Review
Medicine, General & Internal
Ugur Gezer, Abel J. Bronkhorst, Stefan Holdenrieder
Summary: Liquid biopsy is a method of diagnosing pathological conditions by testing biomarkers in body fluids. Cell-free DNA (cfDNA) has significant potential as a biomarker in oncology, prenatal testing, and transplant monitoring. The clinical potential of repeat DNA sequences in cfDNA as an underappreciated marker in liquid biopsy for cancer is highlighted.
Article
Genetics & Heredity
Till Baar, Sebastian Duemcke, Saskia Gressel, Bjoern Schwalb, Alexander Dilthey, Patrick Cramer, Achim Tresch
Summary: Alu elements are a significant group of RNA retrotransposons in the human genome, linked to genetic defects and sequence diversity. This study provides new insights into the origin and life cycle of Alu transcripts, showing that they are more stable and partly transcribed by RNA Polymerase II. Additionally, a novel statistical test for detecting expression of quantitative trait loci in Alu elements is developed.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Hyo Won Ahn, Zelia F. Worman, Arianna Lechsinska, Lindsay M. Payer, Tongguang Wang, Nasir Malik, Wenxue Li, Kathleen H. Burns, Avindra Nath, Henry L. Levin
Summary: Transposable elements (TEs) may contribute to the risk of neuropsychiatric diseases by affecting gene expression and regulation.
Article
Cell Biology
Deborah Ramini, Silvia Latini, Angelica Giuliani, Giulia Matacchione, Jacopo Sabbatinelli, Emanuela Mensa, Maria Giulia Bacalini, Paolo Garagnani, Maria Rita Rippo, Giuseppe Bronte, Massimiliano Bonafe, Maurizio Cardelli, Fabiola Olivieri
Summary: One of the main challenges in aging research is to understand the complex epigenetic mechanisms involved in cellular senescence. This study found that changes in DNA methylation, specifically in transposable element (TE) sequences, are associated with replicative senescence in fibroblasts. The study also showed that the RNA expression of Alu and L1 sequences, as well as the amount of TE DNA copies, were significantly increased in senescent cells. These findings suggest that TEs may play a role in the acquisition of the senescent phenotype.
Article
Genetics & Heredity
Maria E. Morales, Tiffany Kaul, JaNiece Walker, Chelsea Everett, Travis White, Prescott Deininger
Summary: Alu elements, the most abundant source of nonallelic homology in the human genome, play a crucial role in genetic instability. Alu mismatches influence various DNA recombination processes, leading to deletions with different mechanisms depending on DNA repair defects.
Article
Biochemistry & Molecular Biology
Thanit Saeliw, Songphon Kanlayaprasit, Surangrat Thongkorn, Kwanjira Songsritaya, Bumpenporn Sanannam, Chanachai Sae-Lee, Depicha Jindatip, Valerie W. Hu, Tewarit Sarachana
Summary: This study characterized the expression and sequence characteristics of transposable elements, specifically Alu elements, in the prefrontal cortex tissues of individuals with autism spectrum disorder (ASD). The study found that the differential expression of Alu elements was associated with ASD-related genes and cellular processes. Additionally, significant hypomethylation of Alu elements was observed in ASD subphenotypes, suggesting potential epigenetic involvement. These findings provide insights into the role of Alu elements in gene regulation and molecular neuropathology in ASD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biology
Xingyu Liao, Wufei Zhu, Juexiao Zhou, Haoyang Li, Xiaopeng Xu, Bin Zhang, Xin Gao
Summary: This review explores the characteristics of DNA repeats, their functional impacts, and available tools for their analysis.
COMMUNICATIONS BIOLOGY
(2023)
Article
Genetics & Heredity
Shohei Kojima, Satoshi Koyama, Mirei Ka, Yuka Saito, Erica Parrish, Mikiko Endo, Sadaaki Takata, Misaki Mizukoshi, Keiko Hikino, Atsushi Takeda, Asami Gelinas, Steven Heaton, Rie Koide, Anselmo F. Kamada, Michiya Noguchi, Michiaki Hamada, Biobank Japan Project Consortium, Yoichiro Kamatani, Yasuhiro Murakawa, Kazuyoshi Ishigaki, Yukio Nakamura, Kaoru Ito, Chikashi Terao, Yukihide Momozawa, Nicholas F. Parrish
Summary: MEGAnE is a new tool for detecting and genotyping mobile element variants (MEVs) from short-read whole-genome sequencing datasets. This tool has revealed population-specific differences in MEVs and their impact on gene expression variation and disease risk. The integration of MEVs with expression quantitative trait loci (eQTL) maps has shown that MEVs regulate tissue-specific gene expression and contribute to genome diversification and traits.
Editorial Material
Cell Biology
Kathleen Watt, Lynne-Marie Postovit
Summary: In cancer, alternative polyadenylation can result in altered 3' UTRs with varying regulatory effects. A recent study reveals a mechanism that leads to lengthening of 3' UTRs and translational repression of specific metastasis-suppressing genes, introducing a potential therapeutic vulnerability.
NATURE CELL BIOLOGY
(2023)
Article
Hematology
Yohann Jourdy, Nicolas Chatron, Mathilde Fretigny, Amy Dericquebourg, Damien Sanlaville, Christine Vinciguerra
Summary: This study characterized the breakpoint junctions of 24 large F8 deletions and revealed the main causative mechanisms of these deletions. It also identified a possible F8 DNA breakage hotspot involved in non-recurrent rearrangements.
JOURNAL OF THROMBOSIS AND HAEMOSTASIS
(2022)
Article
Biotechnology & Applied Microbiology
Roshan Regmi, Toby E. Newman, Yuphin Khentry, Lars G. Kamphuis, Mark C. Derbyshire
Summary: Our study characterized small non-coding RNAs in S. sclerotiorum and identified their endogenous targets. We found that S. sclerotiorum produces microRNAs and short interfering RNAs, and discovered phased siRNA-producing loci in this pathogen. We also identified a large number of endogenous targets, many of which are repeat element genes. In addition, we predicted and confirmed the existence of miRNA loci and their cleavage targets. Our findings provide new insights into the sRNA populations and functions in S. sclerotiorum, and contribute to the study of sRNAs in this pathogen.
Article
Plant Sciences
Zhi-Zhong Li, Samuli Lehtonen, Jin-Ming Chen
Summary: This study examines the structural complexity and evolutionary history of plastomes in the subclass Alismatidae. Analysis of 38 complete plastomes reveals significant variability in size, structure, repeat elements, and gene content. The results suggest that ndh gene loss and repeat elements contribute to the size of plastomes in Alismatidae.
Article
Neurosciences
Bin Mao, Na Lin, Danhua Guo, Deqin He, Huili Xue, Lingji Chen, Qianqian He, Min Zhang, Meihuan Chen, Hailong Huang, Liangpu Xu
Summary: This study aimed to elucidate the underlying causes of genetic epilepsy in seven Chinese families using whole-exome sequencing and identified 11 variants in seven genes associated with the disease. The study provided genetic counseling, medical suggestions, and prenatal diagnosis for the families. Molecular diagnosis is crucial for improved medical outcomes and recurrence risk evaluation in genetic epilepsy.
FRONTIERS IN NEUROSCIENCE
(2023)
Article
Cell Biology
Siyan Meng, Xiaoxu Liu, Shiqi Zhu, Peng Xie, Haitong Fang, Qingyun Pan, Ke Fang, Fanfan Li, Jin Zhang, Zhuanzhuan Che, Quanyong Zhang, Guangyao Mao, Yan Wang, Ping Hu, Kai Chen, Fei Sun, Wei Xie, Zhuojuan Luo, Chengqi Lin
Summary: ELL3, an RNA polymerase II elongation factor, suppresses the activity of a subset of young LINE-1 elements, which regulate gene activation and signaling pathways in mouse embryonic stem cells. This study reveals the enhancer function of these LINE-1 elements and their importance in early embryo development.
NATURE CELL BIOLOGY
(2023)
Article
Genetics & Heredity
Alba Marino, Alena Kizenko, Wai Yee Wong, Fabrizio Ghiselli, Oleg Simakov
Summary: By reevaluating and annotating repeat elements in the genomes of coleoid cephalopods, and using network sequence divergence approaches, we have identified and characterized the ancient repeat complement shared by at least four species. Surprisingly, lower-copy-number DNA and retroelements were found to be more associated with ancient cephalopod radiation, rather than the most abundant elements in extant genomes.
FRONTIERS IN GENETICS
(2022)
Article
Endocrinology & Metabolism
Freja C. B. Mork, Jens Otto B. Madsen, Andreas K. Jensen, Gerrit Hall, Kasper A. Pilgaard, Flemming Pociot, Jesper Johannesen
Summary: The study found that some children with T1D have impaired insulin sensitivity during the remission phase, and they may still not be in remission 14.5 months after diagnosis despite having stimulated c-peptide levels >300 pmol/L.
Article
Biochemistry & Molecular Biology
Stefan E. Seemann, Aashiq H. Mirza, Claus H. Bang-Berthelsen, Christian Garde, Mikkel Christensen-Dalsgaard, Christopher T. Workman, Flemming Pociot, Niels Tommerup, Jan Gorodkin, Walter L. Ruzzo
Summary: The accelerated evolution of RNA structures in vertebrates, though rare, does not preclude the conservation of their functions, as shown in the study.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Endocrinology & Metabolism
Setareh Soltani, Kamran Mansouri, Shahram Parvaneh, Avnesh S. Thakor, Flemming Pociot, Reza Yarani
Summary: Diabetes is a chronic disorder with serious complications affecting patients' survival and quality of life. Extracellular vesicles (EVs) as a new type of cell-free therapeutic delivery packets have potential in treating diabetic complications.
REVIEWS IN ENDOCRINE & METABOLIC DISORDERS
(2022)
Article
Genetics & Heredity
Sara Juul Mansachs, Sofie Olund Villumsen, Jesper Johannesen, Alexander Lind, Simranjeet Kaur, Flemming Pociot
Summary: Autoantibodies to NPY-LA have been found in individuals with T1D. This study identified three loci (DGKH, DCAF5, and LINC02261) associated with NPY-LA levels, indicating an association with neurologic and vascular disorders. Additionally, SNP variations in six genes were found to be associated with NPY-LA levels, and pathway analysis showed NPY-LA's association with gene transcription, protein modification, immunological functions, and the MAPK pathway.
Article
Multidisciplinary Sciences
Hasim Tekin, Knud Josefsen, Lars Krogvold, Knut Dahl-Jorgensen, Ivan Gerling, Flemming Pociot, Karsten Buschard
Summary: The incidence of type 1 diabetes in children under 18 years of age increases after COVID-19 infection. Decreased expression of PDE12 is associated with T1D development, while rare PDE12 SNPs may increase the risk of T1D.
SCIENTIFIC REPORTS
(2022)
Article
Medicine, General & Internal
Tina Okdahl, Anne-Marie Wegeberg, Flemming Pociot, Birgitte Brock, Joachim Storling, Christina Brock
Summary: The level of low-grade inflammation in type 2 diabetes is associated with obesity, glycaemic regulation, therapeutical management, sex, and complications. Our results underline the importance of addressing inflammatory issues in type 2 diabetes, as these may predispose for crippling comorbidities.
Article
Biochemistry & Molecular Biology
Reza Yarani, Oana Palasca, Nadezhda T. Doncheva, Christian Anthon, Bartosz Pilecki, Cecilie A. S. Svane, Aashiq H. Mirza, Thomas Litman, Uffe Holmskov, Claus H. Bang-Berthelsen, Mogens Vilien, Lars J. Jensen, Jan Gorodkin, Flemming Pociot
Summary: This study identified common conserved pathological UC-related gene expression signatures between humans and mice by comparing gene expression data. These signatures can be used as treatment targets or biomarker candidates. Less known genes with importance in disease pathogenesis were identified and validated in different samples. The findings contribute to disease phenotyping, treatment decisions, drug discovery, and clinical trial design.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Endocrinology & Metabolism
Steffen U. Thorsen, Xiang Liu, Yachana Kataria, Thomas Mandrup-Poulsen, Simranjeet Kaur, Ulla Uusitalo, Suvi M. Virtanen, Jill M. Norris, Marian Rewers, William Hagopian, Jimin Yang, Jin-Xiong She, Beena Akolkar, Stephen Rich, Carin Andren Aronsson, Ake Lernmark, Anette-Gabriele Ziegler, Jorma Toppari, Jeffrey Krischer, Hemang M. Parikh, Christina Ellervik, Jannet Svensson
Summary: It is found that iron intake and genetically determined iron overload may interact in predisposing to the development of childhood islet autoimmunity and type 1 diabetes. A U-shaped association between iron intake and risk of GAD antibody as the first autoantibody in children was found. High iron intake was associated with an increased risk of IA with insulin as the first autoantibody in children with 2 or more iron risk alleles.
Article
Endocrinology & Metabolism
Najda Rudman, Simranjeet Kaur, Vesna Simunovic, Domagoj Kifer, Dinko Soic, Toma Keser, Tamara Stambuk, Lucija Klaric, Flemming Pociot, Grant Morahan, Olga Gornik
Summary: In this study, a genetic association study was conducted to explore the genetic variants contributing to the N-glycosylation of plasma proteins and IgGs in type 1 diabetes. The results confirmed previously known associations and identified novel associations that were not previously reported. These findings highlight the importance of further investigating the potential role of N-glycosylation in complement activation and susceptibility to type 1 diabetes.
Article
Endocrinology & Metabolism
Caroline Frorup, Rebekka Gerwig, Cecilie Amalie Sondergaard Svane, Joana Mendes Lopes de Melo, Kristine Henriksen, Tina Floyel, Flemming Pociot, Simranjeet Kaur, Joachim Storling
Summary: This study provides detailed insight into the effects of cytokines on EndoC-beta H5 cells, including increased apoptosis, MHC-I expression, chemokine production, impaired mitochondrial function, and diminished insulin secretion.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Cell Biology
Valdemar Brimnes Ingemann Johansen, Daisy Faero, Karsten Buschard, Karsten Kristiansen, Flemming Pociot, Pia Kiilerich, Knud Josefsen, Martin Haupt-Jorgensen, Julie Christine Antvorskov
Summary: The incidence of type 1 diabetes is increasing and environmental factors are believed to contribute to it. A gluten-free diet has been shown to improve autoimmune diabetes in non-obese diabetic (NOD) mice and humans. This study conducted analysis of gut microbiota and pancreatic immune environment in NOD mice fed a gluten-free (GF) diet and a gluten-containing standard (STD) diet. The results revealed distinct microbiota compositions and reduced insulitis in GF mice, suggesting a protective effect of a GF diet in humans.
Review
Biochemistry & Molecular Biology
Hamid-Reza Mohammadi-Motlagh, Mona Sadeghalvad, Niloofar Yavari, Rosita Primavera, Setareh Soltani, Shashank Chetty, Abantika Ganguly, Shobha Regmi, Tina Floyel, Simranjeet Kaur, Aashiq H. H. Mirza, Avnesh S. S. Thakor, Flemming Pociot, Reza Yarani
Summary: Pancreatic beta cells play a crucial role in regulating blood sugar levels through insulin production. Research has shown that autophagy, the process of recycling cell components, is vital for beta cell function and survival. Impaired autophagy leads to loss of beta cell function, apoptosis, and the development of diabetes. Factors such as endoplasmic reticulum stress, inflammation, and high metabolic demands can affect autophagy, thereby impacting beta cell function and insulin synthesis. This review highlights the importance of autophagy in determining the fate of beta cells in diabetes and discusses the role of intrinsic and extrinsic factors in modulating autophagy and cellular failure.
