Review
Cell & Tissue Engineering
Hui-Qi Qu, Charlly Kao, Hakon Hakonarson
Summary: Single-cell RNA sequencing (scRNA-seq) is a revolutionary technology that has greatly contributed to our understanding of cellular heterogeneity and gene expression dynamics, particularly in stem cell research. Different types of scRNA-seq technologies have been developed and they offer distinct advantages in capturing cellular heterogeneity and characterizing rare cell populations within complex tissues.
Article
Biochemical Research Methods
Meichen Dong, Aatish Thennavan, Eugene Urrutia, Yun Li, Charles M. Perou, Fei Zou, Yuchao Jiang
Summary: SCDC is a deconvolution method for bulk RNA-seq data that improves the accuracy of cell-type decomposition. It leverages cell-type specific gene expression profiles from multiple scRNA-seq reference datasets and integrates deconvolution results from different experiments and laboratories. The study demonstrates that SCDC outperforms existing methods in both settings.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Immunology
Erich Horeth, Akinsola Oyelakin, Eun-Ah Christine Song, Monika Che, Jonathan Bard, Sangwon Min, Jeremy Kiripolsky, Jill M. Kramer, Satrajit Sinha, Rose-Anne Romano
Summary: Sjogren's Syndrome is a chronic autoimmune disease affecting salivary and lacrimal glands. RNA sequencing and single-cell RNA sequencing have revealed important pathways and regulatory networks in the pathobiology of SS, as well as the diversity in activated state of salivary gland epithelial cells.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Kaile Wang, Zhenna Xiao, Yun Yan, Rui Ye, Min Hu, Shanshan Bai, Emi Sei, Yawei Qiao, Hui Chen, Bora Lim, Steven H. Lin, Nicholas E. Navin
Summary: The newly proposed SNuBar-ATAC method allows for sample multiplexing in ATAC-seq by using a single oligonucleotide adaptor during the existing tagmentation step, without the need for pre-labeling procedures. The accuracy and scalability of this method were demonstrated in cell line mixture experiments and multiplexing of human breast tissue regions.
Article
Biochemical Research Methods
W. J. Pereira, F. M. Almeida, D. Conde, K. M. Balmant, P. M. Triozzi, H. W. Schmidt, C. Dervinis, G. J. Jr Jr Pappas, M. Kirst
Summary: Asc-Seurat is a comprehensive workbench providing an accessible graphical interface for scRNA-seq analysis, significantly reducing the time and effort required to analyze and interpret the information in scRNA-seq datasets. It encapsulates tools for all critical steps of scRNA-seq data analysis in an user-friendly manner.
BMC BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Tao Hu, Lei Wei, Shuailin Li, Tianrun Cheng, Xuegong Zhang, Xiaowo Wang
Summary: This study demonstrates evidence that miRNAs can reduce gene expression noise in mouse cells at the mRNA level, with key features such as miRNA expression level, target number, target pool abundance, and miRNA-target interaction strength contributing to noise repression. miRNAs work cooperatively in cell type-specific subnetworks to synergistically repress target noise, providing resistance to extrinsic fluctuations through accelerated degradation and elevated transcriptional activation of miRNA targets. Through integrated analysis of single-cell RNA and miRNA expression profiles, miRNAs are shown to be important post-transcriptional regulators for reducing gene expression noise and conferring robustness to biological processes.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Amichay Afriat, Vanessa Zuzarte-Luis, Keren Bahar Halpern, Lisa Buchauer, Sofia Marques, Angelo Ferreira Chora, Aparajita Lahree, Ido Amit, Maria M. Mota, Shalev Itzkovitz
Summary: This study characterized the temporal expression programs of the rodent malaria parasite Plasmodium berghei ANKA and the host hepatocyte in a zonally controlled manner using single-cell RNA sequencing and single-molecule transcript imaging. The study identified differences in parasite gene expression in distinct zones and identified a subpopulation of hepatocytes with reduced levels of Plasmodium transcripts and parasitophorous vacuole breakdown. These findings provide insights into the liver stage of Plasmodium infection.
Review
Biotechnology & Applied Microbiology
Ricard Argelaguet, Anna S. E. Cuomo, Oliver Stegle, John C. Marioni
Summary: The development of single-cell multimodal assays has provided a powerful tool for investigating cellular heterogeneity in multiple dimensions. Data integration is a key challenge in analyzing single-cell multimodal data, with existing strategies utilizing similar mathematical ideas but having distinct goals and principles.
NATURE BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Sini Junttila, Johannes Smolander, Laura L. Elo
Summary: This study compared 18 methods for identifying differential states (DS) changes between conditions in multisubject scRNA-seq data, and found that pseudobulk methods and mixed models performed best, showing superior statistical performance compared to naive single-cell methods.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Yunqing Liu, Na Lu, Changwei Bi, Tingyu Han, Guo Zhuojun, Yunchi Zhu, Yixin Li, Chunpeng He, Zuhong Lu
Summary: The study developed a functional expression matrix (FEM) algorithm to utilize information from all expressed genes and showed good performance in cell clustering and cell-type specific function annotation.
Article
Biochemistry & Molecular Biology
Mohamed Nabil Bakr, Haruko Takahashi, Yutaka Kikuchi
Summary: By using gene expression signature classification and Cox regression analyses, a prognosis-related gene signature for melanoma was established and validated in multiple datasets, showing potential for predicting prognosis in melanoma patients.
Article
Cell Biology
Abhijeet R. Patil, Gaurav Kumar, Huanyu Zhou, Liling Warren
Summary: scRNA-seq is a powerful technology for studying cellular processes and cell type diversity. This article introduces scViewer, an interactive graphical user interface application for visualizing scRNA-seq gene expression data. The tool provides various analysis functionalities, such as exploring cell-type-specific gene expression, co-expression analysis of two genes, and differential expression analysis with different biological conditions.
Article
Genetics & Heredity
Wei Vivian Li, Yanzeng Li
Summary: The study presents a method called scLink, which utilizes single-cell RNA sequencing technologies for gene co-expression network analysis. Through simulation and real data studies, the advantages of scLink in improving single-cell gene network analysis are demonstrated.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Zhipeng Sun, Todd G. Nystul, Guohua Zhong
Summary: In this study, the researchers used single-cell RNA sequencing, RNAi screen, and bioinformatic analysis to identify genes involved in germ cell differentiation. They discovered that a gene named eggpl is highly expressed in ovarian germline stem cells and downregulated in early daughter cells. Knockdown of eggpl resulted in defects in germ cell proliferation and differentiation. Furthermore, the downregulation of eggpl was found to link nutritional status to germ cell proliferation and differentiation. This study provides new insights into the signaling networks regulating early germ cell development and identifies eggpl as an important player in this process.
Article
Biochemistry & Molecular Biology
Gayani Perera, Liam Power, Amy Larson, Christina J. J. Codden, Junya Awata, Rebecca Batorsky, Douglas Strathdee, Michael T. T. Chin
Summary: Barth Syndrome is a rare X-linked disorder characterized by cardiomyopathy, muscular hypotonia, and cyclic neutropenia. Single-nucleus RNA sequencing of mouse hearts revealed abnormal cell-cell communication, particularly between adipocytes and cardiomyocytes, in Barth Syndrome patients. These findings suggest that improving mitochondrial function in both adipocytes and cardiomyocytes may benefit patients with Barth Syndrome.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
