Article
Biotechnology & Applied Microbiology
Yuechao Wu, Qiurong Ren, Zhaohui Zhong, Guanqing Liu, Yangshuo Han, Yu Bao, Li Liu, Shuyue Xiang, Shuo Liu, Xu Tang, Jianping Zhou, Xuelian Zheng, Simon Sretenovic, Tao Zhang, Yiping Qi, Yong Zhang
Summary: PAM-relaxed Cas9 nucleases, cytosine base editors, and adenine base editors are promising tools for precise genome editing in plants. However, their genome-wide off-target effects and background mutations are not well understood. In this study, the whole-genome sequencing analyses of transgenic rice plants edited by different editing tools were conducted, revealing distinct gRNA-dependent off-target sites preferred by Cas9 nucleases and base editors. Additionally, the ABE8e base editor showed a high number of A-to-G off-target mutations at TA motif sites. The study also investigated the timeline and mechanism of somaclonal variation caused by tissue culture, which contributes to background mutations.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Raja Rajakani, Pravin Prakash, Dolly Ghosliya, Ranjana Soni, Arpita Singh, Vikrant Gupta
Summary: This study reports the extensive identification of miRNAs and their possible targets in Azadirachta indica for the first time, indicating the therapeutic potential of this medicinal tree. The miRNAs identified in neem range in size between 19 and 23 nt, with a potential negative correlation between miRNA expression and their targets.
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2021)
Article
Genetics & Heredity
Xinting Yu, Shisong Rong
Summary: The present study aimed to summarize and validate genomic association signals for diabetic retinopathy (DR) and its subtypes. A comprehensive list of significant GWAS discoveries was curated from the GWAS catalog and PubMed/MELINE databases. Meta-analysis of the top signals confirmed the association of two SNPs with DR in independent populations, emphasizing the need for consistent validation and replication efforts in the field of DR genetics. Further functional investigation is warranted for the identified gene loci to understand their role in DR pathogenesis.
Article
Cell & Tissue Engineering
Y. Jia, X. Qi, M. Ma, S. Cheng, B. Cheng, C. Liang, X. Guo, F. Zhang
Summary: This study aimed to explore novel regulatory genetic variants associated with bone mineral density (BMD). Through an integrative analysis of BMD genome-wide association study and regulatory single nucleotide polymorphism (rSNP) annotation information, we identified 36 common genes associated with BMD, such as FAM3C, CCDC170, and SOX6. Additionally, multiple gene ontology terms related to BMD were detected. These findings support the implication of regulatory genetic variants in the development of osteoporosis.
BONE & JOINT RESEARCH
(2023)
Article
Biology
C. Yones, J. Raad, L. A. Bugnon, D. H. Milone, G. Stegmayer
Summary: MiRNAs play a key role in gene expression regulation, and computational methods are needed for accurate prediction of new miRNA candidates. A novel computational method, mirDNN, demonstrated high precision on multiple animal and plant genomes. A new validation methodology was used to ensure the effectiveness of this approach.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Endocrinology & Metabolism
Hongmei Zhu, Siu-wai Leung
Summary: This study synthesized the evidence from microRNA-type 2 diabetes association studies and microRNA-regulated type 2 diabetes pathway delineation studies to identify and validate statistically and biologically significant microRNAs as type 2 diabetes biomarkers. Sixteen microRNAs were found to meet the criteria for biomarker selection.
Article
Dermatology
Ryosuke Okuno, Yu Inoue, Yuichi Hasebe, Toshio Igarashi, Mika Kawagishi-Hotta, Takaaki Yamada, Seiji Hasegawa
Summary: The epidermis is a vital organ that serves as a protective barrier and regulates water retention. Aging, ultraviolet damage, and genetic factors can affect epidermal turnover. This study identified a genetic variant, rs2278431, in the 19q13.2 region that is associated with the rate of corneocyte shedding, which is indicative of epidermal turnover. The variant appears to affect the expression of the SPINT2 gene, which is involved in keratinocyte proliferation and corneocyte size regulation.
EXPERIMENTAL DERMATOLOGY
(2023)
Article
Genetics & Heredity
Dulari K. Jayarathna, Miguel E. Renteria, Adil Malik, Emilie Sauret, Jyotsna Batra, Neha S. Gandhi
Summary: Hormone-dependent cancers are a major cause of death globally and are influenced by factors such as unhealthy lifestyles, environment, and genetics. Transcriptome-wide association studies have identified novel associations between HDC risk and protein-coding genes. Using a SMR-HEIDI method, this study found 13 significant miRNAs associated with HDC risk, providing insights into cancer biology and genetic mechanisms.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Matjaz Rokavec, Zekai Huang, Heiko Hermeking
Summary: This study conducted a comprehensive integrative meta-analysis of multiple computational and experimental miR-34 related datasets, and developed tools to identify and characterize novel miR-34 targets. The meta-analysis results were integrated into a user-friendly website, METAmiR34TARGET, which allows for the prediction of relevant miR-34 targets using expression data obtained from cell lines and tumors/tissues. The website also includes information on more than 200 experimentally validated miR-34 target mRNAs. This research is important for further understanding the role of the p53/miR-34 connection in tumor suppression and for identifying potential cancer drug targets.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Yoon-Young Kim, Kwang-Soo Kim, Yong-Jin Kim, Sung-Woo Kim, Hoon Kim, Seung-Yup Ku
Summary: The study extensively investigated premature ovarian insufficiency in females, identifying differentially expressed genes through RNA sequencing and highlighting the crucial role of miRNAs in regulation, especially in different stages of ovarian development impacting key genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Nana Liu, Longjiang Zhang, Tian Tian, Jingliang Cheng, Bing Zhang, Shijun Qiu, Zuojun Geng, Guangbin Cui, Quan Zhang, Weihua Liao, Yongqiang Yu, Hui Zhang, Bo Gao, Xiaojun Xu, Tong Han, Zhenwei Yao, Wen Qin, Feng Liu, Meng Liang, Qiang Xu, Jilian Fu, Jiayuan Xu, Wenzhen Zhu, Peng Zhang, Wei Li, Dapeng Shi, Caihong Wang, Su Lui, Zhihan Yan, Feng Chen, Jiance Li, Jing Zhang, Dawei Wang, Wen Shen, Yanwei Miao, Junfang Xian, Jia-Hong Gao, Xiaochu Zhang, Mulin Jun Li, Kai Xu, Xi-Nian Zuo, Meiyun Wang, Zhaoxiang Ye, Chunshui Yu, CHIMGEN Consortium
Summary: Genome-wide association meta-analyses in populations of East Asian and European ancestries identify variant-trait associations for 44 hippocampal traits and provide insight into the genetic architectures of hippocampal and subfield volumes.
Article
Medicine, Research & Experimental
Chiara De Santi, Frances K. Nally, Remsha Afzal, Conor P. Duffy, Stephen Fitzsimons, Stephanie L. Annett, Tracy Robson, Jennifer K. Dowling, Sally-Ann Cryan, Claire E. McCoy
Summary: Macrophages are crucial in innate immunity, but can lead to inflammatory diseases if persistently in a pro-inflammatory state. Reprogramming macrophages towards an anti-inflammatory phenotype through targeting a mitochondrial enzyme like arginase 2 shows promise in modulating macrophage phenotype.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2022)
Article
Genetics & Heredity
Jian-Yong Wang, Lei Cui, Hong-Yi Shi, Ling-Hao Chen, Ren-Wei Jin, Xiao-Xia Jiang, Zhu-Ling Chen, Jian-Hong Zhu, Xiong Zhang
Summary: This study found that the single nucleotide polymorphisms (SNPs) of the DNMT1 gene are associated with the risk of Parkinson's disease (PD). Among them, rs9305012 is significantly associated with PD risk, and rs9305012/C is a protective allele. The haplotypes of the 4 tag-SNPs show significant differences between PD patients and controls. The ACC module composed of the 3 alleles is the highest-risk haplotype associated with PD.
FRONTIERS IN GENETICS
(2023)
Article
Plant Sciences
Linnell Bentley Randall, Simon Sretenovic, Yuechao Wu, Desuo Yin, Tao Zhang, Joyce Van Eck, Yiping Qi
Summary: The study utilized the A3A/Y130F-BE3 system for efficient C-to-T base editing in tomato and analyzed the edited plants at the genome and transcriptome levels, finding no clear off-target effects. Base-edited plants showed higher levels of SNVs and indels compared to control plants, but there was no significant evidence of distinct off-target effects.
Article
Allergy
Leah C. Kottyan, Michael P. Trimarchi, Xiaoming Lu, Julie M. Caldwell, Avery Maddox, Sreeja Parameswaran, Michael Lape, Rahul J. D'Mello, Madeline Bonfield, Adina Ballaban, Vincent Mukkada, Philip E. Putnam, Pablo Abonia, Netali Ben-Baruch Morgenstern, Amy A. Eapen, Ting Wen, Matthew T. Weirauch, Marc E. Rothenberg
Summary: The study identified 6 replicated association and genome-wide significance loci, as well as 7 additional loci with suggestive significance. Thirteen protein-coding EoE candidate risk genes were expressed in a genotype-dependent manner.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2021)
Review
Endocrinology & Metabolism
Dylan J. M. Bergen, Antonio Maurizi, Melissa M. Formosa, Georgina L. K. McDonald, Ahmed El-Gazzar, Neelam Hassan, Maria-Luisa Brandi, Jose A. Riancho, Fernando Rivadeneira, Evangelia Ntzani, Emma L. Duncan, Celia L. Gregson, Douglas P. Kiel, M. Carola Zillikens, Luca Sangiorgi, Wolfgang Hogler, Ivan Duran, Outi Makitie, Wim Van Hul, Gretl Hendrickx
Summary: This article describes 59 high bone mass disorders and their underlying genetic causes, with a focus on the signaling pathways and mechanisms involved. The authors classify the known genes into subgroups based on a uniform Gene Ontology terminology, providing potential insights for experimental design and genetic screening. Additionally, the authors discuss the application of functional genomics in discovering new genes and mechanisms in high bone mass disorders, highlighting the importance of multidisciplinary collaborations and knowledge transfer from the laboratory to the clinic. (c) 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
JOURNAL OF BONE AND MINERAL RESEARCH
(2023)
Article
Rheumatology
S. J. J. Drummen, S. Balogun, A. Lahham, K. Bennell, R. S. Hinman, M. Callisaya, G. Cai, P. Otahal, T. Winzenberg, Z. Wang, B. Antony, I. P. Munugoda, J. Martel-Pelletier, J. P. Pelletier, F. Abram, G. Jones, D. Aitken
Summary: This study aimed to determine the feasibility of a randomized controlled trial (RCT) examining the effects of outdoor walking on knee osteoarthritis (KOA) clinical outcomes and MRI structural changes. The study found that a full-scale RCT is feasible based on acceptable adherence, retention, randomization, and safety, although recruitment challenges were identified. The significant symptomatic benefits demonstrate the clinical usefulness of a subsequent trial.
CLINICAL RHEUMATOLOGY
(2023)
Article
Endocrinology & Metabolism
Antoine Weihs, Layal Chaker, Tiphaine C. Martin, Kim V. E. Braun, Purdey J. Campbell, Simon R. Cox, Myriam Fornage, Christian Gieger, Hans J. Grabe, Harald Grallert, Sarah E. Harris, Brigitte Kuehnel, Riccardo E. Marioni, Nicholas G. Martin, Daniel L. McCartney, Allan F. McRae, Christa Meisinger, Joyce B. J. van Meurs, Jana Nano, Matthias Nauck, Annette Peters, Holger Prokisch, Michael Roden, Elizabeth Selvin, Marian Beekman, Diana van Heemst, Eline P. Slagboom, Brenton R. Swenson, Adrienne Tin, Pei-Chien Tsai, Andre Uitterlinden, W. Edward Visser, Henry Voelzke, Melanie Waldenberger, John P. Walsh, Anna Koettgen, Scott G. Wilson, Robin P. Peeters, Jordana T. Bell, Marco Medici, Alexander Teumer
Summary: Novel associations between thyroid hormones and DNA methylation were discovered, advancing our understanding of thyroid hormone action particularly related to KLF9. This study demonstrates the utility of integrating EWAS with other -omics data for unraveling thyroid hormone signaling in humans.
Article
Nutrition & Dietetics
Alexandra P. M. de Koning-Backus, Jessica Kiefte-de C. Jong, Jeroen G. J. van Rooij, Andre G. G. Uitterlinden, Trudy A. Voortman, Magda Meester-Smoor, Caroline C. W. Klaver
Summary: Age-related macular degeneration (AMD) has a strong genetic basis, which can be reduced by environmental factors such as smoking and a healthy diet. However, many ophthalmologists do not inform patients about these beneficial lifestyle changes due to lack of trust and measurement methods. To address this, the AMD-Life study aims to investigate if personalized risk-profiling and coaching can motivate patients to change their lifestyle. The study also aims to identify biomarkers that reflect lifestyle changes beneficial for AMD.
Article
Medicine, General & Internal
Jing Tian, Graeme Jones, Xin Lin, Yuan Zhou, Anna King, James Vickers, Feng Pan
Summary: This study investigates the association between the number of chronic pain sites and the risk of dementia and its subtypes. The findings suggest that a greater number of chronic pain sites is associated with an increased risk of all-cause dementia and Alzheimer's disease, but not vascular and frontotemporal dementia.
Article
Public, Environmental & Occupational Health
Grigory Sidorenkov, Ralph Stadhouders, Colin Jacobs, Firdaus A. A. Mohamed Hoesein, Hester A. Gietema, Kristiaan Nackaerts, Zaigham Saghir, Marjolein A. Heuvelmans, Hylke C. Donker, Joachim G. Aerts, Roel Vermeulen, Andre Uitterlinden, Virissa Lenters, Jeroen van Rooij, Cornelia Schaefer-Prokop, Harry J. M. Groen, Pim A. de Jong, Robin Cornelissen, Mathias Prokop, Geertruida H. de Bock, Rozemarijn Vliegenthart
Summary: Trials have shown that low-dose computed tomography (CT) lung cancer screening can reduce lung cancer mortality in long-term (ex-)smokers, although many individuals have been subjected to unnecessary diagnostic procedures. This project aims to improve the efficiency of lung cancer screening by identifying high-risk participants and improving risk discrimination for nodules. The study will gather new data on genetics, air pollution, malignancy risk for lung nodules, and CT biomarkers beyond lung nodules, and develop prediction models for pre-screening and post-baseline-screening participant selection and nodule management.
EUROPEAN JOURNAL OF EPIDEMIOLOGY
(2023)
Article
Cell Biology
Maxim B. Freidin, Nathan Cheetham, Emma L. Duncan, Claire J. Steves, Katherine J. Doores, Michael H. Malim, Niccolo Rossi, Janet M. Lord, Paul W. Franks, Alessandra Borsini, Isabelle Granville Smith, Mario Falchi, Carmine Pariante, Frances M. K. Williams
Summary: Chronic fatigue is a common symptom of post-COVID syndrome, and this study suggests that elevated levels of IL-6 prior to COVID-19 infection may contribute to the development of chronic fatigue.
INFLAMMATION RESEARCH
(2023)
Article
Medicine, General & Internal
Sadiya S. Khan, Wendy S. Post, Xiuqing Guo, Jingyi Tan, Fang Zhu, Daniel Bos, Bahar Sedaghati-Khayat, Jeroen van Rooij, Aaron Aday, Norrina B. Allen, Maxime M. Bos, Andre G. Uitterlinden, Matthew J. Budoff, Donald M. Lloyd-Jones, Jonathan D. Mosley, Jerome I. Rotter, Philip Greenland, Maryam Kavousi
Summary: Coronary artery calcium score and polygenic risk score were evaluated for their ability to predict risk of coronary heart disease (CHD) in two population-based studies. The results showed that coronary artery calcium score had better discrimination and improved risk prediction when added to traditional risk factors compared to the polygenic risk score.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2023)
Article
Rheumatology
Ambrish Singh, Alison Venn, Leigh Blizzard, Lyn March, Felix Eckstein, Graeme Jones, Wolfgang Wirth, Flavia Cicuttini, Changhai Ding, Benny Antony
Summary: This study aims to describe the associations between MRI markers and knee symptoms in young adults. The results showed that bone marrow lesions and cartilage defects were positively associated with knee symptoms, while cartilage volume and thickness were weakly and negatively associated with knee symptoms.
Article
Rheumatology
Zhiqiang Wang, Graeme Jones, Leigh Blizzard, Dawn Aitken, Zhen Zhou, Mengmeng Wang, Saliu Balogun, Flavia Cicuttini, Benny Antony
Summary: This study aimed to describe the prevalence and correlates of the use of complementary and alternative medicines (CAMs) among community-dwelling older adults. The results showed that 35% of the participants reported CAM use, with vitamins/minerals being the most commonly used. CAM users were more likely to be female, be better educated, have more joints with osteoarthritis, and have healthier lifestyles.
INTERNATIONAL JOURNAL OF RHEUMATIC DISEASES
(2023)
Article
Endocrinology & Metabolism
J. A. Kanis, H. Johansson, E. McCloskey, E. Liu, K. E. Akesson, F. A. Anderson, R. Azagra, C. L. Bager, C. Beaudart, H. A. Bischoff-Ferrari, E. Biver, O. Bruyere, J. A. Cauley, J. R. Center, R. Chapurlat, C. Christiansen, C. Cooper, C. J. Crandall, S. R. Cummings, J. A. P. da Silva, B. Dawson-Hughes, A. Diez-Perez, A. B. Dufour, J. A. Eisman, P. J. M. Elders, S. Ferrari, Y. Fujita, S. Fujiwara, C. -c. Glueer, I. Goldshtein, D. Goltzman, V. Gudnason, J. Hall, D. Hans, M. Hoff, R. J. Hollick, M. Huisman, M. Iki, S. Ish-Shalom, G. Jones, M. K. Karlsson, S. Khosla, D. P. Kiel, W. -p. Koh, F. Koromani, M. A. Kotowicz, H. Kroger, T. Kwok, O. Lamy, A. Langhammer, B. Larijani, K. Lippuner, D. Mellstrom, T. Merlijn, A. Nordstrom, P. Nordstrom, T. W. O'Neill, B. Obermayer-Pietsch, C. Ohlsson, E. S. Orwoll, J. A. Pasco, F. Rivadeneira, A. -M. Schott, E. J. Shiroma, K. Siggeirsdottir, E. M. Simonsick, E. Sornay-Rendu, R. Sund, K. M. A. Swart, P. Szulc, J. Tamaki, D. J. Torgerson, N. M. van Schoor, T. P. van Staa, J. Vila, N. J. Wareham, N. C. Wright, N. Yoshimura, M. C. Zillikens, M. Zwart, L. Vandenput, N. C. Harvey, M. Lorentzon, W. D. Leslie
Summary: A large international meta-analysis finds that a previous history of fracture is associated with an increased risk of future fractures, regardless of age, sex, and bone mineral density. The study highlights the importance of considering previous fracture history as a risk factor for fracture prevention strategies.
OSTEOPOROSIS INTERNATIONAL
(2023)
Article
Cardiac & Cardiovascular Systems
Shirin Ibrahim, Jeroen van Rooij, Annemieke J. M. H. Verkerk, Jard de Vries, Linda Zuurbier, Joep Defesche, Jorge Peter, Willemijn A. M. Schonck, Bahar Sedaghati-Khayat, G. Kees Hovingh, Andre G. Uitterlinden, Erik S. G. Stroes, Laurens F. Reeskamp
Summary: This study evaluated the accuracy of a low-cost, high-throughput genotyping array for diagnosing familial hypercholesterolemia (FH). The results showed that the array had a high coverage and sensitivity for FH-causing variants, and could identify additional FH-causing variants. The array has the potential to increase accessibility to genetic testing for FH at a low cost.
CIRCULATION-GENOMIC AND PRECISION MEDICINE
(2023)
Article
Biology
Carolina Medina-Gomez, Benjamin H. Mullin, Alessandra Chesi, Vid Prijatelj, John P. Kemp, Chen Shochat-Carvalho, Katerina Trajanoska, Carol Wang, Raimo Joro, Tavia E. Evans, Katharina E. Schraut, Ruifang Li-Gao, Tarunveer S. Ahluwalia, M. Carola Zillikens, Kun Zhu, Dennis O. Mook-Kanamori, Daniel S. Evans, Maria Nethander, Maria J. Knol, Gudmar Thorleifsson, Ivana Prokic, Babette Zemel, Linda Broer, Fiona E. McGuigan, Natasja M. van Schoor, Sjur Reppe, Mikolaj A. Pawlak, Stuart H. Ralston, Nathalie van der Velde, Mattias Lorentzon, Kari Stefansson, Hieab H. H. Adams, Scott G. Wilson, M. Arfan Ikram, John P. Walsh, Timo A. Lakka, Kaare M. Gautvik, James F. Wilson, Eric S. Orwoll, Cornelia M. van Duijn, Klaus Bonnelykke, Andre G. Uitterlinden, Unnur Styrkarsdottir, Kristina E. Akesson, Timothy D. Spector, Jonathan H. Tobias, Claes Ohlsson, Janine F. Felix, Hans Bisgaard, Struan F. A. Grant, J. Brent Richards, David M. Evans, Bram van der Eerden, Jeroen van de Peppel, Cheryl Ackert-Bicknell, David Karasik, Erika Kague, Fernando Rivadeneira
Summary: Skull bone mineral density (SK-BMD) is a suitable trait for studying bone biology, particularly related to intramembranous ossification. A genome-wide association meta-analysis identified 59 loci associated with SK-BMD, which collectively explained 12.5% of the variance in the trait. These loci are involved in skeletal development and osteoporosis, and four of them are related to intramembranous ossification and craniofacial abnormalities.
COMMUNICATIONS BIOLOGY
(2023)
Article
Pharmacology & Pharmacy
K. J. Ploegmakers, E. P. van Poelgeest, L. J. Seppala, S. C. van Dijk, L. C. P. G. M. de Groot, S. Oliai Araghi, N. M. van Schoor, B. Stricker, K. M. A. Swart, A. G. Uitterlinden, R. A. A. Mathot, N. van Der Velde
Summary: This study investigated whether the use of beta-blockers in older adults increased the risk of falls and found that elevated plasma concentrations of metoprolol were associated with an increased risk of falls. No association was found between nonselective beta-blocker concentrations and fall risk. Changes in concentration over time were also not associated with increased fall risk.
PHARMACOLOGY RESEARCH & PERSPECTIVES
(2023)
Article
Biochemistry & Molecular Biology
Shulan Huang, Hongning Zhang, Wen Chen, Jiawei Wang, Zhen Wu, Meiqi He, Jian Zhang, Xiang Hu, Shuanglin Xiang
Summary: This study used a yeast cDNA library constructed from zebrafish embryos to identify potential interacting proteins of Tnfaip1. Functional annotation and signaling pathway analysis revealed that these proteins are mainly involved in translation, protein catabolic process, ribosome assembly, cytoskeleton formation, amino acid metabolism, and PPAR signaling pathway. Further experiments confirmed four interacting proteins of Tnfaip1. These findings enhance our understanding of the network of Tnfaip1-interacting proteins during embryo development and provide a molecular foundation for future exploration of Tnfaip1's biological functions.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)