Integrated microbiome, transcriptome and metabolome insight into the alleviating mechanisms of sheep milk in a DSS-induced colitis mouse model by Wenna Yao, Ruilin Du, Shuo Yan, Teligun Bao, Huimin Zhang, Fang Yang, Yue Xue, Yulong Zhao, Siqin Bao, Xihe Li, Yongli Song

“…ELISA and qPCR analysis showed that relative mRNA expression levels of TNF-α, IL-1β, IL-6, and IL-17 were decreased in SM treatment compared to DSS-induced colitis mice. …”
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Stromal architecture and fibroblast subpopulations with opposing effects on outcomes in hepatocellular carcinoma by Yifei Cheng, Xiaofang Chen, Li Feng, Zhicheng Yang, Liyun Xiao, Bin Xiang, Xiaodong Wang, Dongbin Liu, Penghui Lin, Jieyi Shi, Guohe Song, Wulei Qian, Boan Zhang, Yanan Xu, Zheng Gao, Lv Chen, Yingcheng Wu, Jiaqiang Ma, Youpei Lin, Haichao Zhao, Lihua Peng, Xuebin Mao, Yang Liu, Hao Hou, Mingyu Yang, Yuan Ji, Xiaoying Wang, Jian Zhou, Xun Xu, Xiyang Liu, Wu Wei, Xiaoming Zhang, Qiang Gao, Hu Zhou, Yidi Sun, Kui Wu, Jia Fan

“…Using paired single-cell RNA and epigenomic sequencing with Stereo-seq, we revealed two fibroblast subsets CAF-FAP and CAF-C7, whose spatial enrichment strongly correlated with the two stromal archetypes and opposing patient prognosis. …”
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Effects of rumen fluid transplantation on the fecal flora of yaks by Man Zhang, Man Zhang, Man Zhang, Yan Li, Yumin Li, Yumin Li, Yumin Li, Chenxu Cheng, Chenxu Cheng, Chenxu Cheng, Shatuo Chai, Shatuo Chai, Shatuo Chai, Yingkui Yang, Yingkui Yang, Yingkui Yang, Xun Wang, Xun Wang, Xun Wang, Shuxiang Wang, Shuxiang Wang, Shuxiang Wang

“…After this, yak feed intake was recorded daily; yaks were weighed on days 1, 30, and 60 of the formal trial; and yak feces were collected directly from the ground on days 1, 4, 7, 14, 30, and 60 to compare the microbial composition of the feces using 16S rRNA sequencing data.ResultsThe results showed that rumen fluid transplantation significantly increased the alpha diversity of fecal microflora (P < 0.05), and on day 30 of the experiment, both the operational taxonomic unit (OTU) and Shannon index were significantly higher in the RT group than the CON group (P < 0.05). …”
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Dicoumarol sensitizes hepatocellular carcinoma cells to ferroptosis induced by imidazole ketone erastin by Ziwei Yang, Ziwei Yang, Tixin Han, Ruibin Yang, Ruibin Yang, Yinuo Zhang, Yinuo Zhang, Yifei Qin, Yifei Qin, Yifei Qin, Jialu Hou, Jialu Hou, Fei Huo, Fei Huo, Zhuan Feng, Zhuan Feng, Yaxin Ding, Yaxin Ding, Jiali Yang, Jiali Yang, Gang Zhou, Gang Zhou, Shijie Wang, Shijie Wang, Xiaohang Xie, Xiaohang Xie, Peng Lin, Peng Lin, Zhi-Nan Chen, Zhi-Nan Chen, Jiao Wu, Jiao Wu

“…The intrinsic factors determining sensitivity to IKE-induced ferroptosis remain to be explored to improve its efficacy.MethodsBulk RNA-sequencing data from hepatocellular carcinoma (HCC) and normal liver tissues were collected from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases. …”
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Reprogramming of iPSCs to NPCEC-like cells by biomimetic scaffolds for zonular fiber reconstruction by Tianhui Chen, Zhongxing Chen, Juan Du, Min Zhang, Zexu Chen, Qingyi Gao, Aodong Chen, Qinghao Meng, Yang Sun, Yan liu, Linghao Song, Xinyue Wang, Pranav Prakash Edavi, Chen Xu, Hongmei Zhang, Jinhai Huang, Yongxiang Jiang

“…Ocular tissue and aqueous humour samples from patients with EL were subjected to RNA sequencing and Olink high-throughput proteomic analysis, revealing the downregulation of pathogenic genes (FBN1, MFAP2) and upregulation of secretory proteins (IL-12, MMP-1). …”
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Impaired inflammatory resolution with severe SARS-CoV-2 infection in leptin knock out obese hamster by Ren-Di Jiang, Yun-Zhe Luo, Hao-Feng Lin, Xiao-Shuang Zheng, Wen-Tao Zeng, Mei-Qin Liu, Hao-Hao Deng, Qi Wang, Ya-Na Lai, Ying Chen, Zi-Shuo Guo, Ya Zeng, Qian-Chun Gong, Chen Qiu, Mei Dong, Xi Wang, Zi-Yi Wang, Li-Na Ji, Pan-Pan Hou, Qian Li, Xu-Rui Shen, Bei Li, Yun Gao, Ai-Hua Zhang, Ting-Ting Jiang, Ai-Min Shi, Peng Zhou, Xin-Hua Lin, Zi-Qing Deng, Jian-Min Li, Zheng-Li Shi

“…Notably, reduced Trem2-dependent efferocytosis pathways in Leptin−/− hamsters indicated weakened inflammation resolution, consistent with the scRNA-seq data from patients with obesity. In summary, our study highlights the obesity-associated mechanisms underlying severe SARS-CoV-2 infections and establishes a reliable preclinical animal model for developing obesity-specific therapeutics for critical COVID-19.…”
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Translational and clinical comparison of whole genome and transcriptome to panel sequencing in precision oncology by Irina A. Kerle, Thomas Gross, Anja Kögler, Jonas S. Arnold, Maximilian Werner, Jan-Niklas Eckardt, Elena E. Möhrmann, Marie Arlt, Barbara Hutter, Jennifer Hüllein, Daniela Richter, Martin M. K. Schneider, Mario Hlevnjak, Lino Möhrmann, Dorothea Hanf, Christoph E. Heilig, Simon Kreutzfeldt, Maria-Veronica Teleanu, Evelin Schröck, Daniel Hübschmann, Peter Horak, Christoph Heining, Stefan Fröhling, Hanno Glimm

“…In this study, we compared whole-exome/whole-genome (WES/WGS) and transcriptome sequencing (TS) with broad panel sequencing by resequencing the same tumor DNA and RNA as well as normal tissue DNA for germline assessment, from 20 patients with rare or advanced tumors, who were originally sequenced by WES/WGS ± TS within the DKFZ/NCT/DKTK MASTER program from 2015 to 2020. …”
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Molecular mechanisms of libido influencing semen quality in geese through the hypothalamic-pituitary-testicular-external genitalia axis by Zhiyu He, Tanze Liu, Xiaoyong He, Yang Song, Guibi Li, Xiaopeng Li, Qingyuan Ouyang, Shenqiang Hu, Hua He, Liang Li, Hehe Liu, Jiwen Wang

“…Through transcriptome sequencing (RNA-seq), we identified 98, 163, 2,474 and 400 differentially expressed genes (DEGs) in the hypothalamus, pituitary, testis and external genitalia, respectively. …”
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AdipoRon ameliorates the progression of heart failure with preserved ejection fraction via mitigating lipid accumulation and fibrosis by Wuping Tan, Yijun Wang, Siyi Cheng, Zhihao Liu, Mengjie Xie, Lingpeng Song, Qinfang Qiu, Xiaofei Wang, Zeyan Li, Tianyuan Liu, Fuding Guo, Jun Wang, Xiaoya Zhou

“…Cardiac function was evaluated using echocardiography, and Postmortem analysis included RNA-sequencing, untargeted metabolomics, transmission electron microscopy and molecular biology methods. …”
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Delivery of dendritic cells targeting 3M2e-HA2 nanoparticles with a CpG adjuvant via lysosomal escape of Salmonella enhances protection against H9N2 avian influenza virus by Futing Jia, Wenfeng Wang, Yawen Tian, Ainul Zahra, Yingkai He, Chongbo Ge, Tongyu Zhang, Mingyue Wang, Jingshuo Gong, Gerui Zhang, Guilian Yang, Wentao Yang, Chunwei Shi, Jianzhong Wang, Haibin Huang, Xin Cao, Yang Zeng, Nan Wang, Zhannan Wang, Chunfeng Wang, Yanlong Jiang

“…All the constructed plasmids were then transformed into the sifA gene-deficient Salmonella vector χYL56 for oral immunization.The results showed that sifA-deficient Salmonella could efficiently increase antigen-specific mucosal sIgA antibody titers, especially in alveolar lavage samples, whereas the presence of the phage-54 nanobody could dramatically increase intracellular IFN-γ mRNA levels, indicating its ability to enhance the Th1-type immune response. …”
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The 2023 dengue outbreak in Lombardy, Italy: A one-health perspective by Francesca Rovida, Marino Faccini, Carla Molina Granè, Irene Cassaniti, Sabrina Senatore, Eva Rossetti, Giuditta Scardina, Manuela Piazza, Giulia Campanini, Daniele Lilleri, Stefania Paolucci, Guglielmo Ferrari, Antonio Piralla, Francesco Defilippo, Davide Lelli, Ana Moreno, Luigi Vezzosi, Federica Attanasi, Marzia Soresini, Manuela Barozzi, Lorenzo Cerutti, Stefano Paglia, Angelo Regazzetti, Maurilia Marcacci, Guido Di Donato, Marco Farioli, Mattia Manica, Piero Poletti, Antonio Lavazza, Maira Bonini, Stefano Merler, Fausto Baldanti, Danilo Cereda, Antonella Sarasini, Milena Furione, Dalila Mele, Federica Bergami, Josè Camilla Sammartino, Alessandro Ferrari, Greta Romano, Antonino Maria Guglielmo Pitrolo, Maya Carrera, Rita Brugnoli, Nunzia Laini, Francesca Bonalda, Sara Arfani, Giuditta Zamboni, Fanny Delfanti, Piergiuseppe Ferrari, Anxhela Dafa, Antonella Negri, Filippa Parisi, Marcello Tirani, Michela Viscardi, Gabriele Del Castillo, Federica Morani, Francesco Scovenna, Sheila Sansebastian, Manuel Maffeo, Mario Chiari, Enrico Tallarita

“…In the case of positive DENV IgM, a second sample was collected to detect DENV RNA and verify seroconversion. Entomological and epidemiological investigations were also performed. …”
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Mechanism of hsa_circ_0069443 promoting early pregnancy loss through ALKBH5/FN1 axis in trophoblast cells by Bai-xue Li, Mei-yao Wu, Zhi-hui Wang, Dong-mei Zhou, Jian-qi Li, Bing-feng Lu, Xiao-ling Lin, Yang Zhao, Xiu-jie Sheng

“…This study also found that hsa_circ_0069443 can bind to the RNA-binding protein demethylase ALKBH5, affecting the overall m6A level of trophoblast cells, and hsa_circ_0069443 and ALKBH5 can regulate the expression level of FN1, verifying the role of the 0069443/ALKBH5/FN1 axis in trophoblast cells and endometrial stromal cells. …”
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Tacedinaline (CI-994), a class I HDAC inhibitor, targets intrinsic tumor growth and leptomeningeal dissemination in MYC-driven medulloblastoma while making them susceptible to anti... by Arndt Borkhardt, Nan Qin, Stephen T Keir, Darell D Bigner, Allison Cole, Matthias Wölfl, Viktoria Marquardt, Johanna Theruvath, David Pauck, Daniel Picard, Lena Blümel, Mara Maue, Jasmin Bartl, Ulvi Ahmadov, Maike Langini, Frauke-Dorothee Meyer, Joselyn Cruz-Cruz, Claus M Graef, Till Milde, Olaf Witt, Anat Erdreich-Epstein, Gabriel Leprivier, Ulf Kahlert, Anja Stefanski, Kai Stühler, Julia Hauer, Thomas Beez, Christiane B Knobbe-Thomsen, Ute Fischer, Jörg Felsberg, Finn K Hansen, Rajeev Vibhakar, Sujatha Venkatraman, Samuel H Cheshier, Guido Reifenberger, Thomas Kurz, Marc Remke, Siddhartha Mitra

“…We tested the combinatorial effect of targeting class I HDACs and the CD47-SIRPa phagocytosis checkpoint pathway using in vitro phagocytosis assays and in vivo orthotopic xenograft models.Results CI-994 displayed antitumoral effects at the primary site and the metastatic compartment in two orthotopic mouse models of MYC-driven MB. Furthermore, RNA sequencing revealed nuclear factor-kB (NF-κB) pathway induction as a response to CI-994 treatment, followed by transglutaminase 2 (TGM2) expression, which enhanced inflammatory cytokine secretion. …”
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Blood immunophenotyping of multiple sclerosis patients at diagnosis identifies a classical monocyte subset associated to disease evolution by Stéphane Rodriguez, Stéphane Rodriguez, Laura Couloume, Juliette Ferrant, Juliette Ferrant, Nicolas Vince, Marion Mandon, Marion Mandon, Rachel Jean, Rachel Jean, Celine Monvoisin, Simon Leonard, Simon Le Gallou, Simon Le Gallou, Nayane S. B. Silva, Nayane S. B. Silva, Sonia Bourguiba-Hachemi, David Laplaud, David Laplaud, Alexandra Garcia, Romain Casey, Romain Casey, Romain Casey, Romain Casey, Helene Zephir, Anne Kerbrat, Gilles Edan, Emmanuelle Lepage, Eric Thouvenot, Eric Thouvenot, Aurelie Ruet, Aurelie Ruet, Guillaume Mathey, Guillaume Mathey, Pierre-Antoine Gourraud, Pierre-Antoine Gourraud, Karin Tarte, Karin Tarte, Celine Delaloy, Patricia Amé, Patricia Amé, Mikael Roussel, Mikael Roussel, Laure Michel, Laure Michel, Laure Michel

“…IntroductionMyeloid cells trafficking from the periphery to the central nervous system are key players in multiple sclerosis (MS) through antigen presentation, cytokine secretion and repair processes.MethodsCombination of mass cytometry on blood cells from 60 MS patients at diagnosis and 29 healthy controls, along with single cell RNA sequencing on paired blood and cerebrospinal fluid (CSF) samples from 5 MS patients were used for myeloid cells detailing.ResultsMyeloid compartment study demonstrated an enrichment of a peculiar classical monocyte population in 22% of MS patients at the time of diagnosis. …”
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A 5-transcript signature for discriminating viral and bacterial etiology in pediatric pneumonia by Sandra Viz-Lasheras, Alberto Gómez-Carballa, Jacobo Pardo-Seco, Xabier Bello, Irene Rivero-Calle, Ana Isabel Dacosta, Myrsini Kaforou, Dominic Habgood-Coote, Aubrey J. Cunnington, Marieke Emonts, Jethro A. Herberg, Victoria J. Wright, Enitan D. Carrol, Stephane C. Paulus, Werner Zenz, Daniela S. Kohlfürst, Michiel Van der Flier, Ronald de Groot, Luregn J. Schlapbach, Philipp Agyeman, Andrew J. Pollard, Colin Fink, Taco T. Kuijpers, Suzanne Anderson, Cristina Calvo, María del Carmen Martínez-Padilla, Ana Pérez-Aragón, Esteban Gómez-Sánchez, Juan Valencia-Ramos, Francisco Giménez-Sánchez, Paula Alonso-Quintela, Laura Moreno-Galarraga, Ulrich von Both, Marko Pokorn, Dace Zavadska, María Tsolia, Clementien L. Vermont, Henriëtte A. Moll, Michael Levin, Federico Martinón-Torres, Antonio Salas

“…Our research seeks to address this gap by identifying host transcriptomic biomarkers in the blood of children with definitive viral and bacterial pneumonia. We performed RNA sequencing on 192 prospectively collected whole blood samples, including 38 controls and 154 pneumonia cases, uncovering a 5-transcript signature (genes FAM20A, BAG3, TDRD9, MXRA7, and KLF14) that effectively distinguishes bacterial from viral pneumonia (area under the curve (AUC): 0.95 [0.88–1.00]). …”
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Advanced delivery systems for gene editing: A comprehensive review from the GenE-HumDi COST Action Working Group by Alessia Cavazza, Francisco J. Molina-Estévez, Álvaro Plaza Reyes, Victor Ronco, Asma Naseem, Špela Malenšek, Peter Pečan, Annalisa Santini, Paula Heredia, Araceli Aguilar-González, Houria Boulaiz, Qianqian Ni, Marina Cortijo-Gutierrez, Kristina Pavlovic, Inmaculada Herrera, Berta de la Cerda, Emilio M. Garcia-Tenorio, Eva Richard, Sergio Granados-Principal, Arístides López-Márquez, Mariana Köber, Marijana Stojanovic, Melita Vidaković, Irene Santos-Garcia, Lorea Blázquez, Emily Haughton, Dongnan Yan, Rosario María Sánchez-Martín, Loubna Mazini, Gloria Gonzalez Aseguinolaza, Annarita Miccio, Paula Rio, Lourdes R. Desviat, Manuel A.F.V. Gonçalves, Ling Peng, Cecilia Jiménez-Mallebrera, Francisco Martin Molina, Dhanu Gupta, Duško Lainšček, Yonglun Luo, Karim Benabdellah

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Identification and subcellular localization of proteins that interact with Duck plague virus pUL14 in infected host cells by Jieyu Wan, Mingshu Wang, Anchun Cheng, Wei Zhang, Qiao Yang, Bin Tian, Xumin Ou, Di Sun, Yu He, Xinxin Zhao, Ying Wu, Shaqiu Zhang, Juan Huang, Zhen Wu, YanLing Yu, Ling Zhang, Dekang Zhu, Renyong Jia, Mafeng Liu, Shun Chen

“…These proteins are associated mainly with the regulation of biological processes, RNA biosynthetic processes, and nuclear export. …”
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