Identification of intratumoral microbiome-driven immune modulation and therapeutic implications in diffuse large B-cell lymphoma by Zheng Yijia, Xiaoyu Li, Lina Ma, Siying Wang, Hong Du, Yun Wu, Jing Yu, Yunxia Xiang, Daiqin Xiong, Huiting Shan, Yubo Wang, Zhi Wang, Jianping Hao, Jie Wang

“…Abstract Objective Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin lymphoma, with significant clinical heterogeneity. …”
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Detection of host-derived sphingosine by Pseudomonas aeruginosa is important for survival in the murine lung. by Annette E LaBauve, Matthew J Wargo

“…These sphingolipids not only play a structural role in lipid membranes, but some are also intracellular and intercellular signaling molecules important in normal eukaryotic cell functions as well as orchestrating immune responses. The members of the SphR transcriptome were identified by microarray analyses, and DNA binding assays showed specific interaction of these promoters with SphR, which enabled us to determine the consensus SphR binding site. …”
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Transcript profiling of plastid ferrochelatase two mutants reveals that chloroplast singlet oxygen signals lead to global changes in RNA profiles and are mediated by Plant U-Box 4 by Snigdha Rai, Matthew D. Lemke, Anika M. Arias, María F. Gómez Méndez, Katayoon Dehesh, Jesse D. Woodson

“…Elevated JA and SA levels were observed in 1O2-stressed fc2 plants. pub4 reversed most of this 1O2-induced gene expression and reduced the JA content in fc2 plants. …”
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Microphysiological gut-on-chip enables extended in vitro development of Cryptosporidium hominis by Samantha Gunasekera, Benjamin Thierry, Brendon King, Paul Monis, Jillian M. Carr, Abha Chopra, Mark Watson, Mark O’Dea, Edward Cheah, Ramesh Ram, Peta L. Clode, Nawal Hijjawi, Una Ryan

“…ConclusionsThese data demonstrate that bioengineered gut-on-chip models support extended C. hominis growth and can be used to interrogate responses of host cells to infection. Owing to its relative simplicity, the pumpless and tubeless gut-on-chip can be accessible to most laboratories with established HCT-8 infection models for Cryptosporidium culture.…”
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Histological and transcriptional characterization of the pancreatic acinar tissue in type 1 diabetes by Louise Granlund, Anders Hedin, Miriam Wahlhütter, Peter Seiron, Olle Korsgren, Oskar Skog, Marcus Lundberg

“…Among these, the two most enriched gene sets were Myc Targets V2 and Estrogen Response Early.Conclusion Taken together, these new data emphasize the involvement of the entire pancreas in type 1 diabetes pathology. …”
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Uncovering the Understanding of the Concept of Patient Similarity in Cancer Research and Treatment: Scoping Review by Iryna Manuilova, Jan Bossenz, Annemarie Bianka Weise, Dominik Boehm, Marvin Döbel, Silke D Werle, Arsenij Ustjanzew, Niklas Reimer, Cosima Strantz, Philipp Unberath, Patrick Metzger, Thomas Pauli, Susann Schulze, Sonja Hiemer, Irmak Oguztürk, Leila Kamkar, Hans A Kestler, Hauke Busch, Benedikt Brors, Jan Christoph

“…ResultsThis scoping review synthesized evidence from 137 studies, emphasizing the multidimensional concept of patient similarity in cancer research, which integrates diverse data types, methodological frameworks, research objectives, and cancer types. Transcriptomic data (92/137, 67.1%) and clinical data (65/137, 47.4%) were the most frequently used, often combined to enhance the comprehensiveness of similarity analyses. …”
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Lactylation Modification as a Promoter of Bladder Cancer: Insights from Multi-Omics Analysis by Yipeng He, Lingyan Xiang, Jingping Yuan, Honglin Yan

“…The high-risk group was more sensitive to most first-line chemotherapy drugs, while the low-risk group had a better response to immunotherapy. …”
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Whole-genome identification of HSF family genes in Cerasus humilis and expression analysis under high-temperature stress by Xiaopeng Mu, Jiating Zhang, Chenyi Wang, Liming Chen, Jianying Zhang, Pengfei Wang, Jiancheng Zhang, Bin Zhang, Junjie Du

“…By analyzing the tissue specific transcriptomes, it was found that most ChHSF genes had higher expression levels in leaves than in other tissues of C.humilis. …”
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The microbiota metabolite, phloroglucinol, confers long-term protection against inflammation by Janire Castelo, Sarai Araujo-Aris, Diego Barriales, Samuel Tanner Pasco, Iratxe Seoane, Ainize Peña-Cearra, Ainhoa Palacios, Carolina Simó, Virginia Garcia-Cañas, Muthita Khamwong, Itziar Martín-Ruiz, Monika Gonzalez-Lopez, Laura Barcena, José Ezequiel Martín Rodríguez, José Luís Lavín, Naiara Gutiez, Raquel Marcos, Estibaliz Atondo, Arantza Cobela, Laura Plaza-Vinuesa, Adrián Plata, Eneko Santos-Fernandez, Alberto Fernandez-Tejada, Mari Carmen Villarán, José Miguel Mancheño, Juana Maria Flores, Ana María Aransay, Aize Pellón, Blanca de las Rivas, Rosario Muñoz, Abelardo Margolles, Patricia Ruas-Madiedo, Maria Victoria Selma, Mercedes Gomez de Agüero, Leticia Abecia, Juan Anguita, Héctor Rodríguez

“…Here, we demonstrate that phloroglucinol tempers macrophage responses to pro-inflammatory pathogens and stimuli. …”
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Inhibition of the nucleolar RNA exosome facilitates adaptation to starvation. by Xi Feng, Xiaoman Wang, Shouhong Guang, Shanshan Pang, Haiqing Tang

“…In response to nutrient scarcity, cells must reallocate their limited energy for cellular maintenance at the expense of certain processes. …”
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Rational therapeutic targeting of myeloid cells in glioblastoma: challenges and perspectives by Faruk Akay, Maya Saleh

“…Multi-omics, single-cell transcriptomics and multi-modal spatial analyses of GB are unraveling the diversity of brain myeloid cells, including activated microglia, border-associated macrophages (BAM), and monocyte-derived glioma-associated macrophages (GAM), instructed by ontogeny, spatial distribution, cell-cell interactions and response to metabolic cues in the TME. …”
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Identification and Expression Analysis of C2H2-Type Zinc Finger Protein (C2H2-ZFP) Genes in <i>Bougainvillea</i> in Different Colored Bracts by Yushan Wang, Yanping Hu, Wen Liu, Wengang Yu, Jian Wang, Yang Zhou

“…Zinc finger proteins (ZFPs), one of the most extensive transcription factor families in plants, are implicated in diverse biological functions, including plant morphogenesis, transcriptional regulation, and responses to abiotic stress. …”
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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

“…The deformity frequency was significantly increased by prolonged exposure duration at dose rates ≥ 0.4 mGy/h. Molecular responses analyzed by RNA-seq at gastrulation (5.5 hpf transcriptome) indicate that the radiation induced adverse effects occurred during the earliest stages of development. …”
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Analysis of glutamate-dependent mechanism and optimization of fermentation conditions for poly-gamma-glutamic acid production by Bacillus subtilis SCP017-03. by Caiyun Wu, Yutao Gou, Shuai Jing, Wei Li, Fanglan Ge, Jiao Li, Yao Ren

“…In this study, we first systematically analyzed the response of Bacillus subtilis SCP017-03 to glutamate addition by comparing transcriptomics and proteomics. …”
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Genome-wide identification, characterization, and expression analysis of the MADS-box gene family in grass pea (Lathyrus sativus) under salt stress conditions by Mohamed Abdelsattar, Ahmed E. Nassar, Khaled H. Mousa, Ahmed Hussein, Manal M. S. El-Baghdady, Khaled H. Radwan, Manar S. Ibrahim, Achraf El Allali, Aladdin Hamwieh, Alsamman M. Alsamman, Zakaria Kehel

“…Annotation analysis revealed variations in the intron-exon structures of the genes, with most type I genes being intronless. Ten distinct conserved motifs were identified across the genes. …”
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Ischemic Preconditioning Confers Epigenetic Repression of Mtor and Induction of Autophagy Through G9a‐Dependent H3K9 Dimethylation by Olof Gidlöf, Andrea L. Johnstone, Kerstin Bader, Bohdan B. Khomtchouk, Jiaqi J. O'Reilly, Selvi Celik, Derek J. Van Booven, Claes Wahlestedt, Bernhard Metzler, David Erlinge

“…Post‐translational modifications of histone residues can confer rapid and drastic switches in gene expression in response to various stimuli, including ischemia. The aim of this study was to investigate the effect of histone methylation in the response to cardiac ischemic preconditioning. …”
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Molecular and pharmacological heterogeneity of ETV6::RUNX1 acute lymphoblastic leukemia by Zhenhua Li, Huanbin Zhao, Wenjian Yang, Maud Maillard, Satoshi Yoshimura, Yu-Chih Hsiao, Xin Huang, Yoshihiro Gocho, Lauren Rowland, Anthony Brown, Landon Choi, Kristine R. Crews, Charles G. Mullighan, Samuel W. Brady, Cheng Cheng, Ti-Cheng Chang, Gang Wu, Mignon L. Loh, Allen Eng Juh Yeoh, Federico Antillon-Klussmann, Sima Jeha, Hiroto Inaba, Jiyang Yu, Ching-Hon Pui, Seth E. Karol, William E. Evans, Jun J. Yang

“…Profiling the genomic and pharmacological landscape of 194 pediatric ETV6::RUNX1 ALL cases, we uncover two transcriptomic clusters, C1 (61%) and C2 (39%). Compared to C1, the C2 subtype features higher white blood cell counts and younger age at diagnosis, as well as better early treatment responses. …”
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Identification of cell adhesion-related subtypes and construction of risk model to predict breast cancer prognostic and immunological properties by De-Ming Lv, Li Yang, Chen Fan, Ling-Hui Fang, Su-Fen Cheng

“…Abstract Background Breast invasive carcinoma is the most common form of breast cancer, often resulting in recurrence or metastasis in patients. …”
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AtMYB72 aggravates photosynthetic inhibition and oxidative damage in Arabidopsis thaliana leaves caused by salt stress by Hongrui Zhang, Yinuo Wu, Hongbo Zhang, Nan Sun, Hongjiao Zhang, Bei Tian, Tanhang Zhang, Kexin Wang, Xu Nan, Huiui Zhang

“…In this study, physiological and transcriptome techniques were used to analyze the effects of the R2R3-MYB transcription factor AtMYB72 on the growth and development, physiological function, and key gene response of Arabidopsis thaliana. …”
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Combining inhibition of galectin-3 with and before a therapeutic vaccination is critical for the prostate-tumor-free outcome by Carolina Tiraboschi, Lucas Gentilini, Carla Velazquez, Enrique Corapi, Felipe Martín Jaworski, José Daniel Garcia Garcia, Yorfer Rondón, Anne Chauchereau, Diego José Laderach, Daniel Compagno

“…In the case of immunotherapy, tumors develop robust immune escape mechanisms that abolish any protective response, and to date why prostate cancer is one of the most resistant diseases remains unresolved.Methods By using a combination of clinical data to study the transcriptome of metastasis samples from patients with castration-refractory prostate cancer, and state of the art cellular and molecular biology assays in samples from tumor-bearing mice that have been submitted to surgical resection of the tumor before receiving a vaccination, we answered several essential questions in the field of immunotherapy for prostate cancer. …”
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