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single cell RNA sequencing

Burak Tepe, Matthew C Hill, Brandon T Pekarek, Patrick J Hunt, Thomas J Martin, James F Martin, Benjamin R Arenkiel
Cellular heterogeneity within the mammalian brain poses a challenge toward understanding its complex functions. Within the olfactory bulb, odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality are influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity and better understand adult-born neuron development, we utilized single-cell RNA sequencing and computational modeling to reveal diverse and transcriptionally distinct neuronal and nonneuronal cell types...
December 4, 2018: Cell Reports
Ying Yao, Asima Zia, Łukasz Wyrożemski, Ida Lindeman, Geir Kjetil Sandve, Shuo-Wang Qiao
By offering high sequencing speed and ultra-high-throughput at a low price, Illumina next-generation sequencing platforms have been widely adopted in recent years. However, an experiment with multiplexed library could be at risk of molecular recombination, known as "index switching", which causes a proportion of the reads to be assigned to an incorrect sample. It is reported that a new advance, exclusion amplification (ExAmp) in conjunction with the patterned flow cell technology introduced on HiSeq 3000/HiSeq 4000/HiSeq X sequencing systems, potentially suffers from a higher rate of index switching than conventional bridge amplification...
2018: PloS One
Michael Bartoschek, Nikolay Oskolkov, Matteo Bocci, John Lövrot, Christer Larsson, Mikael Sommarin, Chris D Madsen, David Lindgren, Gyula Pekar, Göran Karlsson, Markus Ringnér, Jonas Bergh, Åsa Björklund, Kristian Pietras
Cancer-associated fibroblasts (CAFs) are a major constituent of the tumor microenvironment, although their origin and roles in shaping disease initiation, progression and treatment response remain unclear due to significant heterogeneity. Here, following a negative selection strategy combined with single-cell RNA sequencing of 768 transcriptomes of mesenchymal cells from a genetically engineered mouse model of breast cancer, we define three distinct subpopulations of CAFs. Validation at the transcriptional and protein level in several experimental models of cancer and human tumors reveal spatial separation of the CAF subclasses attributable to different origins, including the peri-vascular niche, the mammary fat pad and the transformed epithelium...
December 4, 2018: Nature Communications
Nicholas D Leigh, Garrett S Dunlap, Kimberly Johnson, Rachelle Mariano, Rachel Oshiro, Alan Y Wong, Donald M Bryant, Bess M Miller, Alex Ratner, Andy Chen, William W Ye, Brian J Haas, Jessica L Whited
Regeneration of complex multi-tissue structures, such as limbs, requires the coordinated effort of multiple cell types. In axolotl limb regeneration, the wound epidermis and blastema have been extensively studied via histology, grafting, and bulk-tissue RNA-sequencing. However, defining the contributions of these tissues is hindered due to limited information regarding the molecular identity of the cell types in regenerating limbs. Here we report unbiased single-cell RNA-sequencing on over 25,000 cells from axolotl limbs and identify a plethora of cellular diversity within epidermal, mesenchymal, and hematopoietic lineages in homeostatic and regenerating limbs...
December 4, 2018: Nature Communications
Jie Xiong, Wei-Li Zhao
Natural-killer/T cell lymphoma (NKTCL) represents the most common subtype of extranodal lymphoma with aggressive clinical behavior. Prevalent in Asians and South Americans, the pathogenesis of NKTCL remains to be fully elucidated. Using system biology techniques including genomics, transcriptomics, epigenomics, and metabolomics, novel biomarkers and therapeutic targets have been revealed in NKTCL. Whole-exome sequencing studies identify recurrent somatic gene mutations, involving RNA helicases, tumor suppressors, JAK-STAT pathway molecules, and epigenetic modifiers...
December 4, 2018: Journal of Hematology & Oncology
Li Li, Yulun Huang, Yuge Gao, Tengfei Shi, Yunyun Xu, Huini Li, Marko Hyytiäinen, Jorma Keski-Oja, Qiuying Jiang, Yizhou Hu, Zhimin Du
BACKGROUND: Glioblastoma multiforme (GBM) is the most malignant central nervous system tumor. Alkylating agent, temozolomide (TMZ), is currently the first-line chemotherapeutic agent for GBM. However, the sensitivity of GBM cells to TMZ is affected by many factors. And, several clinic trials, including co-administration of TMZ with other drugs, have failed in successful treatment of GBM. We have previously reported that Netrin-4 (NTN4), a laminin-like axon guidance protein, plays a protective role in GBM cell senescence upon TMZ-triggered DNA damage...
December 4, 2018: BMC Cancer
Rimsha Farooq, Khadim Hussain, Shahid Nazir, Muhammad Rizwan Javed, Nazish Masood
CRISPR/Cas9 is a technology evolved from modified type II immune system of bacteria and archaea. Exploitation of this bacterial immune system in all eukaryotes including plants may lead to site-specific targeted genome engineering. Genome engineering is objectively utilized to express/silence a trait harbouring gene in the plant genome. In this review, different genetic engineering techniques including classical breeding, RNAi and genetic transformation and synthetic sequence-specific nucleases (zinc finger nucleases; ZFNs and transcription activator-like effector nuclease; TALENs) techniques have been described and compared with advanced genome editing technique CRISPR/Cas9, on the basis of their merits and drawbacks...
November 30, 2018: Cellular and Molecular Biology
Haojia Wu, Yuhei Kirita, Erinn L Donnelly, Benjamin D Humphreys
BACKGROUND: A challenge for single-cell genomic studies in kidney and other solid tissues is generating a high-quality single-cell suspension that contains rare or difficult-to-dissociate cell types and is free of both RNA degradation and artifactual transcriptional stress responses. METHODS: We compared single-cell RNA sequencing (scRNA-seq) using the DropSeq platform with single-nucleus RNA sequencing (snRNA-seq) using sNuc-DropSeq, DroNc-seq, and 10X Chromium platforms on adult mouse kidney...
December 3, 2018: Journal of the American Society of Nephrology: JASN
Marco Garieri, Georgios Stamoulis, Xavier Blanc, Emilie Falconnet, Pascale Ribaux, Christelle Borel, Federico Santoni, Stylianos E Antonarakis
X-chromosome inactivation (XCI) provides a dosage compensation mechanism where, in each female cell, one of the two X chromosomes is randomly silenced. However, some genes on the inactive X chromosome and outside the pseudoautosomal regions escape from XCI and are expressed from both alleles (escapees). We investigated XCI at single-cell resolution combining deep single-cell RNA sequencing with whole-genome sequencing to examine allelic-specific expression in 935 primary fibroblast and 48 lymphoblastoid single cells from five female individuals...
December 3, 2018: Proceedings of the National Academy of Sciences of the United States of America
Ashley Untereiner, Shaaban Abdo, Alpana Bhattacharjee, Himaben Gohil, Farzaneh Pourasgari, Neke Ibeh, Mi Lai, Battsetseg Batchuluun, Anthony Wong, Nicholas Khuu, Ying Liu, Dana Al Rijjal, Neil Winegarden, Carl Virtanen, Beverley A Orser, Over Cabrera, Gabor Varga, Jonathan Rocheleau, Feihan F Dai, Michael B Wheeler
γ-Aminobutyric acid (GABA) administration has been shown to increase β-cell mass, leading to a reversal of type 1 diabetes in mice. Whether GABA has any effect on β cells of healthy and prediabetic/glucose-intolerant obese mice remains unknown. In the present study, we show that oral GABA administration ( ad libitum) to mice indeed increased pancreatic β-cell mass, which led to a modest enhancement in insulin secretion and glucose tolerance. However, GABA treatment did not further increase insulin-positive islet area in high fat diet-fed mice and was unable to prevent or reverse glucose intolerance and insulin resistance...
December 3, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
Boris Winterhoff, Shobhana Talukdar, Zenas Chang, Jinhua Wang, Timothy K Starr
PURPOSE OF REVIEW: This article discusses the advances, applications and challenges of using single-cell RNA sequencing data in guiding treatment decisions for ovarian cancer. RECENT FINDINGS: Genetic heterogeneity is a hallmark of ovarian cancer biology and underlies treatment resistance. Defining the different cell types present within a single ovarian cancer is difficult, but could ultimately lead to improvements in diagnosis and treatment. Next-generation sequencing technologies have rapidly increased our understanding of the molecular landscape of epithelial ovarian cancers, but the majority of these studies are conducted on bulk samples, resulting in data that represents an 'average' of all cells present...
November 30, 2018: Current Opinion in Obstetrics & Gynecology
Agnieska Brazovskaja, Barbara Treutlein, J Gray Camp
Three-dimensional (3D) tissues grown in culture from human stem cells offer the incredible opportunity to analyze and manipulate human development, and to generate patient-specific models of disease. Methods to sequence DNA and RNA in single cells are being used to analyze these so-called 'organoid' systems in high-resolution. Single-cell transcriptomics has been used to quantitate the similarity of organoid cells to primary tissue counterparts in the brain, intestine, liver, and kidney, as well as identify cell-specific responses to environmental variables and disease conditions...
November 29, 2018: Current Opinion in Biotechnology
Matthew J Carr, Jeremy S Toma, Adam P W Johnston, Patrick E Steadman, Scott A Yuzwa, Neemat Mahmud, Paul W Frankland, David R Kaplan, Freda D Miller
Peripheral innervation plays an important role in regulating tissue repair and regeneration. Here we provide evidence that injured peripheral nerves provide a reservoir of mesenchymal precursor cells that can directly contribute to murine digit tip regeneration and skin repair. In particular, using single-cell RNA sequencing and lineage tracing, we identify transcriptionally distinct mesenchymal cell populations within the control and injured adult nerve, including neural crest-derived cells in the endoneurium with characteristics of mesenchymal precursor cells...
November 19, 2018: Cell Stem Cell
Simona Ranallo, Alessandro Porchetta, Francesco Ricci
DNA nanotechnology employs synthetic nucleic acid strands to design and engineer nanoscale structural and functional systems of increasing complexity that may find applications in sensing,1-7 computing,8-10 molecular transport,11-13 information processing14 and catalysis.15,16 Several features make synthetic DNA a particularly appealing and advantageous biomaterial for all the above applications but more specifically for sensing. First, synthetic DNA sequences, especially if of limited length (<100 nucleotides), have highly predictable interactions and thermodynamics...
December 1, 2018: Analytical Chemistry
Weng Chuan Peng, Catriona Y Logan, Matt Fish, Teni Anbarchian, Francis Aguisanda, Adrián Álvarez-Varela, Peng Wu, Yinhua Jin, Junjie Zhu, Bin Li, Markus Grompe, Bruce Wang, Roel Nusse
In the healthy adult liver, most hepatocytes proliferate minimally. However, upon physical or chemical injury to the liver, hepatocytes proliferate extensively in vivo under the direction of multiple extracellular cues, including Wnt and pro-inflammatory signals. Currently, liver organoids can be generated readily in vitro from bile-duct epithelial cells, but not hepatocytes. Here, we show that TNFα, an injury-induced inflammatory cytokine, promotes the expansion of hepatocytes in 3D culture and enables serial passaging and long-term culture for more than 6 months...
November 29, 2018: Cell
Kent A Riemondy, Monica Ransom, Christopher Alderman, Austin E Gillen, Rui Fu, Jessica Finlay-Schultz, Gregory D Kirkpatrick, Jorge Di Paola, Peter Kabos, Carol A Sartorius, Jay R Hesselberth
Single-cell RNA sequencing (scRNA-seq) methods generate sparse gene expression profiles for thousands of single cells in a single experiment. The information in these profiles is sufficient to classify cell types by distinct expression patterns but the high complexity of scRNA-seq libraries often prevents full characterization of transcriptomes from individual cells. To extract more focused gene expression information from scRNA-seq libraries, we developed a strategy to physically recover the DNA molecules comprising transcriptome subsets, enabling deeper interrogation of the isolated molecules by another round of DNA sequencing...
November 29, 2018: Nucleic Acids Research
Andrei Rozanski, HongKee Moon, Holger Brandl, José M Martín-Durán, Markus A Grohme, Katja Hüttner, Kerstin Bartscherer, Ian Henry, Jochen C Rink
Flatworms (Platyhelminthes) are a basally branching phylum that harbours a wealth of fascinating biology, including planarians with their astonishing regenerative abilities and the parasitic tape worms and blood flukes that exert a massive impact on human health. PlanMine ( has the mission objective of providing both a mineable sequence repository for planarians and also a resource for the comparative analysis of flatworm biology. While the original PlanMine release was entirely based on transcriptomes, the current release transitions to a more genomic perspective...
November 28, 2018: Nucleic Acids Research
Gang Xin, Ryan Zander, David M Schauder, Yao Chen, Jason S Weinstein, William R Drobyski, Vera Tarakanova, Joseph Craft, Weiguo Cui
During chronic viral infection, the inflammatory function of CD4 T-cells becomes gradually attenuated. Concurrently, Th1 cells progressively acquire the capacity to secrete the cytokine IL-10, a potent suppressor of antiviral T cell responses. To determine the transcriptional changes that underlie this adaption process, we applied a single-cell RNA-sequencing approach and assessed the heterogeneity of IL-10-expressing CD4 T-cells during chronic infection. Here we show an IL-10-producing population with a robust Tfh-signature...
November 28, 2018: Nature Communications
(no author information available yet)
Through single-cell RNA sequencing, two groups of researchers offer new insight into the respective roles of CD8+ T cells and tumor cells in driving immunotherapy resistance. Their studies pinpoint two distinct T-cell states, as well as a T-cell exclusion program promoted by tumor cells, that may influence patients' likelihood of response to immune checkpoint blockade.
November 28, 2018: Cancer Discovery
Vera Zywitza, Aristotelis Misios, Lena Bunatyan, Thomas E Willnow, Nikolaus Rajewsky
Neural stem cells (NSCs) contribute to plasticity and repair of the adult brain. Niches harboring NSCs regulate stem cell self-renewal and differentiation. We used comprehensive and untargeted single-cell RNA profiling to generate a molecular cell atlas of the largest germinal region of the adult mouse brain, the subventricular zone (SVZ). We characterized >20 neural and non-neural cell types and gained insights into the dynamics of neurogenesis by predicting future cell states based on computational analysis of RNA kinetics...
November 27, 2018: Cell Reports
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