Review
Biochemical Research Methods
Zoe A. Clarke, Tallulah S. Andrews, Jawairia Atif, Delaram Pouyabahar, Brendan T. Innes, Sonya A. MacParland, Gary D. Bader
Summary: This tutorial provides guidelines for interpreting single-cell transcriptomic maps to identify cell types, states and other biologically relevant patterns, with a recommended three-step workflow including automatic cell annotation, manual cell annotation, and verification. It also discusses frequently encountered challenges, strategies to address them, as well as guiding principles and specific recommendations for software tools and resources.
Article
Biochemical Research Methods
Pontus Eriksson, Nour-al-dain Marzouka, Gottfrid Sjodahl, Carina Bernardo, Fredrik Liedberg, Mattias Hoglund
Summary: In this study, we evaluated the behavior of gene-pair-based single sample predictors (SSPs) in gene expression-based multiclass prediction tasks. We found that these methods showed excellent performance, with high accuracy and informative prediction scores, in many expression-based classification tasks. However, the compatibility of gene-pair-based predictors with new datasets still needs to be verified.
Article
Biochemistry & Molecular Biology
Ruben Dries, Jiaji Chen, Natalie Del Rossi, Mohammed Muzamil Khan, Adriana Sistig, Guo-Cheng Yuan
Summary: Spatial transcriptomics is a rapidly growing field that characterizes tissue organization and architecture comprehensively at single-cell or subcellular resolution, providing a foundation for mechanistic understanding of biological processes. Computational methods play crucial roles in extracting biological signals from data, while various approaches have been developed to overcome technology-specific limitations. Downstream analysis tools quantify spatial organization and cell-cell communications, and integrative pipelines assemble multiple tools for convenient data analysis.
Article
Multidisciplinary Sciences
Teruo Akuta, Daisuke Minegishi, Nobuhide Kido, Keitaro Imaizumi, Shinji Nakaoka, Shin-Ichiro Tachibana, Kenji Hikosaka, Fumi Hori, Masataka Nakagawa, Chiaki Sakuma, Yuki Oouchi, Yu Nakajima, Sohei Tanaka, Tomoko Omiya, Kouki Morikaku, Minori Kawahara, Yoshifumi Tada, Hiroshi Tarui, Takafumi Ueda, Takane Kikuchi-Ueda, Yasuo Ono
Summary: A study developed an immunodiagnostic test based on RNA-seq data to detect scabies in infected animals' skin, which has the potential to accurately diagnose scabies in wildlife and humans.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Mingyue Wang, Qinan Hu, Tianhang Lv, Yuhang Wang, Qing Lan, Rong Xiang, Zhencheng Tu, Yanrong Wei, Kai Han, Chang Shi, Junfu Guo, Chao Liu, Tao Yang, Wensi Du, Yanru An, Mengnan Cheng, Jiangshan Xu, Haorong Lu, Wangsheng Li, Shaofang Zhang, Ao Chen, Wei Chen, Yuxiang Li, Xiaoshan Wang, Xun Xu, Yuhui Hu, Longqi Liu
Summary: This study utilized Stereo-seq technology to analyze the spatiotemporal transcriptome of developing Drosophila with high resolution and sensitivity. The results revealed the spatial transcriptomic characteristics of Drosophila embryos and larvae, and provided key information for the analysis of transcription factor regulons.
DEVELOPMENTAL CELL
(2022)
Article
Biochemistry & Molecular Biology
Seth A. Ament, Ricky S. Adkins, Robert Carter, Elena Chrysostomou, Carlo Colantuoni, Jonathan Crabtree, Heather H. Creasy, Kylee Degatano, Victor Felix, Peter Gandt, Gwenn A. Garden, Michelle Giglio, Brian R. Herb, Farzaneh Khajouei, Elizabeth Kiernan, Carrie McCracken, Kennedy McDaniel, Suvarna Nadendla, Lance Nickel, Dustin Olley, Joshua Orvis, Joseph P. Receveur, Mike Schor, Shreyash Sonthalia, Timothy L. Tickle, Jessica Way, Ronna Hertzano, Anup A. Mahurkar, Owen R. White
Summary: Scalable technologies for single-cell transcriptome and epigenome sequencing are revolutionizing our understanding of cell types and states. The BICCN, part of the BRAIN Initiative, is utilizing these technologies on an unprecedented scale to map cell types in the mammalian brain. To enhance data accessibility, the NIH has established the NeMO Archive as the primary repository for genomics data from the BRAIN Initiative, containing transcriptomic and epigenomic data from over 50 million brain cells.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Peter Pruisscher, Philipp Lehmann, Soren Nylin, Karl Gotthard, Christopher W. Wheat
Summary: This study conducted a time-course experiment on the head and abdomen of the butterfly Pieris napi, revealing significant differential gene expression dynamics during diapause compared to non-diapausing siblings from the first day of pupal development. The findings suggest a preprogrammed transcriptional landscape that is active during winter, with different biological processes active in the two body parts. Ultimately, adults emerging from either direct or diapause pathways exhibit minimal transcriptomic differences, indicating a strongly canalized adult phenotype.
Article
Biotechnology & Applied Microbiology
Jinding Liu, Kun Lang, Suxu Tan, Wencai Jie, Yihua Zhu, Shiqing Huang, Wen Huang
Summary: LivestockExp is a web-based database server for exploring gene expression and alternative splicing, containing a large number of livestock animals and RNA-seq samples. It provides diverse analysis modules and visualization tools, serving as a valuable data resource and analysis platform.
Article
Biochemistry & Molecular Biology
Miao Zhao, Xian Zou, Shenping Zhou, Jilong Liu, Chong Wang
Summary: In this study, the gene expression profiles of the receptive uterus in guinea pigs were analyzed and compared to the pre-receptive uterus. The results highlighted the importance of the inflammatory response in uterine receptivity and identified several hub genes involved in regulating endometrial receptivity. A cross-species comparison revealed that guinea pigs have a gene expression pattern of uterine receptivity more similar to humans than mice.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Richard C. Tyser, Elmir Mahammadov, Shota Nakanoh, Ludovic Vallier, Antonio Scialdone, Shankar Srinivas
Summary: The single-cell transcriptional profile of a human embryo between 16 and 19 days after fertilization shows similarities and differences in gastrulation compared to mouse and non-human primate models. This study provides new insights into human development and offers valuable information for directed differentiation of human cells in vitro.
Article
Multidisciplinary Sciences
Kiya W. Govek, Emma C. Troisi, Zhen Miao, Rachael G. Aubin, Steven Woodhouse, Pablo G. Camara
Summary: STvEA is a method that combines single-cell RNA sequencing data with mIHC images to achieve transcriptome-guided annotation of highly multiplexed immunohistochemistry data. This approach enables systematic annotation of nuanced cell populations, spatial patterns of transcription, and interactions between cell types, thereby increasing the level of detail in histological analyses.
Article
Agricultural Engineering
Aleya Ferdausi, Xianmin Chang, Meriel Jones
Summary: This study investigated the differential expression of transcripts related to secondary metabolite biosynthesis in Narcissus basal plate and in vitro callus. Enzymes involved in the initial biosynthetic pathways were upregulated in callus, while genes responsible for regulating the later stage of alkaloid biosynthesis were mainly upregulated in field samples. The findings provide insights into the genes and enzymes involved in secondary metabolism in Narcissus plants.
INDUSTRIAL CROPS AND PRODUCTS
(2021)
Article
Physics, Fluids & Plasmas
Silvia Lazzardi, Filippo Valle, Andrea Mazzolini, Antonio Scialdone, Michele Caselle, Matteo Osella
Summary: Large-scale data on single-cell gene expression can be analyzed through the statistics of their basic building blocks, similar to linguistics, ecology, or genomics. A mathematical framework can uncover emergent statistical laws in single-cell transcriptomic data and explore the underlying mechanisms. Treatable statistical models are valuable tools to distinguish biological variability from statistical effects and sampling process in transcriptomics.
Article
Biotechnology & Applied Microbiology
Eoin O'Hara, Allen Herbst, Arun Kommadath, Judd M. Aiken, Debbie McKenzie, Negin Goodarzi, Pamela Skinner, Paul Stothard
Summary: This study utilized RNA sequencing to compare the brain transcriptome of white-tailed deer affected by chronic wasting disease (CWD) to unaffected deer. The results identified significant gene expression changes related to immune activation, providing important insights into the pathogenesis of CWD and potential targets for therapeutic interventions. The study also ruled out an association between CWD and spiroplasma infection.
Article
Genetics & Heredity
Kyrillus S. Shohdy, Rohan Bareja, Michael Sigouros, David C. Wilkes, Princesca Dorsaint, Jyothi Manohar, Daniel Bockelman, Jenny Z. Xiang, Rob Kim, Kentaro Ohara, Kenneth Eng, Juan Miguel Mosquera, Olivier Elemento, Andrea Sboner, Alicia Alonso, Bishoy M. Faltas
Summary: In this study, three exome capture-based methods were used to analyze 32 FFPE tumor samples, showing high correlation and reliable detection of key immune gene expression and outlier gene transcription. The Agilent assay demonstrated the highest molecular subtype concordance with FF-TruSeq in urothelial cancer samples.
NPJ GENOMIC MEDICINE
(2021)
Article
Biochemical Research Methods
Muhadasi Tuerxunyiming, Feng Xian, Jin Zi, Yilihamujiang Yimamu, Reshalaiti Abuduwayite, Yan Ren, Qidan Li, Abulizi Abudula, SiQi Liu, Patamu Mohemaiti
JOURNAL OF PROTEOME RESEARCH
(2018)
Article
Biotechnology & Applied Microbiology
Yongbing Zhao, Chen Sun, Dongyu Zhao, Yadong Zhang, Yang You, Xinmiao Jia, Junhui Yang, Lingping Wang, Jinyue Wang, Haohuan Fu, Yu Kang, Fei Chen, Jun Yu, Jiayan Wu, Jingfa Xiao
Article
Microbiology
Xinyu Chen, Yadong Zhang, Zhewen Zhang, Yongbing Zhao, Chen Sun, Ming Yang, Jinyue Wang, Qian Liu, Baohua Zhang, Meili Chen, Jun Yu, Jiayan Wu, Zhong Jin, Jingfa Xiao
FRONTIERS IN MICROBIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Yongbing Zhao, Jinyue Wang, Fang Liang, Yanxia Liu, Qi Wang, Hao Zhang, Meiye Jiang, Zhewen Zhang, Wenming Zhao, Yiming Bao, Zhang Zhang, Jiayan Wu, Yan W. Asmann, Rujiao Li, Jingfa Xiao
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biotechnology & Applied Microbiology
Yun Shu, Hui Li, Hongjuan Shang, Jun Chen, Xiaoxing Su, Wei Le, Yan Lei, Liming Tao, Cailiang Zou, Wendy Wu
ONCOTARGETS AND THERAPY
(2020)
Article
Oncology
ZeWen Xiao, Wendy Wu, Chunlong Wu, Man Li, Fuming Sun, Lu Zheng, Gaojing Liu, Xiaoling Li, Zhiyuan Yun, Jiebing Tang, Yang Yu, Shengnan Luo, Wenji Sun, Xiaohong Feng, Qian Cheng, Xue Tao, Shuangxiu Wu, Ji Tao
Summary: This study revealed distinct 5hmC signatures in cfDNA of CRC and AD patients compared to healthy controls, potentially aiding in early-stage CRC screening and assessing adenoma malignancy. The findings imply the importance of 5hmC modifications for different pathological subtypes in colorectal diseases, suggesting the need for further large-scale follow-up studies.
MOLECULAR ONCOLOGY
(2021)
Article
Microbiology
Lyubomir Dimitrov Stanchev, Magdalena Marek, Feng Xian, Mara Kloehn, Daniele Silvestro, Gunnar Dittmar, Rosa Laura Lopez-Marques, Thomas Guenther Pomorski
Summary: Pdr11p, a pleiotropic drug resistance transporter in the yeast Saccharomyces cerevisiae, plays a role in facilitating the uptake of exogenous sterols at the plasma membrane under anaerobic growth conditions. Experimental results suggest that all six extracellular cysteine residues in Pdr11p are crucial for its functional integrity.
Article
Multidisciplinary Sciences
Nicole Kiweler, Catherine Delbrouck, Vitaly Pozdeev, Laura Neises, Leticia Soriano-Baguet, Kim Eiden, Feng Xian, Mohaned Benzarti, Lara Haase, Eric Koncina, Maryse Schmoetten, Christian Jaeger, Muhammad Zaeem Noman, Alexei Vazquez, Bassam Janji, Gunnar Dittmar, Dirk Brenner, Elisabeth Letellier, Johannes Meiser
Summary: The study reveals that antifolate treatment results in an uncoupled mitochondrial one-carbon metabolism, which supports cancer cell migration. Inhibition of serine de novo synthesis reduces cancer cell migration, and specifically inhibiting mitochondrial serine catabolism can strongly inhibit pulmonary metastasis.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Wei Zhang, Wenjuan Han, Bo Yu, Xin Zhao, Gaojun Lu, Wendy Wu, Yi Zhang
Summary: Gene mutations in primary and metastatic lesions of NSCLC patients were examined, revealing EGFR gene mutation as the most common with EGFR amplification more prevalent in the metastatic group. Metastatic group showed higher mutant-allele tumor heterogeneity value and shorter progression-free survival than the non-metastatic group.
Article
Biotechnology & Applied Microbiology
YunYu Lin, Yan Lei, LinWei Li, Xiaoxing Su, Qiqi Tian, Wendy Wu
Summary: This study identified a novel BAIAP2-ROS1 rearrangement and provided more knowledge of ROS1 fusion in clinical personalized treatment. The good response to crizotinib therapy emphasizes the importance of DNA-based and RNA-based NGS in rare fusion identification in clinical practice.
ONCOTARGETS AND THERAPY
(2022)
Article
Biology
Feng Xian, Julia Regina Sondermann, David Gomez Varela, Manuela Schmidt, Jungmin Choi
Summary: The age and sex of animals have a significant impact on experimental outcomes in biomedical research. In this study, we used a quantitative proteomics approach to analyze mouse paw skin and sciatic nerves, and discovered significant differences between male and female mice at different ages. These findings provide valuable insights into somatosensory and skin biology, and emphasize the importance of considering age and sex as biological variables in preclinical studies using mouse disease models.
Review
Cell Biology
Wenjuan Zhang, Jian Cao, Ke Liu, Ziwei Qu, Ying Zheng, Jun Yu, Yishan Yu, Yongsheng Wang, Wendy Wu
Summary: Immunotherapy has become the main systemic therapy for cancer patients, but current biomarkers are limited by tumor tissue accessibility. Rare mutations in CD274 gene's UTR region have been suggested as potential biomarkers for immunotherapy efficacy. This study explores the multi-omics analysis of CD274 UTR region using cSMART 2.0 technology and finds that rare structural variants exist in different Chinese cancer populations, which can predict response to immune checkpoint inhibitors. Liquid biopsy-based cSMART 2.0 technology offers a more sensitive and accurate detection method when tissue samples are unavailable.
CELL DEATH DISCOVERY
(2023)
Article
Oncology
Ernesto Gargiulo, Elodie Viry, Pablo Elias Morande, Anne Largeot, Susanne Gonder, Feng Xian, Nikolaos Ioannou, Mohaned Benzarti, Felix Bruno Kleine Borgmann, Michel Mittelbronn, Gunnar Dittmar, Petr Nazarov, Johannes Meiser, Basile Stamatopoulos, Alan G. Ramsay, Etienne Moussay, Jerome Paggetti
Summary: This study investigated the interactions between cancer cells and the microenvironment using mouse models of chronic lymphocytic leukemia (CLL). It found that small extracellular vesicles (sEVs) derived from CLL tissue contain specific miRNA and immune-checkpoint ligands, which alter the function and exhaustion of CD8+ T cells. Blocking sEV biogenesis delayed CLL pathogenesis and high expression of sEV-related genes correlated with poor outcomes in CLL patients.
BLOOD CANCER DISCOVERY
(2023)