title: Single cut products of Microprocessor on pri-miRNAs

city: Hong Kong

first: Duc

middle: Trung

address: Clear Water Bay

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

summary: The human Microprocessor complex cleaves primary microRNA (miRNA) transcripts (pri-miRNAs) to initiate miRNA synthesis. Microprocessor consists of DROSHA (an RNase III enzyme), and DGCR8. DROSHA has two conserved RNase III domains, which make double cuts on each of pri-miRNA strands. In this study, we show that Microprocessor has an unexpected single-cut activity, which creates a single cut on just one of the pri-miRNA strands using one of the two RNase III domains of DROSHA. This cleavage does not lead to the production of miRNA but instead it downregulates miRNA expression. We also demonstrate that certain RNA elements facilitate the single-cut activity of Microprocessor, and by manipulating these elements, we can regulate the ratio of single-cut to double-cut activities, thus controlling miRNA production both in vitro and in vivo.

overall_design: The 2 samples were generated from two experiments. 1)  The single cut products of pri-mir-92a-1 in in vitro cleavage assay of Microprocessor were confirmed by sequencing. 2) The single cut products of some pri-miRNAs, which contain a large asymmetric internal loop  in their lower stem in in vitro cleavage assay of Microprocessor were also confirmed by sequencing.

first: Tuan

first: Thuy

first: Trung

middle: D


title: Effect of cold atmospheric plasma (CAP) in MCF-7

status: Public on Jan 24 2020

city: Goyang-si

first: sung bin

last: park

state: Gyeonggi-do

address: 32, Dongguk-ro, Ilsandong-gu

department: Department of Life Science

country: South Korea

institute: Dongguk University-Seoul

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: DNMT1 is required for proximal-distal patterning of the lung endoderm and restraining alveolar type 2 cell fate

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

country: USA

institute: Perelman School of Medicine at the University of Pennsylvania

type: Expression profiling by high throughput sequencing

summary: Lung endoderm development occurs through a series of finely coordinated transcriptional processes that are regulated by epigenetic mechanisms. However, the role of DNA methylation in regulating lung endoderm development remains poorly understood. We demonstrate that DNA methyltransferase 1 (Dnmt1) is required for early branching morphogenesis of the lungs and for restraining epithelial fate specification. Loss of Dnmt1 leads to an early branching defect, a loss of proximal endodermal cell differentiation, and an expansion of the distal endoderm compartment. Dnmt1 deficiency also leads to precocious distal endodermal cell differentiation with premature expression of alveolar type 2 cell restricted genes. These data reveal an important requirement for Dnmt1 mediated DNA methylation in early lung development to promote proper branching morphogenesis, maintain proximal endodermal cell fate, and suppress premature activation of the distal epithelial fate.

overall_design: Lung were harvested from E12.5 wild-type littermate and ShhCre-Dnmt1KO mice.

first: Jarod

middle: A

last: Zepp

first: Micheal

middle: P

first: Edward

middle: E

last: Morrisey


title: Effect of cold atmospheric plasma (CAP) in MCF-7/TxR breast cancer cell [dataset 2]

summary: Paclitaxel is a widely used therapeutic chemical for breast cancer treatment, however, cancer recurrence remains obstacle for improved prognosis of cancer patients. In the current study, cold atmospheric plasma (CAP) was examined for its potential use to overcome the drug resistance, which mainly comprised of reactive oxygen and nitrogen species. After developing a paclitaxel (Tx)-resistant MCF-7 (MCF-7/TxR) breast cancer cell, CAP was applied to the cells and its effect on recovery of drug sensitivity was examined in cellular as well as molecular aspect. The MCF-7/TxR cells restored sensitivity against Tx up to 70% by CAP. Comparison of genome-wide expression profiles between the Tx resistance cell and its CAP-treated cell identified 86 genes that commonly appeared with significant change. Notably, 48 genes including DAGLA and CEACAM1, which are known to contribute to the acquisition of Tx resistance, showed opposite expression in the two cellular status. The protein expression level of selected genes, DAGLA and CEACAM1, was recovered to that of their parental cell by CAP. Furthermore, the dysregulation of DAGLA and CEACAM1 in MCF-7/TxR alleviated the drug sensitivity recovery effect of CAP. Taken together, CAP inhibited the growth of Tx-resistant MCF-7 cancer cells and recovered Tx sensitivity by resetting expression of multiple drug resistance–related genes. These findings may contribute to extending the application of CAP to the treatment of Tx-resistant cancer.

overall_design:
genom-wide expression profiling of MCF-7/TxR, MCF-7/TxR and CAP treated MCF-7/TxR cell. In result, cold atmospheric plasma different effect the CAP-treated MCF-7/TxR breast cancer cell.
Total RNA is obtained from MCF-7/TxR and CAP treated MCF-7/TxR

first: Sungbin

last: Park

first: Sunjung

last: Kim


title: Anatomical-spatial dissection of single-cell retinal transcriptomics paves the road for new horizons in complement immunology [Mm]

first: Dwight

middle: Edward

last: Stambolian

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

summary:
Purpose: We present the first comprehensive map of the murine retinal complement expression at a single-cell resolution from ~92,000 retinal cells, spanning 11 cell types.
Methods: Retinal mRNA profiles from 10-week-old wild-type (WT) Black 6 mouse eyes were generated by scRNA sequencing. The data was normalized using Seurat.
Results: Using an optimized data analysis workflow, we found novel patterns of complement expression in the retina
Conclusions: Our landmark atlas provides crucial mechanistic insights in complement immunology

overall_design:
Retinal cell mRNA data from 10-week old wild type (WT) Black 6 eyes were generated by scRNA sequencing.
~92,000 retinal cells, spanning 11 cell types (Amacrine Cells, Cone BCs, Cone Photoreceptors, Endothelial Cells, Horizontal Cells, Microglia, Muller Glia, Pericytes, Retinal Ganglion Cells, Rod BCs, Rod Photoreceptors).

first: Divyansh

last: Agarwal

first: Nicolas

last: Dana


title: NGS of 3'-termini of tRNA from E. coli

city: Hamburg

first: Andreas

last: Czech

address: Martin-Luther-King-Platz 6

country: Germany

institute: University of Hamburg

type: Non-coding RNA profiling by high throughput sequencing

summary:
To avoid biases from secondary structure and modifications we sequenced the hypomodified 3'-terminus of tRNA
This allowed assessment of relative levels of mature tRNA as well as low abundant fractions like non-intact tRNA or precuresor tRNA

overall_design: Purified tRNA from E. coli (wt, cca K.O., rnt K.O.) from exponential (exp) and stationary (stat) phase was analysed


title: Chromatin accessibility of human monocyte-derived dendritic cells in response to infection with HIV-1

city: Paris

first: Mickael

middle: Mathieu

last: Menager

address: 24 Boulevard du Montparnasse

country: France

institute: Institut Imagine

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcriptional programming of the innate immune response is pivotal for host protection. The transcriptional mechanisms that link pathogen sensing with innate activation remain poorly understood. During infection with HIV-1, human dendritic cells (DCs) can detect the virus through an innate sensing pathway leading to antiviral type I interferon and DC maturation. Here, we have developed an iterative experimental and computational approach to map the innate response circuitry during HIV-1 infection. By integrating genome-wide chromatin accessibility with expression kinetics, we have inferred a gene regulatory network that links 542 transcription factors (TFs) with 21,862 target genes. Through genetic perturbation and drug treatments we identify PRDM1 and RARA as essential regulators of the interferon response and DC maturation, respectively. This work provides a resource for interrogation of regulators of HIV replication and innate immunity, highlighting the complexity and cooperativity in the regulatory circuit controlling the DC response to HIV-1 infection.

overall_design: DCs were derived from the peripheral blood from three deidentified human donors and infected with a single cycle HIV-1 reporter virus (HIV-1-GFP) in the presence of Vpx.  Mock conditions were treated only with Vpx.  Cells were sorted by flow cytometry at the indicated times and according to the indicated conditions (GFP +/- or CD86 high/low) and immediately processed for an assay of transposase-accessible chromatin (ATAC-seq).

middle: M

first: Jarrod

middle: S

last: Johnson

first: Nicholas

last: De Veaux

first: Alexander

middle: W

last: Rives

first: Lynn

last: Amon

last: Manel

first: Alan

last: Aderem

first: Dan

middle: R

last: Littman

first: Richard

last: Bonneau


title: PLIN2 knockdown alters the genome-wide gene transcription profile of leiomyoma cells

city: Chicago

first: Ping

last: Yin

state: IL

address: 303 East Superior Street, Lurie 10-107

institute: Northwestern University

summary:
Purpose: To investigate the function of PLIN2 in human uterine leiomyoma tumorigenesis, we generated genome-wide transcription profile of leiomyoma cells after PLIN2 knockdown.
Methods:  Primary leiomyoma cells were isolated from fresh uterine leiomyoma tissues and transfected with PLIN2 small interfering RNA (siRNA; 100 nM, #4392422) or non-targeting siRNA (100 nM, #4390844; Ambion, Foster City, CA) for 72 hours. Total RNA was isolated using the RNeasy Mini kit and RNA-seq library was completed per the manufacturer’s instructions using the KAPA Stranded RNA-seq Kit with RiboErase (#KK8483; KAPA Biosystems, Wilmington, MA).  cDNA libraries were sequenced as single-end, 75 base-length reads on an Illumina NextSeq 500 instrument (Illumina, San Diego, CA) with an average read count of 27 million reads per sample. The quality of DNA reads, in fastq format, was evaluated using FastQC. Adapters were trimmed, and reads of poor quality or aligning to rRNA sequences were filtered. The cleaned reads were aligned to the Homo sapiens genome (hg19) using STAR. Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for hg19 obtained from University of California Santa Cruz (http://genome.ucsc.edu).
Results: A total of 3877 genes were found to be differentially expressed, with 2557 genes found to be upregulated and 1320 genes found to be downregulated by PLIN2 knockdown. Gene Ontology analysis (DAVID, https://david.ncifcrf.gov) identified cellular component organization/biogenesis (P=1.4E-27) and metabolic processes (P=1.6E-10) as the top two biological processes of genes upregulated by PLIN2 depletion. Kyoto Encyclopedia of Genes and Genomes (KEGG; DAVID) pathway analysis identified enrichment of genes involved in the cell cycle, pyruvate metabolism, fatty acid metabolism and degradation, purine and pyrimidine metabolism, apoptosis, and extracellular matrix component organization after PLIN2 depletion.
Conclusions: These findings provide support for a role of PLIN2 depletion in activating metabolic activity within leiomyoma cells.

overall_design: Genome-wide transcription profiling of primary human uterine leiomayoma cells with or without PLIN2 depletion using RNA-Seq

first: Ijeoma

last: Okeigwe

first: Serdar

last: Bulun

first: Shimeng

last: Liu

first: Alfred

last: Rademaker

first: John

last: Coon

first: Stacy

last: Kujawa

first: Jared

last: Robins


title: HCC prediction after clearance of HCV in chronic hepatitis C I

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

country: Japan

institute: Toray Industries, Inc.

summary:
We attempted to development prediction methods for hepatocellular carcinoma (HCC) in chronic hepatitis C patients who have been successfully treated by anti-viral therapy.
2565 miRNAs in 43 liver tissues specimens were analyzed.

overall_design: Fourty three patients were enrolled and 36 patients had not developed HCC and 7 had developed HCC

first: Y

last: Murakami


title: Alanyl-glutamine in peritoneal dialysis fluids - a randomized controlled phase I/II trial

city: Wien

first: Klaus

last: Kratochwill

address: Lazarettgasse 14

country: Austria

institute: Medical University of Vienna

summary:
In this open-label randomized controlled phase I/II trial, 20 stable peritoneal dialysis patients underwent two 4 h dwells with acidic glucose-based PDF, with and without 8 mM alanyl-glutamine (AlaGln) in a cross-over design.
Unsupervised hierarchical clustering of transcriptomics data suggested specific effects of AlaGln in patients who had previously suffered from peritonitis.

overall_design: Expression profiles could be generated from 3 patients' RNA under both treatment conditions in the study.

first: Michael

last: Böhm

first: Rebecca

last: Herzog

first: Katharina

last: Gruber

first: Anton

last: Lichtenauer

first: Lilian

last: Kuster

first: Andreas

last: Gleiss

first: Martin

last: Bilban

first: Christoph

last: Aufricht

last: Vychytil


title: RNA sequencing on circulating tumor cells from prostate cancer patients

city: San Antonio

first: Chun-Lin

last: Lin

state: Texas

address: 7703 Floyd Curl Dr., MC8257, 233 STRF

institute: University of Texas Health Science Center at San Antonio

summary: Circulating tumor cells (CTCs) undergo considerable stress in the bloodstream. To understand the underlying phenomenon, we conducted single-cell genomic or transcriptomic analyses of primary tumor cells shed in urine and CTCs in blood of prostate cancer patients. Of more than four hundred focal genomic alterations analyzed, increased and decreased copy-numbers of 113 recurrent regions were found in CTCs relative to primary tumor cells. Tumor cells with these pre-existing genomic alterations can be adaptively selected, allowing for transcription reprogramming during blood circulation. These regions harbored genes associated with oxidative phosphorylation machineries that are exploited by CTCs for alternative energy metabolism.

overall_design: Examination of prostate CTCs transcriptomic profile in single cell level

last: Liss


title: Analysis of Grp78 deficiency in lung epithelial type 2 cells.

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

summary: RNA-Seq reveals activation of ER stress/UPR signaling and impaired cell function in Grp78 KO AT2 cells

overall_design: Grp78 KO AT2 cells vs. wild-type AT2 cells

first: Beiyun

last: Zhou

first: Zea

last: Borok


title: Transcriptomic responses and Chromatin accessibility of human monocyte-derived dendritic cells to infection with HIV-1

first: Mickael

last: Menager


title: Mal2 drives immune evasion by reducing antigen presentation on tumor cells

status: Public on Jan 23 2020

city: Indianapolis

first: Chi

last: Zhang

state: IN

institute: INDIANA UNIVERSITY

summary: Current cancer immunotherapies are assumed to improve infiltration and cytotoxicity of immune cells in the tumor. However, tumor cells have developed a variety of resistance mechanisms to suppress the MHC class I antigen presentation, and thereby impair the cytotoxicity of CD8+ T cells. Here, we identified Mal2 as a key player that mediates the turnover of the antigen-MHC-I complex and reduce the antigen presentation on tumor cells. Mal2 promotes the endocytosis of tumor antigen via direct interaction with the MHC-I complex and endosome-associated Rab5/7. In mouse and human breast tumor models, inhibition of Mal2 profoundly enhanced the cytotoxicity of tumor-infiltrating CD8+ T cells and suppressed breast tumor growth, suggesting that Mal2 is a potential target for breast cancer immunotherapy.

overall_design: Examination of wildtype, knock out and overexpression of MAL2 in cancer microenvironment

first: Yuanzhang

last: Fang

first: Xinna


title: Goat's milk feeding enhances innate and adaptive immunities and alleviates allergen-induced airway inflammation in offspring mice

city: Tainan

first: Jiu Yao

last: Wang

address: No.138,Sheng Li Road,Tainan

country: Taiwan

institute: Nation Cheng Kung University

summary:
Goat’s milk (GM), as compared to Cow’s milk (CM), is easier for human to digest and absorb. GM feeding can improve colic, minor digestive disorders, asthma or eczema in infants. It has been demonstrated that GM have antioxidant and anti-inflammatory effects. Whether GM consumed in pregnant mothers has any immune-modulating effects on their newborns is still unclear. In this study, we used pregnant mothers and their offspring mice to verify this hypothesis.
we collected feces of offspring before allergen sensitization (day 0) and two days after i.t. allergen challenge (day 16). Detection of cDNA of feces using Applied Biosystems™ Axiom™ Microbiome Array found the phyla of Bacteroidia, Clostridia, Flavobacteriia, Deferribacteres, Verrucomicrobiae and Gammaproteobacteria as well as some unclassified viruses. Comparison in ratio of Firmicutes to Bacteroidetes (F/B ratio), water-fed (W0) group had higher F/B ratio (0.79) than GM-fed (G0) (0.50) and CM-fed (C0) group (0.54) at Day 0. After HDM allergen sensitization and challenge, there was a remarkable increase of F/B ratio in water-fed mice (0.63 in WN vs. 0.84 in WA), while there was no change of F/B ratio in GM-fed (GN vs. GA) and CM-fed mice (CN vs. CA)

overall_design: 44 total sample were analyzed

first: Hui-Fang

last: Kao

first: Yu-Chin

first: Hsiu-Ying

last: Tzseng

first: Lawrence

last: Shih-Hsin Wu

first: Hui-Ju

last: Tsai

first: Miao-Hsi

last: Hsieh

first: Pei-Chi

last: Chen

first: Wen-Shou

last: Kuo

first: Li-Fan

last: Liu

first: Zhi-Gang

first: Jiu-Yao


title: Single cell transcriptome analysis of distal adult murine lung airway epithelium

city: San Francisco

first: Jaymin

middle: J

last: Kathiriya

state: CA

address: 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

summary: To comprehensively study the heterogeneity within distal airway epithelium, we performed single cell transcriptomic analysis of the naive lung samples. Our analysis reveals that distal lung airway epithelial cells are highly heterogenous. We employed supervised clustering to identify a rare group of cells with transcriptional similiarities to embryonic distal lung bud tip progenitors. This approach identified a quiescent progenitor population of airway cells that accounted for all in vitro regenerative activity. Furthermore, these cells were also required for in vivo transplantation, reconstitution of alveoli, and functional recovery of injured mice. These findings indicate that small subpopulations of specialized stem/progenitors are required for effective lung regeneration and could potentially be used as therapeutic adjuncts after major lung injury.

overall_design: We performed single cell transcriptomic sequencing of flow purified Epcam+/Itgb4+/CD200+ cells via 10X Genomics platform

first: Harold

last: Chapman


title: Adrenergic signaling in muscularis macrophages limits infection-induced neuronal loss

city: New York

first: Paul

middle: Andrew

last: Muller

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: Enteric–associated neurons (EAN) are closely associated with immune cells and continuously monitor and modulate homeostatic intestinal functions, including motility. Bidirectional interactions between immune and neuronal cells are altered during disease processes such as neurodegeneration or irritable bowel syndrome. We investigated how infection-induced inflammation affects intrinsic EAN (iEAN) and the role of intestinal muscularis macrophages (MM) in this process. Using murine models of enteric infections, we observed long-term gastrointestinal symptoms including reduced motility and loss of excitatory iEAN, which was mediated by an NLRP6 and caspase 11 mechanism, depended on infection history, and could be reversed by microbiota manipulation. MM responded to luminal infection by upregulating a neuroprotective program dependent on β2-adrenergic receptor (β2-AR) signaling, and mediated neuronal protection via an arginase 1-polyamine axis. Our results identify a mechanism of neuronal cell death post–infection and point to a role for tissue–resident MM in limiting neuronal damage.

overall_design:
Actively translated mRNA profiles from immunoprecipitated ribosome-bound mRNA from the ileum muscularis and nodose ganglion of Snap25:RiboTag mice were prepared by deep sequencing on an Illumina NextSeq
Actively translated mRNA profiles from immunoprecipitated ribosome-bound or input mRNA from the ileum muscularis of LysM:Adrb2floxflox:RiboTag or LysM:Adrb2floxplus:RiboTag mice were prepared by deep sequencing on an Illumina NextSeq

first: Fanny

last: Matheis

first: Christina

middle: L

last: Graves

first: Ilana

last: Gabanyi

first: Zachary

last: Kerner

first: Diego

last: Costa-Borges

first: Tomasz

last: Ahrends

first: Philip

last: Rosenstiel

first: Daniel

last: Mucida


title: The mRNA decay factor CAR-1 regulates axon regeneration via mitochondrial calcium dynamics

city: La Jolla

first: Ngang Heok

last: Tang

address: 9500 Gilman Drive

institute: UC San Diego

summary: mRNA decay factors regulate mRNA turnover by recruiting non-translating mRNAs and targeting them for degradation, yet it remains poorly understood how mRNA decay factors function in vivo to regulate specific cellular processes. Here we show that mRNA decay factors form cytoplasmic puncta in C. elegans neurons and have opposing roles in axon maintenance and regrowth. While the decapping enzymes DCAP-1/DCP1 and DCAP-2/DCP2 regulate developmental axon guidance and promote axon regrowth upon injury, the translational repressors CAR-1/LSM14 and CGH-1/DDX6 regulate axon maintenance and inhibit axon regrowth in adult animals. We identified mRNA targets of CAR-1 in neurons and found that the mitochondrial calcium uptake regulator micu-1 is repressed by CAR-1. We show that axon injury triggers a transient mitochondrial calcium influx via the MCU-1 uniporter that is more sustained in car-1 loss of function mutants. The enhanced axon regrowth and defective axon maintenance of car-1 mutants are dependent on MICU-1 function. Our results uncover specific roles for mRNA decay regulators in neurons and reveal a novel pathway that controls axon regrowth through mitochondrial calcium uptake.

overall_design: seCLIP-seq in C. elegans strains CZ25180 and CZ26430

first: Ngang-Heok

first: Kyung-Won

last: Kim

first: Suhong

last: Xu

first: Stephen

last: Blazie

first: Brian

last: Yee

first: Gene

last: Yeo

first: Yishi

last: Jin

first: Andrew

last: Chisholm


title: Gene expression during recovery from different forms of trauma in the sea anemone, Nematostella vectensis

city: Charlotte

first: Whitney

middle: at

last: Leach

address: 9201 University City Blvd.

department: Biological Sciences

institute: University of North Carolina at Charlotte

summary: We exposed N. vectensis to three forms of trauma (streptomycin, cytochalasin D, or calcium-free seawater) to determine differences in gene expression during recovery from the trauma. Gene expression was monitored during different time points of recovery for animals exposed to cytochalasin D or calcium-free seawater. Gene expression was monitored following designated times of exposure and after 1 hour of recovery for animals exposed to streptomycin.

overall_design: total 84 samples: 14 time points (3 replicates each) for 2 conditions. (14*3*2 = 84)

first: Shelcie

last: Menard-Harvey

first: Adam

last: Reitzel


title: Transcriptomes of clonal palms with different fruit phenotypes.

city: Bandar Baru Bangi

first: Norashikin

last: Sarpan

state: Selangor

address: 6 Persiaran Institusi

department: Advanced Biotechnology and Breeding Centre

country: Malaysia

institute: Malaysian Palm Oil Board

summary: Leaf tissue was sampled from clonal palms producing normal and mantled fruits. RNAseq libraries were generated and sequenced on Illumina  platform. Differential expression analysis was carried out between the normal and mantled groups of palms.

overall_design: Leaf tissue used in this study was collected from clonal palms of a single ortet (mother palm). A total of 10 clonal palms bearing normal (5 palms) and mantled fruits (5 palms) were identified based on the fruit bunch cencus data and hereafter designated as biological replicates. Leaf tissues extended from frond 0 were sampled and used for isolation of total RNA. Expression profiling of the two groups were assessed through transcriptome sequencing data. For differential analysis, the normal group was designated as the reference.

first: Tatiana

middle: V

last: Tatarinova

first: Eng-Ti

last: Low

first: Meilina

last: Ong-Abdullah

first: Siew-Eng

last: Ooi


title: MicroRNA-1 regulates goat uterine NK cells function by targeting tumor necrosis factor-like weak inducer of apoptosis (TWEAK)

city: Yangling

first: Xuefeng

last: Qi

state: Shaanxi

address: Taicheng Road

country: China

institute: Northwest A&F University

summary: MicroRNAs (miRNAs) play important roles in regulating immune response of natural killer (NK) cells, a critical effectors against malignancy and infection. Here, miRNAs profiles of goat uterine NK (uNK) cells and peripheral blood NK (pNK) cells were examined, and a novel miRNAs, miR-1, that is lowly expressed in uNK cells compared to pNK cells were identified. We further demonstrated that miR-1 directly target TWEAK gene in NK cells, a negative regulator of NK cell cytotoxicity. Moreover, our data revealed that an increased miR-1 expression was observed in uNK cells incubated with somatic cell nuclear transfer (SCNT) conditioned medium compared to those incubated with in vitro fertilization (IVF) conditioned medium, and an inverse correlation was detected between miR-1 expression and TWEAK mRNA and protein expression in both groups. Interestingly, miR-1 mediated suppression of TWEAK in uNK cells in response to SCNT conditioned medium incubation was accompanied with an increased cytotoxicity and IFN-γ expression compared to control group. Furthermore, miR-1 inhibitor transfection abrogate the enhanced cytotoxicity of uNK cells incubated with SCNT conditioned medium, which was accompanied with an increased TWEAK expression. Taken together, our results demonstrated that TWEAK regulated by miR-1 may play a key role in regulating goat uNK cells cytotoxicity and IFN-γ expression levels. In particularly, miR-1 mediated suppression of TWEAK may involved in the increased cytotoxicity of uNK cells in response to SCNT embryo incubation. These results provide a resource for studying the roles of miRNAs in goat NK cell biology and contribute to a better understanding of the physiologic significance of miRNAs in the regulation of NK cell function.

overall_design: uNK and NK cells were separated from uterus and peripheral blood of goat.uNK group and NK group were subjected to analysis.

first: Mingzhu

last: Lei


title: MicroRNA expression difference between radiosensitive group and radioresistant group in atypical meningioma with gross total resection and adjuvant radiotherapy

city: Beijing

first: Yonggang

last: Wang

address: South 4th Ring West Road 119, Fengtai District

department: Neurosurgery

institute: Beijing Tiantan Hospital, Capital Medical University

summary: For atypical meningiomas (AM), the combination of gross total resection (GTR) and adjuvant radiotherapy (ART) is still a controversial therapeutic strategy to improve prognosis. This study analysed the factors influencing the prognosis on AM patients treated with GTR+ART by investigating both clinical characteristics and the change in microRNA (miRNA) expression.Adult AM patients who were admitted to the Tiantan hospital from 2008 to 2015 and underwent GTR+ART were included. Patients who suffered recurrence within 3 years after operation were considered radioresistant, while the others were considered radiosensitive. Clinical characterizations were compared between these two groups. The miRNAs expression was detected via miRNA microarray in 10 patients, 5 from the radiosensitive group and 5 from the radioresistant group.No significant difference was found in the clinical characteristics. between radiosensitive and radioresistant patients. We found 7 significantly upregulated miRNAs and 7 significantly downregulated miRNAs  in patients resistant to radiotherapy. The differentially expressed miRNAs were enriched mostly in the Fatty acid metabolic pathways (hsa00061, hsa01212) and TGF-β signalling pathway (hsa04350). For AM patients treated with GTR+ART, the changes in miRNA expression discovered in this study may be a potential predictor of individual sensitivity to adjuvant radiotherapy. Further research is needed regarding the predictive power and mechanism by which these miRNAs influence prognosis.

overall_design: A total of 55 AM cases with GTR+ART were followed up to at least 3 years. Patients suffered recurrence within 3 years were considered as radioresistant and the others were taken as radiosensitive. 10 tumor samples were detected by miRNA arry test, 5 from radioresistant group and 5 from radiosensitive group. Comparison between the miRNA profiles of the radioresistant and radiosensitive group AM samples revealed 1466 common miRNAs.

first: Xiaokang

last: Zhang

first: Guobin


title: Ventral midbrain-type neural stem/precursor cells (VM-NSCs) derived from human midbrain organoids as a stable source for treating symptoms of Parkinson’s disease

city: seoul

first: Hyun-Seob

last: Lee

address: 71 Daehak-ro, Jongno-gu

department: Biomedical research institute

institute: Seoul national University Hospital

summary: In this study, midbrain-like organoids were yielded from hPSCs to prepare cells suitable for PD therapy. Neural stem/precursor cells (NSCs) isolated from midbrain organoids (Og-NSCs) expanded stably and differentiated into mDA neurons, and an unprecedentedly high proportion express midbrain-specific factors.

overall_design: mRNA profile of 2D culture system derived NSCs, Midbrain Organoid derived NSCs

first: Lee

last: Sang-Hun

first: Chang

last: Mi-Yoon

first: Kim

last: Seung Won

first: Woo

last: Hye Ji


title: Human iPSC-derived GABAergic Interneuron Transplants Attenuate Neuropathic Pain

city: Sydney

first: John

middle: William

last: Manion

address: Charles Perkins Centre, John Hopkins Drive

department: SOLES

country: Australia

institute: The University of Sydney

summary: Neuropathic pain causes severe suffering and most patients are resilient to current therapies. A core element of neuropathic pain is the loss of inhibitory tone in the spinal cord. Previous studies have shown that foetal GABAergic neuron precursors can provide relief from pain. However, the source of these precursor cells and their multipotent status make them unsuitable for therapeutic use. Here we extend these findings by showing, for the first time, that spinally transplanted, terminally differentiated hiPSC-derived GABAergic (iGABAergic) neurons provide significant, long-term and safe relief from neuropathic pain induced by peripheral nerve injury in mice. Furthermore, iGABAergic Neuron transplants survive long term in the injured spinal cord and show evidence of synaptic integration. Together, this provides the proof in principle for the first viable GABAergic transplants to treat human neuropathic pain patients.

overall_design: 4 replicates Sensory neurons 4 replicates GABAergic neurons 3 replicates hiPSC


title: A CRISPRi system for efficient and rapid gene knockdown in Caulobacter crescentus

city: Seattle

first: Monica

last: Guo

state: WA

address: 750 Republican St

department: Microbiology

institute: University of Washington

summary: CRISPR interference (CRISPRi) is a powerful new tool used in different organisms that provides a fast, specific, and reliable way to knockdown gene expression. Caulobacter crescentus is a well-studied model bacterium, and although a variety of genetic tools have been developed, it currently takes several weeks to delete or deplete individual genes, which significantly limits genetic studies. Here, we optimized a CRISPRi approach to specifically downregulate the expression of genes in C. crescentus. Although the Streptococcus pyogenes CRISPRi system commonly used in other organisms does not work efficiently in Caulobacter, we demonstrate that a catalytically-dead version of Cas9 (dCas9) derived from the type II CRISPR3 module of Streptococcus thermophilus or from Streptococcus pasteurianus can each be effectively used in Caulobacter. We show that these CRISPRi systems can be used to rapidly and inducibly deplete ctrA or gcrA, two essential well-studied genes in Caulobacter, in either asynchronous or synchronized populations of cells. Additionally, we demonstrate the ability to multiplex CRISPRi-based gene knockdowns, opening new possibilities for systematic genetic interaction studies in Caulobacter.

overall_design: RNA-sequencing experiments from Caulobacter crescentus CB15N cells expressing dCas9 and sgRNA targeting ctrA. (i) RNA-seq in ML3173 (Pxyl-dcas9(Sth3)) repressed in glucose, (ii) RNA-seq in ML3173 (Pxyl-dcas9(Sth3)) induced in xylose, (iii) RNA-seq in ML3174 (Pxyl-dcas9(Sth3) Pconstitutive-sgRNA(Sth3)_ctrA) repressed in glucose, and (iv) RNA-seq in ML3174 (Pxyl-dcas9(Sth3) Pconstitutive-sgRNA(Sth3)_ctrA) induced in xylose.

first: Mathilde

last: Guzzo

first: Lennice

middle: K

last: Castro

first: Christopher

last: Reisch

first: Michael

middle: T

last: Laub


title: Single cell transcriptome analysis of bleomycin injured distal adult murine lung airway epithelium

first: Jaymin

last: Kathiriya

first: Harold

middle: A

last: Chapman


title: The gene expression of the brain/pituitary from oxt/oxtr1 homozygous mutants and WT medaka in both sexes

city: Sapporo

first: Saori

last: Yokoi

state: Hokkaido

address: Kita 12-jo Nishi 6-chome, Kita-ku

department: Faculty of Pharmaceutical Sciences

institute: Hokkaido university

summary: Differential gene expression in the brain/pituitary of oxt/oxtr1 homozygous mutants in both sexes.

overall_design: Examination of expression profiles of wild-type, oxytocin mutant and oxytocin receptor mutants in both sexes.

first: Mari

last: Mito

first: Shintaro

last: Iwasaki

first: Shinichi

last: Nakagawa

first: Hideaki

last: Takeuchi


title: A suite of haploid genetic screens identifies SPRING as a novel determinant of SREBP signaling and cholesterol metabolism

city: Amsterdam

first: Noam

last: Zelcer

address: Meibergdreef 9

department: Medical Biochemistry

country: Netherlands

institute: AUMC

summary: The sterol-regulatory element binding protein (SREBP) transcription factors are central transcriptional regulators of sterol- and fatty acid metabolism. Using a suite of human haploid genetic screens, we identify the SREBP Regulating Gene (SPRING; C12ORF49) as a novel regulator of this pathway. SPRING is a glycosylated Golgi-resident membrane protein. Genetic ablation of SPRING in human Hap1 cells, murine Hepa1-6 hepatoma cells, and in primary murine hepatocytes leads to a marked reduction in SREBP signaling. In mice, deletion of Spring results in embryonic lethality. However, we show that adenoviral-mediated silencing of hepatic Spring expression also attenuates the SREBP response. Mechanistically, we demonstrate that attenuated SREBP signaling in SPRINGKO cells is a result of reduced SREBP cleavage-activating protein (SCAP) and its mislocalization. Whereas in control cells SCAP cycles between the ER and the Golgi in a sterol-dependent manner, in SPRINGKO cells SCAP is trapped in the Golgi irrespective of the cellular sterol status. Consistent with limited functional SCAP in SPRINGKO cells, reintroducing SCAP restores SREBP-dependent signaling, cholesterol biosynthesis, and lipoprotein uptake. Consistent with SREBP signaling being required for cell growth and proliferation, a wide range of human tumor cell lines display dependency on SPRING expression. In conclusion, we identify SPRING as a previously unrecognized determinant of the SREBP pathway that is essential for proper SCAP function.

overall_design: Identification of a gene, SPRING (C12ORF49), as a novel regulator of the SREBP pathway and cholesterol homeostasis

first: Thijn

last: Brummelkamp


title: Transcriptomes in the Sciatic Nerves of Lewis Rats with Experimental Autoimmune Neuritis

status: Public on Jan 22 2020

city: Harbin

first: Yang

last: Xue

address: 23 You Zheng Street

institute: The First Affiliated Hospital of Harbin Medical University

summary: Guillain-Barré syndrome (GBS) is characterized by acute immune-mediated peripheral neuropathy, which may result in rapidly progressive paralysis and fatal respiratory failure. As the underlying pathological mechanisms of GBS are unclear, we surveyed the transcriptome of rats with experimental autoimmune neuritis (EAN), a model of GBS. Briefly, sciatic nerves on both sides were collected from 8–10-week-old Lewis rats during early (10 days post-induction), peak (19 days), and late neuritis (30 days). Total RNA was sequenced to identify differentially expressed genes. Compared to control rats without induced neuritis, 33 genes were differentially expressed in the early phase (14 upregulated and 19 downregulated), with an adjusted P-value < 0.05 and |log2 fold-change| > 1, as were 137 genes in the peak phase (126 upregulated and 11 downregulated) and 60 genes in the late phase (58 upregulated and 2 downregulated). Eleven of these genes were common to all stages, suggesting their crucial roles throughout the disease course. Analysis of protein-protein interactions revealed Fos, Ccl2, Itgax and C3 as node genes at different stages. Functional analysis of differentially expressed genes identified biological processes and pathways that are activated as neuritis progresses. This is the first genome-wide gene expression study of peripheral nerves in experimental autoimmune neuritis model. Dynamic gene expression and significantly altered biological functions were detected in different phases of the disease, increasing our understanding of the molecular mechanisms underlying EAN and highlighting potential targets for its diagnosis and treatment.

overall_design: Sciatic RNA sequencing data were collected from 8–10-week-old Lewis rats within four groups, including the control, early neuritis (10 days post-induction), peak neuritis (19 days), and late neuritis (30 days) groups (n = 3 per group).

first: Pengqi

last: Yin

first: Guozhong

last: Li

first: Di

last: Zhong


title: Widespread transcriptional scanning in the testis modulates gene evolution rates

city: NEW YORK

first: Bo

last: Xia

state: New York

address: 550 1ST AVE

department: Institute for Computational Medicine

institute: New York University School of Medicine

summary: The testis expresses the largest number of genes of any mammalian organ, a finding that has long puzzled molecular biologists. Our detailed transcriptomic map of human and mouse spermatogenesis provides evidence that this widespread transcription serves to maintain DNA sequence integrity in the male germline by correcting DNA damage through “transcriptional scanning”. Supporting this model, we find that genes expressed during spermatogenesis display lower mutation rates on the transcribed strand and have low diversity in the population, while unexpressed genes evolve faster and are enriched for sensory and immune-defense functions. Thus, we propose that transcriptional scanning modulates mutation rates in a gene-specific manner, maintaining germline DNA sequence integrity for the bulk of genes but allowing for fast evolution in a specific subset.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The project contains data from single cell RNA-seq of both human (two biological replicates, each with two technical replicates) and mouse (two biological replicates) testicular cells.

first: Itai

last: Yanai


title: Silencing Trisomy 21 with XIST in Neural Stem Cells Promotes Neuronal Differentiation

city: Worcester

first: Jan

last: Czerminski

state: Massachusetts

address: 55 Lake Ave N, S6-241

department: Neurology

institute: UMass Medical School

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules (RNA-Seq)

city: Cambridge

first: Natasha

last: Patel-Murray

address: 77 Massachusetts Avenue

institute: Massachusetts Institute of Technology

summary: High-throughput screening and gene signature analyses frequently identify lead therapeutic compounds with unknown modes of action (MoAs), and the resulting uncertainties can lead to the failure of clinical trials. We developed a multi-omics approach for uncovering MoAs through an interpretable machine learning model of the effects of compounds on transcriptomic, epigenomic, metabolomic, and proteomic data.    We applied this approach to examine compounds with beneficial effects in models of Huntington’s disease, finding common MoAs for previously unrelated compounds that were not predicted based on similarities in the compounds’ structures, connectivity scores, or binding targets. We experimentally validated two such disease-relevant MoAs, autophagy activation and bioenergetics manipulation. This interpretable machine learning approach can be used to find and evaluate MoAs in future drug development efforts.

overall_design: Cells expressing mutant huntingtin were treated in triplicate with serum-free DMEM with vehicle (Q111SST) or serum-free DMEM with one of 14 protective compounds for 24 hours. Wild type cells were also treated with serum-free DMEM with vehicle (Q7SST) as an additional control for 24 hours. We examined the compounds' transcriptomic effects on the cells using RNA-Seq.

first: Ernest

last: Fraenkel


title: A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules


title: An optimised protocol harnessing laser capture microdissection for transcriptomic analysis on matched primary and metastatic colorectal tumours to identify novel biomarker

city: Singapore

first: Johnny

middle: Chin-Ann

last: Ong

state: Singapore

address: 11 Hospital Drive

department: Division of Surgical Oncology

country: Singapore

institute: National Cancer Centre Singapore

summary:
Purpose: To develop a methodology to obtain high-quality expression data from matched primary tumours and metastases by utilizing LCM to isolate pure cellular populations
Methods: Snap frozen biopsies of matched primary tumour, metastasis and the associated normal tissues were microdissected to obtain stromal and epithelial components. RNA was extracted from the respective microdissected samples and subsequently subjected to RNA sequencing.
Results: We demonstrated an optimised LCM protocol which reproducibly delivered intact RNA used for RNA sequencing and quantitative polymerase chain reaction (qPCR). This framework helped to uncover multiple differentially expressed cancer-associated genes and qPCR verification of 9 chosen targets confirmed the high fidelity of the RNA sequencing process.
Conclusion: This study suggests that the combination of matched tissue specimens with tissue microdissection and NGS provides a viable platform to unmask hidden biomarkers and provides insight into tumour biology at a higher resolution.

first: Melissa

last: Ching Ching

middle: O

last: Chin-Ann


title: Probing secretome of hematopoietic and mesenchymal stem cell interactions in single and co-cultures

city: Urbana

first: Aidan

last: Gilchrist

address: 1206 W Gregory Dr., suite 2200

institute: University of Illinois at Urbana-Champaign

summary: Hematopoietic stem cells (HSCs) primarily reside in the bone marrow, where they receive external cues from their local microenvironment. The complex milieu of biophysical cues, cellular components, and cell-secreted factors regulates the process by which HSC produce the blood and immune system. We previously showed direct co-culture of primary murine hematopoietic stem and progenitor cells with a population of marrow-derived mesenchymal stromal and progenitor cells (MSPCs) in a methacrylamide-functionalized gelatin (GelMA) hydrogel improves hematopoietic progenitor maintenance. However, the mechanism by which MSPCs influenced HSC fate decisions remained unknown. Herein, we report the use of proteomic analysis to correlate HSC phenotype to a broad candidate pool of 200 soluble factors produced by combined mesenchymal and hematopoietic progeny. Partial Least Squares Regression (PLSR), along with an iterative filter method, identified TGFβ-1, MMP-3, c-RP, and TROY as positively correlated with HSC maintenance. Experimentally, we then observe exogenous stimulation of HSC monocultures in GelMA hydrogels with these combined cytokines increases the ratio of hematopoietic progenitors to committed progeny after a 7-day culture 7.52 ± 3.65 fold compared to non-stimulated monocultures. Findings suggest a cocktail of the downselected cytokines amplify hematopoietic maintenance potential of HSCs beyond that of MSPC-secreted factors alone. This work integrates empirical and computation methods to identify cytokine combinations to improve HSC maintenance within an engineered HSC niche, suggesting a route towards identifying feeder-free culture platforms for HSC expansion.

sample_organism:
Mus musculus
synthetic construct

overall_design: HSPCs and MSPCs were cultured at increasing ratios of 1:0, 1:1, 1:10, 0:1, 0:10 (HSPCs:MSPCs) in 4, 5, 7.5 wt% methacrylamide-functionalized gelatin (GelMA) for a total of 15 conditions. Media collected from days 2, 4, and 6 was pooled for each sample and used for subsequent proteomic analysis: 15 conditions, in triplicate.

middle: E

first: Brendan

last: Harley


title: Expression data of health individuals and newly diagnosed multiple myeloma

first: Zhiyao

last: Zhang

address: No. 8 Gongti South Road, Beijing

institute: Beijing Chao-yang hospital

summary:
Multiple myeloma is a multi-stage disease. Based on its laboratory and clinical presentation it can be summarized as MGUS, smoldering myeloma, and multiple myeloma. Previous studies have shown that the expression levels of miRNAs in different stages of the disease are different. This study analyzes the expression levels of miRNAs in healthy individuals and myeloma serum exosomes.
We used microarrays to detail the miRNAs expressionin between 12 healthy individuals and 12 multiple myeloma and identified distinct classes of dys-regulated genes.

overall_design: Collecting multiple myeloma patients and healthy individuals peripheral blood and serum and extract exosomes, extract exosome RNA, and hybridize on Affymetrix microarrays.

first: Zhi-yao


title: Genome-wide occupancy profiling of FoxO1 in human primary chondrocytes

first: Tomas

last: Duffy

address: 10550 N Torrey Pines Rd

institute: TSRI

summary: FoxO1 regulates extracellular matrix and circadian rhythm genes in human primary chondrocytes

overall_design: Genome-wide occupancy profiling of FoxO1 was independently assessed in human primary chondrocytes from 3 different donors.

first: Martin

last: Lotz


title: Prom1-deficiency effects on mouse primary hepatocyte transcriptomes in serum-free condition

city: Seoul

first: Young-Gyu

last: Ko

address: 145, Anam-ro, Seongbuk-gu

department: Division of Life Sciences

institute: Korea University

summary:
Purpose: The function of Prom1, a penta-transmembrane glycoprotein  which is a used as cancer stem cell marker, in the liver is unclear. The goal of this study is to examine the effect of Prom1 -/- in mouse primary hepatocyte transcriptomes.
Prominin-1 (Prom1) is a major cell surface marker of cancer stem cells, but its physiological functions in the liver have not been elucidated. We analyzed the levels of mRNA transcripts in serum-starved primary Prom1+/+ and Prom1-/- mouse hepatocytes using RNA-sequencing (RNA-seq) data, and found that CREB target genes were down-regulated. This initial observation led us to determine that the Prom1 deficiency inhibited cAMP response element binding protein (CREB) activation and gluconeogenesis, but not cyclic AMP (cAMP) accumulation, in glucagon-, epinephrine-, or forskolin-treated liver tissues and primary hepatocytes, and mitigated glucagon-induced hyperglycemia. Because Prom1 interacted with radixin, the Prom1 deficiency prevented radixin from localizing to the plasma membrane. Moreover, systemic adenoviral knockdown of radixin inhibited CREB activation and gluconeogenesis in glucagon-treated liver tissues and primary hepatocytes, and mitigated glucagon-elicited hyperglycemia. Based on these results, we conclude that Prom1 regulates hepatic PKA signaling via radixin functioning as an A kinase-anchored protein (AKAP).

overall_design: Two mouse primary hepatocyte groups were studied: WT hepatocytes and Prom1-deficient (Prom1 -/-) hepatocytes in serum-free condition. Two biological replicates for each group were selected; all are age-matched males.

first: Hyun

last: Lee

first: Dong-Min

last: Yu

first: Jun-Sub

last: Park

first: Hwayeon

first: Jun-Seok

last: Kim

first: Seung-Hoi

last: Koo

first: Jae-Seon

first: Sungsoo


title: Long-term absence of Langerhans cells alters the gene expression 2 profile of keratinocytes and dendritic epidermal T cells

city: Dallas

first: Uthra

last: Balaji

address: 3434 Live Oak St

department: Biostatistics Core

institute: Baylor Scott & White Research Institute

summary: In this study, with the help of RNA-sequencing, we show for the first time that long-term absence of epidermal resident Langerhans cells (LCs) led to significant gene expression changes in the local keratinocytes and resident dendritic epidermal T cells

overall_design: A total of 11 samples are included in this study with 3 replicates each fpr LC-/- and WT groups in the KC cell population and 3 replicates for WT and 2 replicates for LC-/- groups in the DETC cell population

first: Botond

last: Igyarto

first: Qingtai

last: Su


title: The Evening Complex Establishes Repressive Chromatin Domains via H2A.Z-Nucleosome Deposition in Arabidopsis

first: Phillip

last: Wigge

address: Bateman Street

department: Sainsbury Laboratory

country: United Kingdom

institute: University of Cambridge

summary: The Evening Complex (EC) is a core component of the circadian clock, which represses target gene expression at the end of the day and integrates temperature information in order to coordinate environmental and endogenous signals. Despite its importance, the mechanism of EC function remains unknown. Here we show that the EC recruits repressive chromatin domains to regulate the evening transcriptome. The EC component EARLY FLOWERING 3 (ELF3) directly interacts with a protein from the Swi2/Snf2-Related 1 (SWR1) complex to control deposition of H2A.Z-nucleosomes at the EC target genes. The SWR1 components display a circadian oscillation in gene expression with a peak at dusk, suggesting that the circadian clock controls the expression and function of SWR1. In turn, SWR1 is required for the circadian clockwork as defects in SWR1 activity alters morning-expressed genes. The EC-SWR1 complex binds to the promoters of the core clock genes PSEUDORESPONSE REGULATOR 7 (PRR7) and PRR9 and catalyzes H2A.Z deposition coincident with their repression at dusk. This provides a mechanism by which the circadian clock temporally establishes repressive chromatin domains to shape oscillatory gene expression around dusk.

overall_design: HTA11 ChIP-seq and Mnase-seq were generated in Arabidopsis seedlings growing at 17 ºC

first: Phil

first: Meixuezi

last: Tong


title: Functional heritage: the evolution of chimeric RNA into a gene

city: Changsha

first: Wu

last: Hao

state: Hunan

address: 138 Tongzipo Road

department: Department of General Surgery

institute: The Third Xiangya Hospital of Central South University

summary: Once believed to be unique features of neoplasia, chimeric RNAs have been discovered in normal physiology. We speculated that some chimeric RNAs may be functional precursors of genes and that forming chimeric RNA at the transcriptional level may be a “trial” mechanism before the functional element is fixed into the genome. Supporting this idea, we identified a chimeric RNA, HNRNPA1L2-SUGT1 (H-S), whose sequence is highly similar to the pseudogene MRPS31P5. Evolutionarily, H-S precedes MRPS31P5, as it can be detected bioinformatically and experimentally in marmoset monkeys, which do not possess MRPS31P5 in their genome. Conversely, H-S is minimally expressed in humans, while instead, MRPS31P5 is abundantly expressed. Here, we provide multiple lines of evidence supporting that MRPS31P5 is not truly a pseudogene, but a functional descendent of the H-S chimera. We also show that H-S is a product of cis-splicing between adjacent genes, while MRPS31P5 is likely produced by genome rearrangement.

sample_organism:
Callithrix jacchus
Homo sapiens

platform_organism:
Callithrix jacchus
Homo sapiens

overall_design: Human foreskin fibroblast cell transfected with si-hMRPS31P5 and si-gl2, marmoset fibroblast cell CJ-157 cell transfected with si-HNRNPA1L2-SUGT1 and si-gl2 were subjected to RNA sequence

first: Hao

last: Wu

first: Sandeep

last: Singh

first: Xinrui

last: Shi

first: Emily

last: Lin

first: Xiaorong

last: Li

first: Hui


title: Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period

city: La Jolla

first: Kun

last: Tan

address: 2880 Torrey Pines Scenic Dr. Room 4812

department: Department of Obstetrics, Gynecology, and Reproductive Sciences

institute: UCSD

summary: Pro-spermatogonia (SG) serve as the gateway to spermatogenesis. Using single-cell RNA sequencing (RNAseq), we studied the development of ProSG, their SG descendants, and testicular somatic cells, during the perinatal period in mice. We identified both gene and protein markers for 3 temporally distinct ProSG cell subsets, including a migratory cell population with a distinct transcriptome from the previously defined T1- and T2-ProSG stages. This intermediate (I)-ProSG subset translocates from the center of seminiferous tubules to the spermatogonial stem cell (SSC) “niche” in its periphery soon after birth. We identified 3 undifferentiated SG subsets at postnatal day 7, each of which express distinct genes, including transcription factor and signaling genes. Two of these subsets have the characteristics of newly emergent SSCs. We also molecularly defined the development of Sertoli, Leydig, and peritubular myoid cells during the perinatal period, allowing us to identify candidate signaling pathways acting between somatic and germ cells in a stage-specific manner during the perinatal period. Our study provides a rich resource for those investigating testicular germ and somatic cell developmental during the perinatal period.

overall_design: Single cell sequencing (10X genomics) from unfractionated perinatal testicular cells (embryonic day [E] 18.5, postnatal day [P] 2, and P7; with two biological replicates for each timepoint) were performed for this study.

first: Hye-Won

last: Song

first: Miles

middle: F

last: Wilkinson


title: A cancer-specific ubiquitin ligase drives alternative polyadenylation by targeting PCF11

city: Irvine

first: Lei

address: University of California, Irvine

institute: University of California, Irvine

summary: Alternative polyadenylation (APA) contributes to the complexity of the transcriptome by generating mRNA isoforms with varying 3' UTR lengths. APA leading to 3' UTR shortening (3'-US) of mRNAs is a common feature of most cancer cells. However, the molecular mechanisms promoting APA in cancer are not well established. Here, we describe a widespread mechanism promoting 3'-US in cancer through ubiquitination and degradation of the 3' processing complex protein, PCF11, by the cancer-specific MAGE-A11-HUWE1 ubiquitin ligase. MAGE-A11 is normally expressed only in the male germline but is frequently re-activated in human cancers. MAGE-A11 is necessary for cancer cell viability and is sufficient to drive tumorigenesis. Screening for targets of MAGE-A11 revealed that it ubiquitinates PCF11 for degradation. This leads to APA of many transcripts in ovarian and lung tumors from both mouse xenografts and human tumor specimens. Importantly, expression of a non-degradable PCF11 degron mutant suppressed MAGE-A11 oncogenic activity and 3'-US. Analysis of the transcripts affected by MAGE-A11, revealed core oncogenic and tumor suppressor genes and pathways. This includes 3'-US of the cyclin D2 oncogene leading to deregulation of the Rb tumor suppressor pathway. Furthermore, competing endogenous RNA (ceRNA) partners of 3'-US transcripts include many tumor suppressor genes, such as PTEN that is downregulated by MAGE-A11 resulting in activation of the Akt growth signaling pathway. These findings provide insights into the function of MAGE-A11 and help explain the molecular mechanisms driving APA in cancer.

overall_design: Examination of alternative polyadenylation and gene expression upon MAGEA11 expression in HEK293FT, DAOY, A2780, and OV56 cells.

first: SeungWook

last: Yang

first: Wei

first: Patrick

last: Potts


title: Macrophages in eutopic endometrium endometriosis

city: San Francisco

first: Julia

last: Vallve Juanico

state: California

address: 513 Parnassus Ave HSE1619

department: Obstetrics and Gynecology Department

institute: University of California San Francisco

summary: Comparison of macrophages M1 (M1) and M2 (M2) from eutopic endometrium from women with and without endometriosis

overall_design: M1 and M2 populations were isolated from human endometrium by fluorescence activating cell sorting using a unique cell-specific flow cytometry panel of conjugated antibodies from six women with endometriosis and 5 controls without disease, all in the secretory phase of the menstrual cycle. Transcriptomes were determined by RNA high sequencing.

first: J

first: S

last: Houshdaran

first: L

middle: C

last: Giudice


title: A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules (ChIP-Seq)

first: Natasha

last: Patel-Murray

overall_design: Cells expressing mutant huntingtin were treated in triplicate with serum-free DMEM with vehicle (Q111SST) or serum-free DMEM with one of 14 protective compounds for 24 hours. Wild type cells were also treated with serum-free DMEM with vehicle (Q7SST) as an additional control for 24 hours. We examined the compounds' epigenomic effects on the cells using H3K4me3 ChIP-Seq.

first: Ernest

last: Fraenkel


title: Folate deficiency in vascular smooth muscle cells

city: Aberdeen

first: Claus

last: Mayer

address: Greenburn Road

institute: Biomathematics & Statistics Scotland

summary: Folate deficiency promotes differentiation of vascular smooth muscle cells, but shifts the overall phenotype towards skeletal muscle

overall_design: A7r5 rat vascular smooth muscle cells were grown in medium containing 100ng/ml (excess), 10ng/ml (sufficient) or 2.5ng/ml of folic acid (deficient) for 7, 14 and 21 days

first: Andreas

last: Kolb


title: Distinct Transcriptomic Profile of Monocyte-Derived Macrophages in Response to Escherichia Coli: When Genetics Rules

status: Public on Jan 21 2020

city: Guelph

first: Mehdi

last: Emam

state: ON

address: 419 Gordon St

department: Pathobiology

country: Canada

institute: University of Guelph

summary: The proinflammatory response of Monocyte-Derived Macrophages is controlled by host genetics

overall_design: The transcriptomic profile of monocyte-derived macrophages were compared between two groups of genetically distinct high and low responder group

first: Emam

last: Mehdi

first: Mallard

last: Bonnie

first: Juan

last: Medrano

first: Angela

last: Canovas


title: Transcriptome analysis of B cell lymphomas in several c-myc Igh transgenic mice

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: Investigation of B cell lymphomas (IgM+ IgD+) located in various places (lung, mesenteric lymph nodes,…) of three different c-myc Igh transgenic mice. Insertion of c-myc in 5' to Emu (cr), in 5' to Cmu with Emu deletion (hv), and in Calpha (co).

overall_design: B220+ purified B cells from spleen of healthy wt, hv, cr, and co mice (stimulated or not with LPS for two days). B220+ purified B cell lymphomas from various hv, cr, co mice (19 samples).

first: Y

last: Denizot

first: F

last: Boyer


title: MicroRNA-204-5p is a tumor suppressor and potential therapeutic target in head and neck squamous cell carcinoma.

city: Guangzhou

first: Cheng

last: Wang

address: 56 Lingyuan Road West

institute: Sun Yat-sen University

summary: To understand molecular mechanisms underlying miR-204-5p mediated suppression of HNSCC progression, we performed RNA-seq analysis in UM-SCC1 cells transfected with miR-204-5p mimics and control mimics. The expression of JAK2, SNAI2, TGFBR2, MAP2K4, involved in both EMT and STAT3 signaling, were all decreased in cells treated with miR-204-5p mimics.

overall_design: UM-SCC1 cells were transfected with miR-204-5p mimics or corresponding control oligos. MiR-204-5p induced gene expression in UM-SCC1 cells was measured at 48 hours after transfection. Three independent experiments were performed for each group.

first: Zehang

last: Zhuang

first: Pei

last: Yu

last: Xie

first: Hongzhang

last: Huang


title: Genome-wide study the fruit ripening associated lncRNAs in strawberry

city: Nanchang

first: Dong

state: JiangXi

address: Hong Gu Tan New Road, No. 999

institute: Nanchang University

summary: With the development of high throughput sequencing technologies, plenty of non-coding RNAs (ncRNAs) have been discovered to play important roles in diverse plant biological processes. Although these ncRNAs extensively exist in plant, their biological functions are still remained to characterize. To obtain a comprehensive understanding of long non-coding RNA (lncRNA) function in strawberry fruit ripening progress, we performed transcriptomic analyses on the diploid strawberry Fragaria vesca in a time-course during fruit ripening. Here, we have identified 25,613 lncRNAs based on RNA-seq data from poly(A)-depleted libraries and rRNA-depleted libraries. Among them, most of lncRNAs exhibit stage-specific expression pattern. Functional analysis on F.vesca endogenous FRUIT RIPENING-RELATED LONG ANTISENSE INTERGENIC RNA (FRILAIR) in octaploid strawberry Falandi, we found that overexpression FRILAIR can compete miR397 to regulate its target laccase genes (LACs), and it may contribute to strawberry ripening. Our findings demonstrate that FRILAIR can act as a competing endogenous RNA (ceRNA) by disturbing miR397 to repress expression level of LACs, and would be valuable for strawberry ripening.

overall_design: High-depth paired-end RNA-seq from polyA depleted and rRNA depleted RNAs

first: Yajun

last: Tang


title: Induction of YAP5SA-GFP vs nGFP expression in FlipinTrex293 cells

city: Boston

first: Doaa

middle: AS

last: Megahed

state: MA

address: 200 Longwood Avenue, Harvard Medical schooL, WaB 536D

department: Systems Biology

institute: Harvard Medical School

summary: Dox-inducible YAP5SA-GFP/nGFP were treated with Doxycycline for 24 hours each and compared to non-treated controls

overall_design: Cells were grown to confluence in Tet-free medium (using Tet-compatible FBS from Clontech®) after which they were induced with 1or 0 ug/ml Doxycyline for 24 hours. One cell line expressed nGFP and the other GFP-tagged YAP5SA.


title: Genes expressed in the pleuropodia from embryos of the locust Schistocerca gregaria (Insecta, Orthoptera).

city: Ceske Budejovice

first: Barbora

last: Konopova

address: Branisovska 31

department: Institute of Entomology

country: Czech Republic

institute: Biology Centre CAS

summary: RNA-seq was used to study the genes expressed in peculiar glandular organs that transiently appear in insect embryos and are called the pleuropodia. The locust Schistocerca gregaria (Orthoptera) was used as a model. The purpose of the study is to identify the function of these organs. Our results suport the hypothesis (Slifer, 1937) that the pleuropodia secrete enzymes that digest the serosal cuticle before hatching. Additionally, we found that the pleuropodia may also have other functions, such as in embryonic immunity. The pleuropodia are peculiarly modified limbs. We show that in their early stages both legs and pleuropodia share a similar genetic landscape, but as the appendages become more morphologically diverse they became also more diverse genetically.

overall_design: Pleuropodia and legs of the third pair ("T3") at an equal age were compared. To identify DEGs upregulated in the mature pleuropodia that have morphological markers of active (secreting) organs samples from stages 10, 11 and 12 days were merged (legs and pleuropodia separately).

first: Elisa

last: Buchberger

first: Alastair

last: Crisp


title: Identification of Stretch Responsive microRNAs in Embyonic Mouse Cardiomyocytes

city: Seattle

first: Vishal

last: Nigam

address: 1900 9th Ave

department: Pediatrics

institute: Seattle Childrens Research Institute

summary: The goal of this study was to identify microRNAs that are modulated by cyclic stretch. miRNA-Seq was performed comparing samples from cultured E16.5 mouse cardiomyocytes exposed to either cyclic stretch of 16% at 1Hz for 24h or static conditions.

overall_design: 3 samples from cardiomyocytes cultured under static conditions were used as the controls. The 3 experimental samples were from cardiomyocytes exposed to cyclic stretch of 16% at 1Hz for 24h.

first: Nigam

last: Vishal


title: Adaptation of human cells to protein synthesis errors

city: Aveiro

first: Ana Sofia

last: Varanda

address: Campus Universitário Santiago

department: Health Sciences

country: Portugal

institute: University of Aveiro

summary: Protein synthesis is a highly regulated process and maintenance of its fidelity is essential to life. Alterations in the components of the protein synthesis machinery, namely RNAs, aminoacyl-tRNA synthetases (aaRS) or tRNA modifying enzymes, increase the level of protein synthesis errors (PSE), and are associated with several conditions, from cancer to neurodegeneration. Still, the cause-effect mechanisms remain to be elucidated in many conditions. In order to have a global picture of how human cells respond and adapt in culture we created stable HEK293 cell lines that express mutant tRNAs. For this, we modified the anticodon of a human serine transfer RNA (tRNASer), to incorporate the amino acid serine (Ser) at various non-cognate sites and overexpressed the wild type tRNASer to evaluate the effects of tRNA misexpression. DNA microarrays were then performed to identify the transcriptional deregulation induced by PSE of cells in culture at different time points (cells passages).

overall_design: HEK293 cells were stably transfected with a plasmid carrying modified tRNAs and five cell lines were created; Mock (empty plasmid, our control), tRNASer(S) (carrying the wild type serine tRNA); tRNASer(A) (carrying a serine tRNA with Alanine anticodon); tRNASer(L) (carrying a serine tRNA with Leucine anticodon) and tRNASer(H) (carrying a serine tRNA with Histidine anticodon). After the creation of stable cell lines (designed passage 1, P1), cells were kept in culture dishes and subcultured ever 3 days using the same dilution (1/6) until passage 30. Three biological replicates of each of the five cell lines was extracted at three time points; P1 (cells passage 1, after the creation of the stable cell lines); P15 (cells passage 15, an intermediary time point) and P30 (cells passage 30, end of evolution experiment). All 45 samples were hybridized in Sure Print G3 Human Gene Expression 8x60k v2 microarrays (Agilent Technologies, Cat.G4851B).

first: Ana

middle: S

first: Mafalda

last: Santos

last: Soares

first: Carla

last: Oliveira

first: Manuel


title: MicroRNA-204-5p is a tumor suppressor and potential therapeutic target in head and neck squamous cell carcinoma

first: Cheng

summary: To screen microRNAs (miRNAs) that are deregulated in head and neck squamous cell carcinoma (HNSCC), we comparatively analyzed the miRNA profiles by using 10 HNSCC patient samples and paired adjacent non-cancerous counterparts. Microarray analysis revealed that 24 miRNAs were downregulated and 19 miRNAs were elevated in HNSCC samples when compared with adjacent non-cancerous tissue. These miRNAs included upregulated miR-21-5p, miR-21-3p, and downregulated miR-99a-5p, which have been reported to regulate malignant progression of HNSCC in previous studies.

overall_design: A total of 10 fresh human HNSCC specimens and their paired adjacent non-cancerous counterparts were enrolled in this study, which were pathologically diagnosed. All patients received radical surgery and none received any form of pre-surgical adjuvant therapy.


title: scRNA-sequencing of ILC2 sorted from the choroid plexus and meninges of IL-33 treated aged (20-22 mos) mice

city: Albany

first: Ivan Ting Hin

last: Fung

address: 47 New Scotland Ave

institute: Albany Medical College

summary: ILC2 are potent producers of IL-5 and IL-13 and Th2 cytokines. We have found that they promote neurogenesis and cognitive functions in aged mice . We report that CP and meningeal ILC2 from IL-33 treated aged mice have differential expression of Th2 cytokines as well as genes involved in metabolism through scRNA-sequencing.

overall_design: We used the 10X Genomics platform to prepare scRNA-seq libraries to detail the global programme of different gene expression between ILC2 in the choroid plexus and meninges of IL-33 treated 20-22 mos aged mice

first: Qi

last: Yang

first: Ivan


title: Genome-wide studies of circular RNAs in Marek's tumorigenesis in Chicken (circRNA-Seq)

city: Beijing

first: lulu

last: wang

address: Malianwa

institute: China Agricultural University

summary: Marek's disease (MD), induced by Marek's disease virus (MDV), is a lymphotropic neoplastic disease and causes huge economic losses to the poultry industry. Non-coding RNAs play important regulatory roles in disease pathogenesis. To investigate host circRNA and miRNA expression profile, RNA sequencing was performed in tumorous spleens (TS), spleens from the survivors (SS) without any lesion after MDV infection, and noninfected chicken spleens (NS).

overall_design: we investigated the circular RNA (circRNA) profiles in the Marker's tumorigenesis disease in chicken through sequencing 14 samples for different stages of Marek's disease and analyzing the RNA-seq data using existing software

first: Lulu

last: Wang

first: Zhen

last: You

first: Mingyue

first: Yiming

last: Yuan

first: Changjun

last: Liu

first: Ning

first: Hao

last: Zhang

first: Ling

last: Lian


title: Genome-wide studies of microRNAs in Marek's tumorigenesis in Chicken (miRNA-Seq)

summary: Marek's disease (MD), induced by Marek's disease virus (MDV), is a lymphotropic neoplastic disease and causes huge economic losses to the poultry industry. Non-coding RNAs play important regulatory roles in disease pathogenesis. To investigate host miRNA expression profile, RNA sequencing was performed in tumorous spleens (TS), spleens from the survivors (SS) without any lesion after MDV infection, and noninfected chicken spleens (NS).

overall_design: we investigated the microRNA (miRNA) profiles in the Marker's tumorigenesis disease in chicken through sequencing 14 samples for different stages of Marek's disease and analyzing the RNA-seq data using existing software


title: A unified allosteric/torpedo mechanism for transcriptional termination on human protein-coding genes

city: Exeter

first: Steven

last: West

state: Devon

address: Stocker Rd

department: Living Systems Institute

institute: University of Exeter

summary: The so-called allosteric and torpedo models have been used for the past thirty years to explain how transcription terminates on protein-coding genes.  The former invokes conformational changes in the transcription complex and the latter involves degradation of the downstream product of poly(A) signal (PAS) processing.  Here, we describe a single mechanism incorporating features of both models.  We show that CPSF73 is indispensable for transcriptional termination on protein-coding and its loss causes profound read-through genome-wide.  CPSF73 functions upstream of allosteric modifications to the elongation complex that cause Pol II to slow down after the PAS.  This state is enriched by rapid depletion of XRN2 and promoted by protein phosphatase 1 (PP1), the inhibition of which confers runaway read-through in the absence of XRN2.  These allosteric changes facilitate XRN2-dependent termination, by aiding its capture of Pol II, rather than constituting a termination pathway in themselves.  Our experiments unify the long-standing allosteric and torpedo models for transcriptional termination.

overall_design: Chromatin-associated and nuclear RNA-seq was performed on a CPSF73 tagged auxin-inducible degron (AID) cell line treated with or without auxin to induce rapid depletion of the CPSF73 protein. The AID cassette consists of an in-frame insertion of the AID tag at the 3' exon, P2A cleavage sequence, antibiotic resistance marker and SV40 polyA site. Two repair plasmids containing either Hygromycin or Neomycin resistance markers were used to select for biallelic insertions of the repair cassettes by CRISPR/Cas9. This HCT116 cell line was additionally modified at the AAVS1 safe-habour locus by ectopic integration of a doxycycline-inducible TIR1 gene using a pMK243 repair template plasmid (addgene #72835) via CRISPR/Cas9. The TIR1 protein is the E3 ubiquitin ligase required to induce degradation of AID containing proteins in the presence auxin.

first: Joshua

middle: D

last: Eaton

first: Laura

last: Francis

first: Lee

last: Davidson


title: Preclinical Evaluation of Dual mTOR inhibitor, AZD2014, and Castration in Prostate Cancer

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

summary:
Purpose: RNA sequence analysis identified active proliferation of T cells in the combination therapy
Methods: Pten-null tumours were collected 4 hours after the last dose (18th day). Total RNA from tumor samples was isolated using the Allprep kit (Qiagen, Germany). The quantity of the RNA was assessed by Qubit (Life technologies) and quality was measured by Bioanalyzer 2100 (Agilent). Samples with 8 or more RNA integrity number (RIN) were used for library preparation and subsequent RNA sequencing. Library preparation was carried out using the Illumina® TruSeq Stranded mRNA Library Preparation Kit (Life Technologies) according to manufacturer recommendations. Single-end 50 bp sequencing reads were generated using Illumina HiSeq and were aligned to the human genome version hg19 or the mouse genome version mm10 using TopHat v2.0.4. Normalisation of read counts and identification of differential expression of genes (DEGs) were carried out using the DESeq v1.10.1 work flow.
Results: RNA sequence analysis identified differential gene expression between treatment groups and combination therapy clearly demonstrated active proliferation of cytotoxic lymphocytes.
Conclusions: Our study represents the first detailed analysis of Pten-null transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Pten-null tumours collected within 4 hours after the last dose of the specified dosing regimen. Single-end 50 bp sequencing reads were generated using Illumina HiSeq and were aligned to the human genome version hg19 or the mouse genome version mm10 using TopHat v2.0.4. Normalisation of read counts and identification of differential expression of genes (DEGs) were carried out using the DESeq v1.10.1 work flow.

first: Sandi

last: Chiranjeevi

first: Messie

last: Charlie

first: Antonio

last: Ramos-Montoya

first: Sérgio

last: Felisbino

first: Davies

last: Barry

first: Pacey

last: Simon


title: microRNA repertoire of wild-type C57BL/6 mice T cell blasts and their secreted small extracellular vesicles (Evs)

status: Public on Jan 20 2020

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: T cell blasts were obtained from wild-type  C57BL/6 mice. Six-day culture blast supernatants were ultracentrifuged for small EV obtention and small EV pellet obtained after from 100,000g ultracentrifugation and T cell blasts RNA were isolated for small RNA sequencing;  (N=3) independent experiments

overall_design: Total splenocytes were isolated from spleens of 8-to-12-week old WT C57BL/6 mice.Cells were cultured in the presence of Concanavalin and EVs were isolated from supernatants of 6-day lymphoblast cultures by serial ultracentrifugation. Total RNA from cells and secreted small EVs was isolated using the miRNeasy RNA Isolation Kit (QIAGEN). RNA was amplified and prepared for small RNA-Seq using the SmallRNA NEBNext Library Prep Set (New England Biolabs) following the manufacturer’s recommendations and sequenced using the Illumina HiSeq 2500 System. Three biological replicates were analyzed.

first: L

last: Fernandez-Messina

first: A

last: Rodríguez-Galán

first: V

middle: G

last: García de Yébenes

first: C

last: Gutiérrez-Vázquez

first: S

last: Tenreiro

middle: R

last: Ramiro

first: F

last: Sanchez-Madrid


title: Targeted deletion of mouse Slc25a28 (Mitoferrin2) reveals Mitoferrin1 and Mitoferrin2 are necessary for liver regeneration and cell proliferation

city: Salt Lake City

first: Diane

middle: M

last: Ward

state: UT

address: 15 N Medical Dr Suite 1100

department: Pathology Department - School of Medicine

institute: University of Utah

summary: Hepatocyte-specific loss of Slc25a37 (Mitoferrin1) in Mitoferrin2-/- mice did not affect animal viability or liver size suggesting that there must be alternative hepatocyte mitochondrial iron importers that function in the absence of Mitoferrins.

overall_design: Liver mRNA profiles  from aged-matched  controls and hepatocyte-specific loss of both mitoferrins (Alb-cre Mfnr1-/- Mfrn2-/-) animals.

first: Alexandra

last: Seguin


title: Imprinted Cdkn1c Genomic Locus Cell-Autonomously Promotes Cell Survival in Cerebral Cortex Development [cdkn1c_KO]

city: Klosterneuburg

first: Florian

last: Pauler

address: Am Campus 1

institute: Institute of Science and Technology Austria (IST Austria)

summary: The cyclin-dependent kinase inhibitor p57KIP2 is encoded by the imprinted Cdkn1c locus, exhibits maternal expression, and is essential for cerebral cortex development. How Cdkn1c regulates corticogenesis is however not clear. To this end we employ Mosaic Analysis with Double Markers (MADM) technology to genetically dissect Cdkn1c gene function in corticogenesis at single cell resolution. We find that the previously described growth-inhibitory Cdkn1c function is a non-cell-autonomous one, acting on the whole organism. In contrast we reveal a growth-promoting cell-autonomous Cdkn1c function which at the mechanistic level mediates radial glial progenitor and nascent projection neuron survival. Strikingly, the growth-promoting function of Cdkn1c is highly dosage sensitive but not subject to genomic imprinting. Collectively, our results suggest that the Cdkn1c locus regulates cortical development through distinct cell-autonomous and non-cell-autonomous mechanisms. More generally, our study highlights the importance to probe the relative contributions of cell intrinsic gene function and tissue-wide mechanisms to the overall phenotype.

overall_design: Transcriptome changes upon deletion of Cdkn1c gene locus in cortical projection neurons

first: Susanne

last: Laukoter

first: Robert

last: Beattie

first: Simon

last: Hippenmeyer


title: Establishing hematopoietic stem cell gene therapy for breast cancer brain metastases using intratumoral myeloid cell-specific gene promoters

city: Leeds

first: Mihaela

last: Lorger

address: Beckett street

department: Leeds Institute of Cancer and Pathology

institute: University of Leeds

summary: The goal was to identify genes that are differentially expressed between the bone marrow-derived CD11b+ myeloid cells infiltrating intracranial tumors and the peripheral myeloid cells (e.g. infiltrating the spleen and bone marrow).

overall_design: Murine breast cancer cells (EO771 or PyMT, respectively) were injected intracranially into C57Bl6 mice with chimeric green fluorescent protein (GFP)-tagged bone marrow. Approximately 2 weeks later, the intracranial tumors, the spleens and the bone marrow were harvested, the GFP+CD11b+ cells were isolated by FACS and processed for RNA isolation.


title: Dynamic changes in gene expression during early differentiation of embryonic stem cells

city: Toronto

first: Jennifer

last: Mitchell

state: Ontario

address: 25 Harbord Street

department: Cell and Systems Biology

institute: University of Toronto

summary: We monitor the changes in genome-wide gene expression 6, 12 and 24 hours after removal of LIF and 2i from the ES cell culture media.

overall_design: Examination of PolyA+ RNA after LIF/2i removal from mouse enbryonic stem cells

first: Gurdeep

last: Singh

first: Scott

last: Davidson


title: microRNA expression changes in DICER-KO B cells after OVA-specific immune synapse formation

first: Manuel

last: Gomez

summary: Intercellular communication orchestrates effective immune responses against disease-causing agents. Extracellular vesicles (EVs) are potent mediators of cell-cell communication. EVs carry bioactive molecules, including microRNAs, which modulate gene expression and function in the recipient cell. Here, we show that formation of cognate primary OVA-specific T-B lymphocyte immune contacts promotes transfer to the B cell of a very restricted set of OTII-derived CD4+ T cell exosomal microRNAs (mmu-miR20a-5p, mmu-miR-25-3p and mmu-miR-155-3p). To discriminate exogenously transferred microRNAs from microRNAs induced in B cells after immune synaps, small RNAseq of CD19Cre/Ki DICERfl/fl (DICER-KO) B cells, virtually lacking mature microRNAs, alone and cocultured with OTII CD4+T cells in the presence and absence of OVA was performed; (N=3) independent experiments

overall_design: B cells isolated from CD19Cre/Ki DICERfl/fl (DICER-KO) mice were either left alone or cocultured with OVA-specific OTII-derived CD4+T cells in a 1B:4T ratio, either in the presence or absence of OVA peptide. After 16h culture, B lymphocytes were sorted and total RNA was isolated using the miRNeasy RNA Isolation Kit (QIAGEN). RNA was amplified and prepared for small RNA-Seq using the SmallRNA NEBNext Library Prep Set (New England Biolabs) following the manufacturer’s recommendations and sequenced using the Illumina HiSeq 2500 System. Three biological replicates were analyzed.

last: Fernandez-Messina


title: Transcriptome analysis defines ToF and ASD myocardial gene signatures and reveals disease-specific gene reprogramming upon surgery with cardiopulmonary bypass

city: Genova

first: Davide

last: Cangelosi

address: Via Gerolamo Gaslini 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

summary: Tetralogy of Fallot (ToF) and Atrial Septal Defects (ASD) are the most common types of congenital heart disease and a major cause of childhood morbidity and mortality. Cardiopulmonary bypass (CPB) is used during corrective cardiac surgery to support circulation and heart stabilization. However, this technique triggers systemic inflammatory and stress response and consequent increased risk of postoperative complications. The aim of this study was to define the molecular bases of ToF and ASD pathogenesis and response to CPB and identify new specific biomarkers. We conducted comparative transcriptome analysis of right atrial biopsies from 10 ToF and 10 ASD patients before (Pre-CPB) and after (Post-CPB) surgery. Pre-CPB samples showed significant differential expression of 72 genes (DEGs), 28 of which were overexpressed in ToF and 44 in ASD. According to Gene Ontology annotation, the mostly enriched biological processes were represented by matrix organization and cell adhesion in ToF and by muscle development and contractility in ASD specimens. GSEA highlighted the specific enrichment of known hypoxia gene sets in ToF samples, pointing to a role for hypoxia in disease pathogenesis. The post-CPB myocardium exhibited significant alterations in the expression profile of genes related to transcription regulation, growth/apoptosis, inflammation, cell adhesion/matrix organization, and oxidative stress. Among DEGs, only 70 were common to the two disease groups, whereas 110 and 24 were unique in ToF and ASD, respectively. Interestingly, gene expression changes in ASD samples followed a consensus hypoxia profile. These data define ToF- and ASD-specific myocardial transcriptional signatures and demonstrate differential gene reprogramming in response to CPB in the two pathologies, with potential prognostic and therapeutic implications.

overall_design: Transcriptome analysis of human atrial tissues from children affected by TOF or ASD following surgery with cardio-pulmonary bypass.

first: Federica

last: Raggi

first: Martina

last: Morini

first: Pamela

last: Becherini

first: Fabiola

last: Blengio

first: Massimo

last: Acquaviva

first: Luisa

last: Belli

first: Giuseppe

last: Panizzon

last: Cervo

first: Luigi

last: Varesio

first: Alessandra

last: Eva

first: Maria

last: Bosco


title: Conjunctival and mucosal melanoma

city: Copenhagen

first: Lauge Hjorth

last: Mikkelsen

address: Frederik V's Vej 11, 1st Floor

department: Pathology

country: Denmark

institute: Copenhagen University Hospital

summary:
NanoString data on 12 conjunctival melanomas and mucosal melanoma
The objective was to compare conjunctival melanoma with other mucosal melanomas at the RNA level using NanoString expression analysis of FFPE material.

overall_design: approximately 10 samples of melanome from each anatomical mucosal location (conjunctiva, nasal, rectal, and vaginal mucosal were compared.

first: Lauge

middle: H

first: Steffen

last: Heegaard


title: CircRNAs function as a new layer of regulation in rice-Magnaporthe oryzae interaction

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: We reported effects of Magnaporthe oryzae infection on  expression of circRNA in  the young leaves of the blast-resistant accession IRBLkm-Ts (IR25) and the blast-susceptible accession Lijiangxin Tuan Heigu (LTH)

overall_design: Leaves of three-week-old seedlings of LTH and IR25  were collected at 0, 12, 24 hour post inoculation (hpi) with spores of Magnaporthe oryzae

first: Jin

last: fan


title: Imprinted Cdkn1c Genomic Locus Cell-Autonomously Promotes Cell Survival in Cerebral Cortex Development

first: Florian

last: Pauler

overall_design: RNA-Seq of sorted neurons

first: Susanne

last: Laukoter

first: Robert

last: Beattie

first: Simon

last: Hippenmeyer


title: The Habenular G-Protein-Coupled Receptor 151 regulates synaptic plasticity and nicotine intake

status: Public on Jan 18 2020

city: New York

first: Laura

last: Kus

state: NY

address: 1230 York Avenue # 260

department: Heintz Laboratory

country: USA

institute: The Rockefeller University

summary: The habenula, an ancient small brain area in the epithalamus, densely expresses nicotinic acetylcholine receptors and is critical for nicotine intake and aversion. As such, identification of strategies to manipulate habenular activity may yield new approaches to treat nicotine addiction.  Here we show that GPR151, an orphan G protein-coupled receptor (GPCR) highly enriched in the habenula of humans and rodents is expressed at presynaptic membranes and synaptic vesicles, and associates with synaptic components controlling vesicle release and ion transport. Deletion of Gpr151 inhibits evoked neurotransmission but enhances spontaneous miniature synaptic currents and eliminates short-term plasticity induced by nicotine. We find that GPR151 couples to the G-alpha inhibitory protein Gao1 to reduce cAMP levels in mice and in GPR151 expressing cell lines that are amenable to ligand screens. Gpr151-KO mice show diminished behavioral responses to nicotine, and self-administer greater quantities of the drug, phenotypes rescued by viral re-expression of Gpr151 in the habenula. These data identify GPR151 as a critical modulator of habenular function that controls nicotine addiction vulnerability.

overall_design: TRAP-Seq of neurons in the medial habenula of adult Gpr151-KO::Chat-TRAP DW167 mice

first: Beatriz

last: Antolin-Fontes

first: Li

last: Kun

first: Jessica

middle: L

last: Ables

first: Michael

last: Riad

first: Andreas

last: Görlich

first: Maya

last: Williams

first: Nathaniel

last: Heintz

first: Paul

last: Kenny

first: Ines

last: Ibañez-Tallon


title: Transcriptome analysis of blast Side and Main populations cells in patients with acute myeloid leukemia

city: VILLEJUIF

first: christophe

last: desterke

address: 14-16 avenue Paul Vaillant Couturier

department: UFR medecine institute Andre Lwoff

country: France

institute: university Paris Sud11

summary: Acute myeloid leukemia (AML) represent a series of hemopathies characterized by the clonal expansion in bone marrow and blood of immature myeloid cells blocked in differentiation, called blasts. Despite significant supportive care progresses, few medical discoveries radically changed LAM prognosis (5 year survival rate of 30%). An aggressive conventional chemotherapy is used to kill AML cells. However, many patients relapse mainly due to the persistence of rare AML cells able to re-initiate the disease. Quiescence and protection against environmental stresses (chemoresistance) are major characteristics of these cells. Drug efflux leading to chemoresistance is observed by Side Population (SP) detection through ABC transporter activation. So, AML blasts presenting SP functionality could represent a chemoresistant population. This SP phenotype is essentially acquired by circulating AML blasts after contact with medullar mesenchymal stromal cells (MSC). A transcriptome analysis of AML blasts sorted according to their SP functionality or not (Non SP cells or Main Population, ie MP) after co-culture on MSCs was realized.

overall_design: Transcriptome analysis was performed on Side population (SP) AML blasts versus Non Side population (NSP) AML blasts, also named main population (MP). Cells were sorted after a 3-day co-culture of peripheral blood AML blast sample at diagnosis with human medullar mesenchymal stromal cells.

first: Laetitia

last: Boutin

first: Pierre

last: Arnautou

first: Christophe

last: Desterke

first: Emmanuel

last: Raffoux

first: Jean-Valère

last: Malfuson

first: Jean-Jacques

last: Lataillade

first: Marie-Caroline

last: Le Bousse-Kerdilès

first: Adrienne

last: Anginot


title: The chromatin remodeler Snf2h is essential for oocyte meiotic cell cycle progression

status: Public on Jan 19 2020

city: Cincinnati

first: Zhiyuan

last: Chen

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: Oocytes are indispensable for mammalian life. Thus, it is important to understand how mature oocytes are generated. As a critical stage of oocytes development, meiosis has been extensively studied, yet how chromatin remodeling contributes to this process is largely unknown. Here, we demonstrate that the ATP-dependent chromatin remodeling factor Snf2h (also known as Smarca5) plays a critical role in regulating meiotic cell cycle progression. Females with oocyte-specific depletion of Snf2h are infertile and oocytes lacking Snf2h fail to undergo meiotic resumption. Mechanistically, depletion of Snf2h results in dysregulation of meiosis-related genes, which causes failure of maturation-promoting factor (MPF) activation. ATAC-seq analysis in oocytes revealed that Snf2h regulates transcription of a key meiotic gene, Prkar2b, by increasing its promoter chromatin accessibility. Our studies thus not only demonstrate the importance of Snf2h in oocyte meiotic resumption, but also reveal the mechanism underlying how a chromatin remodeling factor can regulate oocyte meiosis.

overall_design:
RNA-seq were performed for Snf2h WT and KO oocytes at different developmental stages [i.e., Growing1 (40-45um), Growing2 (50-55um), Fully-grown oocytes (>70um)]. For each stage, two RNA-seq replicates were performed for each group. For FGO, oocytes were collected without or with prior hormon stimulation, which are referred to as non-hormone stimulated FGO (nFGO) and FGO, respectively.
Two ATAC-seq replicates were performed in Growing1 and fully grown oocytes from both Snf2h WT and conditional KO female mice.

first: Chunxia

last: Zhang

first: Qiangzong

last: Yin

first: Xudong

last: Fu

first: Yisi

last: Li

first: Tomas

last: Stopka

first: Arthus

last: Skoultchi

first: Yi


title: Identification of tRFs&tiRNAs Expression Profile in Breast Cancer Tissues

city: Nanjing

first: Yining

last: Yang

state: Jiangsu

address: 42 Baiziting Road

department: Clinical Laboratory

institute: Jiangsu Cancer Hospital

summary:
Purpose:In recent years, tRFs(transfer RNA-Derived Fragments) & tiRNAs (transfer RNA-Derived Stress-induced RNAs or tRNA halves) have been shown to have vital roles in cancer biology. We aimed to reveal the expression profile of tRFs&tiRNAs in breast cancer tissues in the study, and to explore their potential as biomarkers of breast cancer.
Methods:We characterize tRFs&tiRNAs expression profiles in 6 pairs of breast cancer tissues and adjacent normal samples.Then we selected six tRFs&tiRNAs with significant expression and added 10 pairs of samples to verify the selected genes by qPCR in 16 pairs of breast cancer tissues along with the previous 6 pairs.
Results:We found 31 differentially expressed tRFs&tiRNAs across our dataset, out of which 17 were up-regulated, 14 were down-regulated. Compared with 16 breast cancer tissues and healthy controls by qPCR, the results demonstrated that AS-tDR-001430, AS-tDR-001130 and AS-tDR-000779 were significantly expressed in breast cancer tissues (p < 0.001). AS-tDR-000779 was significantly up-regulated, AS-tDR-001430 and AS-tDR-001130 were significantly down-regulated which the expression patterns were similar to the sequencing results.
Conclusions:Our studies have demonstrated that there were significantly expressed tRFs&tiRNAs in breast cancer tissues. They are hopefully to become biomarkers and would be valuable researches in this area.

overall_design: tRFs&tiRNAs profiles of 6 pairs of breast cancer tissues and adjacent normal samples by deep sequencing, using Illumina NextSeq 500.

first: Xiaoming

last: Wang


title: Circulating CD1c+ myeloid dendritic cells are precursors to Langerhans cell histiocytosis (LCH) lesion CD1a+CD207+cells

city: Houston

first: Carl

last: Allen

state: TX

address: 1102 Bates Street, C1024.25

department: Department of Pediatrics- Cancer

institute: Baylor College of Medicine

summary:
Expression data from LCH lesion subpopulations and healthy donors' peripheral blood specimens
Langerhans cell histiocytosis (LCH) is a myeloproliferative disorder that is characterized by the inflammatory lesions with pathogenic CD1a+CD207+ dendritic cells (DCs).  BRAFV600E and other somatic activating MAPK gene mutations have been identified in differentiating bone marrow and blood myeloid cells, but the origin of the LCH lesion CD1a+CD207+DCs and mechanisms of lesion formation remain incompletely defined.   In order to identify candidate LCH CD1a+CD207+DCs’ precursor populations, gene expression profiles of LCH lesion CD1a+CD207+DCs were first compared to established gene signatures from human myeloid cell subpopulations. Interestingly, the CD1c+ myeloid DC (mDC) gene signature was most enriched in the LCH CD1a+CD207+DC’ transcriptome.  Additionally, the BRAFV600E allele was not only localized to CD1a+CD207-DCs and CD1a+CD207+DCs, but it was also identified in CD1c+mDCs in LCH lesions. Transcriptomes of CD1a+CD207-DCs were nearly indistinguishable from CD1a+CD207+DCs (both CD207low and CD207high subpopulations).  Transcription profiles of LCH lesion CD1a+CD207+DCs and peripheral blood CD1c+mDCs from healthy donors were compared to identify potential LCH DC-specific biomarkers. HLADQB2 expression was significantly increased in LCH lesion CD1a+CD207+DCs compared to circulating CD1c+mDCs from healthy donors, and HLA-DQB2 antigen was identified on LCH lesion CD1a+CD207- and CD1a+CD207+DCs as well as on CD1c+(CD1a+CD207-) mDCs, but not in any other lesion myeloid subpopulations. Interestingly, HLADQB2 expression was specific to peripheral blood of patients with BRAFV600E+ peripheral blood mononuclear cells (PBMC), and HLA-DQB2+CD1c+blood cells were highly enriched for the BRAFV600E in these patients. These data support a model where blood CD1c+mDCs with activated ERK migrate to lesion sites where they differentiate into pathogenic CD1a+CD207+ DCs.

overall_design: 57 samples: 18 healthy donor peripheral blood/skin subpopulations and 39 LCH lesion subpopulation specimens

first: Karen Phaik Har

last: Lim

first: Paul

last: Milne

first: Florent

last: Ginhoux

first: Matthew

last: Collin


title: MGA represses MYC-target genes [ChIP-seq]

first: Xiaoyang

address: 1950 CIrcle of Hope

summary: We used ChIP-seq to map the binding sites of MGA and MYC in the lung adenocarcinoma cell line A549 cells

overall_design: ChIP-seq of MGA and c-MYC in A549 cells