The impact of dropouts in scRNAseq dense neighborhood analysis by Alisa Pavel, Manja Gersholm Grønberg, Line H. Clemmensen

“…Single cell RNA sequencing (scRNAseq) provides the possibility to investigate transcriptomic profiles on a single cell level. …”
Get full text

Epigenomic disorder and partial EMT impair luminal progenitor integrity in Brca1-associated breast tumorigenesis by Camille Landragin, Melissa Saichi, Marthe Laisné, Adeline Durand, Pacôme Prompsy, Renaud Leclere, Jérémy Mesple, Kyra Borgman, Amandine Trouchet, Marisa M. Faraldo, Aurélie Chiche, Anne Vincent-Salomon, Hélène Salmon, Céline Vallot

“…Abstract In breast cancer related to the BRCA1 mutation, luminal progenitor cells are believed to be the cells of origin, yet how these cells transform into invasive cancer cells remain poorly understood. Here, we combine single-cell epigenomic and transcriptomic data to reconstitute sequences of events in luminal cells that lead to tumorigenesis. …”
Get full text

multiDGD: A versatile deep generative model for multi-omics data by Viktoria Schuster, Emma Dann, Anders Krogh, Sarah A. Teichmann

“…Abstract Recent technological advancements in single-cell genomics have enabled joint profiling of gene expression and alternative modalities at unprecedented scale. …”
Get full text

Expression characteristics, molecular mechanisms, and clinical significance of DICER1 in breast cancer by Xi Zhang, Long Yu, Cuizhi Geng

“…ObjectiveThis study aims to investigate the expression patterns, molecular mechanisms, and clinical significance of DICER1 in breast cancer (BRCA), providing new biomarkers and therapeutic targets for prognosis assessment and personalized treatment of breast cancer.MethodsBy integrating RNA-seq data, clinical data, and tumor mutation burden (TMB) data from The Cancer Genome Atlas (TCGA) database, as well as single-cell transcriptomic data from the Gene Expression Omnibus (GEO) database, we analyzed the expression characteristics of DICER1 in breast cancer. …”
Get full text

Stimulation of regulatory dendritic cells suppresses cytotoxic T cell function and alleviates DEN-induced liver injury, fibrosis and hepatocellular carcinoma by Junjie Wang, Pixu Gong, Qingqing Liu, Menglei Wang, Dengfang Wu, Mengyu Li, Shujie Zheng, Han Wang, Han Wang, Qiaoming Long

“…LAP-treated mice are protected from DEN-induced liver injury, fibrosis and HCC in a TLR2-dependent manner. Single-cell transcriptome profiling revealed that LAP treatment determines an immunosuppressive hepatic T-cell program that is characterized by a significantly reduced cytotoxic activity. …”
Get full text

Exploring the Role of Bifenthrin in Recurrent Implantation Failure and Pregnancy Loss Through Network Toxicology and Molecular Docking by Shengyuan Jiang, Yixiao Wang, Haiyan Chen, Yuanyuan Teng, Qiaoying Zhu, Kaipeng Xie

“…The diagnostic model based on these genes exhibited good predictive performance in the RIF cohort and was successfully validated in the RPL cohort. Single-cell transcriptomic analysis revealed a significant increase in the proportion of myeloid cells in RPL patients, while immune infiltration analysis showed a consistent downregulation of M2 macrophages in both RIF and RPL. …”
Get full text

Overexpression of MMP14 is associated with poor prognosis and immune cell infiltration in colon cancer by Na Li, Nan Zhang, Guanghui Wang

“…Single-cell transcriptome data were analyzed to explore MMP14 expression and immune microenvironment changes. mRNA expression profiles and clinical data were retrieved from public databases (TCGA and GEO). …”
Get full text

Functional Analysis of Promoters, mRNA Cleavage, and mRNA Secondary Structure on <i>esxB-esxA</i> in <i>Mycolicibacterium smegmatis</i> by Ryan G. Peters, Jessica M. Kelly, Sarah Bibeau, Ying Zhou, Scarlet S. Shell

“…Consistent with this, there was no detectable correlation between mRNA half-life and secondary structure near the 5′ ends of 5′ UTRs on a transcriptome-wide basis. Collectively, these data shed light on the determinants of <i>esxB-esxA</i> expression in <i>M. smegmatis</i> as well as provide broader insight into the determinants of mRNA cleavage in mycobacteria and the relationship between 5′ UTR secondary structure and mRNA stability.…”
Get full text

Multi-modal comparison of molecular programs driving nurse cell death and clearance in Drosophila melanogaster oogenesis. by Shruthi Bandyadka, Diane P V Lebo, Albert A Mondragon, Sandy B Serizier, Julian Kwan, Jeanne S Peterson, Alexandra Y Chasse, Victoria K Jenkins, Anoush Calikyan, Anthony J Ortega, Joshua D Campbell, Andrew Emili, Kimberly McCall

“…We also integrated two publicly available single-cell RNAseq atlases of the Drosophila ovary to define the transcriptomic profiles of follicle cells. …”
Get full text

Prognostic analysis of bladder cancer with neddylation-related genes by Huang Xiaolong, Deng Min, Zhang Sizhou, Hu Daorong, Pan Juncheng, Wang Yanjian, Li Jie Gu Hong, Zheng Ji, Wu Qingjian

“…Abstract Background Previous studies have demonstrated a close association between neddylation modifications and tumor progression as well as alterations in the microenvironment. This study aimed to explore the role of neddylation in bladder cancer (BLCA) progression and its prognostic significance. …”
Get full text

Re-evaluating evidence for giant genomes in amoebae by Daniel Barzilay, João P. B. Alcino, Giulia M. Ribeiro, Alfredo L. P. Sousa, Daniel J. G. Lahr

“…Fully sequenced amoebozoa genomes range from 14.4 to 52.37 mega basepairs, well within the typical single-celled eukaryote expectation. …”
Get full text

Comprehensive bioinformatics analysis identified HMGB3 as a promising immunotherapy target for glioblastoma multiforme by Libin Wang, Peizhi Xu, Xinglong Li, Qinghua Zhang

“…Results HMGB3 was highly expressed in GBM tissues and influenced the interpatient and intratumoral transcriptomic heterogeneity as well as immunosuppression in GBM. …”
Get full text

The role of B cell-activating factor system in autoimmune diseases: mechanisms, disease implications, and therapeutic advances by Liang Li, Shengxian Shen, Shuai Shao, Erle Dang, Gang Wang, Hui Fang, Hongjiang Qiao

“…Despite progress, mechanistic gaps in BAFF-mediated crosstalk between innate and adaptive immunity, as well as interspecies-specific pathogenesis warrant further investigation using humanized disease models and single-cell transcriptomic profiling. …”
Get full text

mRNA Vaccines Against Infectious Diseases and Cancer by Alexander Meisel, Steve Pascolo

“…In addition, advances in next-generation sequencing (NGS) technology allow the genome, exome, and transcriptome of a single cancer patient to be deciphered. …”
Get full text

Integration of machine learning and experimental validation to identify the prognostic signature related to diverse programmed cell deaths in breast cancer by Longpeng Li, Longpeng Li, Jinfeng Zhao, Yaxin Wang, Zhibin Zhang, Wanquan Chen, Jirui Wang, Yue Cai

“…In addition, we analyzed PCDRS in relation to immune as well as therapeutic responses. The distribution of genes in different cells was explored by single-cell analysis and spatial transcriptome analysis. …”
Get full text

Cocaine-induced gene regulation in D1 and D2 neuronal ensembles of the nucleus accumbens by Philipp Mews, Autumn VA Mason, Emily G. Kirchner, Molly Estill, Eric J. Nestler

“…Notably, we identified a discrete D1 MSN population characterized by the upregulation of immediate early genes, as well as another group of D1 MSNs linked to prolonged withdrawal, uncovering novel regulators of withdrawal-related transcriptome dynamics. …”
Get full text

Glutamate transporter SLC1A6 promotes resistance to immunotherapy in cancer by Chenchen Li, Yi Lin, Haoran Zheng, Hengda Zeng, Longhao Xu, Daqin Wu, Jianwen Lao, Peicong Cai, Shuai Liang, Chunhui Wang, Tianxin Lin, Wenlong Zhong

“…The clinical prognostic value of SLC1A6 in cancer was validated using publicly available lung cancer single-cell datasets, as well as transcriptomic data from both bladder and lung cancer cohorts. …”
Get full text

Identification of the "Collagen-Macrophage" sub-category of patients with colorectal cancer as an extension of the CMS4 subtype with THBS2 as a therapeutic target by Shuwen Chen, Zhaoyan Jiang, Wanxuan Song, Chuqiao Lu, Yanbing Lin, Shiyao Xu, Kunxin Xie, Li Wan, Xiaoqin Yuan

“…Abstract We identified a subset of patients with colorectal cancer (CRC) enriched with “collagen-TAMs,” designated the CM class, using large integrated colon cancer transcriptome and single-cell transcriptome datasets. …”
Get full text

Soluble TIM-3, likely produced by myeloid cells, predicts resistance to immune checkpoint inhibitors in metastatic clear cell renal cell carcinoma by Ivan Pourmir, Nadine Benhamouda, Thi Tran, Hugo Roux, Joséphine Pineau, Alain Gey, Andyara Munoz, Nesrine Mabrouk, Nicolas Epaillard, Virginie Verkarre, Yann-Alexandre Vano, Eric Tartour, Stéphane Oudard

“…The origin and role of sTIM-3 are studied on tumor and blood samples, using multiplex immunohistochemistry and flow cytometry, as well as analyses of publicly available single-cell transcriptomic (scRNAseq) and mass cytometry data. …”
Get full text

Evidence for thermosensitivity of the cotton (Gossypium hirsutum L.) immature fiber (im) mutant via hypersensitive stomatal activity. by Hee Jin Kim, Naohiro Kato, Ruth Ndathe, Gregory N Thyssen, Don C Jones, Harish H Ratnayaka

“…However, the mechanisms altering the stress responses in im mutant are not well understood. Thus, we characterized growth and gas exchange in im and TM-1 under no stress and also investigated their stress responses by comparing gas exchange and transcriptomic profiles under high temperature. …”
Get full text