Exploring the tumor microenvironment of breast cancer to develop a prognostic model and predict immunotherapy responses by Ye Tian, Yong Yang, Lei He, Xiaocheng Yu, Hu Zhou, Juan Wang

“…Abstract Breast cancer is the most prevalent malignancy in women and exhibits significant heterogeneity. …”
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Molecular Functional and Transcriptome Analysis of <i>Arabidopsis thaliana</i> Overexpression <i>BrBBX21</i> from Zicaitai (<i>Brassica rapa</i> var. <i>purpuraria</i>) by Mei Fu, Mengting Lu, Juxian Guo, Shizheng Jiang, Imran Khan, Umer Karamat, Guihua Li

“…The <i>BrBBX21-1</i> gene is most closely linked to the <i>AtBBX21</i> gene based on phylogeny and protein sequence similarities. …”
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Molecular underpinnings of exceptional response in primary malignant melanoma of the esophagus to anti-PD-1 monotherapy by Yu Chen, Xuan Wang, Jie Dai, Li Zhou, Xuefeng Xia, Jun Guo, Xue Bai, Lu Si, Bixia Tang, Chuanliang Cui, Xiaoting Wei, Xinan Sheng, Siming Li, Zhihong Chi, Lili Mao, Bin Lian, Xieqiao Yan, Yan Kong, Caili Li, Xuan Gao, Lirui Tang, Linzi Sun, Zhonghui Qi, Zelong Xu

“…Genomic sequencing analysis revealed that the genomic aberration landscape of PMME predominated in classical cancer driver genes, with approximately half of PMME cases harboring mutations in BRAF, N/KRAS, and NF1. In contrast, most NEMM cases were triple wild-type. Transcriptome analysis revealed that, compared with NEMM, PMME displayed more significant proliferation and inflammatory features with higher expression of genes related to antigen presentation and differentiation, and a less immunosuppressive signature with lower expression of inhibitory immune checkpoints and dedifferentiation-related genes. …”
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Comprehensive pan-cancer analysis indicates key gene of p53-independent apoptosis is a novel biomarker for clinical application and chemotherapy in colorectal cancer by Jianing Yan, Jingzhi Wang, Min Miao, Yongfu Shao

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Mycobacterium tuberculosis PhoP integrates stress response to intracellular survival by regulating cAMP level by Hina Khan, Partha Paul, Harsh Goar, Bhanwar Bamniya, Navin Baid, Dibyendu Sarkar

“…Survival of Mycobacterium tuberculosis within the host macrophages requires the bacterial virulence regulator PhoP, but the underlying reason remains unknown. 3′,5′-Cyclic adenosine monophosphate (cAMP) is one of the most widely used second messengers, which impacts a wide range of cellular responses in microbial pathogens including M. tuberculosis. …”
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Aquaporins modulate the cold response of Haemaphysalis longicornis via changes in gene and protein expression of fatty acids by Han Wang, Ruwei Bai, Tingwei Pei, Jianglei Meng, Chuks F. Nwanade, Yuchao Zhang, Xiujie Liang, Yunsheng Tang, Jingze Liu, Zhijun Yu

“…RNA interference was used to explore the relationship between AQP and the cold response of H. longicornis. Additionally, proteomic and transcriptomic analyses were used to investigate the mechanisms underlying the effects of AQPs on cold response in ticks. …”
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Immunotherapy biomarkers in brain metastases: insights into tumor microenvironment dynamics by Mu Li, Yi Zhang, Duo Yu, Yaoyu Yu, Wenxue Ma

“…Brain metastases (BM), represent the most common intracranial malignancies in adults and remain a major clinical challenge due to their poor prognosis and limited therapeutic options. …”
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Comprehensive Characterization of Mesenchymal Stem Cells from Human Placenta and Fetal Membrane and Their Response to Osteoactivin Stimulation by C. M. Raynaud, M. Maleki, R. Lis, B. Ahmed, I. Al-Azwani, J. Malek, F. F. Safadi, A. Rafii

“…Mesenchymal stem cells (MSCs) are the most promising seed cells for cell therapy and can be isolated from various sources of human adult tissues such as bone marrow (BM-MSC) and adipose tissue. …”
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Multi-omics profiling of cross-resistance between ceftazidime-avibactam and meropenem identifies common and strain-specific mechanisms in Pseudomonas aeruginosa clinical isolates by Bartosz J. Bartmanski, Anja Bösch, Steven Schmitt, Niranjan R. Ireddy, Qun Ren, Jacqueline Findlay, Adrian Egli, Maria Zimmermann-Kogadeeva, Baharak Babouee Flury

“…Whole-genome sequencing revealed strain heterogeneity and different evolutionary paths, with three genes mutated in three or more strains: dacB in CZA-treated strains and oprD and ftsI in MEM-treated strains. Transcriptomic and proteomic analysis underlined heterogeneous strain response to antibiotic treatment with few commonly regulated genes and proteins. …”
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Embryonic thermal conditioning and post-hatch heat challenge alter hypothalamic expression of genes related to appetite, thermoregulation, and stress modulation in broiler chicks by Reagan Vaughan, Usman Sulaiman, Annalise Flynn, Fernando Biase, Noam Meiri, Dongmin Liu, Paul Siegel, Mark Cline, Elizabeth Gilbert

“…The results revealed pathways associated with energy metabolism were altered in response to EHC, with most differences in the nCPa. …”
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Eliciting Clavulanic Acid Biosynthesis: The Impact of <i>Bacillus velezensis</i> FZB42 on the Metabolism of <i>Streptoyces clavuligerus</i> ATCC 27064 by Luisa F. Patiño, Carlos Caicedo-Montoya, Laura Pinilla-Mendoza, Jaison H. Cuartas, Rigoberto Ríos-Estepa

“…Most of the genes from the cephamycin C and CA clusters were up-regulated, which correlates well with the increase in CA production. …”
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The janus face of astrocytes in multiple sclerosis: Balancing protection and pathology by Ahmad A. Abulaban, Hayder M. Al-kuraishy, Ali I. Al-Gareeb, Ali K. Albuhadily, Mustafa M. Shokr, Athanasios Alexiou, Marios Papadakis, Gaber El-Saber Batiha

“…While the pathogenesis of MS involves complex interactions between peripheral immune cells and CNS glia, astrocytes—the most abundant glial cells—play a dual role in disease progression. …”
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Profiling type I and II interferon responses reveals distinct subgroups of pediatric patients with autoinflammatory disorders by Anaïs Nombel, PharmD, Magali Perret, MSc, Sophie Trouillet-Assant, PhD, Marine Villard, PhD, Christine Lombard, PharmD, Lorna Garnier, PharmD, Anne-Perrine Foray, MD, PhD, Sarah Benezech, MD, Remi Pescarmona, PharmD, Samira Khaldi-Plassart, PhD, Thierry Walzer, PhD, Alexandre Belot, MD, PhD, Sébastien Viel, PharmD, PhD

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Integrative Omics reveals changes in the cellular landscape of peroxisome-deficient pex3 yeast cells by Tjasa Kosir, Hirak Das, Marc Pilegaard Pedersen, Ann-Kathrin Richard, Marco Anteghini, Vitor Martins dos Santos, Silke Oeljeklaus, Ida J van der Klei, Bettina Warscheid

“…Our integrative omics analysis reveals that the absence of peroxisomes induces distinct responses at the level of the transcriptome and proteome. …”
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Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis by Hongbin Chen, Tianqi Qi, Siyu Guo, Xiaoyang Zhang, Minghua Zhan, Si Liu, Yuyao Yin, Yifan Guo, Yawei Zhang, Chunjiang Zhao, Xiaojuan Wang, Hui Wang

“…The upregulated differentially expressed genes (DEGs) in the LRTIs group were mainly enriched in infection immune response-related pathways. Klebsiella pneumoniae had the most significant increase in abundance in LRTIs, which was strongly correlated with host infection or inflammation genes TNFRSF1B, CSF3R, and IL6R. …”
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In vivo structure profiling reveals human cytosolic and mitochondrial tRNA structurome and interactome in response to stress by Noah Peña, Yichen Hou, Christopher P. Watkins, Sihao Huang, Wen Zhang, Christopher D. Katanski, Tao Pan

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The heme-regulated inhibitor kinase Hri1 is activated in response to aminolevulinic acid deficiency in Schizosaccharomyces pombe. by Samuel Plante, Ariane Brault, Mariano Avino, Hajer Sakouhi, Florie Lo Ying Ping, Tobias Vahsen, Simon Labbé

“…Using a strain that is unable to synthesize heme de novo (hem1Δ), global transcriptome analysis reveals that among the genes encoding these kinases, hri1+ is the most strongly induced under δ-aminolevulinate (ALA)-limiting conditions. …”
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Ceramides play a significant role in the response of Pogostemon cablin to bacterial wilt by regulating the ABA pathway by Jian Li, Dan-Xia Wu, He-Nan Bao, Ke-Yu Li, Ming-Yong Zhang, Yun-Hao Sun, Kuai-Fei Xia

“…Bacterial wilt represents one of the most significant threats to patchouli cultivation; however, the molecular mechanisms underlying P. cablin’s response to bacterial wilt remain unexplored. …”
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Neutrophil prime unique transcriptional responses in intestinal organoids during infection with nontyphoidal Salmonella enterica serovars by Anna-Lisa E. Lawrence, Ryan P. Berger, David R. Hill, Sha Huang, Veda K. Yadagiri, Brooke Bons, Courtney Fields, Jason S. Knight, Christiane E. Wobus, Jason R. Spence, Vincent B. Young, Basel H. Abuaita, Mary X. O'Riordan

“…Using a transcriptomics approach, we identified a dominant role for PMNs in mounting differential immune responses including production of pro-inflammatory cytokines, chemokines, and antimicrobial peptides. …”
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Combination therapies induce cancer cell death through the integrated stress response and disturbed pyrimidine metabolism by Goetz Hartleben, Kenji Schorpp, Yun Kwon, Barbara Betz, Foivos‐Filippos Tsokanos, Zahra Dantes, Arlett Schäfer, Ina Rothenaigner, José Manuel Monroy Kuhn, Pauline Morigny, Lisa Mehr, Sean Lin, Susanne Seitz, Janina Tokarz, Anna Artati, Jerzy Adamsky, Oliver Plettenburg, Dominik Lutter, Martin Irmler, Johannes Beckers, Maximilian Reichert, Kamyar Hadian, Anja Zeigerer, Stephan Herzig, Mauricio Berriel Diaz

“…Abstract By accentuating drug efficacy and impeding resistance mechanisms, combinatorial, multi‐agent therapies have emerged as key approaches in the treatment of complex diseases, most notably cancer. Using high‐throughput drug screens, we uncovered distinct metabolic vulnerabilities and thereby identified drug combinations synergistically causing a starvation‐like lethal catabolic response in tumor cells from different cancer entities. …”
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