Patient-derived iPSCs link elevated mitochondrial respiratory complex I function to osteosarcoma in Rothmund-Thomson syndrome. by Brittany E Jewell, An Xu, Dandan Zhu, Mo-Fan Huang, Linchao Lu, Mo Liu, Erica L Underwood, Jun Hyoung Park, Huihui Fan, Julian A Gingold, Ruoji Zhou, Jian Tu, Zijun Huo, Ying Liu, Weidong Jin, Yi-Hung Chen, Yitian Xu, Shu-Hsia Chen, Nino Rainusso, Nathaniel K Berg, Danielle A Bazer, Christopher Vellano, Philip Jones, Holger K Eltzschig, Zhongming Zhao, Benny Abraham Kaipparettu, Ruiying Zhao, Lisa L Wang, Dung-Fang Lee

“…RTS iPSC-derived osteoblasts showed defective osteogenic differentiation and gain of in vitro tumorigenic ability. Transcriptome analysis of RTS osteoblasts validated decreased bone morphogenesis while revealing aberrantly upregulated mitochondrial respiratory complex I gene expression. …”
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Revealing the role of increased SK3 expression in sulfonylurea resistance triggered by prolonged exposure by Jung Gyu Park, Minseok Kim, Sungje Yoo, Sun Wook Hwang, Jongsoo Mok, Joonghoon Park, Keon Wook Kang

“…Results Insulinoma cells resistant to sulfonylureas exhibited elevated resting membrane potentials compared to sensitive cells. Transcriptome analysis revealed differential expression of genes, notably highlighting the significance of kcnn3 (Potassium Calcium-Activated Channel Subfamily N Member 3) in SR insulinoma cells. …”
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Intratracheal Aerosolization of <i>Nocardia farcinica</i> in Mice Optimizes Bacterial Distribution and Enhances Pathogenicity Compared to Intranasal Inoculation and Intratracheal I... by Bingqian Du, Ziyu Song, Jirao Shen, Jiang Yao, Shuai Xu, Xiaotong Qiu, Min Yuan, Zhenjun Li

“…Furthermore, ITA resulted in better lung bacterial distribution and delivery efficiency than ITI and IN. Transcriptome analysis of lungs from <i>N. farcinica</i> infected mice via IN, ITA and ITI revealed significant differential gene expression, whereas ITA route resulted in a larger fold change. …”
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Effects of Dietary β-Carotene on the Gonadal Color, Pigmentation, and Regulation Mechanisms in Sea Urchin Strongylocentrotus Intermedius by Weixiao Di, Yinuo Zhang, Huinan Zuo, Haijing Liu, Lina Wang, Jun Ding, Yaqing Chang, Rantao Zuo

“…Several differential genes, enriched in the pathways of steroid biosynthesis, oxidative phosphorylation, and ubiquitination, were screened based on transcriptome analysis. Real-time PCR further demonstrated that β-carotene significantly upregulated the expression of <i>cholesterol 25-hydroxylase</i> (<i>CH25H</i>), <i>NADH dehydrogenase subunit 1</i> (<i>ND1</i>), <i>NADH dehydrogenase subunit 2</i> (<i>ND2</i>), and <i>NADH dehydrogenase subunit 4</i> (<i>ND4</i>) while it downregulated the expression of <i>24-dehydrocholesterol reductase</i> (<i>DHCR24</i>). …”
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Immunomodulatory gene networks predict treatment response and survival to de-escalated, anthracycline-free neoadjuvant chemotherapy in triple-negative breast cancer in the WSG-ADAP... by Darren Korbie, Clare Stirzaker, Oleg Gluz, Christine zu Eulenburg, Ulrike Nitz, Matthias Christgen, Sherko Kuemmel, Eva-Maria Grischke, Helmut Forstbauer, Michael Braun, Mathias Warm, John Hackmann, Christoph Uleer, Bahriye Aktas, Claudia Schumacher, Rachel Wuerstlein, Enrico Pelz, Hans Heinrich Kreipe, Susan J. Clark, Matt Trau, Monika Graeser, Nadia Harbeck

“…Conclusion Polygenic scores incorporating immunoregulatory genes can predict pCR and survival and represent an opportunity to select patients for de-escalated, anthracycline-free NACT. This transcriptome network analysis also identifies potential new targets for personalized medicine approaches in patients without response to NACT. …”
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ELABELA promotes the migration and homing of bone marrow mesenchymal stem cells to myocardial injury sites through the ERK1/2/miR-299a-5p/Exo70 pathway by Jing-Yu Hou, Hao Wu, Shuang-Mei Li, Xiao-Jing Li, Shu-Jun Yang, Xu-Xiang Chen, Chang-Qing Zhou, Hui-Bao Long, Hai-Dong Wu, Jia-Ying Fu, Ya-Jie Guo, Tong Wang

“…Cardiac repair was evaluated through fluorescence imaging, echocardiography, and histological analysis. Transcriptome sequencing and bioinformatics analysis were employed to identify and validate the mechanisms by which ELA promoted the migration of BMSCs. …”
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The intersection between circulatory microRNAs and biomarkers of neurodegeneration by Amber Yaqub, Rima Mustafa, M. Arfan Ikram, Mohsen Ghanbari

“…Plasma levels of 591 well-expressed circulatory miRNAs were measured by the HTG EdgeSeq Whole Transcriptome Assay, while t-tau, NfL, Aβ-40 and Aβ-42 were analysed using the Simoa NF-light® and N3PA assays. …”
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Dose-dependent effects of gamma radiation on the early zebrafish development and gene expression. by Selma Hurem, Leonardo Martín Martín, Dag Anders Brede, Eystein Skjerve, Rasoul Nourizadeh-Lillabadi, Ole Christian Lind, Terje Christensen, Vidar Berg, Hans-Christian Teien, Brit Salbu, Deborah Helen Oughton, Peter Aleström, Jan Ludvig Lyche

“…A dose-response relationship was found in the numbers of differentially regulated genes in exposure groups compared to controls at a total dose as low as 1.62 mGy. Ingenuity Pathway Analysis identified retinoic acid receptor activation, apoptosis, and glutathione mediated detoxification signaling as the most affected pathways in the lower dose rate (0.54 mGy/h), while eif2 and mTOR, i.e., involved in the modulation of angiogenesis, were most affected in higher dose rates (5.4 and 10.9 mGy/h). …”
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Genome-wide identification of starch metabolism gene families in Potentilla anserina and the expression pattern in response to abiotic stress factors by Yangmiao Jiao, Qin He, Xu Li, Yang Chen, Tingting Tian, Liang Cao, Zaiqi Zhang

“…In the tuberous roots, when compared with the control conditions, 2 AMYs and 4 BAMs were upregulated, while 3 BAMs were downregulated, meanwhile, the contents of maltose and glucose-6-phosphate (G6P) were decreased, while the content of glucose-1-phosphate (G1P) was increased under drought treatment. …”
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Integrative Proteomics and Genomics Identify Novel Biomarkers and Therapeutic Targets in Vitiligo via Mendelian Randomization by Chenjue Yan, Ling Jiang, Yibo Hu, Ting You, Jing Chen, Songjiang Wu

“…Abstract Introduction Given that the proteome is a major source of therapeutic targets, we conducted a proteome-wide Mendelian randomization (MR) combined with transcriptome sequencing analysis to identify candidate protein markers and therapeutic targets for vitiligo. …”
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Prognostic risk model of six m7 g-related lncRNAs in lung adenocarcinoma by Kaijun Long, Kai Wang, Manjun Gao, Yao Wang, Yang Tang, Cheng Chen, Xixian Ke

“…Subsequently, a nomogram, KEGG analysis, GO analysis and immune infiltration analysis were applied successively to reveal potential prognosis of LUAD patients based on prognostic model. …”
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Porcine β-defensin 5 (pBD-5) modulates the inflammatory and metabolic host intestinal response to infection by Arthur Nery Finatto, Christine Yang, Matheus de Oliveira Costa

“…Pathway analysis revealed the downregulation of immune-related pathways, including IL-17, toll-like receptor (TLR), and NOD-like receptor signalling pathways, upon pBD-5 exposure. …”
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Sideroflexin family genes were dysregulated and associated with tumor progression in prostate cancers by Hua Huang, Huibo Lian, Wang Liu, Benyi Li, Runzhi Zhu, Haiyan Shao

“…SFXN2/4 genes were significantly upregulated while the SFXN3 expression was significantly downregulated in malignant tissues compared to benign tissues. …”
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Dietary exposure of the water flea Daphnia galeata to microcystin-LR by Eun-jeong Kim, Donggu Jeon, Yeon-jeong Park, Hyunmin Woo, Seong-il Eyun

“…Furthermore, functional protein classification revealed an upregulation of lipid and inorganic ion transport processes, while amino acid and carbohydrate transport processes were found to be downregulated. …”
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Ox-LDL induces a non-inflammatory response enriched for coronary artery disease risk in human endothelial cells by Jiahao Jiang, Thomas K. Hiron, Anil Chalisey, Yashaswat Malhotra, Thomas Agbaedeng, Chris A. O’Callaghan

“…An integrative analysis implicates the role of AP-1, NFE-2 and CEBP transcription factors in regulating ox-LDL-induced transcription. …”
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Pseudomonas plecoglossicida infection induces neutrophil autophagy-driven NETosis in large yellow croaker Larimichthys crocea by Jia-Feng Cao, Jia-Feng Cao, Jia-Feng Cao, Jiong Chen, Jiong Chen, Jiong Chen

“…To further explore the underlying mechanism, we performed transcriptome analysis and western blotting, which revealed that P. plecoglossicida triggers NETosis through activation of the autophagy pathway. …”
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Purification and identification of anti-inflammatory peptides from sturgeon (Acipenser schrenckii) cartilage by Li Yuan, Qian Chu, Bei Yang, Wei Zhang, Quancai Sun, Ruichang Gao

“…Transcriptome analysis suggested the inhibition of activated mitogen-activated protein kinase (MAPK) and interleukin-17 (IL-17) signaling pathways after LLEL intervention. …”
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Spatio-Temporal Regulation of Gibberellin Biosynthesis Contributes to Optimal Rhizome Bud Development by Kanako Bessho-Uehara, Tomoki Omori, Stefan Reuscher, Keisuke Nagai, Ayumi Agata, Mikiko Kojima, Yumiko Takebayashi, Takamasa Suzuki, Hitoshi Sakakibara, Motoyuki Ashikari, Tokunori Hobo

“…We propose that precise regulation of gibberellin (GA) biosynthesis plays a pivotal role in optimal rhizome bud development, as demonstrated by a comparative transcriptome analysis between tiller buds and rhizome buds and quantification of phytohormones. …”
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Alternative splicing dynamics during gastrulation in mouse embryo by Wei Wang, Yu Zhang, Yuanyuan Zhai, Wuritu Yang, Yongqiang Xing

“…Subsequently, the dynamic expression of splicing factors (SFs) during gastrulation was characterized, while the expression patterns and functions of germ layer-specific SFs were identified. …”
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An insulin-sensitive Drosophila insulin-like receptor mutant remodels methionine metabolism to extend lifespan. by Marc Tatar, Wenjing Zheng, Shweta Yadav, Rochele Yamamoto, Noelle Curtis-Joseph, Shengxi Li, Lin Wang, Andrey A Parkhitko

“…Because abrogation of S-adenosylhomocysteine hydrolase blocks the longevity benefit conferred by dInr353, we conclude the methionine cycle reprogramming of Type II is sufficient to slow aging. Metabolomic analysis further revealed the Type II mutant is metabolically flexible: unlike aged wildtype, aged dInr353 adults can reroute methionine toward the transsulfuration pathway, while Type I mutant flies upregulate the transsulfuration pathway continuously from young age. …”
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