Integrative multi-omic analysis of NLRP3 inflammasome dysregulation and subtyping for personalized treatment in acute myeloid leukemia by Hong Zhang, Linlin Yang, Yukexin Liu, Dongju Wang, Liming Shi, Changyu Tian

“…The NLRP3 inflammasome, a multi-protein complex involved in innate immunity and inflammation, has been implicated in various diseases; however, its role in AML development and progression is not well understood. In this study, we analyzed genomic, bulk-, and single-cell transcriptomic data to assess the contribution of NLRP3 inflammasome genes to AML. …”
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Hepatitis B virus modulates store-operated calcium entry to enhance viral replication in primary hepatocytes. by Jessica C Casciano, Nicholas J Duchemin, R Jason Lamontagne, Laura F Steel, Michael J Bouchard

“…Many viruses modulate calcium (Ca2+) signaling to create a cellular environment that is more permissive to viral replication, but for most viruses that regulate Ca2+ signaling, the mechanism underlying this regulation is not well understood. The hepatitis B virus (HBV) HBx protein modulates cytosolic Ca2+ levels to stimulate HBV replication in some liver cell lines. …”
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The role of HSPA14 in breast cancer: implications for tumorigenesis, immune response modulation, and personalized therapies by Ruipeng Zhao, Xiaocun Zhu, Wan Wei, Linlin Zhen

“…Spearman’s correlation analysis was performed to examine the correlation between HSPA14 expression and immune cell infiltration, as well as immune checkpoint genes. Single cell transcriptomic data from GSE114727 was utilized to calculate the expression of HSPA14 in different cell subpopulations. …”
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Regulatory and disruptive variants in the CLCN2 gene are associated with modified skin color pattern phenotypes in the corn snake by Sophie A. Montandon, Pierre Beaudier, Asier Ullate-Agote, Pierre-Yves Helleboid, Maya Kummrow, Sergi Roig-Puiggros, Denis Jabaudon, Leif Andersson, Michel C. Milinkovitch, Athanasia C. Tzika

“…In humans and mice, disruption of CLCN2 results in leukoencephalopathy, as well as retinal and testes degeneration. Our single-cell transcriptomic analyses in snakes reveal that CLCN2 is indeed expressed in chromatophores during embryogenesis and in the adult brain, but the behavior and fertility of Motley and Stripe corn snakes are not impacted. …”
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Sequential emergence and contraction of epithelial subtypes in the prenatal human choroid plexus revealed by a stem cell model by Haley Masters, Shuxiong Wang, Christina Tu, Quy Nguyen, Yutong Sha, Matthew K. Karikomi, Pamela Shi Ru Fung, Benjamin Tran, Cristina Martel, Nellie Kwang, Michael Neel, Olga G. Jaime, Victoria Espericueta, Brett A. Johnson, Kai Kessenbrock, Qing Nie, Edwin S. Monuki

“…In simplified differentiations from human pluripotent stem cells, derived CPECs (dCPECs) display canonical properties and dynamic motile multiciliated phenotypes that interact with Aβ uptake. Single dCPEC transcriptomes over time correlate well with human organoid and fetal CPECs, while pseudotemporal and cell cycle analyses highlight the direct CPEC origin from neuroepithelial cells. …”
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Regulation of revival stem cell differentiation by CREPT/RPRD1B during intestinal regeneration by Tingwei Lan, Mengdi Li, Xiaolin Duan, Huihui Jia, Yajun Cao, Yinyin Wang, Fangli Ren, Jianqiu Sheng, Junfeng Xu, Zhijie Chang

“…Interestingly, revSCs were remarkably accumulated, but enterocytes were decreased in Vil-CREPT KO mice. Our single-cell transcriptome analyses demonstrated that CREPT deletion impaired the stem potential of revSCs and inhibited their differentiation into enterocytes and goblet cells. …”
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Determinants of response to daratumumab in Epstein-Barr virus-positive natural killer and T-cell lymphoma by Jennifer Yang, Anand D Jeyasekharan, Joanne Lee, Wee Joo Chng, Tae-Hoon Chung, Nurulhuda Mustafa, Adina Huey Fang Nee, Jing Yuan Chooi, Sabrina Hui Min Toh, Viknesvaran Selvarajan, Shuangyi Fan, Siok Bian Ng, Michelle Poon, Esther Chan, Yen Lin Chee, Longen Zhou

“…This is corroborated recently by a phase II clinical trial which established that daratumumab monotherapy is well tolerated and displayed encouraging response in relapsed/refractory NKTL patients. …”
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FNDC5 and ACOX1 as Biomarkers of Peroxisomal Activity with Contrast Outcomes in Colon Adenocarcinoma by Yuan Hepei, Zeng Jun, Khan Muhammad, Wang Baiyao, Hu Xiaoshan, Wei Hao, Wang Zhaotong, Yuan Yawei

“…Tumor microenvironment features were assessed using ESTIMATE, MCP-counter, and CIBERSORT. Single-cell RNA-seq data (TISCH; EMTAB8107) were used to examine cell-type-specific PRG expression. …”
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PRMT1-mediated methylation of UBE2m promoting calcium oxalate crystal-induced kidney injury by inhibiting fatty acid metabolism by Tianhui Yuan, Zehua Ye, Shuqin Mei, Miao Zhang, Ming Wu, Fangyou Lin, Weimin Yu, Wei Li, Xiangjun Zhou, Fan Cheng

“…In this study, mice with specific deletion or overexpression of PRMT1 in tubular epithelial cells were developed, and a CaOx crystal-induced kidney injury mouse model was established. Single-cell RNA-sequencing, metabolomic, proteomic, and transcriptomic analyses, together with immunoprecipitation, mass spectrometry, GST-pulldown assays, oxygen consumption rate assays, and other methods, were used to reveal the mechanism of PRMT1 in renal injury caused by CaOx crystals. …”
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Identification and Validation of NK Marker Genes in Ovarian Cancer by scRNA-seq Combined with WGCNA Algorithm by Xin He, Weiwei Feng

“…Therefore, we analyzed four high-grade serous ovarian cancer scRNA-seq data, screening NK cell marker genes at the single-cell level. The WGCNA algorithm screens NK cell marker genes based on bulk RNA transcriptome patterns. …”
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Investigation of granuloma-targeted host-pathogen interactions identify vaccine correlates of immune protection associated with control of M. tuberculosis replication by David Forrest Ackart, Dr. Faye Lanni, Victoria Mitcham, Dr. G. Brooke Anderson, Dr. Michael Lyons, Dr. Marcela Henao-Tamayo, Dr Brendan Podell

“…Results: Mice left unvaccinated have a bimodal distribution of granulomas containing Mtb populations with either low or high replication, indicating variable response across granulomas within a single group of mice. Early in the course of infection, granulomas permitting a high Mtb replication rate have an early accumulation of CD138 plasma cells and low recruitment as well as low proliferation rate of Tbet- and Ki67-expressing Th1 CD4 T cells. …”
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Application of root exudates derived from peanut/maize intercropping system promotes peanut growth and yield via modulating nitrogen turnover processes by Tong Si, Lijian Yang, Jinhao Lu, Yimin Lin, Xiaona Yu, Xiaojun Zhang, Xiaoxia Zou

“…Results Agronomical and physiological assesses indicated that single application of SUC and the combination application of “OA + SUC” showed better performance on peanut growth, pod yield, and soil nitrogen (N) turnover processes including total N and NO3 −-N contents as well as activities of N turnover enzymes. …”
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Chronic stress in mice: how gut bacteria influence gene activity in key brain neurons by Wenxia Jiang, Yifan Li, Jie Yang, Xunmin Tan, Ruimin Tian, Guojing Ma, Jing Wu, Jianping Zhang, Yu Huang, Ping Liu, Minghao Yuan, Xiaodong Song, Leyao Luo, Xingyu Zhou, Hongzhou Zuo, Ma-Li Wong, Julio Licino, Peng Zheng

“…We characterized the microbial composition and function of control, bedding exchange, and CUMS mice through 16S rRNA gene and metagenomic sequencing. Additionally, single-nucleus RNA sequencing (snRNA-seq) was used to compare the transcriptomic changes in the hypothalamus of these three groups. …”
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Whole Genome Sequencing of Greater Amberjack (Seriola dumerili) for SNP Identification on Aligned Scaffolds and Genome Structural Variation Analysis Using Parallel Resequencing by Kazuo Araki, Jun-ya Aokic, Junya Kawase, Kazuhisa Hamada, Akiyuki Ozaki, Hiroshi Fujimoto, Ikki Yamamoto, Hironori Usuki

“…We carried out de novo sequencing of the greater amberjack genome to construct a reference genome sequence to identify single nucleotide polymorphisms (SNPs) for breeding amberjack by marker-assisted or gene-assisted selection as well as to identify functional genes for biological traits. …”
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Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases by Daniela Michlmayr, Theodore R Pak, Adeeb H Rahman, El‐Ad David Amir, Eun‐Young Kim, Seunghee Kim‐Schulze, Maria Suprun, Michael G Stewart, Guajira P Thomas, Angel Balmaseda, Li Wang, Jun Zhu, Mayte Suaréz‐Fariñas, Steven M Wolinsky, Andrew Kasarskis, Eva Harris

“…Serum cytokine measurements confirmed significant acute‐phase upregulation of monocyte chemoattractants. Distinct transcriptomic signatures were associated with infection timepoint, as well as convalescent‐phase anti‐CHIKV antibody titer, acute‐phase viremia, and symptom severity. …”
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NXPE1 alters the sialoglycome by acetylating sialic acids in the human colon by Bum Seok Lee, Ashley Cook, Surojit Sur, Laura Dobbyn, Maria Popoli, Sana Khalili, Shibin Zhou, Chetan Bettegowda, Nickolas Papadopoulos, Kathy Gabrielson, Phillip Buckhaults, Bert Vogelstein, Kenneth W. Kinzler, Nicolas Wyhs

“…Of the genes in this region, only haplotypes containing NXPE1 correlate perfectly with mPAS staining in the original cohort used for whole genome sequencing, as well as in a validation cohort. Transcriptomic analysis indicates that linked haplotypes are associated with altered expression of NXPE1 suggesting a possible genetic mechanism. …”
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Human and Mouse Bone Marrow CD45⁺ Erythroid Cells Have a Constitutive Expression of Antibacterial Immune Response Signature Genes by Roman Perik-Zavodskii, Olga Perik-Zavodskaia, Julia Shevchenko, Kirill Nazarov, Anastasia Gizbrekht, Saleh Alrhmoun, Vera Denisova, Sergey Sennikov

“…<b>Methods</b>: The objective of this study was to comprehensively explore the traits of human bone marrow Erythroid cells through protein–protein interaction network analysis using cytokine secretion analysis, and single-cell immunoproteomic analysis using flow cytometry, as well as the re-analysis of publicly available human and mouse bone marrow Erythroid-cell transcriptomic data. …”
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PAQR6 as a prognostic biomarker and potential therapeutic target in kidney renal clear cell carcinoma by Tao Zou, Zongming Jia, Jixiang Wu, Xuxu Liu, Minghao Deng, Xuefeng Zhang, Yuxin Lin, Yuxin Lin, Jigen Ping

“…TIDE algorithm was used to assess how well various patient cohorts responded to immune checkpoint therapy. …”
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The immune system in cardiovascular diseases: from basic mechanisms to therapeutic implications by Xiaoyan Wang, Liming Chen, Jianming Wei, Hao Zheng, Ning Zhou, Xinjie Xu, Xin Deng, Tao Liu, Yunzeng Zou

“…This progress has been facilitated by advancements in various technological approaches, including multi-omics analysis (single-cell sequencing, spatial transcriptome et al.) and significant improvements in immunotherapy techniques such as chimeric antigen receptor (CAR)-T cell therapy. …”
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Identification and Expression Pattern Analysis of Odorant Receptor Family Genes of Tuta absoluta by Zhonglin ZHOU, Gang LIAO, Tingting XIANG, Zhongxiang SUN

“…Phylogenetic analysis revealed that four genes (TabsOR01, TabsOR28, TabsOR34, and TabsOR38) clustered in a well-defined branch, while the remaining genes were distributed across other branches. …”
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