Article
Plant Sciences
Yi Wu, Fangbin Cao, Lupeng Xie, Feibo Wu, Shenlong Zhu, Chengwei Qiu
Summary: Aluminum toxicity is a major constraint to crop production in acidic soils. This study investigated the changes in miRNA expression in the roots of two olive genotypes with contrasting aluminum tolerance. A total of 352 miRNAs were discovered, and 11 miRNAs showed significantly different expression patterns between the tolerant and sensitive genotypes under aluminum stress. In silico prediction identified potential target genes involved in transcriptional regulation, hormone signaling, transportation, and metabolism. These findings provide new insights into the regulatory roles of miRNAs in enhancing aluminum tolerance in olives.
Article
Cell Biology
Ana Paula Azambuja, Marcos Simoes-Costa
Summary: Cell fate commitment is mainly regulated by cis-regulatory elements that propagate signaling inputs to network components. This study provides insights into the three-dimensional organization of the neural crest genome and how signaling systems provide spatial cues for progenitors to transform their molecular identity.
DEVELOPMENTAL CELL
(2021)
Article
Oncology
Jikui Sun, Quanfeng Ma, Chang Shu, Jinbiao Xiong, Banban Li, Jingchao Wu, Shusheng Zhang, Jialin Li, Jun Liu, Jinhuan Wang
Summary: MicroRNA-mediated mRNA dysregulation and multiple signaling pathways play important roles in various cancers, including gliomas. MiR-301a was found to be significantly upregulated in gliomas and associated with poor prognosis. Zinc and ring finger 3 (ZNRF3) were identified as critical mediators of miR-301a effects on proliferation and apoptosis in gliomas. Furthermore, a novel feedback loop involving miR-301a/ZNRF3/wnt/beta-catenin signaling was discovered, which may serve as a potential therapeutic target for glioma tumorigenesis.
INTERNATIONAL JOURNAL OF ONCOLOGY
(2021)
Article
Neurosciences
Kaiyue Zhao, Li Zeng, Zhongdi Cai, Mimin Liu, Ting Sun, Zhuorong Li, Rui Liu
Summary: This study investigated the potential mechanism and biomarkers of vascular dementia (VaD) through studying the miRNA, TF, and their co-regulatory networks in the cortex of rats. The results revealed differentially expressed miRNAs, TFs, and genes in VaD rats, indicating their involvement in various signaling pathways and biological processes.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Plant Sciences
Qingyou Zheng, Wenxing Chen, Man Luo, Liqing Xu, Qinglin Zhang, Zhengrong Luo
Summary: The study characterized three genotypes of persimmon with different PA accumulation patterns using PacBio full-length sequencing and Illumina-based RNA sequencing. Transcriptome dynamics at four key fruit developmental stages were analyzed, revealing potential regulators for PA accumulation and enhancing the understanding of molecular pathways underlying PA accumulation in persimmon fruit.
Article
Plant Sciences
Heng-Ling Meng, Pei-Yuan Sun, Jia-Rui Wang, Xiao-Qian Sun, Chuan-Zhi Zheng, Ting Fan, Qing-Fu Chen, Hong-You Li
Summary: This study conducted comparative physiological and transcriptomic analyses of two Tartary buckwheat genotypes with contrasting drought resistance. The drought-tolerant genotype exhibited higher water content, proline, and soluble sugar, as well as lower electrolyte leakage under drought stress. Transcriptome sequencing identified potential drought-responsive genes, with transcription factors and abscisic acid playing important roles. These findings enhance our understanding of the drought tolerance mechanisms in Tartary buckwheat.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Medicine, General & Internal
Fuxing Tang, Xiaohong Jiang, Shijie Liao, Yun Liu, Maolin He
Summary: This study investigates the potential regulatory mechanism of transcription factor (TF)-miRNA-mRNA in osteosarcoma using bioinformatics methods and validates the findings through qRT-PCR. The study identifies differentially expressed miRNAs and genes and constructs a TF-miRNA-mRNA regulatory network. Two genes, LAMC1 and THBS1, in the network are found to have prognostic value. Survival analysis and experimental validation establish a TF-miRNA-mRNA sub-network, providing insights into the pathological mechanisms of osteosarcoma for diagnosis and treatment.
Article
Biochemistry & Molecular Biology
Jian Sun, Yijun Lin, Nayoung Ha, Jianfei Zhang, Weiqi Wang, Xudong Wang, Qian Bian
Summary: In this study, researchers used single-cell RNA-Seq to investigate the transcriptional dynamics during mouse maxillary development. They identified distinct mesenchymal cell populations and their developmental trajectory, as well as key transcription factors associated with mesenchymal fate transitions. This study provides important insights for understanding craniofacial morphogenesis and abnormalities at a systems-level.
JOURNAL OF GENETICS AND GENOMICS
(2023)
Article
Genetics & Heredity
Lu Li, Bo Sun, Yingpu Sun
Summary: This study investigates the molecular mechanism of endometriosis by analyzing differentially expressed genes and their predicted transcription factors and miRNAs. The findings provide novel insights for clinical diagnosis and treatment of endometriosis.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Yanhong Li, Jie Wang, Mauricio A. Elzo, Mingchuan Gan, Tao Tang, Jiahao Shao, Tianfu Lai, Yuan Ma, Xianbo Jia, Songjia Lai
Summary: Through experiments, it was found that in rabbits induced to be obese by a high-fat diet, there were significant differences in the expression of certain miRNAs and core genes, with the miRNAs being able to regulate transcription factors that impact lipid metabolism. These results contribute to a better understanding of the molecular mechanisms of skeletal muscle metabolism in rabbits.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Jinhuan Dou, Hanpeng Luo, Abdul Sammad, Wenqi Lou, Di Wang, Flavio Schenkel, Ying Yu, Lingzhao Fang, Yachun Wang
Summary: This study reveals the epigenetic and transcriptional alterations induced by heat stress in the liver of rats, and identifies potential heat stress response markers. The integration of ATAC-seq, RNA-Seq, and WGBS data provides comprehensive insights into the molecular responses to heat stress in mammals.
Article
Genetics & Heredity
Rinku Sharma, Shashankaditya Upadhyay, Sudeepto Bhattacharya, Ashutosh Singh
Summary: This study constructed a multiple abiotic stress-responsive TF-miRNA-gene regulatory network for O. sativa, demonstrating a stable and efficient transmission of biological signals within the network to combat multiple stresses with TFs, miRNAs, and genes working together.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Jiahuan Luo, Rongxia Huang, Pengying Xiao, Anli Xu, Zhaomei Dong, Lirong Zhang, Rui Wu, Yunlin Qiu, Li Zhu, Ruopeng Zhang, Li Tang
Summary: This study identified hub transcription factors of recurrent implantation failure (RIF) and constructed a regulatory network. Three potential molecular biomarkers for the diagnosis of RIF were discovered, providing novel insights into the molecular mechanisms underlying RIF. However, further validation is required to confirm these results.
JOURNAL OF ASSISTED REPRODUCTION AND GENETICS
(2023)
Article
Biochemical Research Methods
Dania Machlab, Lukas Burger, Charlotte Soneson, Filippo M. Rijli, Dirk Schuebeler, Michael B. Stadler
Summary: Proteins binding to specific nucleotide sequences, such as transcription factors, have significant roles in regulating gene expression. The monaLisa package, an R/Bioconductor package, provides methods to identify relevant transcription factors from experimental data. It allows seamless motif analyses without relying on software outside of R.
Article
Genetics & Heredity
Zhaoxu Gao, Jun Li, Li Li, Yanzhi Yang, Jian Li, Chunxiang Fu, Danmeng Zhu, Hang He, Huaqing Cai, Lei Li
Summary: This study reconstructed an integrated miRNA network in Arabidopsis, which includes core transcription factors, miRNAs, and downstream genes. The study found that miRNAs occupy distinct niches and enrich miRNA-containing feed-forward loops in gene regulatory networks. Further analyses revealed how miRNA-containing feed-forward loops coordinate transcription factors in different hierarchical layers and their association with miRNA hubs.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Review
Biochemical Research Methods
Mohammad Reza Karimi, Amir Hossein Karimi, Shamsozoha Abolmaali, Mehdi Sadeghi, Ulf Schmitz
Summary: Holistic perspectives are crucial in understanding the complexity of tumors and current single-layer analysis has limitations. Integrative multilayer approaches are emerging as effective tools in achieving systemic views on cancer biology.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Gabriela Loscalzo, Julia Scheel, Jose Santiago Ibanez-Cabellos, Eva Garcia-Lopez, Shailendra Gupta, Jose Luis Garcia-Gimenez, Salvador Mena-Molla, Alfredo Perales-Marin, Jose Morales-Rosello
Summary: In this study, 48 fetuses were evaluated using Doppler ultrasound and overexpressed miRNAs were identified in the cord blood of fetuses with late-onset fetal growth restriction (LO-FGR). The overexpressed miRNAs, including miR-25-3p, miR-185-5p, and miR-132-3p, were found to be associated with certain molecular pathways and gene ontologies related to cardiac development and neuron death. Furthermore, two miRNAs, miR-185-5p and miR-25-3p, were highlighted as important in cholesterol efflux and starvation responses associated with LO-FGR phenotypes. These findings suggest that evaluation of miR-25-3p, miR-132-3p, and miR-185-5p could serve as molecular biomarkers for the diagnosis and management of LO-FGR.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Editorial Material
Genetics & Heredity
Justin J. -L. Wong, Ulf Schmitz
Summary: Recent research has highlighted the physiological significance of intron retention (IR) in various domains of life and has uncovered unexpected functions in a wide range of biological processes. Despite significant progress in the field, there are still some challenges to be addressed, which, once overcome, will enable the discovery of more functions of IR.
TRENDS IN GENETICS
(2022)
Review
Chemistry, Multidisciplinary
Suchi Smita Gupta, Krishna P. Singh, Shailendra Gupta, Maria Dusinska, Qamar Rahman
Summary: This review compares CNTs and asbestos fibers in terms of their structural characteristics, bio-persistence, surface to volume ratio, and ability to adsorb toxins/pollutants. The study also examines the mechanisms underlying the toxicity caused by certain types of CNTs and asbestos fibers, using altered gene expression data. The results suggest that certain types of CNTs do indeed mimic asbestos fibers in terms of associated toxicity.
Review
Biochemical Research Methods
Ryley Dorney, Bijay P. Dhungel, John E. J. Rasko, Lionel Hebbard, Ulf Schmitz
Summary: This review highlights the importance of gene fusions in cancer, including chromosomal rearrangement-independent fusion transcripts and complex fusion structures. It proposes a classification system for gene and transcript fusions and discusses the use of long-read sequencing and bioinformatic tools to detect and characterize fusions.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Veronika Petrova, Renhua Song, Karl J. Nordstroem, Joern Walter, Justin J. L. Wong, Nicola J. Armstrong, John E. J. Rasko, Ulf Schmitz
Summary: This study investigates the regulation of intron retention in cells of the innate immune system and identifies the importance of chromatin accessibility and intrinsic characteristics of introns. The findings provide insights for understanding the pathogenic alterations linked to RNA processing and may contribute to the development of novel therapeutic approaches.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Pharmacology & Pharmacy
Alf Spitschak, Shailendra Gupta, Krishna P. P. Singh, Stella Logotheti, Brigitte M. M. Puetzer
Summary: Cancer cells can avoid recognition and destruction by the immune system, and cancer is associated with chronic inflammation, while certain autoimmune diseases can lead to tumor development. Although cancer immunotherapy has revolutionized anti-tumor treatment, immune-related toxicities and adverse events can limit the clinical utility of advanced drugs, especially in patients with metastatic cancer and pre-existing autoimmune diseases. In this review, we analyze the dynamic links between cancer, autoimmune diseases, and drugs using multi-omics, data-driven computational approaches, and network concepts. By focusing on molecular and epigenetic metastasis-related processes in cancer cells and the immune microenvironment, we identify vulnerabilities for drug development to control cancer progression and immune responses. Drug repurposing allows for faster access and optimal management of cancer treatment by leveraging existing safety profiles and established pharmacokinetic properties of approved agents. These approaches provide new opportunities for predicting and applying targeted and clinically used drugs at the interface of immune-mediated diseases and cancer towards next-generation immunotherapies.
Article
Biochemistry & Molecular Biology
Matti Hoch, Jannik Rauthe, Konstantin Cesnulevicius, Myron Schultz, David Lescheid, Olaf Wolkenhauer, Valerio Chiurchiu, Shailendra Gupta
Summary: Lipid mediators play important roles in regulating inflammatory responses, and their biosynthetic pathways are targeted by common anti-inflammatory drugs. Transitioning from pro-inflammatory lipid mediators (PIMs) to specialized pro-resolving mediators (SPMs) is crucial for resolving acute inflammation and preventing chronic inflammation. This study used the Atlas of Inflammation Resolution to construct a gene regulatory network associated with SPM and PIM biosynthesis. By analyzing single-cell sequencing data and using machine learning approaches, the researchers identified cell type-specific gene regulatory networks and demonstrated the impact of immune cell activation on PIM and SPM profiles. This research provides insights into the gene regulation of lipid mediators in immune responses and highlights the contribution of specific cell types in their biosynthesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Mehdi Sadeghi, Mohammad Reza Karimi, Amir Hossein Karimi, Nafiseh Ghorbanpour Farshbaf, Abolfazl Barzegar, Ulf Schmitz
Summary: In this study, a differentially expressed co-expression module of mRNAs in EMT-type gastric tumors was identified using Weighted Gene Co-expression Network Analysis (WGCNA). Through network analysis and linear discriminant analysis, mRNA motifs and microRNA-based models with strong prognostic and diagnostic relevance were determined. Additionally, the DMD/ITGA1/CAV1 motif was identified as the top motif with consistent relevance to prognosis. The molecular functions of the identified models indicate the central roles of MAPK, Hh, and cGMP/cAMP signaling in the pathology of the EMT subtype of gastric cancer and highlight their potential utility in precision therapeutic approaches.
Article
Multidisciplinary Sciences
Farzaneh Jafary, Farzane Abasi Joozdani, Kiana Shahzamani, Sepideh Jafari, Hossein Mirhendi, Mohamad Reza Ganjalikhany
Summary: During replication, mutations in SARS-CoV-2 can affect the virus' ability to bind to human cell receptors, evade the immune system, transmit efficiently, and respond to vaccines. The Omicron variant shows increased binding affinity to ACE2 and decreased flexibility in the spike protein compared to other variants.
Review
Biochemistry & Molecular Biology
Siyuan Wu, Ulf Schmitz
Summary: Single-cell sequencing technologies have revolutionized life sciences and biomedical research by providing high-resolution data on cell heterogeneity. Computational algorithms and mathematical models have been developed to make sense of the data and simulate biological processes, leading to breakthroughs in understanding cell differentiation and tissue composition. Long-read sequencing technologies have further enhanced the investigation of alternative splicing, isoform expression, genome assembly, and the detection of complex structural variants.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Rhys Gillman, Matt A. Field, Ulf Schmitz, Rozemary Karamatic, Lionel Hebbard
Summary: Cancer, a heterogeneous disease with a strong genetic component, can benefit from precision medicine approaches to identify molecular drivers. Single-tumour methods based on gene interaction networks have limitations and require further research for evaluation.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Oncology
Jaynish S. S. Shah, Michael J. G. Milevskiy, Veronika Petrova, Amy Y. M. Au, Justin J. L. Wong, Jane E. E. Visvader, Ulf Schmitz, John E. J. Rasko
Summary: After years of neglect, the importance of intron retention (IR) in cancer has been recognized. Many tumors are associated with increased IR, while breast cancer is the only tumor type with reduced IR. It was found that normal breast tissue has unusually high IR, and low IR in breast tumors is associated with poor prognosis.
BREAST CANCER RESEARCH
(2022)