Activation of FGFR genes by genetic and epigenetic alterations in uterine leiomyomas by Vilja Jokinen, Aurora Taira, Åsa Kolterud, Isa Ahlgren, Kimmo Palin, Riku Katainen, Maritta Räisänen, Eevi Kaasinen, Sini Ilves, Anniina Raitila, Helena Kopp Kallner, Emma Siili, Ralf Bützow, Oskari Heikinheimo, Annukka Pasanen, Auli Karhu, Niko Välimäki, Lauri A. Aaltonen

“…Although ULs can be classified to molecular subtypes based on genetic drivers, potential secondary drivers are not well characterised. Methods We performed mutation analysis of RNA-sequencing data of ULs, followed by screening of FGFR alterations in our Finnish (n = 2677) and Swedish (n = 372) UL collections, utilising Sanger-, next-generation and Nanopore sequencing and SNP array data. …”
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Application of multi-omics technology in pathogen identification and resistance gene screening of sheep pneumonia by Kai Huang, Lvfeng Yuan, Jia Liu, Xiaolong Li, Dan Xu, Xiaoxue Zhang, Jie Peng, Huibin Tian, Fadi Li, Weimin Wang

“…Mycoplasma ovipneumoniae was identified as the primary pneumonia pathogen, and its presence was further validated by load quantification and immunohistochemical analysis. Integration of genome-wide association study (GWAS) data from 266 lung pathological scores with transcriptome-based differentially expressed genes analysis enabled the identification of five single nucleotide polymorphisms (SNPs) and three potential candidate genes associated with Mycoplasma pneumonia. …”
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Phylogenetic and DNA barcoding study on Dehaasia pugerensis Koord. & Valeton, an endemic and critically endangered species from East Java, Indonesia by Aulia Hasan Widjaya, Andi Salamah, Tety Maryenti, Iyan Robiansyah, Irfan Martiansyah, Muhammad Rifqi Hariri, Weibang Sun

“…A single sample from each population of Dehaasia pugerensis underwent DNA sequencing utilizing DNA barcoding markers from three chloroplast genes: ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL), maturase K (matK), and the transfer RNA-histidine and the photosystem II protein D1 (trnH-psbA) intergenic spacer, as well as one nuclear ITS region. …”
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ARMH1 is a novel marker associated with poor pediatric AML outcomes that affect the fatty acid synthesis and cell cycle pathways by Mojtaba Bakhtiari, Sean C. Jordan, Sean C. Jordan, Hope L. Mumme, Hope L. Mumme, Richa Sharma, Mala Shanmugam, Swati S. Bhasin, Swati S. Bhasin, Manoj Bhasin, Manoj Bhasin, Manoj Bhasin

“…IntroductionDespite remarkable progress in Pediatric Acute Myeloid Leukemia (pAML) treatments, the relapsed disease remains difficult to treat, making it pertinent to identify novel biomarkers of prognostic/therapeutic significance.Material and methodsBone marrow samples from 21 pAML patients were analyzed using single cell RNA sequencing, functional assays with ARMH1 knockdown and overexpression were performed in leukemia cell lines to evaluate impact on proliferation and migration, and chemotherapy sensitivity. …”
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WISP1 drives esophageal squamous cell carcinoma progression via modulation of cancer-associated fibroblasts and immune microenvironment by Zhiqiang Yi, Qiqi Zhang, Ting Tao, Xiaojia Liu, Hui Li, Xiujuan Li, Zhiqiang Zhang

“…To date, no in-depth research has been conducted to explore the role and importance of WISP1 in ESCC.MethodsIn this study, we downloaded the expression data of WISP1 (CCN4), Single-Cell RNA Sequencing (scRNA) data, and clinical information from public databases. …”
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Machine learning-based integration identifies plasma cells-related gene signature ST6GAL1 in idiopathic pulmonary fibrosis by Fanjie Lin, Ken Lin, Donglei Li, Weiguo Kong, Jiayu Zhuang, Wei He, Xinguang Wei, Tianchi Xiao, Hao Zu, Zili Zhang, Wenju Lu

“…Methods The marker genes for plasma cells were extracted via single-cell RNA sequencing (scRNA-seq) analysis. Hub genes most relevant to the IPF state and plasma cells infiltration level were screened by weighted gene co-expression network analysis (WGCNA). …”
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Low-dose radiotherapy enhances the efficacy of PD-L1 blockade and induces the abscopal effect by Pierre-Antoine Laurent, Eric Deutsch, Charlotte Robert, Antonin Levy, Michele Mondini, Marine Gerbé De Thoré, Winchygn Liu, Lydia Meziani, Céline Clémenson, Flavie Naulin, Liu Shi, Lisa Bouarroudj, Nathan Benzazon, Marine Aglave, Paul Bergeron, Lisa Sitterlé, Daphné Morel

“…Subsequently, we showed that low-dose RT to one tumor enhances the efficacy of anti-PD-L1 consolidation therapy in a distant, unirradiated tumor, thereby inducing an abscopal effect comparable to that observed with high-dose RT. Single-cell RNA sequencing analysis highlighted the polarization of tumor-associated macrophages (TAMs) within distant unirradiated tumors towards a pro-inflammatory phenotype following low-dose RT and anti-PD-L1. …”
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The role and mechanism of CLEC7A in regulating PD-L1 to promote ovarian cancer growth by CHEN Yao, SUN Sibai, XU Jun, HE Jie

“…The GSE184880 single-cell sequencing dataset was analyzed to reveal differences in immune cell proportions and cellular communication between CLEC7A low-expression and high-expression HGSOC tumors. …”
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Results of the Campaign Dedicated to World Hepatitis Day by V. V. Klushkina, Z. S. Rodionova, T. V. Tyrgina, E. V. Tivanova, I. V. Solovieva, V. V. Orlov, L. V. Telminova, E. B. Lapteva, R. S. Amirov, V. S. Kichatova, F. A. Asadi Mobarhan, A. A. Karlsen, O. V. Isaeva, A. N. Gerasimov, S. N. Kuzin, K. K. Kyuregyan, M. I. Mikhailov, V. G. Akimkin

“…With the exception of two genotype 1b sequences that clustered together, the identified HCV sequences were not similar, confirming the absence of cross-contamination during reflex HCV RNA testing. …”
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Identification of glycolysis-related gene signatures for prognosis and therapeutic targeting in idiopathic pulmonary fibrosis by Han Gao, Zhongyi Sun, Xingxing Hu, Weiwei Song, Yuan Liu, Menglin Zou, Menglin Zou, Minghui Zhu, Zhenshun Cheng, Zhenshun Cheng, Zhenshun Cheng

“…A prognostic signature was developed using LASSO regression, and time-dependent receiver operating characteristic (ROC) curves were generated to evaluate predictive performance. Single-cell RNA sequencing (scRNA-seq) data were analyzed to examine GRG expression across various cell types. …”
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TNFR2 blockade promotes antitumoral immune response in PDAC by targeting activated Treg and reducing T cell exhaustion by Eliane Piaggio, Allan Thiolat, Anais Debesset, Caroline Pilon, Benoît Laurent Salomon, José Laurent Cohen, Sylvain Baulande, Sylvain Meunier, Orianne Cuelenaere-Bonizec, Wilfrid Richer, Claire Houppe, Matteo Ponzo, Jeanne Magnan, Jonathan Caron, Pamela Caudana, Jimena Tosello Boari, Nhu Han To, Ilaria Cascone

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Transcriptomic and proteomic characterization of cell and protein biomarkers of checkpoint inhibitor-induced liver injury by Changhua Ji, Steven Kumpf, Jessie Qian, Joel D. Federspiel, Mark Sheehan, Darien Capunitan, Edmond Atallah, Stuart Astbury, Seda Arat, Elias Oziolor, Mireia Fernandez Ocana, Shashi K. Ramaiah, Jane Grove, Guruprasad P. Aithal, Thomas A. Lanz

“…Single-cell RNA sequencing revealed that these changes were primarily found in select T cell subtypes (including CD8 + effector memory cells), while CD16 + monocytes exhibited enrichment in metabolic pathways. …”
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RAB26 promotes prostate cancer progression via the MAPK/ERK-TWIST1 signaling axis by Hexi Wang, Simin Liang, Xiaoyi Du, Guozhi Zhao, Yuanyuan Bai, Junwu Li, Haoyu Xu, Senlin Peng, Ye Yuan, Wei Tang

“…However, the functional role of RAB26 in prostate cancer (PCa) remains to be elucidated. Single-cell RNA sequencing data (GSE141445) analysis indicated that RAB26 was widely expressed in PCa cells, especially in luminal cells and basal cells. …”
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FOXL2 drives the differentiation of supporting gonadal cells in early ovarian development by Laura Danti, Karolina Lundin, Petra Nedeczey-Ruzsák, Timo Tuuri, Juha S. Tapanainen

“…Furthermore, a comparative analysis with existing single cell RNA sequencing data from human in vivo-derived samples elucidated that FOXL2 initiates the downregulation of coelomic epithelial genes GATA4, LHX9 and UPK3B at day 6. …”
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m6A-methylase METTL3 promotes retinal angiogenesis through modulation of metabolic reprogramming in RPE cells by Qian Zhou, Xianyang Liu, Huiping Lu, Na Li, Jiayu Meng, Jiaxing Huang, Zhi Zhang, Jiangyi Liu, Wei Fan, Wanqian Li, Xingran Li, Xiaoyan Liu, Hangjia Zuo, Peizeng Yang, Shengping Hou

“…Abstract Retinal neovascularization (RNV) disease is one of the leading causes of blindness, yet the molecular underpinnings of this condition are not well understood. To delve into the critical aspects of cell-mediated angiogenesis, we analyzed our previously published single-cell data. …”
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Investigating the mechanisms by which low NAT1 expression in tumor cells contributes to chemo-resistance in colorectal cancer by Zheng Yuan, Kai Fang, Xinsheng Miao, Yan Zhang, Menghui Gu, Wei Xu, Hao Li, Dawei Zhu, Jiahui Zhou, Jian Sun, Xinhua Gu

“…Additionally, we utilized single-cell RNA sequencing (scRNA-seq), the Cellchat assay, and western blot to explore the intercellular communication between tumor and endothelial cells in the context of anti-PD-1 therapy and NAT1’s impact. …”
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Acquired DNA damage repairs deficiency-driven immune evolution and involved immune factors of local versus distant metastases in non-small cell lung cancer by Wen-Fang Tang, Xiao-Jun Fan, Hua Bao, Rui Fu, Yi Liang, Min Wu, Chao Zhang, Jian Su, Yi-Long Wu, Wen-Zhao Zhong

“…Primary tumors with high levels of CD4+ T cells were associated with distant metastases rather than local metastases. Analysis of TCGA data and a single-cell RNA-sequencing dataset revealed a decreasing trend of major immune cells, such as CD8+ T cells, and an increasing trend of CD4 T helper cells (Th2 and Th1) in primary tumors with metastases from local to distant sites. …”
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Programmed cell death regulates hematopoietic cell homeostasis under radiation conditions by Manling Shu, Jinfu Zhang, Yuhong Peng, Zhengyang Li, Xin Shu, Jie Wang, Huihong Zeng, Lijian Shao

“…In vivo spleen colony formation, competitive bone marrow transplantation and secondary transplantation were used to verify the protective effect of inhibiting Caspase-1 on hematopoietic stem cells damaged by radiation. RNA sequencing (RNA-Seq) using Lin−c-Kit+ cell populations revealed the mechanism by which inhibition of Caspase-1 mitigates post-irradiation hematopoietic stem cell damage. …”
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Exploring the diversity of Gardnerella vaginalis in the genitourinary tract microbiota of monogamous couples through subtle nucleotide variation. by A Murat Eren, Marcela Zozaya, Christopher M Taylor, Scot E Dowd, David H Martin, Michael J Ferris

“…This study also highlights the fact that a few, reproducible nucleotide variations within the 16S rRNA gene can reveal clinical or epidemiological associations that would be missed by genus-level or species-level categorization of 16S rRNA data.…”
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Microbiological and clinical evaluation of ultrasonic debridement with/without erythritol air polishing during supportive periodontal therapy in arches with full-arch fixed implant... by Qi Liu, Lin Tang, Zhaoguo Yue, Jianxia Hou, Jingwen Yang, Pingyi Jia, Jianzhang Liu, Zhongning Liu

“…Peri-implant submucosal plaque will be collected at each re-examination, and the bacterial flora will be analysed by 16s ribosomal RNA gene sequencing. X-ray examinations will be conducted at 12-month intervals to evaluate the marginal bone level around implants.Ethics and dissemination This prospective single-centre, randomised controlled trial (PKUSSIRB-202054045) has been approved by the Ethics Committee of Stomatology School and Hospital of Peking University. …”
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