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Race, ethnicity, ancestry, and aspects that impact HLA data and matching for transplant Front. Genet. (IF 3.7) Pub Date : 2024-03-15 Abeer Madbouly, Yung-Tsi Bolon
Race, ethnicity, and ancestry are terms that are often misinterpreted and/or used interchangeably. There is lack of consensus in the scientific literature on the definition of these terms and insufficient guidelines on the proper classification, collection, and application of this data in the scientific community. However, defining groups for human populations is crucial for multiple healthcare applications
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Impact of deep phenotyping: high diagnostic yield in a diverse pediatric population of 172 patients through clinical whole-genome sequencing at a single center Front. Genet. (IF 3.7) Pub Date : 2024-03-15 Ozlem Akgun-Dogan, Ecenur Tuc Bengur, Beril Ay, Gulsah Sebnem Ozkose, Emre Kar, Fuat Baris Bengur, Aybike S. Bulut, Ayca Yigit, Eylul Aydin, Fatma Nisa Esen, Ozkan Ozdemir, Ahmet Yesilyurt, Yasemin Alanay
Background: Pediatric patients with undiagnosed conditions, particularly those suspected of having Mendelian genetic disorders, pose a significant challenge in healthcare. This study investigates the diagnostic yield of whole-genome sequencing (WGS) in a pediatric cohort with diverse phenotypes, particularly focusing on the role of clinical expertise in interpreting WGS results.Methods: A retrospective
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Complete genome sequence of a novel Prescottella sp. R16 isolate from deep-sea sediments in the western Pacific Front. Genet. (IF 3.7) Pub Date : 2024-03-14 Lingqi Ma, Yuqi Bai, Weili Wang, Shengxiang Pei, Gaiyun Zhang
Prescottella, a distinct genus separate from Rhodococcus, has garnered attention for its adaptability and ecological versatility. In this study, a Gram-stain positive and ovoid-rod shaped the actinobacterium strain R16 was isolated from deep-sea sediment (with a depth of 6,310 m) in the Western Pacific. On the basis of 16S rRNA gene sequence analysis, average nucleotide identity and phylogenomic analysis
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Intelligent computation in cancer gene therapy Front. Genet. (IF 3.7) Pub Date : 2024-03-14 Roee Samuel, Ramez Daniel
In recent years, the use of gene therapy for the treatment of disease has gained substantial interest, both in academic research and in the biomedical industry. Initial experimentation in gene therapy has generated positive results, as well as questions regarding safety. However, lessons have been learned from these first investigations, among them a realization that such treatments require a method
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Non-coding RNA and reprogrammed mitochondrial metabolism in genitourinary cancer Front. Genet. (IF 3.7) Pub Date : 2024-03-13 Sandiya Thirunavukkarasu, Shouryarudra Banerjee, Ishaq Tantray, Rani Ojha
Non-coding ribonucleic acids (ncRNAs) have been recently shown to contribute to tumorigenesis by mediating changes in metabolism. ncRNAs act as key molecules in metabolic pathways regulation. The dysregulation of ncRNAs during cancer progression contributes to altered metabolic phenotypes leading to reprogrammed metabolism. Since ncRNAs affect different tumor processes by regulating mitochondrial dynamics
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Genetic architecture of body weight, carcass, and internal organs traits of Ghanaian local chickens Front. Genet. (IF 3.7) Pub Date : 2024-03-13 Roland A. Kanlisi, Esinam N. Amuzu-Aweh, Augustine Naazie, Hope R. Otsyina, Terra R. Kelly, Rodrigo A. Gallardo, Susan J. Lamont, Huaijun Zhou, Jack Dekkers, Boniface B. Kayang
Information on the genetic architecture of the production traits of indigenous African chicken is limited. We performed a genome-wide association study using imputed Affymetrix Axiom® 600K SNP-chip genotypes on 1,113 chickens from three agroecological zones of Ghana. After quality control, a total of 382,240 SNPs remained. Variance components and heritabilities for some growth, carcass and internal
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TCRpred: incorporating T-cell receptor repertoire for clinical outcome prediction Front. Genet. (IF 3.7) Pub Date : 2024-03-13 Meiling Liu, Yang Liu, Li Hsu, Qianchuan He
T-cell receptor (TCR) plays critical roles in recognizing antigen peptides and mediating adaptive immune response against disease. High-throughput technologies have enabled the sequencing of TCR repertoire at the single nucleotide level, allowing researchers to characterize TCR sequences with high resolutions. The TCR sequences provide important information about patients’ adaptive immune system, and
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Comprehensive whole-genome resequencing unveils genetic diversity and selective signatures of the Xiangdong black goat Front. Genet. (IF 3.7) Pub Date : 2024-03-13 Ziao Liu, Haobang Li, Yang Luo, Jianbo Li, Ao Sun, Zulfiqar Ahmed, Baizhong Zhang, Chuzhao Lei, Kangle Yi
Xiangdong black goats, indigenous to Hunan Province, China, exhibit remarkable adaptation to challenging environments and possess distinct black coat coloration alongside exceptional meat quality attributes. Despite their significance, comprehensive genomic investigations of this breed have been notably lacking. This study involved a comprehensive examination of population structure, genomic diversity
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Association of glutamate receptor gene polymorphisms with attention-deficit hyperactivity disorder susceptibility: a systematic review and meta-analysis Front. Genet. (IF 3.7) Pub Date : 2024-03-13 Dehua Zou, Qiaoli Zeng, Pei Liu, Yue Wei, Runmin Guo, Yizhun Zhu, Rong-Rong He
Background: There is a growing body of evidence indicating a possible association between genetic variations and attention-deficit hyperactivity disorder (ADHD), although the results have been inconsistent. The objective of this study was to evaluate the correlation between the GRIN2A, GRIN2B and GRM7 gene polymorphisms and ADHD.Methods: A comprehensive meta-analysis and subgroup evaluation was conducted
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Long-read sequencing reveals chromothripsis in a molecularly unsolved case of Cornelia de Lange syndrome Front. Genet. (IF 3.7) Pub Date : 2024-03-13 Ilaria Bestetti, Milena Crippa, Alessandra Sironi, Matteo Bellini, Francesca Tumiatti, Sara Ballabio, Ferruccio Ceriotti, Luigi Memo, Maria Iascone, Lidia Larizza, Palma Finelli
Thanks to a long-read sequencing (LRS) approach, in this study, we have reported a molecularly solved case of a proband with a clinical diagnosis of Cornelia de Lange syndrome (CDLS), which is a multisystemic disorder whose causative molecular defects involve cohesin complex genes, with NIPBL located at 5p13.2 accounting for approximately 50%–60% of CDLS cases. The first-tier tests revealed an abnormal
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PCGIMA: developing the web server for human position-defined CpG islands methylation analysis Front. Genet. (IF 3.7) Pub Date : 2024-03-13 Ming Xiao, Yi Xiao, Jun Yu, Le Zhang
Introduction: CpG island (CGI) methylation is one of the key epigenomic mechanisms for gene expression regulation and chromosomal integrity. However, classical CGI prediction methods are neither easy to locate those short and position-sensitive CGIs (CpG islets), nor investigate genetic and expression pattern for CGIs under different CpG position- and interval- sensitive parameters in a genome-wide
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LncRNA-mediated ceRNA network reveals the mechanism of action of Saorilao-4 decoction against pulmonary fibrosis Front. Genet. (IF 3.7) Pub Date : 2024-03-12 Xinyue Fu, Xinni Song, Shufang Niu, Songli Shi, Hong Chang, Jun Qi, Peng Wang, Wanfu Bai
Introduction: Pulmonary fibrosis (PF), a type of interstitial pneumonia with complex etiology and high mortality, is characterized by progressive scarring of the alveolar interstitium and myofibroblastic lesions. In this study, we screened for potential biomarkers in PF and clarified the role of the lncRNA-miRNA-mRNA ceRNA network in the inhibitory effect of SRL-4 on PF.Methods: Healthy male SPF SD
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Integrative analysis identifies cancer cell-intrinsic RARRES1 as a predictor of prognosis and immune response in triple-negative breast cancer Front. Genet. (IF 3.7) Pub Date : 2024-03-12 Zhengheng Yu, Hongjin Liu, Jingming Ye, Yinhua Liu, Ling Xin, Qian Liu, Yuanjia Cheng, Lu Yin, Ling Xu
Triple-negative breast cancer (TNBC) is a subtype of breast cancer with poor prognosis and limited treatment options. Although immune checkpoint inhibitors (ICIs) have been proven to improve outcomes in TNBC patients, the potential mechanisms and markers that determine the therapeutic response to ICIs remains uncertain. Revealing the relationship and interaction between cancer cells and tumor microenvironment
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Salivary miRNAs as auxiliary liquid biopsy biomarkers for diagnosis in patients with oropharyngeal squamous cell carcinoma: a systematic review and meta-analysis Front. Genet. (IF 3.7) Pub Date : 2024-03-11 Huy Nguyen, Taichiro Nonaka
Objective: The healthcare system needs a novel approach to improve and diagnose early oropharyngeal squamous cell carcinoma against its low survival rate. We conduct a systematic review and a comprehensive meta-analysis for the diagnostic role of blood and salivary microRNAs (miRNAs).Methods: An unbiased and thorough literature search in PubMed yielded appropriate data from qualified articles regarding
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A case report of Pallister-Killian syndrome with an unusual mosaic supernumerary marker chromosome 12 with interstitial 12p13.1-p12.1 duplication Front. Genet. (IF 3.7) Pub Date : 2024-03-11 T. V. Karamysheva, I. N. Lebedev, L. I. Minaycheva, L. P. Nazarenko, A. A. Kashevarova, D. A. Fedotov, N. A. Skryabin, M. E. Lopatkina, A. D. Cheremnykh, E. A. Fonova, T. V. Nikitina, E. A. Sazhenova, M. M. Skleimova, N. A. Kolesnikov, G. V. Drozdov, Y. S. Yakovleva, G. N. Seitova, K. E. Orishchenko, N. B. Rubtsov
Pallister-Killian syndrome (PKS) is a rare inherited disease with multiple congenital anomalies, profound intellectual disability, and the presence in the karyotype of sSMC - i(12)(p10). The frequency of PKS may be underestimated due to problems with cytogenetic diagnosis caused by tissue-specific mosaicism and usually a low percentage of peripheral blood cells containing sSMC. Such tissue-specific
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Case report: Novel SIN3A loss-of-function variant as causative for hypogonadotropic hypogonadism in Witteveen–Kolk syndrome Front. Genet. (IF 3.7) Pub Date : 2024-03-11 Lourdes Correa Brito, Ana Keselman, Florencia Villegas, Paula Scaglia, María Esnaola Azcoiti, Sebastián Castro, Nora Sanguineti, Agustín Izquierdo, Marianela Maier, Ignacio Bergadá, Claudia Arberas, Rodolfo A. Rey, María Gabriela Ropelato
Pubertal delay can be due to hypogonadotropic hypogonadism (HH), which may occur in association with anosmia or hyposmia and is known as Kallmann syndrome (OMIM #308700). Recently, hypogonadotropic hypogonadism has been suggested to overlap with Witteveen–Kolk syndrome (WITKOS, OMIM #613406) associated with 15q24 microdeletions encompassing SIN3A. Whether hypogonadotropic hypogonadism is due to haploinsufficiency
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Fibroblast heterogeneity and functions: insights from single-cell sequencing in wound healing, breast cancer, ovarian cancer and melanoma Front. Genet. (IF 3.7) Pub Date : 2024-03-08 Omar Lujano Olazaba, Jeffrey Farrow, Teresa Monkkonen
Cancer has been described as the wound that does not heal, in large part due to fibroblast involvement. Activation of cancer-associated fibroblasts (CAFs) contributes to critical features of the tumor microenvironment, including upregulation of key marker proteins, recruitment of immune cells, and deposition of extracellular matrix (ECM)—similar to fibroblast activation in injury-induced wound healing
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Dual-transgenic BiFC vector systems for protein-protein interaction analysis in plants Front. Genet. (IF 3.7) Pub Date : 2024-03-08 Piaojuan Chen, Meiling Ye, Yadi Chen, Qin Wang, Qiongli Wang, Ming Zhong
Protein-protein interaction (PPI) play a pivotal role in cellular signal transduction. The bimolecular fluorescence complementation (BiFC) assay offers a rapid and intuitive means to ascertain the localization and interactions of target proteins within living cells. BiFC is based on fluorescence complementation by reconstitution of a functional fluorescent protein by co-expression of N- and C-terminal
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Impact of persistent barrier to gene flow and catastrophic events on red algae evolutionary history along the Chilean coast Front. Genet. (IF 3.7) Pub Date : 2024-03-08 Oscar R. Huanel, Alejandro E. Montecinos, Francisco Sepúlveda-Espinoza, Marie-Laure Guillemin
Historical vicariance events, linked to the existence of stable physical barriers to gene flow, generate concordant genetic breaks in co-distributed species while stochastic processes (e.g., costal uplift) could cause species-specific genetic breaks as a result of local strong demographic bottlenecks or extinction. In Chile, previous studies show that the area of the 30°S-33°S could correspond to a
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Neurodevelopmental disorders as a risk factor for temporomandibular disorder: evidence from Mendelian randomization studies Front. Genet. (IF 3.7) Pub Date : 2024-03-08 Xueqiang Wu, Zefang Li, Yiping Cui, Zhaojun Yan, Tingting Lu, Song Cui
Objective: This study aims to clarify the incidence rate of temporomandibular joint disease in patients with mental disorders.Methods: Data extracted from the Psychiatric Genomics Consortium and FinnGen databases employed the Mendelian Randomization (MR) method to assess the associations of three neurodevelopmental disorders (NDDs)—Attention-Deficit/Hyperactivity Disorder (ADHD), Autism Spectrum Disorder
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Searching for gene-gene interactions through variance quantitative trait loci of 29 continuous Taiwan Biobank phenotypes Front. Genet. (IF 3.7) Pub Date : 2024-03-07 Wan-Yu Lin
Introduction: After the era of genome-wide association studies (GWAS), thousands of genetic variants have been identified to exhibit main effects on human phenotypes. The next critical issue would be to explore the interplay between genes, the so-called “gene-gene interactions” (GxG) or epistasis. An exhaustive search for all single-nucleotide polymorphism (SNP) pairs is not recommended because this
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Uganda chicken genetic resources: II. genetic diversity and population demographic history inferred from mitochondrial DNA D-loop sequences Front. Genet. (IF 3.7) Pub Date : 2024-03-07 Illyass Yussif, Donald Rugira Kugonza, Charles Masembe
The genetic diversity of indigenous chickens, which comprise over 80% of the chicken resources in Uganda, is largely not well-characterized for their genetic contribution. This study assessed the genetic diversity and population structure of the indigenous chicken population in Uganda to serve as an essential component for improvement and conservation strategies. A set of 344 mitochondrial DNA (mtDNA)
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High-resolution genomic profiling and locus-specific FISH in subcutaneous and visceral adipose tissue of obese patients Front. Genet. (IF 3.7) Pub Date : 2024-03-07 Vivian-Pascal Brandt, Heidrun Holland, Matthias Blüher, Nora Klöting
Obesity is known as a heterogeneous and multifactorial disease. The distribution of body fat is crucial for the development of metabolic complications. Comprehensive genetic analyses on different fat tissues are rare but necessary to provide more detailed information. Therefore, we performed genetic analyses of three patients with obesity using high resolution genome wide SNP array (blood, visceral
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Frontiers | Transcriptome profiling and analysis of patients with esophageal squamous cell carcinoma from Kazakhstan Front. Genet. (IF 3.7) Pub Date : 2024-03-06 Aigul Sharip, Saule Rakhimova, Askhat Molkenov, Ainur Ashenova, Ulan Kozhamkulov, Ilyas Akhmetollayev, Andrei Zinovyev, Yuri Zhukov, Marat Omarov, Mukhtar Tuleutaev, Venera Rakhmetova, Joseph D. Terwilliger, Joseph H. Lee, Zhaxybay Zhumadilov, Ainur Akilzhanova, Ulykbek Kairov
Esophageal squamous cell carcinoma (ESCC) is the predominant subtype of esophageal cancer in Central Asia, often diagnosed at advanced stages. Understanding population-specific patterns of ESCC is crucial for tailored treatments. This study aimed to unravel ESCC’s genetic basis in Kazakhstani patients and identify potential biomarkers for early diagnosis and targeted therapies. ESCC patients from Kazakhstan
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Mendelian randomization study shows no causal relationship between psychiatric disorders and glaucoma in European and East Asian populations Front. Genet. (IF 3.7) Pub Date : 2024-03-06 Yan Zhang, Longhui Fu, Fang Feng, Bo Liu, Ying Lei, Qianyan Kang
Background: Glaucoma is a leading cause of blindness strongly associated with psychiatric disorders, but the causal association between glaucoma and psychiatric disorders remains uncertain because of the susceptibility of observational studies to confounding and reverse causation. This study aims to explore the potential causal association between glaucoma and three highly related psychiatric disorders
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tRNA engineering strategies for genetic code expansion Front. Genet. (IF 3.7) Pub Date : 2024-03-06 YouJin Kim, Suho Cho, Joo-Chan Kim, Hee-Sung Park
The advancement of genetic code expansion (GCE) technology is attributed to the establishment of specific aminoacyl-tRNA synthetase/tRNA pairs. While earlier improvements mainly focused on aminoacyl-tRNA synthetases, recent studies have highlighted the importance of optimizing tRNA sequences to enhance both unnatural amino acid incorporation efficiency and orthogonality. Given the crucial role of tRNAs
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Long read sequencing on its way to the routine diagnostics of genetic diseases Front. Genet. (IF 3.7) Pub Date : 2024-03-06 Giulia Olivucci, Emanuela Iovino, Giovanni Innella, Daniela Turchetti, Tommaso Pippucci, Pamela Magini
The clinical application of technological progress in the identification of DNA alterations has always led to improvements of diagnostic yields in genetic medicine. At chromosome side, from cytogenetic techniques evaluating number and gross structural defects to genomic microarrays detecting cryptic copy number variants, and at molecular level, from Sanger method studying the nucleotide sequence of
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Identification of a novel KCNT2 variant in a family with developmental and epileptic encephalopathies: a case report and literature review Front. Genet. (IF 3.7) Pub Date : 2024-03-06 Fengji Cui, Tuoya Wulan, Qian Zhang, Victor Wei Zhang, Yuhua Jiang
Background: Developmental and epileptic encephalopathies (DEEs) are a group of heterogeneous neurodevelopmental diseases characterized mainly by developmental delay/intellectual disability and early-onset epilepsy. Researchers have identified variations in the KCNT2 gene (OMIM* 610044) as the cause of DEE type 57 (MIM# 617771).Case presentation: We report in this study a 46-year-old woman who presented
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Elucidating the role of TWIST1 in ulcerative colitis: a comprehensive bioinformatics and machine learning approach Front. Genet. (IF 3.7) Pub Date : 2024-03-06 Wenjie Ou, Zhaoxue Qi, Ning Liu, Junzi Zhang, Xuguang Mi, Yuan Song, Yanqiu Fang, Baiying Cui, Junjie Hou, Zhixin Yuan
Background: Ulcerative colitis (UC) is a common and progressive inflammatory bowel disease primarily affecting the colon and rectum. Prolonged inflammation can lead to colitis-associated colorectal cancer (CAC). While the exact cause of UC remains unknown, this study aims to investigate the role of the TWIST1 gene in UC.Methods: Second-generation sequencing data from adult UC patients were obtained
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Comparative stigmatic transcriptomics reveals self and cross pollination responses to heteromorphic incompatibility in Plumbago auriculata Lam. Front. Genet. (IF 3.7) Pub Date : 2024-03-06 Di Hu, Di Lin, Shouli Yi, Suping Gao, Ting Lei, Wenji Li, Tingdan Xu
“Heteromorphic self-incompatibility” (HetSI) in plants is a mechanism of defense to avoid self-pollination and promote outcrossing. However, the molecular mechanism underlying HetSI remains largely unknown. In this study, RNA-seq was conducted to explore the molecular mechanisms underlying self-compatible (SC, “T × P” and “P × T”) and self-incompatible (SI, “T × T” and “P × P”) pollination in the two
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Hybrid de novo and haplotype-resolved genome assembly of Vechur cattle — elucidating genetic variation Front. Genet. (IF 3.7) Pub Date : 2024-03-06 Poorvishaa V. Muthusamy, Rajesh Vakayil Mani, Shivani Kumari, Manpreet Kaur, Balu Bhaskar, Rajeev Raghavan Pillai, Thankappan Sajeev Kumar, Thapasimuthu Vijayamma Anilkumar, Nongmaithem Sadananda Singh
Cattle contribute to the nutritional needs and economy of a place. The performance and fitness of cattle depend on the response and adaptation to local climatic conditions. Genomic and genetic studies are important for advancing cattle breeding, and availability of relevant reference genomes is essential. In the present study, the genome of a Vechur calf was sequenced on both short-read Illumina and
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Flexible gold standards for transcription factor regulatory interactions in Escherichia coli K-12: architecture of evidence types Front. Genet. (IF 3.7) Pub Date : 2024-03-05 Paloma Lara, Socorro Gama-Castro, Heladia Salgado, Claire Rioualen, Víctor H. Tierrafría, Luis J. Muñiz-Rascado, César Bonavides-Martínez, Julio Collado-Vides
Post-genomic implementations have expanded the experimental strategies to identify elements involved in the regulation of transcription initiation. Here, we present for the first time a detailed analysis of the sources of knowledge supporting the collection of transcriptional regulatory interactions (RIs) of Escherichia coli K-12. An RI groups the transcription factor, its effect (positive or negative)
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Role of circular RNAs in lung cancer Front. Genet. (IF 3.7) Pub Date : 2024-03-04 Maksat Babayev, Patricia Silveyra
Lung cancer remains a global public health concern with significant research focus on developing better diagnosis/prognosis biomarkers and therapeutical targets. Circular RNAs (circRNAs) are a type of single-stranded RNA molecules that covalently closed and have ubiquitous expression. These molecules have been implicated in a variety of disease mechanisms, including lung cancer, as they exhibit oncogenic
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Genetic interrogation for sequence and copy number variants in systemic lupus erythematosus Front. Genet. (IF 3.7) Pub Date : 2024-03-04 Nicholas Kim-Wah Yeo, Che Kang Lim, Katherine Nay Yaung, Nicholas Kim Huat Khoo, Thaschawee Arkachaisri, Salvatore Albani, Joo Guan Yeo
Early-onset systemic lupus erythematosus presents with a more severe disease and is associated with a greater genetic burden, especially in patients from Black, Asian or Hispanic ancestries. Next-generation sequencing techniques, notably whole exome sequencing, have been extensively used in genomic interrogation studies to identify causal disease variants that are increasingly implicated in the development
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Establishment and analysis of artificial neural network diagnosis model for coagulation-related molecular subgroups in coronary artery disease Front. Genet. (IF 3.7) Pub Date : 2024-03-02 Biwei Zheng, Yujing Li, Guoliang Xiong
Background: Coronary artery disease (CAD) is the most common type of cardiovascular disease and cause significant morbidity and mortality. Abnormal coagulation cascade is one of the high-risk factors in CAD patients, but the molecular mechanism of coagulation in CAD is still limited.Methods: We clustered and categorized 352 CAD paitents based on the expression patterns of coagulation-related genes
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Frontiers | Single nucleotide variants in nuclear pore complex disassembly pathway associated with poor survival in osteosarcoma Front. Genet. (IF 3.7) Pub Date : 2024-03-01 James E. Jacobs, Lara Davis, Shannon McWeeney
Introduction: The bone tumor, osteosarcoma, remains challenging to treat in children and young adults, especially when patients present with metastatic disease. Developing new therapies based on genomic data from sequencing projects has proven difficult given the lack of recurrent genetic lesions across tumors. MYC overexpression has been associated with poor outcomes in osteosarcoma. However, other
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Compositional features analysis by machine learning in genome represents linear adaptation of monkeypox virus Front. Genet. (IF 3.7) Pub Date : 2024-03-01 Sen Zhang, Ya-Dan Li, Yu-Rong Cai, Xiao-Ping Kang, Ye Feng, Yu-Chang Li, Yue-Hong Chen, Jing Li, Li-Li Bao, Tao Jiang
Introduction: The global headlines have been dominated by the sudden and widespread outbreak of monkeypox, a rare and endemic zoonotic disease caused by the monkeypox virus (MPXV). Genomic composition based machine learning (ML) methods have recently shown promise in identifying host adaptability and evolutionary patterns of virus. Our study aimed to analyze the genomic characteristics and evolutionary
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Genome-wide identification of dysregulated alternative splicing and RNA-binding proteins involved in atopic dermatitis Front. Genet. (IF 3.7) Pub Date : 2024-03-01 Yaqi Yang, Hao Chen, Qing Jiang, Lin Yang, Rongfei Zhu, Nan Huang
Objectives: We explored the role and molecular mechanisms of RNA-binding proteins (RBPs) and their regulated alternative splicing events (RASEs) in the pathogenesis of atopic dermatitis (AD).Methods: We downloaded RNA-seq data (GSE121212) from 10 healthy control skin samples (healthy, Ctrl), 10 non-lesional skin samples with AD damage (non-lesional, NL), and 10 lesional skin samples with AD damage
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Metabolic syndrome traits exhibit genotype-by-environment interaction in relation to socioeconomic status in the Mexican American family heart study Front. Genet. (IF 3.7) Pub Date : 2024-03-01 Vincent P. Diego, Eron G. Manusov, Xi Mao, Marcio Almeida, Juan M. Peralta, Joanne E. Curran, Michael C. Mahaney, Harald Göring, John Blangero, Sarah Williams-Blangero
Background: Socioeconomic Status (SES) is a potent environmental determinant of health. To our knowledge, no assessment of genotype-environment interaction has been conducted to consider the joint effects of socioeconomic status and genetics on risk for metabolic disease. We analyzed data from the Mexican American Family Studies (MAFS) to evaluate the hypothesis that genotype-by-environment interaction
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Finding potential lncRNA–disease associations using a boosting-based ensemble learning model Front. Genet. (IF 3.7) Pub Date : 2024-03-01 Liqian Zhou, Xinhuai Peng, Lijun Zeng, Lihong Peng
Introduction: Long non-coding RNAs (lncRNAs) have been in the clinical use as potential prognostic biomarkers of various types of cancer. Identifying associations between lncRNAs and diseases helps capture the potential biomarkers and design efficient therapeutic options for diseases. Wet experiments for identifying these associations are costly and laborious.Methods: We developed LDA-SABC, a novel
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ACPPfel: Explainable deep ensemble learning for anticancer peptides prediction based on feature optimization Front. Genet. (IF 3.7) Pub Date : 2024-02-29 Mingyou Liu, Tao Wu, Xue Li, Yingxue Zhu, Sen Chen, Jian Huang, Fengfeng Zhou, Hongmei Liu
Background: Cancer is a significant global health problem that continues to cause a high number of deaths worldwide. Traditional cancer treatments often come with risks that can compromise the functionality of vital organs. As a potential alternative to these conventional therapies, Anticancer peptides (ACPs) have garnered attention for their small size, high specificity, and reduced toxicity, making
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Megalencephalic leukoencephalopathy with subcortical cysts: a variant update and review of the literature Front. Genet. (IF 3.7) Pub Date : 2024-02-29 Emma M. J. Passchier, Quinty Bisseling, Guy Helman, Rosalina M. L. van Spaendonk, Cas Simons, René C. L. Olsthoorn, Hieke van der Veen, Truus E. M. Abbink, Marjo S. van der Knaap, Rogier Min
The leukodystrophy megalencephalic leukoencephalopathy with subcortical cysts (MLC) is characterized by infantile-onset macrocephaly and chronic edema of the brain white matter. With delayed onset, patients typically experience motor problems, epilepsy and slow cognitive decline. No treatment is available. Classic MLC is caused by bi-allelic recessive pathogenic variants in MLC1 or GLIALCAM (also called
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Mechanistic causes of sign epistasis and its applications Front. Genet. (IF 3.7) Pub Date : 2024-02-28 Jinqiu Zhang, Feiyu Chen, Xianghua Li
Mapping genetic variations to phenotypic variations poses a significant challenge, as mutations often combine unexpectedly, diverging from assumed additive effects even in the same environment. These interactions are known as epistasis or genetic interactions. Sign epistasis, as a specific type of epistasis, involves a complete reversal of mutation effects within altered genetic backgrounds, presenting
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Transcriptome-wide 1-methyladenosine functional profiling of messenger RNA and long non-coding RNA in bladder cancer Front. Genet. (IF 3.7) Pub Date : 2024-02-28 Jian-jian Yin, Yan-liang Song, Yu-feng Guo, Yuan-heng Dai, Qi Chang, Tao Wang, Guo-qiang Sun, Ping Lu, Dong-kui Song, Li-rong Zhang
Introduction: Post-transcriptional RNA modifications are crucial regulators of tumor development and progression. In many biological processes, N1-methyladenosine (m1A) plays a key role. However, little is known about the links between chemical modifications of messenger RNAs (mRNAs) and long noncoding RNAs (lncRNAs) and their function in bladder cancer (BLCA).Methods: Methylated RNA immunoprecipitation
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Population genomic analysis reveals genetic divergence and adaptation in Brachymystax lenok Front. Genet. (IF 3.7) Pub Date : 2024-02-28 Ping Li, Le Niu, Jianbo Chang, Xiaomei Kou, Wentian Wang, Wenjing Hu, Qigen Liu
Studying how populations in various environments differ genetically is crucial for gaining insights into the evolution of biodiversity. In order to pinpoint potential indicators of divergence and adaptation to diverse environments, we conducted a comprehensive analysis of 3,491,868 single nucleotide polymorphisms (SNPs) derived from five populations of Brachymystax lenok. We discovered significant
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Revealing the association between vitamin D metabolic pathway gene variants and lung cancer risk: a systematic review and meta-analysis Front. Genet. (IF 3.7) Pub Date : 2024-02-28 Mohamed I. Elsalahaty, Samar Sami Alkafaas, Aya O. Bashir, Khaled A. El-Tarabily, Mohamed T. El-Saadony, Eman H. Yousef
Lung cancer is a crucial global issue, with more than one million deaths annually. While smoking is considered the main etiology of the disease, several genetic variants are associated with it. Alterations in vitamin D pathway genes have also been studied in regards to lung cancer, but the findings have been inconclusive. We here present a systematic review and meta-analysis of seven genes in this
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Association between missense variants of uncertain significance in the CHEK2 gene and hereditary breast cancer: a cosegregation and bioinformatics analysis Front. Genet. (IF 3.7) Pub Date : 2024-02-27 Natalia Alonso, Sebastián Menao, Rodrigo Lastra, María Arruebo, María P. Bueso, Esther Pérez, M. Laura Murillo, María Álvarez, Alba Alonso, Soraya Rebollar, Mara Cruellas, Dolores Arribas, Mónica Ramos, Dolores Isla, Juan José Galano-Frutos, Helena García-Cebollada, Javier Sancho, Raquel Andrés
Inherited mutations in the CHEK2 gene have been associated with an increased lifetime risk of developing breast cancer (BC). We aim to identify in the study population the prevalence of mutations in the CHEK2 gene in diagnosed BC patients, evaluate the phenotypic characteristics of the tumor and family history, and predict the deleteriousness of the variants of uncertain significance (VUS). A genetic
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Comparative genomics and bioinformatics approaches revealed the role of CC-NBS-LRR genes under multiple stresses in passion fruit Front. Genet. (IF 3.7) Pub Date : 2024-02-26 Komal Zia, Muhammad Sadaqat, Baopeng Ding, Kinza Fatima, Norah A. Albekairi, Abdulrahman Alshammari, Muhammad Tahir ul Qamar
Passion fruit is widely cultivated in tropical, subtropical regions of the world. The attack of bacterial and fungal diseases, and environmental factors heavily affect the yield and productivity of the passion fruit. The CC-NBS-LRR (CNL) gene family being a subclass of R-genes protects the plant against the attack of pathogens and plays a major role in effector-triggered immunity (ETI). However, no
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Connecting epigenetics and inflammation in vascular senescence: state of the art, biomarkers and senotherapeutics Front. Genet. (IF 3.7) Pub Date : 2024-02-26 Oscar Fraile-Martinez, Diego De Leon-Oliva, Diego Liviu Boaru, Patricia De Castro-Martinez, Cielo Garcia-Montero, Silvestra Barrena-Blázquez, Joaquin García-García, Natalio García-Honduvilla, Melchor Alvarez-Mon, Laura Lopez-Gonzalez, Raul Diaz-Pedrero, Luis G. Guijarro, Miguel A. Ortega
Vascular diseases pose major health challenges, and understanding their underlying molecular mechanisms is essential to advance therapeutic interventions. Cellular senescence, a hallmark of aging, is a cellular state characterized by cell-cycle arrest, a senescence-associated secretory phenotype macromolecular damage, and metabolic dysregulation. Vascular senescence has been demonstrated to play a
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Differentially expressed microRNAs targeting genes in key pathways in keratoconus Front. Genet. (IF 3.7) Pub Date : 2024-02-26 Dorota M. Nowak-Malczewska, Joanna Swierkowska, Marzena Gajecka
Introduction: Keratoconus (KTCN) is a corneal ectasia, characterized by a progressive thinning and protrusion of the cornea, with a complex etiology involving genetic, behavioral, lifestyle, and environmental factors. Previous studies indicated that microRNAs (miRNAs) could be involved in KTCN pathogenesis. This in silico study aimed to identify precursor microRNAs (pre-miRNAs) differentially expressed
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Functional polymorphisms of NOS3 and GUCY1A3 affect both nitric oxide formation and association with hypertensive disorders of pregnancy Front. Genet. (IF 3.7) Pub Date : 2024-02-26 Daniela A. Pereira, Marcelo R. Luizon, Ana C. Palei, José E. Tanus-Santos, Ricardo C. Cavalli, Valeria C. Sandrim
Impaired nitric oxide (NO) formation may be associated with endothelial dysfunction and increased cardiovascular disease risk in preeclampsia (PE). Functional single-nucleotide polymorphisms (SNPs) of nitric oxide synthase 3 (NOS3) (rs3918226) and guanylate cyclase 1, soluble, alpha 3 (GUCY1A3) (rs7692387) increase susceptibility to the adverse consequences due to inadequate generation of NO by the
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External proficiency testing for histocompatibility and immunogenetics in today and future Front. Genet. (IF 3.7) Pub Date : 2024-02-26 Fatma Savran Oguz
The Histocompatibility and Immunogenetics laboratories provide disease association and pharmacogenetic analyses as well as the tests required for transplantation immunology and transfusion medicine. They perform Human Leukocyte Antigen (HLA) genotyping in patients/recipients and potential donor candidates for solid organ and stem cell transplants using various molecular methods, and determine mismatches
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Comparison of RNA-Seq and microarray in the prediction of protein expression and survival prediction Front. Genet. (IF 3.7) Pub Date : 2024-02-23 Won-Ji Kim, Bo Ram Choi, Joseph J. Noh, Yoo-Young Lee, Tae-Joong Kim, Jeong-Won Lee, Byoung-Gie Kim, Chel Hun Choi
Gene expression profiling using RNA-sequencing (RNA-seq) and microarray technologies is widely used in cancer research to identify biomarkers for clinical endpoint prediction. We compared the performance of these two methods in predicting protein expression and clinical endpoints using The Cancer Genome Atlas (TCGA) datasets of lung cancer, colorectal cancer, renal cancer, breast cancer, endometrial
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Genotype-by-environment interactions govern fitness changes associated with adaptive mutations in two-component response systems Front. Genet. (IF 3.7) Pub Date : 2024-02-23 Brittany R. Sanders, Jordan E. Miller, Noor Ahmidouch, Joseph L. Graves, Misty D. Thomas
Introduction: Two-component response systems (TCRS) are the main mechanism by which prokaryotes acclimate to changing environments. These systems are composed of a membrane bound histidine kinase (HK) that senses external signals and a response regulator (RR) that activates transcription of response genes. Despite their known role in acclimation, little is known about the role TCRS play in environmental
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Comparative transcriptome and metabolome profiles of the leaf and fruits of a Xianjinfeng litchi budding mutant and its mother plant Front. Genet. (IF 3.7) Pub Date : 2024-02-23 Ning Xu, Xian-quan Qin, Dong-bo Li, Yan-jie Hou, Chen Fang, Shu-wei Zhang, Jing-yi You, Hong-Li Li, Hong-ye Qiu
Background: Litchi (Litchi chinensis) is an important sub-tropical fruit in the horticulture market in China. Breeding for improved fruit characteristics is needed for satisfying consumer demands. Budding is a sustainable method for its propagation. During our ongoing breeding program, we observed a litchi mutant with flat leaves and sharp fruit peel cracking in comparison to the curled leaves and
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DeepCBS: shedding light on the impact of mutations occurring at CTCF binding sites Front. Genet. (IF 3.7) Pub Date : 2024-02-23 Yiheng Wang, Xingli Guo, Zhixin Niu, Xiaotai Huang, Bingbo Wang, Lin Gao
CTCF-mediated chromatin loops create insulated neighborhoods that constrain promoter-enhancer interactions, serving as a unit of gene regulation. Disruption of the CTCF binding sites (CBS) will lead to the destruction of insulated neighborhoods, which in turn can cause dysregulation of the contained genes. In a recent study, it is found that CTCF/cohesin binding sites are a major mutational hotspot
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A maternally derived complex small supernumerary marker chromosome involving chromosomes 8 and 14: case report and review of the literature Front. Genet. (IF 3.7) Pub Date : 2024-02-23 Fatima Ouboukss, Zhour El Amrani, Hicham Bouchahta, Ilham Ratbi, Aziza Sbiti, Thomas Liehr, Abdelaziz Sefiani, Abdelhafid Natiq
Introduction: The majority of small supernumerary marker chromosomes (sSMCs) are derived from one single chromosome. Complex sSMCs, on the other hand, consist of genetic material derived from more than one, normally two chromosomes. Complex sSMCs involving chromosomes 8 and 14 are rarely encountered.Case presentation: We present here a 14-month-old boy born from an unrelated couple. At birth, the baby
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Potential causal associations of PM2.5 and osteoporosis: a two-sample mendelian randomization study Front. Genet. (IF 3.7) Pub Date : 2024-02-22 Yi Zhang, Jinsheng Yu, Hang Pei, Xinzheng Zhao, Chao Wang, Guanyin Wang, Zan Shen, Jiang Hua, Bangjian He
Background: Observational studies suggest a potential association between atmospheric particulate matter 2.5 (PM2.5) and osteoporosis, but a causal association is unclear due to the presence of confounding factors.Methods: We utilized bone mineral density indices at four specific sites to represent osteoporosis: femoral neck (FN-BMD), lumbar spine (LS-BMD), forearm (FA-BMD), and heel (HE-BMD). The
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Association of sleep traits with male fertility: a two-sample Mendelian randomization study Front. Genet. (IF 3.7) Pub Date : 2024-02-22 Shikuan Lu, Ziyang Ma, Wanzhen Zhou, Hongsen Zeng, Jian Ma, Hang Deng, Peihai Zhang
Background: Previous observational studies have investigated the association between sleep-related traits and male fertility; however, conclusive evidence of a causal connection is lacking. This study aimed to explore the causal relationship between sleep and male fertility using Mendelian randomisation.Methods: Eight sleep-related traits (chronotype, sleep duration, insomnia, snoring, dozing, daytime
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Linkage mapping and genomic prediction of grain quality traits in tropical maize (Zea mays L.) Front. Genet. (IF 3.7) Pub Date : 2024-02-21 Noel Ndlovu, Rajashekar M. Kachapur, Yoseph Beyene, Biswanath Das, Veronica Ogugo, Dan Makumbi, Charles Spillane, Peter C. McKeown, Boddupalli M. Prasanna, Manje Gowda
The suboptimal productivity of maize systems in sub-Saharan Africa (SSA) is a pressing issue, with far-reaching implications for food security, nutrition, and livelihood sustainability within the affected smallholder farming communities. Dissecting the genetic basis of grain protein, starch and oil content can increase our understanding of the governing genetic systems, improve the efficacy of future