Article
Biology
Hanako Ono, Yasuhito Arai, Eisaku Furukawa, Daichi Narushima, Tetsuya Matsuura, Hiromi Nakamura, Daisuke Shiokawa, Momoko Nagai, Toshio Imai, Koshi Mimori, Koji Okamoto, Yoshitaka Hippo, Tatsuhiro Shibata, Mamoru Kato
Summary: This study investigated the dynamics of intra-tumor heterogeneity in a mouse colorectal cancer model through single-cell exome and transcriptome sequencing. The results showed an increase in transcriptome diversity and a decrease in genome diversity after serial transplantation. The emergence of new transcriptional subpopulations was found to be key for cancer cells to adapt to microenvironmental changes with genetic alterations at later tumor stages.
Review
Immunology
Bhoomi Madhu, Brittany M. Miller, Maayan Levy
Summary: Research in the past decade has shown that the composition and function of the gut microbiome have a significant impact on intestinal and extra-intestinal diseases. While a common pattern of microbial dysbiosis associated with these diseases has not been identified, disrupted spatial organization of the gut microbiome is often a common feature in disease pathogenesis. Therefore, recent focus has shifted towards understanding the gut microbiome in a spatial context.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Review
Immunology
Tiffany Shi, Krishna Roskin, Brian M. Baker, E. Steve Woodle, David Hildeman
Summary: Solid organ transplant recipients require long-term immunosuppression to prevent rejection. Limited knowledge exists on the effects of immunosuppressive regimens, such as CNI-based therapies, on immune cell populations in grafts. Novel genomics tools, including single cell sequencing techniques, offer insights into rejection processes at a single cell level.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Joao Almeida, Joao M. Alves, Monica Valecha, Sonia Prado-Lopez, Pilar Alvarino, Miguel M. Fonseca, David Posada, Andres Perez-Figueroa, Jose Manuel Cameselle-Teijeiro, Debora Chantada
Summary: This study found that single-cell mitochondrial genomes in both normal and tumor cells of colorectal cancer patients can carry various mitochondrial haplotypes. Moreover, intra-cellular heteroplasmy that exists before tumor development can be maintained in specific tumor cell subpopulations. Somatic mutations in single cells do not seem to play a prominent role in tumorigenesis in these colorectal cancer patients.
Review
Biochemistry & Molecular Biology
Nayoung Kim, Hye Hyeon Eum, Hae-Ock Lee
Summary: Single-cell genomics is highly valued in the field of cancer for its ability to address cellular heterogeneity, impacting clinical decisions and molecular-targeted therapies. Unlike conventional genomics, it focuses more on intratumoral heterogeneity and treatment response influences, offering a potential to improve cancer diagnosis and treatment as an exploratory tool. However, further innovations are needed to enhance its clinical relevance and widespread use.
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
Biotechnology & Applied Microbiology
Isar Nassiri, Benjamin Fairfax, Angela Lee, Yanxia Wu, David Buck, Paolo Piazza
Summary: This study presents an R package, scQCEA, for quality control and enrichment analysis of single-cell RNA sequencing data. It can generate reports and visualize quality scores for comparison and evaluation. It also provides automated cell type annotation and reference gene sets. The tool allows examination of biases and outliers and objective selection of optimal cluster numbers before downstream analysis. Rating: 8/10.
Article
Microbiology
Masato Kogawa, Yohei Nishikawa, Tatsuya Saeki, Takuya Yoda, Koji Arikawa, Haruko Takeyama, Masahito Hosokawa
Summary: Single-cell genomics is a promising approach for studying uncultured bacteria. In this study, a single-cell amplified genome long-read assembly (scALA) workflow was developed to construct complete circular single-amplified bacterial genomes. Through scALA, 16 complete circular genomes of specific bacteria were obtained from human fecal samples, providing insights into microbial evolution, adaptation to environmental changes, and interactions with hosts.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Zaoqu Liu, Huanyun Li, Qin Dang, Siyuan Weng, Mengjie Duo, Jinxiang Lv, Xinwei Han
Summary: Immunotherapy is gaining popularity in oncology, but its efficacy varies among patients. Single-cell sequencing provides insights into the complexity of the tumor microenvironment and cellular characteristics, facilitating the development of more effective personalized treatment strategies.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Review
Oncology
Shengqin Yue, Qian Wang, Jiajun Zhang, Qinyong Hu, Chao Liu
Summary: This review provides an overview of the recent advances made in understanding the heterogeneity of the cervical cancer ecosystem through single-cell sequencing studies. It highlights the potential of high-resolution single-cell dissection in driving targeted therapies and personalized medicine.
Review
Oncology
Yijie Zhang, Dan Wang, Miao Peng, Le Tang, Jiawei Ouyang, Fang Xiong, Can Guo, Yanyan Tang, Yujuan Zhou, Qianjin Liao, Xu Wu, Hui Wang, Jianjun Yu, Yong Li, Xiaoling Li, Guiyuan Li, Zhaoyang Zeng, Yixin Tan, Wei Xiong
Summary: Single-cell RNA sequencing is a crucial technology in tumor research, revealing tumor cell heterogeneity, monitoring tumor development, and aiding in the classification of immune cells and drug resistance mechanisms.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2021)
Article
Genetics & Heredity
Stefano Cheloni, Roman Hillje, Lucilla Luzi, Pier Giuseppe Pelicci, Elena Gatti
Summary: XenoCell is the first stand-alone pre-processing tool that can accurately classify host and graft cellular barcodes in single-cell sequencing experiments. They demonstrated the application of XenoCell in a mixed species 50:50 cell line experiment and a publicly available PDX dataset.
BMC MEDICAL GENOMICS
(2021)
Review
Genetics & Heredity
Varun K. A. Sreenivasan, Saranya Balachandran, Malte Spielmann
Summary: Single-cell sequencing is a powerful method for detecting genetic alterations and their phenotypic consequences at a cellular resolution. It allows for the comparison of cellular lineage between normal and diseased conditions, establishing genotype-phenotype relationships. Unlike bulk-sequencing, it can detect small diseased subpopulations of cells within normal tissues. This technology has potential applications in the detection, diagnosis, and treatment of rare genetic diseases and cancer.
JOURNAL OF MEDICAL GENETICS
(2022)
Article
Microbiology
Wataru Aoki, Masato Kogawa, Shuhei Matsuda, Keisuke Matsubara, Shintaro Hirata, Yohei Nishikawa, Masahito Hosokawa, Haruko Takeyama, Toru Matoh, Mitsuyoshi Ueda
Summary: This study developed a pipeline to analyze the genomic diversity of the rice rhizosphere microbiome at single-cell resolution. By isolating microbial cells from paddy soil and determining their genomic sequences using massively parallel whole-genome amplification, the researchers obtained a large number of genomic sequences that provided insights into microbial functions in the paddy ecosystem. This approach offers a promising platform for gaining novel insights into the roles of microbes in the rice rhizomicrobiome and developing microbial technologies for improved and sustainable rice production.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Medicine, General & Internal
Ying Wang, Jian-Ye Wang, Angelika Schnieke, Konrad Fischer
Summary: Single-cell RNA sequencing (scRNA-seq) is a powerful tool for analyzing intracellular and intercellular interaction data in biomedical research, particularly in studying the immune system during organ transplantation and rejection. This technology offers a comprehensive map of cell populations, allowing researchers to explore the progression of allograft dysfunction and improve personalized organ rejection treatment by identifying decisive cellular subgroups and cell-specific interactions.
MILITARY MEDICAL RESEARCH
(2021)