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single cell rna-seq

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https://www.readbyqxmd.com/read/29784918/early-lineage-segregation-of-multipotent-embryonic-mammary-gland-progenitors
#1
Aline Wuidart, Alejandro Sifrim, Marco Fioramonti, Shigeru Matsumura, Audrey Brisebarre, Daniel Brown, Alessia Centonze, Anne Dannau, Christine Dubois, Alexandra Van Keymeulen, Thierry Voet, Cédric Blanpain
The mammary gland is composed of basal cells and luminal cells. It is generally believed that the mammary gland arises from embryonic multipotent progenitors, but it remains unclear when lineage restriction occurs and what mechanisms are responsible for the switch from multipotency to unipotency during its morphogenesis. Here, we perform multicolour lineage tracing and assess the fate of single progenitors, and demonstrate the existence of a developmental switch from multipotency to unipotency during embryonic mammary gland development...
May 21, 2018: Nature Cell Biology
https://www.readbyqxmd.com/read/29784674/clinically-relevant-cytotoxic-immune-cell-signatures-and-clonal-expansion-of-t-cell-receptors-in-high-risk-mycn-not-amplified-human-neuroblastoma
#2
Jun S Wei, Igor B Kuznetsov, Shile Zhang, Young K Song, Shahab Asgharzadeh, Sivasish Sindiri, Xinyu Wen, Rajesh Patidar, Sushma Nagaraj, Ashley Walton, Jaime M Guidry Auvil, Daniela S Gerhard, Aysen Yuksel, Daniel R Catchpoole, Stephen M Hewitt, Paul M Sondel, Robert C Seeger, John M Maris, Javed Khan
PURPOSE: High-risk neuroblastoma is an aggressive disease. DNA sequencing studies have revealed a paucity of actionable genomic alterations and a low mutation burden, posing challenges to develop effective novel therapies. We used RNA sequencing (RNA-seq) to investigate the biology of this disease including a focus on tumor-infiltrating lymphocytes (TILs). EXPERIMENTAL DESIGN: We performed deep RNA-seq on pre-treatment diagnostic tumors from 129 high-risk and 21 low- or intermediate-risk patients with neuroblastomas...
May 21, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29777657/mcv-mir-m1-targets-the-host-cell-immune-response-resulting-in-the-attenuation-of-neutrophil-chemotaxis
#3
P Akhbari, D Tobin, K Poterlowicz, W Roberts, J R Boyne
Virus-encoded miRNAs are emerging as key regulators of persistent infection and host-cell immune evasion. Merkel cell polyomavirus (MCPyV), the predominant aetiological agent of Merkel cell carcinoma (MCC), encodes a single miRNA, MCV-miR-M1, which targets the oncogenic MCPyV large T antigen (LT). MCV-miR-M1 has previously been shown to play an important role in establishment of long-term infection, however, the underlying mechanism is not fully understood. A key unanswered question is whether, in addition to auto-regulating LT, MCV-miR-M1 also targets cellular transcripts to orchestrate an environment conducive for persistent infection...
May 16, 2018: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29771290/single-cell-clustering-based-on-cell-pair-differentiability-correlation-and-variance-analysis
#4
Hao Jiang, Lydia Sohn, Haiyan Huang, Luonan Chen
Motivation: The rapid advancement of single cell technologies has shed new light on the complex mechanisms of cellular heterogeneity. Identification of intercellular transcriptomic heterogeneity is one of the most critical tasks in single-cell RNA-sequencing studies. Results: We propose a new cell similarity measure based on cell-pair differentiability correlation, which is derived from gene differential pattern among all cell pairs. Through plugging into the framework of hierarchical clustering with this new measure, we further develop a variance analysis based clustering algorithm 'Corr' that can determine cluster number automatically and identify cell types accurately...
May 16, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29767365/current-and-future-methods-for-mrna-analysis-a-drive-toward-single-molecule-sequencing
#5
Anthony Bayega, Somayyeh Fahiminiya, Spyros Oikonomopoulos, Jiannis Ragoussis
The transcriptome encompasses a range of species including messenger RNA, and other noncoding RNA such as rRNA, tRNA, and short and long noncoding RNAs. Due to the huge role played by mRNA in development and disease, several methods have been developed to sequence and characterize mRNA, with RNA sequencing (RNA-Seq) emerging as the current method of choice particularly for large high-throughput studies. Short-read RNA-Seq which involves sequencing of short cDNA fragments and computationally assembling them to reconstruct the transcriptome, or aligning them to a reference is the most widely used approach...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29765956/transcriptomic-profiling-of-zebrafish-hair-cells-using-ribotag
#6
Maggie S Matern, Alisha Beirl, Yoko Ogawa, Yang Song, Nikhil Paladugu, Katie S Kindt, Ronna Hertzano
The zebrafish inner ear organs and lateral line neuromasts are comprised of a variety of cell types, including mechanosensitive hair cells. Zebrafish hair cells are evolutionarily homologous to mammalian hair cells, and have been particularly useful for studying normal hair cell development and function. However, the relative scarcity of hair cells within these complex organs, as well as the difficulty of fine dissection at early developmental time points, makes hair cell-specific gene expression profiling technically challenging...
2018: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29764370/-tuberculosis-in-advanced-hiv-infection-is-associated-with-increased-expression-of-ifn%C3%AE-and-its-downstream-targets
#7
Sheetal Verma, Peicheng Du, Damalie Nakanjako, Sabine Hermans, Jessica Briggs, Lydia Nakiyingi, Jerrold J Ellner, Yukari C Manabe, Padmini Salgame
BACKGROUND: Tuberculosis (TB) is the major cause of death in Human Immunodeficiency Virus (HIV)-infected individuals. However, diagnosis of TB in HIV remains challenging particularly when HIV infection is advanced. Several gene signatures and serum protein biomarkers have been identified that distinguish active TB from latent infection. Our study was designed to assess if gene expression signatures and cytokine levels would distinguish active TB in advanced HIV. METHODS: We conducted a case-control study of whole blood RNA-Seq and plasma cytokine/chemokine analysis in HIV-infected with CD4+ T cell count of ≤ 100 cells/μl, with and without active TB...
May 15, 2018: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29762913/an-online-compendium-of-cho-rna-seq-data-allows-identification-of-cho-cell-line-specific-transcriptomic-signatures
#8
Ankita Singh, Helene F Kildegaard, Mikael R Andersen
Chinese hamster ovary (CHO) cell lines can fold, assemble and modify proteins post-translationally to produce human-like proteins; as a consequence, it is the single most common expression systems for industrial production of recombinant therapeutic proteins. A thorough knowledge of cultivation conditions of different CHO cell lines has been developed over the last decade, but comprehending gene or pathway-specific distinctions between CHO cell lines at transcriptome level remains a challenge. To address these challenges, we compiled a compendium of 23 RNA-Seq studies from public and in-house data on CHO cell lines, i...
May 15, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29761220/transcriptomic-analysis-of-the-harvested-endothelial-cells-in-a-swine-model-of-mechanical-thrombectomy
#9
Nasren Jaff, Rikard Grankvist, Lars Muhl, Arvin Chireh, Mikael Sandell, Stefan Jonsson, Fabian Arnberg, Ulf Eriksson, Staffan Holmin
PURPOSE: In mechanical thrombectomy (MT) for ischemic stroke, endothelial cells (ECs) from intracranial blood vessels adhere to the stent retriever device and can be harvested. However, understanding the molecular biology and the role of the endothelium in different pathological conditions remains insufficient. The purpose of the study was to characterize and analyze the molecular aspect of harvested ECs using cell culture and transcriptomic techniques in an MT swine model relevant to clinical ischemic stroke...
May 14, 2018: Neuroradiology
https://www.readbyqxmd.com/read/29761043/differential-expression-patterns-of-housekeeping-genes-increase-diagnostic-and-prognostic-value-in-lung-cancer
#10
Yu-Chun Chang, Yan Ding, Lingsheng Dong, Lang-Jing Zhu, Roderick V Jensen, Li-Li Hsiao
Background: Using DNA microarrays, we previously identified 451 genes expressed in 19 different human tissues. Although ubiquitously expressed, the variable expression patterns of these "housekeeping genes" (HKGs) could separate one normal human tissue type from another. Current focus on identifying "specific disease markers" is problematic as single gene expression in a given sample represents the specific cellular states of the sample at the time of collection. In this study, we examine the diagnostic and prognostic potential of the variable expressions of HKGs in lung cancers...
2018: PeerJ
https://www.readbyqxmd.com/read/29760697/hookworm-secreted-extracellular-vesicles-interact-with-host-cells-and-prevent-inducible-colitis-in-mice
#11
Ramon M Eichenberger, Stephanie Ryan, Linda Jones, Geraldine Buitrago, Ramona Polster, Marcela Montes de Oca, Jennifer Zuvelek, Paul R Giacomin, Lindsay A Dent, Christian R Engwerda, Matthew A Field, Javier Sotillo, Alex Loukas
Gastrointestinal (GI) parasites, hookworms in particular, have evolved to cause minimal harm to their hosts, allowing them to establish chronic infections. This is mediated by creating an immunoregulatory environment. Indeed, hookworms are such potent suppressors of inflammation that they have been used in clinical trials to treat inflammatory bowel diseases (IBD) and celiac disease. Since the recent description of helminths (worms) secreting extracellular vesicles (EVs), exosome-like EVs from different helminths have been characterized and their salient roles in parasite-host interactions have been highlighted...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29758359/probing-flecainide-block-of-i-na-using-human-pluripotent-stem-cell-derived-ventricular-cardiomyocytes-adapted-to-automated-patch-clamping-and-2d-monolayers
#12
Lin Geng, Chi-Wing Kong, Andy O T Won, Angie Man-Yee Shum, Maggie Z Y Chow, Hui Che, Chenzi Zhang, Ka-Long Yau, Camie W Chan, Wendy Keung, Ronald A Li
Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) are emerging tools for applications such as drug discovery and screening for pro-arrhythmogenicity and cardiotoxicity as leading causes for drug attrition. Understanding the electrophysiology (EP) of hPSC-CMs is essential but conventional manual patch-clamping is highly laborious and low-throughput. Here we adapted hPSC-CMs derived from two human embryonic stem cell (hESC) lines, HES2 and H7, for a 16-channel automated planar-recording approach for single-cell EP characterization...
May 11, 2018: Toxicology Letters
https://www.readbyqxmd.com/read/29752298/single-cell-rna-seq-of-human-induced-pluripotent-stem-cells-reveals-cellular-heterogeneity-and-cell-state-transitions-between-subpopulations
#13
Quan Nguyen, Samuel Lukowski, Han Chiu, Anne Senabouth, Timothy Bruxner, Angelika Christ, Nathan Palpant, Joseph Powell
Heterogeneity of cell states represented in pluripotent cultures have not been described at the transcriptional level. Since gene expression is highly heterogeneous between cells, single-cell RNA sequencing can be used to identify how individual pluripotent cells function. Here, we present results from the analysis of single-cell RNA sequencing data from 18,787 individual WTC CRISPRi human induced pluripotent stem cells. We developed an unsupervised clustering method, and through this identified four subpopulations distinguishable on the basis of their pluripotent state including: a core pluripotent population (48...
May 11, 2018: Genome Research
https://www.readbyqxmd.com/read/29752286/genetic-and-cellular-sensitivity-of-caenorhabditis-elegans-to-the-chemotherapeutic-agent-cisplatin
#14
Francisco Javier García-Rodríguez, Carmen Martínez-Fernández, David Brena, Dmytro Kukhtar, Xènia Serrat, Ernest Nadal, Mike Boxem, Sebastian Honnen, Antonio Miranda-Vizuete, Alberto Villanueva, Julián Cerón
Cisplatin and derivatives are commonly used as chemotherapeutic agents. Although the cytotoxic action of cisplatin on cancer cells is very efficient, clinical oncologists need to deal with two major difficulties: (i) the onset of resistance to the drug, and (ii) the cytotoxic effect in patients. Here we use Caenorhabditis elegans to investigate factors influencing the response to cisplatin in multicellular organisms. In this hermaphroditic model organism, we observed that sperm failure is a major cause in cisplatin-induced infertility...
May 10, 2018: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/29739332/characterization-and-remediation-of-sample-index-swaps-by-non-redundant-dual-indexing-on-massively-parallel-sequencing-platforms
#15
Maura Costello, Mark Fleharty, Justin Abreu, Yossi Farjoun, Steven Ferriera, Laurie Holmes, Brian Granger, Lisa Green, Tom Howd, Tamara Mason, Gina Vicente, Michael Dasilva, Wendy Brodeur, Timothy DeSmet, Sheila Dodge, Niall J Lennon, Stacey Gabriel
BACKGROUND: Here we present an in-depth characterization of the mechanism of sequencer-induced sample contamination due to the phenomenon of index swapping that impacts Illumina sequencers employing patterned flow cells with Exclusion Amplification (ExAmp) chemistry (HiSeqX, HiSeq4000, and NovaSeq). We also present a remediation method that minimizes the impact of such swaps. RESULTS: Leveraging data collected over a two-year period, we demonstrate the widespread prevalence of index swapping in patterned flow cell data...
May 8, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29735606/allele-specific-control-of-replication-timing-and-genome-organization-during-development
#16
Juan Carlos Rivera-Mulia, Andrew Dimond, Daniel Vera, Claudia Trevilla-Garcia, Takayo Sasaki, Jared Zimmerman, Catherine Dupont, Joost Gribnau, Peter Fraser, David M Gilbert
DNA replication occurs in a defined temporal order known as the replication-timing (RT) program. RT is regulated during development in discrete chromosomal units, coordinated with transcriptional activity and 3D genome organization. Here, we derived distinct cell types from F1 hybrid musculus X castaneus mouse crosses and exploited the high single nucleotide polymorphism (SNP) density to characterize allelic differences in RT (Repli-seq), genome organization (Hi-C and promoter-capture Hi-C), gene expression (total nuclear RNA-seq) and chromatin accessibility (ATAC-seq)...
May 7, 2018: Genome Research
https://www.readbyqxmd.com/read/29733404/spar-small-rna-seq-portal-for-analysis-of-sequencing-experiments
#17
Pavel P Kuksa, Alexandre Amlie-Wolf, Živadin Katanic, Otto Valladares, Li-San Wang, Yuk Yee Leung
The introduction of new high-throughput small RNA sequencing protocols that generate large-scale genomics datasets along with increasing evidence of the significant regulatory roles of small non-coding RNAs (sncRNAs) have highlighted the urgent need for tools to analyze and interpret large amounts of small RNA sequencing data. However, it remains challenging to systematically and comprehensively discover and characterize sncRNA genes and specifically-processed sncRNA products from these datasets. To fill this gap, we present Small RNA-seq Portal for Analysis of sequencing expeRiments (SPAR), a user-friendly web server for interactive processing, analysis, annotation and visualization of small RNA sequencing data...
May 4, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29731977/constraint-based-modeling-of-metabolism-allows-finding-metabolic-cancer-hallmarks-and-identifying-personalized-therapeutic-windows
#18
Sergio Bordel
In order to choose optimal personalized anticancer treatments, transcriptomic data should be analyzed within the frame of biological networks. The best known human biological network (in terms of the interactions between its different components) is metabolism. Cancer cells have been known to have specific metabolic features for a long time and currently there is a growing interest in characterizing new cancer specific metabolic hallmarks. In this article it is presented a method to find personalized therapeutic windows using RNA-seq data and Genome Scale Metabolic Models...
April 13, 2018: Oncotarget
https://www.readbyqxmd.com/read/29727680/efficient-generation-of-ca3-neurons-from-human-pluripotent-stem-cells-enables-modeling-of-hippocampal-connectivity-in-vitro
#19
Anindita Sarkar, Arianna Mei, Apua C M Paquola, Shani Stern, Cedric Bardy, Jason R Klug, Stacy Kim, Neda Neshat, Hyung Joon Kim, Manching Ku, Maxim N Shokhirev, David H Adamowicz, Maria C Marchetto, Roberto Jappelli, Jennifer A Erwin, Krishnan Padmanabhan, Matthew Shtrahman, Xin Jin, Fred H Gage
Despite widespread interest in using human induced pluripotent stem cells (hiPSCs) in neurological disease modeling, a suitable model system to study human neuronal connectivity is lacking. Here, we report a comprehensive and efficient differentiation paradigm for hiPSCs that generate multiple CA3 pyramidal neuron subtypes as detected by single-cell RNA sequencing (RNA-seq). This differentiation paradigm exhibits characteristics of neuronal network maturation, and rabies virus tracing revealed synaptic connections between stem cell-derived dentate gyrus (DG) and CA3 neurons in vitro recapitulating the neuronal connectivity within the hippocampus...
May 3, 2018: Cell Stem Cell
https://www.readbyqxmd.com/read/29727663/single-cell-transcriptomics-and-fate-mapping-of-ependymal-cells-reveals-an-absence-of-neural-stem-cell-function
#20
Prajay T Shah, Jo A Stratton, Morgan Gail Stykel, Sepideh Abbasi, Sandeep Sharma, Kyle A Mayr, Kathrin Koblinger, Patrick J Whelan, Jeff Biernaskie
Ependymal cells are multi-ciliated cells that form the brain's ventricular epithelium and a niche for neural stem cells (NSCs) in the ventricular-subventricular zone (V-SVZ). In addition, ependymal cells are suggested to be latent NSCs with a capacity to acquire neurogenic function. This remains highly controversial due to a lack of prospective in vivo labeling techniques that can effectively distinguish ependymal cells from neighboring V-SVZ NSCs. We describe a transgenic system that allows for targeted labeling of ependymal cells within the V-SVZ...
May 3, 2018: Cell
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