Integrating bioinformatics and machine learning to identify AhR-related gene signatures for prognosis and tumor microenvironment modulation in melanoma by Qianru Li, Qianru Li, Heli Li

“…The stability of the machine learning models and the relationship between gene expression and immune infiltrating cells were validated using three independent melanoma datasets. …”
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Identification and Functional Characterization of P159L Mutation in in a Family with Maturity-Onset Diabetes of the Young 5 (MODY5) by Eun Ky Kim, Ji Seon Lee, Hae Il Cheong, Sung Soo Chung, Soo Heon Kwak, Kyong Soo Park

“…These findings suggests that the impaired insulin secretion in this family with the P159L HNF1B mutation may be related to altered GLUT2 expression in β-cells rather than decreased insulin gene expression. In conclusion, we have identified a Korean family with an HNF1B mutation and characterized its effect on the pathogenesis of diabetes.…”
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Screening and Functional Pathway Analysis of Pulmonary Genes Associated with Suppression of Allergic Airway Inflammation by Adipose Stem Cell-Derived Extracellular Vesicles by Sung-Dong Kim, Shin Ae Kang, Yong-Wan Kim, Hak Sun Yu, Kyu-Sup Cho, Hwan-Jung Roh

“…DEG profiles and hierarchical clustering of the identified genes were analyzed to evaluate changes in gene expression. Real-time PCR was performed to determine the expression levels of genes upregulated after treatment with ASC-derived EVs. …”
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Spinal cord injury enhances lung inflammation and exacerbates immune response following exposure to LPS by Bradford C. Berk, Bradford C. Berk, Amanda Pereira, Velia Sofia Vizcarra, Christoph Pröschel, Chia George Hsu, Chia George Hsu, Chia George Hsu

“…ResultsLPS markedly induced proinflammatory gene expression (SAA3, IRG1, NLRP3, IL-1beta, MCP-1) and cytokine release (IL-1beta, IL-6, MCP-1) in SCI mice compared to controls, indicating an exaggerated inflammatory response. …”
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Oral Fusobacterium nucleatum resists the acidic pH of the stomach due to membrane erucic acid synthesized via enoyl-CoA hydratase-related protein FnFabM by Xiaocong Li, Shipeng Zhang, Huafang Sheng, Yan Zhen, Buling Wu, Zhuang Li, Dingqiang Chen, Hongwei Zhou

“…Phylogenetic tree analysis revealed that C22:1(n9) synthesis was significantly associated with FnFabM gene expression in F. nucleatum at pH 1.5. Inhibition of FnFabM expression by cerulenin reduced the C22:1(n9) content and decreased the colonization efficiency of F. nucleatum in the stomach and jejunum of mice.Conclusions Oral F. nucleatum translocate to the intestine by resisting the acidic environment owing to the presence of erucic acid in its cell membrane, which is regulated by FnFabM. …”
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Functional analysis of the PcCDPK5 gene in response to allelopathic substances on p-hydroxybenzoic acid (p-HBA) stress in patchouli by Xiaofeng Liu, Jingru Zhou, Muhammad Zeeshan Ul Haq, Zhineng Fu, Guangtao Gu, Jing Yu, Ya Liu, Dongmei Yang, Huageng Yang, Yougen Wu

“…In this study, we further found that the subcellular localization of PcCDPK5 protein is in the cytoplasm, and its gene expression is closely related to continuous cropping (CC) and p-HBA stress. …”
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The bioinfomatics analysis of the M1 macrophage-related gene CXCL9 signature in cervical cancer by Wenxin Liao, Tingting Liu, Yang Li, Hua Liang, Juexiao Deng, Fujin Shen

“…And the CXCL9-expressing tumour-associated macrophage has been poorly reported in cervical cancer.Methods To clarify the regulatory gene network of M1 macrophage in cervical cancer, we downloaded gene expression profiles of cervical cancer patients in TCGA database to identify M1 macrophage coexpression genes. …”
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MMP9-Associated Tumor Stem Cells, CCL1-Silenced Dendritic Cells, and Cytokine-Induced Killer Cells Have a Remarkable Therapeutic Efficacy for Acute Myeloid Leukemia by Activating T... by Min Dong, Guozhen Zhang, Jie Meng, Biou Liu, Duanfeng Jiang, Feng Liu

“…However, the underlining mechanism and function of DC-CIK cells in acute myeloid leukemia (AML) remain largely elusive. Methods. Gene expression profiles of leukemia patients were obtained from TCGA, DC cell components were evaluated using the quanTIseq method, and cancer stem cell scores were estimated using machine learning methods. …”
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Identification and Analysis of Circular RNAs in Mammary Gland from Yaks Between Lactation and Dry Period by Yilin Shi, Xiaoyun Wu, Guangyao Meng, Xiaoming Ma, Yongfu La, Pengjia Bao, Min Chu, Ping Yan

“…Circular RNA (circRNA), a non-coding RNA, acts as a molecular sponge that sequesters microRNAs (miRNAs) to regulate target gene expression. Although circRNA has been linked to mammary gland lactation, its specific role in yaks remains underexplored. …”
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Qualitative and Quantitative Detection of Virulence-Associated Genes in Escherichia Coli Isolates from Women with Urinary Tract Infections by Zainab Hussein Mahdi, Lina S. Alsaadi, Zainab Amer Hatem, Saade Abdalkareem Jasim

“…Following the extraction of RNA from twenty-five pathogenic isolates of E. coli and ten non-pathogenic isolates, gene expression of fimA and kpsMTII was quantified using quantitative real-time reverse transcription PCR (qRT-PCR). …”
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Investigating the role of cathepsins in breast cancer progression: a Mendelian randomization study by Shengyi Zhou, Shengyi Zhou, Shengyi Zhou, Yizhou Sun, Yizhou Sun, Wenzhang Zha, Wenzhang Zha, Guangjun Zhou, Guangjun Zhou

“…Furthermore, we conducted MR analysis using eQTL data to investigate how gene expression, mediated by cathepsins, affects the occurrence of different types of breast cancer and assessed the regulatory effects of cathepsins.ResultsMR analysis revealed that increased levels of cathepsin E are associated with a greater risk of malignant breast tumors (IVW: p = 0.006, OR = 1.103, 95% CI = 1.028–1.184), and increased levels of cathepsin F are associated with an increased risk of in situ breast cancer (IVW: p = 0.031, OR = 1.190, 95% CI = 1.016–1.394). …”
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BIMSSA: enhancing cancer prediction with salp swarm optimization and ensemble machine learning approaches by Pinakshi Panda, Sukant Kishoro Bisoy, Amrutanshu Panigrahi, Abhilash Pati, Bibhuprasad Sahu, Zheshan Guo, Haipeng Liu, Prince Jain

“…Initially, Boruta and IMRMR were applied to extract relevant gene expression aspects. Then, SSA was implemented to optimize feature size. …”
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The Use of Machine Learning to Create a Risk Score to Predict Survival in Patients with Hepatocellular Carcinoma: A TCGA Cohort Analysis by Samer Tohme, Hamza O Yazdani, Amaan Rahman, Sanah Handu, Sidrah Khan, Tanner Wilson, David A Geller, Richard L Simmons, Michele Molinari, Christof Kaltenmeier

“…Long-term outcomes of patients with HCC can be predicted using a simplified scoring system based on tumor mRNA gene expression levels. This tool could assist clinicians and researchers in identifying patients at increased risks for recurrence to tailor specific treatment and follow-up strategies for individual patients.…”
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HPV-Based Screening, Triage, Treatment, and Followup Strategies in the Management of Cervical Intraepithelial Neoplasia by Oscar Peralta-Zaragoza, Jessica Deas, Claudia Gómez-Cerón, Wendy Argelia García-Suastegui, Geny del Socorro Fierros-Zárate, Nadia Judith Jacobo-Herrera

“…It is known that during the development of cervical cancer associated with HPV infection, a cascade of abnormal events is induced, including disruption of cellular cycle control, alteration of gene expression, and deregulation of microRNA expression. …”
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Lysine deacetylase inhibitors have low selectivity in cells and exhibit predominantly off‐target effects by Kiara E. Bornes, Marcus A. Moody, Thomas M. Huckaba, Megan C. Benz, Emily C. McConnell, Maryam Foroozesh, Van H. Barnes, Bridgette M. Collins‐Burow, Matthew E. Burow, Terry J. Watt, Tasha B. Toro

“…Genetic inactivation results in much stronger deacetylation defects on known targets compared to inhibitor treatment. Gene expression analysis revealed that both inhibitors have extensive and extensively overlapping off‐target effects in cells, even at low inhibitor doses. …”
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Protein Kinase Cε, Which Is Linked to Ultraviolet Radiation-Induced Development of Squamous Cell Carcinomas, Stimulates Rapid Turnover of Adult Hair Follicle Stem Cells by Ashok Singh, Anupama Singh, Jordan M. Sand, Erika Heninger, Bilal Bin Hafeez, Ajit K. Verma

“…In the WT mice, the percent of double positive HSCs retaining BrdU label was 28.4±0.6% compared to 4.0±0.06% for the TG mice, an approximately 7-fold decrease. A comparison of gene expression profiles of FACS sorted double positive HSCs showed increased expression of Pes1, Rad21, Tfdp1 and Cks1b genes in TG mice compared to WT mice. …”
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The epidermal lipid-microbiome loop and immunity: Important players in atopic dermatitis by Junchao Wu, Lisha Li, Tingrui Zhang, Jiaye Lu, Zongguang Tai, Quangang Zhu, Zhongjian Chen

“…Immune responses participate in lipid abnormalities within the EIME by downregulating barrier gene expression and are further cascade-amplified by microbial dysregulation which is instigated by barrier impairment. …”
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Low regulatory T-cells frequency is associated with graft rejection after small bowel transplantation: Clinical and experimental evidence. by Rodrigo Papa-Gobbi, Pablo Stringa, Maria Virginia Gentilini, Ivana Ivanoff, Mariana Machuca, Nidia Monserrat Arreola, Javier Serradilla, Karla Estefanía-Fernández, Paloma Talayero, María Velayos, Elena Sánchez-Zapardiel, Gabriel Gondolesi, Ane Andrés-Moreno, Martin Rumbo, Francisco Hernández-Oliveros

“…Acute cellular rejection (ACR) was diagnosed based on clinical and histological findings, graft gene expression of pro- and anti-inflammatory mediators assessed by RT-qPCR, serum IL-6 and IL-10 levels by Luminex, and Treg frequency analyzed by flow cytometry (CD4+CD25highFoxP3+).…”
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siRNA-mediated inhibition of hTERT enhances the effects of curcumin in promoting cell death in precursor-B acute lymphoblastic leukemia cells: an in silico and in vitro study by Muhammad Hossein Ashoub, Ali Afgar, Alireza Farsinejad, Razieh Razavi, Samira Anvari, Ahmad Fatemi

“…Ferroptotic and oxidative markers were quantified using commercial assays, while cell death parameters and gene expression were evaluated through flow cytometry and qRT-PCR analyses. …”
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Reduced UPF1 levels in senescence impair nonsense-mediated mRNA decay by Dahyeon Koh, Yebin Lee, Kyuchan Kim, Hyeong Bin Jeon, Chaehwan Oh, Sangik Hwang, Minjung Lim, Kwang-Pyo Lee, Yeonkyoung Park, Yong Ryoul Yang, Yoon Ki Kim, Donghwan Shim, Myriam Gorospe, Ji Heon Noh, Kyoung Mi Kim

“…Abstract Cells regulate gene expression through various RNA regulatory mechanisms, and this regulation often becomes less efficient with age, contributing to accelerated aging and various age-related diseases. …”
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