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Single cell RNA seq

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https://www.readbyqxmd.com/read/28798667/the-foxp2-driven-network-in-developmental-disorders-and-neurodegeneration
#1
Franz Oswald, Patricia Klöble, André Ruland, David Rosenkranz, Bastian Hinz, Falk Butter, Sanja Ramljak, Ulrich Zechner, Holger Herlyn
The transcription repressor FOXP2 is a crucial player in nervous system evolution and development of humans and songbirds. In order to provide an additional insight into its functional role we compared target gene expression levels between human neuroblastoma cells (SH-SY5Y) stably overexpressing FOXP2 cDNA of either humans or the common chimpanzee, Rhesus monkey, and marmoset, respectively. RNA-seq led to identification of 27 genes with differential regulation under the control of human FOXP2, which were previously reported to have FOXP2-driven and/or songbird song-related expression regulation...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28790351/whole-transcriptome-profiling-of-taste-bud-cells
#2
Sunil K Sukumaran, Brian C Lewandowski, Yumei Qin, Ramana Kotha, Alexander A Bachmanov, Robert F Margolskee
Analysis of single-cell RNA-Seq data can provide insights into the specific functions of individual cell types that compose complex tissues. Here, we examined gene expression in two distinct subpopulations of mouse taste cells: Tas1r3-expressing type II cells and physiologically identified type III cells. Our RNA-Seq libraries met high quality control standards and accurately captured differential expression of marker genes for type II (e.g. the Tas1r genes, Plcb2, Trpm5) and type III (e.g. Pkd2l1, Ncam, Snap25) taste cells...
August 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28768204/single-cell-landscape-of-transcriptional-heterogeneity-and-cell-fate-decisions-during-mouse-early-gastrulation
#3
Hisham Mohammed, Irene Hernando-Herraez, Aurora Savino, Antonio Scialdone, Iain Macaulay, Carla Mulas, Tamir Chandra, Thierry Voet, Wendy Dean, Jennifer Nichols, John C Marioni, Wolf Reik
The mouse inner cell mass (ICM) segregates into the epiblast and primitive endoderm (PrE) lineages coincident with implantation of the embryo. The epiblast subsequently undergoes considerable expansion of cell numbers prior to gastrulation. To investigate underlying regulatory principles, we performed systematic single-cell RNA sequencing (seq) of conceptuses from E3.5 to E6.5. The epiblast shows reactivation and subsequent inactivation of the X chromosome, with Zfp57 expression associated with reactivation and inactivation together with other candidate regulators...
August 1, 2017: Cell Reports
https://www.readbyqxmd.com/read/28768198/enhanced-neuronal-regeneration-in-the-cast-ei-mouse-strain-is-linked-to-expression-of-differentiation-markers-after-injury
#4
Véronique Lisi, Bhagat Singh, Michel Giroux, Elmer Guzman, Michio W Painter, Yung-Chih Cheng, Eric Huebner, Giovanni Coppola, Michael Costigan, Clifford J Woolf, Kenneth S Kosik
Peripheral nerve regeneration after injury requires a broad program of transcriptional changes. We investigated the basis for the enhanced nerve regenerative capacity of the CAST/Ei mouse strain relative to C57BL/6 mice. RNA sequencing of dorsal root ganglia (DRG) showed a CAST/Ei-specific upregulation of Ascl1 after injury. Ascl1 overexpression in DRG neurons of C57BL/6 mice enhanced their neurite outgrowth. Ascl1 is regulated by miR-7048-3p, which is downregulated in CAST/Ei mice. Inhibition of miR-7048-3p enhances neurite outgrowth...
August 1, 2017: Cell Reports
https://www.readbyqxmd.com/read/28759029/simultaneous-epitope-and-transcriptome-measurement-in-single-cells
#5
Marlon Stoeckius, Christoph Hafemeister, William Stephenson, Brian Houck-Loomis, Pratip K Chattopadhyay, Harold Swerdlow, Rahul Satija, Peter Smibert
High-throughput single-cell RNA sequencing has transformed our understanding of complex cell populations, but it does not provide phenotypic information such as cell-surface protein levels. Here, we describe cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), a method in which oligonucleotide-labeled antibodies are used to integrate cellular protein and transcriptome measurements into an efficient, single-cell readout. CITE-seq is compatible with existing single-cell sequencing approaches and scales readily with throughput increases...
July 31, 2017: Nature Methods
https://www.readbyqxmd.com/read/28758056/single-cell-transcriptome-analysis-of-developing-and-regenerating-spiral-ganglion-neurons
#6
Kelvin Y Kwan
The spiral ganglion neurons (SGNs) of the cochlea are essential for our ability to hear. SGN loss after exposure to ototoxic drugs or loud noise results in hearing loss. Pluripotent stem cell-derived and endogenous progenitor cell types have the potential to become SGNs and are cellular foundations for replacement therapies. Repurposing transcriptional regulatory networks to promote SGN differentiation from progenitor cells is a strategy for regeneration. Advances in the Fludigm C1 workflow or Drop-seq allow sequencing of single cell transcriptomes to reveal variability between cells...
October 2016: Current Pharmacology Reports
https://www.readbyqxmd.com/read/28757360/fusion-of-regionally-specified-hpsc-derived-organoids-models-human-brain-development-and-interneuron-migration
#7
Yangfei Xiang, Yoshiaki Tanaka, Benjamin Patterson, Young-Jin Kang, Gubbi Govindaiah, Naomi Roselaar, Bilal Cakir, Kun-Yong Kim, Adam P Lombroso, Sung-Min Hwang, Mei Zhong, Edouard G Stanley, Andrew G Elefanty, Janice R Naegele, Sang-Hun Lee, Sherman M Weissman, In-Hyun Park
Organoid techniques provide unique platforms to model brain development and neurological disorders. Whereas several methods for recapitulating corticogenesis have been described, a system modeling human medial ganglionic eminence (MGE) development, a critical ventral brain domain producing cortical interneurons and related lineages, has been lacking until recently. Here, we describe the generation of MGE and cortex-specific organoids from human pluripotent stem cells that recapitulate the development of MGE and cortex domains, respectively...
July 26, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28746860/integrating-rna-sequencing-into-neuro-oncology-practice
#8
REVIEW
David S Rogawski, Nicholas A Vitanza, Angela C Gauthier, Vijay Ramaswamy, Carl Koschmann
Malignant tumors of the central nervous system (CNS) cause substantial morbidity and mortality, yet efforts to optimize chemo- and radiotherapy have largely failed to improve dismal prognoses. Over the past decade, RNA sequencing (RNA-seq) has emerged as a powerful tool to comprehensively characterize the transcriptome of CNS tumor cells in one high-throughput step, leading to improved understanding of CNS tumor biology and suggesting new routes for targeted therapies. RNA-seq has been instrumental in improving the diagnostic classification of brain tumors, characterizing oncogenic fusion genes, and shedding light on intratumor heterogeneity...
July 8, 2017: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/28720143/mhc-class-ii-expression-and-potential-antigen-presenting-cells-in-the-retina-during-experimental-autoimmune-uveitis
#9
Deborah A Lipski, Rémi Dewispelaere, Vincent Foucart, Laure E Caspers, Matthieu Defrance, Catherine Bruyns, François Willermain
BACKGROUND: Controversy exists regarding which cell types are responsible for autoantigen presentation in the retina during experimental autoimmune uveitis (EAU) development. In this study, we aimed to identify and characterize the retinal resident and infiltrating cells susceptible to express major histocompatibility complex (MHC) class II during EAU. METHODS: EAU was induced in C57BL/6 mice by adoptive transfer of autoreactive lymphocytes from IRBP1-20-immunized animals...
July 18, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28709640/genome-wide-identification-of-genes-essential-for-podocyte-cytoskeletons-based-on-single-cell-rna%C3%A2-sequencing
#10
Yuqiu Lu, Yuting Ye, Wenduona Bao, Qianqian Yang, Jinquan Wang, Zhihong Liu, Shaolin Shi
Gene expression differs substantially among individual cells of the same type. We speculate that genes that are expressed in all but a portion of cells of a given cell type would be likely essential and required for either the cell survival (housekeeping) or for the cell type's unique structure and function, enabling the organism to survive. Here, we performed RNA-seq of 20 mouse podocytes using the Fluidigm C1 system and identified 335 genes that were expressed in all of them. Among them, 239 genes were also expressed in mesangial and endothelial cells and were involved in energy metabolism, protein synthesis, etc...
July 11, 2017: Kidney International
https://www.readbyqxmd.com/read/28706128/transcriptome-analysis-reveals-a-role-for-the-endothelial-anp-gc-a-signaling-in-interfering-with-pre-metastatic-niche-formation-by-solid-cancers
#11
Takashi Nojiri, Miki Arai, Yutaka Suzuki, Motofumi Kumazoe, Takeshi Tokudome, Koichi Miura, Jun Hino, Hiroshi Hosoda, Mikiya Miyazato, Meinoshin Okumura, Shinpei Kawaoka, Kenji Kangawa
Cancer establishes a microenvironment called the pre-metastatic niche in distant organs where disseminated cancer cells can efficiently metastasize. Pre-metastatic niche formation requires various genetic factors. Previous studies suggest that inhibiting a single niche-factor is insufficient to completely block pre-metastatic niche formation especially in human patients. Here we show that the atrial natriuretic peptide (ANP), an endogenous hormone produced by the heart, inhibits pre-metastatic niche formation and metastasis of murine solid cancer models when pharmacologically supplied in vivo...
May 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28698542/genome-wide-differential-mrna-expression-profiles-in-follicles-of-two-breeds-and-at-two-stages-of-estrus-cycle-of-gilts
#12
Qingpo Chu, Bo Zhou, Feilong Xu, Ruonan Chen, Chunyan Shen, Tingting Liang, Yuan Li, Allan P Schinckel
Estrus expression by gilts and sows is hereditable and important for heat detection. To better understand the molecular biological mechanisms of estrus expression in gilts, the mRNA expression profiles of follicular tissue from Large White gilts in diestrus (LD, n = 3) and estrus (LE, n = 3), and Chinese indigenous Mi gilts in diestrus (MD, n = 2) and estrus (ME, n = 3) were investigated using RNA sequencing. We detected 122,804-335,295 SNPs, 6,140-14,947 InDel and 12 types of AS events (39...
July 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28695489/lack-of-human-cytomegalovirus-expression-in-single-cells-from-glioblastoma-tumors-and-cell-lines
#13
Travis S Johnson, Zachary B Abrams, Xiaokui Mo, Yan Zhang, Kun Huang
The relationship between human cytomegalovirus (HCMV) and glioblastoma (GBM) is an ongoing debate with extensive evidence supporting or refuting its existence through molecular assays, pre-clinical studies, and clinical trials. We focus primarily on the crux of the debate, detection of HCMV in GBM samples using molecular assays. We propose that these differences in detection could be affected by cellular heterogeneity. To take this into account, we align the single-cell RNA sequencing (scRNA-seq) reads from five GBM tumors and two cell lines to HCMV and analyze the alignments for evidence of (i) complete viral transcripts and (ii) low-abundance viral reads...
July 10, 2017: Journal of Neurovirology
https://www.readbyqxmd.com/read/28694456/single-cell-transcriptomics-of-east-asian-pancreatic-islets-cells
#14
Rajkumar Dorajoo, Yusuf Ali, Vanessa S Y Tay, Jonathan Kang, Sudhagar Samydurai, Jianjun Liu, Bernhard O Boehm
Single-cell RNA-seq (scRNA-seq) of pancreatic islets have reported on α- and β-cell gene expression in mice and subjects of predominantly European ancestry. We aimed to assess these findings in East-Asian islet-cells. 448 islet-cells were captured from three East-Asian non-diabetic subjects for scRNA-seq. Hierarchical clustering using pancreatic cell lineage genes was used to assign cells into cell-types. Differentially expressed transcripts between α- and β-cells were detected using ANOVA and in silico replications of mouse and human islet cell genes were performed...
July 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28686870/intestinal-enteroendocrine-lineage-cells-possess-homeostatic-and-injury-inducible-stem-cell-activity
#15
Kelley S Yan, Olivier Gevaert, Grace X Y Zheng, Benedict Anchang, Christopher S Probert, Kathryn A Larkin, Paige S Davies, Zhuan-Fen Cheng, John S Kaddis, Arnold Han, Kelly Roelf, Ruben I Calderon, Esther Cynn, Xiaoyi Hu, Komal Mandleywala, Julie Wilhelmy, Sue M Grimes, David C Corney, Stéphane C Boutet, Jessica M Terry, Phillip Belgrader, Solongo B Ziraldo, Tarjei S Mikkelsen, Fengchao Wang, Richard J von Furstenberg, Nicholas R Smith, Parthasarathy Chandrakesan, Randal May, Mary Ann S Chrissy, Rajan Jain, Christine A Cartwright, Joyce C Niland, Young-Kwon Hong, Jill Carrington, David T Breault, Jonathan Epstein, Courtney W Houchen, John P Lynch, Martin G Martin, Sylvia K Plevritis, Christina Curtis, Hanlee P Ji, Linheng Li, Susan J Henning, Melissa H Wong, Calvin J Kuo
Several cell populations have been reported to possess intestinal stem cell (ISC) activity during homeostasis and injury-induced regeneration. Here, we explored inter-relationships between putative mouse ISC populations by comparative RNA-sequencing (RNA-seq). The transcriptomes of multiple cycling ISC populations closely resembled Lgr5(+) ISCs, the most well-defined ISC pool, but Bmi1-GFP(+) cells were distinct and enriched for enteroendocrine (EE) markers, including Prox1. Prox1-GFP(+) cells exhibited sustained clonogenic growth in vitro, and lineage-tracing of Prox1(+) cells revealed long-lived clones during homeostasis and after radiation-induced injury in vivo...
July 6, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28679385/q-a-using-patch-seq-to-profile-single-cells
#16
Cathryn R Cadwell, Rickard Sandberg, Xiaolong Jiang, Andreas S Tolias
Individual neurons vary widely in terms of their gene expression, morphology, and electrophysiological properties. While many techniques exist to study single-cell variability along one or two of these dimensions, very few techniques can assess all three features for a single cell. We recently developed Patch-seq, which combines whole-cell patch clamp recording with single-cell RNA-sequencing and immunohistochemistry to comprehensively profile the transcriptomic, morphologic, and physiologic features of individual neurons...
July 6, 2017: BMC Biology
https://www.readbyqxmd.com/read/28674382/the-destiny-of-the-resistance-susceptibility-against-gcrv-is-controlled-by-epigenetic-mechanisms-in-cik-cells
#17
Xueying Shang, Chunrong Yang, Quanyuan Wan, Youliang Rao, Jianguo Su
Hemorrhagic disease caused by grass carp reovirus (GCRV) has severely threatened the grass carp (Ctenopharyngodon idella) cultivation industry. It is noteworthy that the resistance against GCRV infection was reported to be inheritable, and identified at both individual and cellular levels. Therefore, this work was inspired and dedicated to unravel the molecular mechanisms of fate decision post GCRV infection in related immune cells. Foremost, the resistant and susceptible CIK (C. idella kidney) monoclonal cells were established by single cell sorting, subculturing and infection screening successively...
July 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28673928/transcriptional-profiling-of-biofilm-regulators-identified-by-an-overexpression-screen-in-saccharomyces-cerevisiae
#18
Gareth A Cromie, Zhihao Tan, Michelle Hays, Amy Sirr, Eric W Jeffery, Aimée M Dudley
Biofilm formation by microorganisms is a major cause of recurring infections and removal of biofilms has proven to be extremely difficult given their inherent drug resistance . Understanding the biological processes that underlie biofilm formation is thus extremely important and could lead to the development of more effective drug therapies, resulting in better infection outcomes. Using the yeast Saccharomyces cerevisiae as a biofilm model, overexpression screens identified DIG1, SFL1, HEK2, TOS8, SAN1, and ROF1/YHR177W as regulators of biofilm formation...
August 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28672168/regulating-cellular-trace-metal-economy-in-algae
#19
REVIEW
Crysten E Blaby-Haas, Sabeeha S Merchant
As indispensable protein cofactors, Fe, Mn, Cu and Zn are at the center of multifaceted acclimation mechanisms that have evolved to ensure extracellular supply meets intracellular demand. Starting with selective transport at the plasma membrane and ending in protein metalation, metal homeostasis in algae involves regulated trafficking of metal ions across membranes, intracellular compartmentalization by proteins and organelles, and metal-sparing/recycling mechanisms to optimize metal-use efficiency. Overlaid on these processes are additional circuits that respond to the metabolic state as well as to the prior metal status of the cell...
June 30, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28666115/ifn%C3%AE-dependent-tissue-immune-homeostasis-is-co-opted-in-the-tumor-microenvironment
#20
Christopher J Nirschl, Mayte Suárez-Fariñas, Benjamin Izar, Sanjay Prakadan, Ruth Dannenfelser, Itay Tirosh, Yong Liu, Qian Zhu, K Sanjana P Devi, Shaina L Carroll, David Chau, Melika Rezaee, Tae-Gyun Kim, Ruiqi Huang, Judilyn Fuentes-Duculan, George X Song-Zhao, Nicholas Gulati, Michelle A Lowes, Sandra L King, Francisco J Quintana, Young-Suk Lee, James G Krueger, Kavita Y Sarin, Charles H Yoon, Levi Garraway, Aviv Regev, Alex K Shalek, Olga Troyanskaya, Niroshana Anandasabapathy
Homeostatic programs balance immune protection and self-tolerance. Such mechanisms likely impact autoimmunity and tumor formation, respectively. How homeostasis is maintained and impacts tumor surveillance is unknown. Here, we find that different immune mononuclear phagocytes share a conserved steady-state program during differentiation and entry into healthy tissue. IFNγ is necessary and sufficient to induce this program, revealing a key instructive role. Remarkably, homeostatic and IFNγ-dependent programs enrich across primary human tumors, including melanoma, and stratify survival...
June 29, 2017: Cell
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