Integrated Single-Cell Analysis Revealed Novel Subpopulations of Foamy Macrophages in Human Atherosclerotic Plaques by Yunrui Lu, Shuang Wu, Shiyu Zhu, Jian Shen, Chang Liu, Chaoyue Zhao, Sheng’an Su, Hong Ma, Meixiang Xiang, Yao Xie

“…Here, we integrate published single-cell RNA-sequencing, spatial transcriptomic, and chromatin accessibility sequencing datasets of human atherosclerotic lesions across eight distinct studies. …”
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Single-cell RNA sequencing uncovers abnormal Sertoli-cell elevation and testicular niche impairment in the transfemales’s testis by Jun Yu, Longfei Hu, Huixia Li, Xiaofeng Li, Chaoye Ma, Ting Jiang, Yongxin Liu, Xue Wang, Xia Li, Liandong Zuo, Haocheng Lin, Wenming Xu, Yiwen Zhou, Yang Liu, Hao Chen

“…Method In this study, we analyzed approximately 49,385 single-cell transcriptomes from transfemale human testicular tissue, comparing cellular composition with that of cisgender male individuals across a range of ages. …”
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Triggering tumorigenic signaling: Succinate dehydrogenase inhibitor (SDHi) fungicides induce oncometabolite accumulation and metabolic shift in human colon cells by Carolina Duarte Hospital, Arnaud Tête, Kloé Debizet, Clémence Rives, Jules Imler, Sofiane Safi-Stibler, Lara Gales, Floriant Bellvert, Julien Dairou, Auriane Hagimont, Agnès Burel, Dominique Lagadic-Gossmann, Robert Barouki, Jerry W. Shay, Jean Bastin, Sophie Mouillet-Richard, Anthony Lemarié, Fatima Djouadi, Sandrine Ellero-Simatos, Xavier Coumoul, Judith Favier, Sylvie Bortoli

“…SDHi exposure also induces a Warburg-like metabolic reprogramming typical of cancer cells, associated with transcriptomic and morphological changes promoting cell migration and invasion. …”
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THERAPEUTIC IMPLICATIONS OF TARGETED SEQUENCING AND miRNA-SEQ OF B CELL LYMPHOMAS by Esra Esmeray Sönmez, Tevfik Hatipoğlu, Xiaozhou Hu, Hongling Yuan, Ayça Erşen Danyeli, Ayla Anar Arıcı, Ahmet Şeyhanlı, Zuhal Önder Siviş, Bengü Demirag, Eda Ataseven, Dilek İnce, Zekiye Altun, Safiye Aktaş, İnci Alacacıoğlu, Tuğba Önal Süzek, Nazan Özsan, Taner Kemal Erdağ, Elvan Çağlar Çıtak, Sermin Özkal, Mehmet Ali Özcan, Nazan Çetingül, Erdener Özer, Tezer Kutluk, Nur Olgun, Can Küçük

“…Objective: Next-generation sequencing (NGS)-based approaches facilitated the identification of genomic and transcriptomic alterations associated with the development of B-cell lymphomas. …”
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ATRX, OLIG2, MGMT, and IDH2 in Glioblastoma: Essential Molecular Mechanisms and Therapeutic Significance by Andrea Pop-Crisan, Radu Pirlog, Lavinia-Lorena Pruteanu, Constantin Busuioc, Ovidiu-Laurean Pop, Deo Prakash Pandey, Cornelia Braicu, Ioana Berindan-Neagoe

“…The 2021 WHO classification highlights the importance of molecular diagnostics, integrating genetic, transcriptomic, and epigenetic alterations alongside histological and immunohistochemical criteria. …”
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Itaconate: A Nexus Metabolite Fueling <i>Leishmania</i> Survival Through Lipid Metabolism Modulation by Ayyoub Kihel, Hajar El Filaly, Dounia Darif, Aicha Assouab, Myriam Riyad, Imane Nait Irahal, Khadija Akarid

“…Accordingly, targeting itaconate-associated pathways could provide a novel therapeutic strategy for leishmaniasis.…”
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ARTEMISIA: a mechanistic study of a novel Janus kinase 1 inhibitor to advance molecular understanding and precision medicine in asthma by Davinder Paul Singh Dosanjh, Erika Darrah, Tina Jellesmark Jensen, Zala Jevnikar, Alese Halvorson, Mathias Cardner, Rod Hughes, Sarah S. Grant, Adam Platt, Chris E. Brightling

“…The ARTEMISIA mechanistic study aims to provide a clear understanding of the pathways impacted by londamocitinib in the lung, determine how this impact is reflected in the nose and periphery, and identify candidate biomarkers of londamocitinib-treatment response in asthma. …”
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Enabling malic acid production from corn-stover hydrolysate in Lipomyces starkeyi via metabolic engineering and bioprocess optimization by Jeffrey J. Czajka, Ziyu Dai, Tijana Radivojević, Joonhoon Kim, Shuang Deng, Teresa Lemmon, Marie Swita, Meagan C Burnet, Nathalie Munoz, Yuqian Gao, Young-Mo Kim, Beth Hofstad, Jon K. Magnuson, Hector Garcia Martin, Kristin E. Burnum-Johnson, Kyle R. Pomraning

“…The fermentation characterization and omic analyses provide a rich dataset for understanding L. starkeyi physiology and metabolic response to growth in hydrolysates. …”
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Unveiling tumor-infiltrating immune cell-driven immune-mediated drug resistance in clear cell renal cell carcinoma: prognostic insights and therapeutic strategies by Jifeng Yang, Yixuan Xing, Jiusong Luan, Wenbo Yang, Xin Zhang, Yanhua Tian, Haisong Zhang

“…Methods Integrative analyses of transcriptomic and single-cell RNA sequencing data from multiple cohorts were employed to characterize immune and metabolic landscapes in ccRCC. …”
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Oxygen level alters energy metabolism in bovine preimplantation embryos by Nina Boskovic, Marilin Ivask, Gamze Yazgeldi Gunaydin, Barış Yaşar, Shintaro Katayama, Andres Salumets, Tõnis Org, Ants Kurg, Karolina Lundin, Timo Tuuri, Carsten O. Daub, Juha Kere

“…We conclude that constant hypoxia culture of in vitro embryos provided the highest blastocyst formation rate and appropriate energy metabolism. …”
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Functional Characterization of <i>MaSPL8</i> Reveals Its Different Roles in Biotic and Abiotic Stress Responses in Mulberry by Longyan Zheng, Wenhao Zhang, Liuqing Wei, Mengqi Li, Li Liu

“…This study highlights <i>MaSPL8</i> as a negative regulator of abiotic stress tolerance and positive regulator of biotic (<i>C. shiraiana</i>) stress tolerance in mulberry and provides insights into its integration with phytohormone pathways. …”
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Kidney diseases and single-cell sequencing research: a bibliometric analysis from 2015 to 2024 by Yaotan Li, Jinyi Hou, Xinghua Zhang, Xiaochang Wu, Shijia Lin, Weijing Liu, Yaoxian Wang, Huijuan Zheng

“…Background Single-cell RNA sequencing (scRNA-seq) has revolutionized kidney disease research by enabling high-resolution transcriptomic analysis at the cellular level. This technology can overcome the limitations of traditional bulk-sequencing; reveal disease-progression trajectories, intercellular communication networks, and cellular heterogeneity; and provide crucial insights into disease mechanisms, thereby facilitating the development of targeted therapies and personalized treatment strategies. …”
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Comparative miRNome analysis of colostrum- and mature milk–derived extracellular vesicles from Holstein and Jersey cows by Daye Mun, Sangdon Ryu, Dong-Hyun Lim, Sangnam Oh, Younghoon Kim

“…Sequencing of miRNAs within milk-derived extracellular vesicles (EVs) provides valuable insights into the molecular mechanisms through which these EVs influence recipient cells. …”
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Artificial Intelligence in Ovarian Cancer: A Systematic Review and Meta-Analysis of Predictive AI Models in Genomics, Radiomics, and Immunotherapy by Mauro Francesco Pio Maiorano, Gennaro Cormio, Vera Loizzi, Brigida Anna Maiorano

“…Unlike earlier reviews, this study synthesizes a broader range of AI applications in ovarian cancer and provides pooled performance metrics across diverse models. …”
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Obese individuals exhibit distinct temporal gene expression dynamics in response to influenza vaccination by Megan Hockman, Julia Matthews, Michael A. Carlock, Ted M. Ross, David Gresham, Elodie Ghedin

“…Previously, we identified a transcriptomic signature prior to seasonal influenza vaccination that is predictive of an individual’s response to the influenza vaccine. …”
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Integrative multi-omics identifies AP-1 transcription factor as a targetable mediator of acquired osimertinib resistance in non-small cell lung cancer by Bengisu Dayanc, Sude Eris, Nazife Ege Gulfirat, Gulden Ozden-Yilmaz, Ece Cakiroglu, Ozlem Silan Coskun Deniz, Gökhan Karakülah, Serap Erkek-Ozhan, Serif Senturk

“…Our findings reveal a robust concordance between epigenetic regulome and transcriptomic changes that characterize the osimertinib resistant state. …”
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Arginine methylation modulates tumor fate and prognosis in clear cell renal cell carcinoma by Jiahao Wang, Dan Bao, Xiaochao Chen, Zijie Yu, Weiyu Kong, Chen Xu, Songtao Li, Yulin Yue

“…Methods We utilized public transcriptomic datasets from TCGA, E-MTAB-1980 and ICGC, for model construction and validation. …”
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Selection of reliable reference genes in Colletotrichum scovillei during different growth stages, host interactions, and plant extract treatment for qRT-PCR by Guo Geng Jia, Sun Ha Kim, Jiyoung Min, Nelson Villalobos Zamora, Silvia Soto Montero, Dong-Keun Yi, Soo-Yong Kim, Sang-Keun Oh

“…Eight candidate reference genes (CsUCE, CsCK, CsTBP, CsTIF, CsPP2A, CsTUB, CsCAL, and CsNADH) were selected from C. scovillei based on transcriptomic and genomic data. Several statistical methods, including the comparative quantification cycle threshold (Ct) method, geNorm, NormFinder, and Bestkeeper, were used to assess the stabilities of reference gene transcripts. …”
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EBV Reactivation-associated gene signature predicts poor prognosis in nasopharyngeal carcinoma by Qingshuang Luo, Jingyi Long, Longtai Hu, Moyed Alsaadawe, Oluwasijibomi Damola Faleti, Xiaoming Lyu

“…Methods An in vitro EBV reactivation model was established to investigate molecular changes associated with viral reactivation. Transcriptomic (RNA-seq) and proteomic (LC-MS/MS) analyses were performed to identify differentially expressed genes. …”
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Cross-tissue MiRNA profiling of extracellular vesicles and PBMCs from amyotrophic lateral sclerosis patients by Francesca Dragoni, Rosalinda Di Gerlando, Luca Diamanti, Bartolo Rizzo, Matteo Bordoni, Eveljn Scarian, Camilla Viola, Giovanni Cerchia, Susanna Zucca, Orietta Pansarasa, Stella Gagliardi

“…Abstract RNA-mediated toxicity, which can be controlled by alteration of gene expression, is considered a key event in Amyotrophic Lateral Sclerosis (ALS). Transcriptomic deregulation of miRNAs expression can spread via “horizontal” RNA transfer through extracellular vesicles (EVs) to act in conjunction with proteins, leading to changes in mRNA, which can provide early signals to indicate forthcoming neuropathological changes in the brain. …”
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