Jagtap, Erik S. Anderson, Frank J. Slack
Summary: Circular RNAs (circRNA) have gained significant attention as new components of disease mechanisms and potential biomarkers in various diseases, including cancer. They are highly conserved and show specific expression patterns in different developmental stages and diseases. Numerous studies have identified circRNA expression patterns associated with specific cancer types and patient prognosis. This article provides an overview of registered clinical trials investigating the value of circRNAs as cancer biomarkers and discusses their potential in clinical cancer care. Overall, circRNAs are actively being studied as diagnostic, predictive, and prognostic biomarkers, and their potential as therapeutic targets support ongoing translational and clinical research.
Article
Biochemistry & Molecular Biology
Soo Mi Lee, Michael T. Winters, Ivan Martinez, Frank J. Slack
Summary: The Keystone Symposium 'Small Regulatory RNAs: From Bench to Bedside' focused on the biology and therapeutic applications of small regulatory RNAs. The conference aimed to facilitate the translation of research findings into clinical tools and foster collaboration between academia and industry. It provided a platform for scientists to present and discuss their research in the field of small regulatory RNAs.
Review
Biochemistry & Molecular Biology
Latika Matai, Frank J. Slack
Summary: Aging is associated with protein misfolding diseases and the failure to maintain proteostasis, due to the accumulation of damaged and misfolded proteins and weakened cellular stress response pathways. MiRNAs play important roles in controlling aging and regulating proteostasis and stress responses during aging and age-related diseases. This review focuses on the role of individual miRNAs in age-associated protein folding and degradation, as well as their relationships with organelle-specific stress response pathways.
Article
Cell Biology
Maria Mavrikaki, Jonathan D. Lee, Isaac H. Solomon, Frank J. Slack
Summary: COVID-19 infection is associated with brain aging and emphasizes the value of neurological follow-up in recovered individuals.
