title: Genome-wide maps of histone modifications in mouse tumor-derived cell lines

city: Macau

first: Ning-Yi

last: Shao

address: E12-3009, University of Macau

institute: University of Macau

summary: Amplification of chromosomal region 8p11-12 is a frequent genetic alteration implicated in the etiology of lung squamous cell carcinoma (LUSC). Here we identify the H3K36 methyltransferase NSD3 (nuclear receptor binding SET domain protein 3), an 8p11-12-localized gene, as a key regulator of LUSC tumorigenesis. We identify NSD3T1232A as an LUSC-associated variant that increases H3K36 dimethylation (H3K36me2) catalytic activity in vitro and in vivo. NSD3T1232A expression in vivo in LUSC mouse models accelerates tumorigenesis and decreases overall survival. Pathologic generation of H3K36me2 by NSD3T1232A rewires the chromatin landscape to promote oncogenic gene expression programming. Together, our work identifies NSD3 as a principal 8p11-12 amplicon-associated oncogenic driver in LUSC and suggests that NSD3-dependency renders LUSC therapeutically vulnerable to BETi.  Here we report the application of Cut and Run technology for high-throughput prolifiling of histone modiifcations in mouse tumor-derived cell lines. We found NSD3 loss leads to decrase of histone H3 lysine 36 dimethylation over gene body regions and intergenic regions, while histone H3 lysine 27 trimethylation is increased over these regions. We also reported that NSD3 depletion mainly down-regulates the expression of genes in PI3K-Akt-mTORC1 pathway and Myc targets through total RNA-seq.

overall_design: Examination of 2 different histone modifications in mouse tumor-derived cell lines in 2 different conditions

first: Gang

last: Yuan

first: Or

last: Gozani


title: The small transcriptome of Escherichia coli in exponential and stationary phase

status: Public on Nov 21 2020

city: Bern

first: Norbert

last: Polacek

address: Freiestrasse 3

department: Chemistry and Biochemistry

country: Switzerland

institute: University of Bern

type: Non-coding RNA profiling by high throughput sequencing

summary: We have deep sequenced the small transcriptome of Escherichia coli growing in LB and in MOPS, in exponential and stationary phase, and analyzed the resulting reads by a novel pipeline STARPA (Stable RNA Processing Product Analyzer). Our analysis reveals over 14,000 small transcripts enriched during both growth stages. RNA samples were collected from total RNA pools or from crude ribosome pools and then size selected by electrophoresis to limit the products to 20-300nt.

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Differential expression analysis demonstrates the presence of enriched small transcripts in stationary phase, likely mediating regulatory functions.

first: Luidalep

last: Hannes

first: Raad

last: Nicole

first: Fasnacht

last: Michel

first: Polacek

last: Norbert


title: An integrated RNA-Seq and network study reveals the effect of nicotinamide on adrenal androgen synthesis

status: Public on Nov 19 2020

city: Jinan

first: Xueying

last: Gao

address: Jingliu Rd.

country: China

institute: Shandong University

type: Expression profiling by high throughput sequencing

summary: Acne vulgaris is a chronic inflammatory disease of the skin resulting from androgeninduced  increased sebum production and altered keratinization. Nicotinamide (NAM),  an amide form of vitamin B3 with a well-established safety profile, has shown good  therapeutic potential in treating acne and its complications. NAM has anti-inflammatory  effects and reduces sebum but its function in androgen biosynthesis remains  unknown. In this study, we used a widely used cell model, starved human adrenal  NCI-H295R cells, to examine the effects of NAM in androgen production and its mediated  network changes. By treating NCI-H295R cells with 1-25 mmol/L of NAM, we  found that cell viability was only slightly inhibited at the highest dose (25 mmol/L).  NAM reduced testosterone production in a dose-dependent manner. Transcriptomic  analysis demonstrated that key enzymes of androgen biosynthesis were significantly  decreased under NAM treatment. In addition, gene set enrichment analysis (GSEA)  showed that gene sets of cell cycle, steroid biosynthesis, TGFβ signalling, and targets  of IGF1 or IGF2 were enriched in NAM-treated cells. Kyoto Encyclopaedia of Genes  and Genomes (KEGG) pathway and Gene ontology (GO) analysis of the differentially  expressed genes also suggested that steroidogenesis and SMAD signalling were affected  by NAM. Overall, these crucial genes and pathways might form a complex  network in NAM-treated NCI-H295R cells and result in androgen reduction. These  findings help explain the potential molecular actions of NAM in acne vulgaris, and  position NAM as a candidate for the treatment of other hyperandrogenic disorders.

overall_design: starved NCI-H295R cells treated  with or without 25 mmol/L NAM for 24 hours

first: Xue-Ying

first: Wei

last: Zhang


title: Epigenome-Wide Association Study for Atrazine Induced Transgenerational Histone Retention Sperm Epigenetic Biomarkers for Disease

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

country: USA

institute: WSU

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Atrazine is a common agricultural herbicide previously shown to promote epigenetic transgenerational inheritance of disease to subsequent generations. The current study was designed as an epigenome-wide association study (EWAS) to identify transgenerational sperm disease associated differential histone retention regions (DHRs). Gestating female F0 generation rats were transiently exposed to atrazine during the period of embryonic gonadal sex determination, and then subsequent F1, F2, and F3 generations obtained in the absence of any continued exposure. The transgenerational F3 generation males were assessed for disease and sperm collected for epigenetic analysis. Pathology was observed in late pubertal onset and for testis disease, prostate disease, kidney disease, lean pathology, and multiple disease. For these pathologies, sufficient numbers of individual males with only a single specific disease were identified. The sperm DNA and chromatin were isolated from adult one-year animals with the specific diseases and analyzed for DHRs with histone chromatin immunoprecipitation (ChIP) sequencing. Transgenerational F3 generation males with or without disease were compared to identify the disease specific epimutation biomarkers. No common DHRs were found among all the pathologies. Epimutation gene associations were identified and found to correlate to previously known disease linked genes.

overall_design: Analysis of the transgenerational actions of atrazine used outbred Sprague Dawley female rats (F0 generation) transiently exposed (25 mg/kg body weight atrazine daily) during days 8 to 14 of gestation. The F1 generation animals (direct fetal exposure) were bred to generate the F2 generation (direct germline exposure), which were bred to generate the F3 generation (transgenerational so no direct exposure). A control lineage used F0 generation gestating females administered vehicle control dimethyl sulfoxide (DMSO). The control and atrazine lineages were aged to 1 year and euthanized for pathology and sperm epigenetic analysis. No sibling or cousin breedings (crosses) were used to avoid any inbreeding artifacts in either the control or atrazine lineages. Generally 6–8 founder gestating females from different litters were bred and 25–50 individuals of each sex obtained for each generation.

first: Jennifer

middle: L

last: Thorson

first: Daniel

last: Beck

first: Millissia

middle: B

last: Maamar

first: Eric

last: Nilsson

first: McBirney

last: Margaux


title: Interaction of preimplantation factor with the global bovine endometrial transcriptome

city: Aberystwyth

first: Ruth

middle: Elizabeth

last: Wonfor

state: Ceredigion

address: Penglais

department: IBERS

country: United Kingdom

institute: Aberystwyth University

summary: We report the effect of synthetic preimplantation factor (sPIF) on the bovine endometrial transcriptome in an ex vivo model. Bovine endometrial explant tissues were cultured from heifers in the follicular stage of the oestrous cycle (n=7). Explants from each animal were cultured in media alone or in the presence of sPIF for a total of 30h and total RNA extracted and RNA-sequencing performed on Illumina HiSeq. Following quality assessment, trimming via Trimmomatic and alignment through Bowtie 2, featureCounts was used to calculate read abundance and deSeq2 to analyse differentially expressed genes following sPIF treatment. As a result of sPIF treatment, 102 genes were differentially expressed compared to the control (Padj<0.1), although none by more than 2-fold. Pathway analysis revealed targeting of several immune based pathways. Steroid biosynthesis was the only over-represented pathway with all genes upregulated. We demonstrate that sPIF can modulate the bovine endometrial transcriptome in an immune modulatory manner, like that in the human endometrium, however, the regulation of genes was much weaker than in previous human work.

overall_design: Evaluation of total RNA via RNA-seq from bovine endometrial tissue with or without sPIF treatment. Seven animals used with RNA extracted from 2 explants per animal (with or without sPIF treatment) Giving a total of 14 RNA-seq samples.

middle: E

first: Christopher

middle: J

last: Creevey

first: Manuela

last: Natoli

first: Matthew

last: Hegarty

first: Deborah

middle: M

last: Nash

middle: T

last: Rose


title: H3K79me2 naïve and in vitro activated B cells

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

summary: We studied the role of the histone methyltransferase DOT1L in B cell development and differentiation. H3K79me2 ChIP-sequencing data was generated from sorted B cells. This was compared to RNA-sequencing data from WT and Dot1L KO mice in order to study the link between H3K79me2 and transcription.

overall_design: Examination of H3K79me2 in naïve and activated B cells

first: Teun

middle: A

last: van den Brand

first: Muhammad

last: Aslam

first: Tibor

last: van Welsem


title: De novo DNA methyltransferase activity in colorectal cancer is directed towards H3K36me3 marked CpG island (RRBS)

status: Public on Nov 24 2020

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

institute: University of Edinburgh

type: Methylation profiling by high throughput sequencing

summary: The aberrant gain of DNA methylation at CpG islands (CGIs) is frequently observed in colorectal tumours and may silence the expression of tumour suppressors such as MLH1. Current models propose that these CGIs are targeted by de novo DNA methyltransferases (DNMTs) in a sequence-specific manner but this has not been tested. Using ectopically integrated CGIs, we find that aberrantly methylated CGIs are subject to low levels of de novo DNMT activity in colorectal cancer cells. By delineating DNMT targets, we find that instead de novo DNMT activity is targeted primarily to CGIs marked by the histone modification H3K36me3, a mark associated with transcriptional elongation. These H3K36me3 marked CGIs are heavily methylated in colorectal tumours and the normal colon suggesting that de novo DNMT activity at CGIs in colorectal cancer is focused on similar targets to normal tissues and not greatly remodelled by tumourigenesis.

overall_design: This series contains RRBS from human cancer cell lines


title: Characterization of FOXA1 mutations in breast cancer

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

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

overall_design: Refer to individual Series


title: Plasma cells are enriched in localized prostate cancer in black men and are associated with improved outcomes

status: Public on Nov 18 2020

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St, Suite 430

country: Canada

institute: Decipher Biosciences, Inc.


title: Regulation of Ex-Translational Activities Is Primary Function of Multi-tRNA Synthetase Complex

city: La Jolla

first: Paul

last: Schimmel

state: California

address: 10550 North Torrey Pines Road, BCC379

department: Molecular Medicine

institute: The Scripps Research Institute

summary: During mRNA translation, tRNAs are charged by aminoacyl-tRNA synthetases (aaRS) and subsequently used by ribosomes. A multi-enzyme aminoacyl-tRNA synthetase complex (MSC) has long been proposed to increase protein synthesis efficiency by passing charged tRNAs directly to ribosomes. An alternative is that the MSC repurposes specific synthetases for ex-translational functions that are activated by cues that direct specific enzymes to novel targets. To explore this question, we generated mammalian cell clones in which ArgRS and GlnRS were absent from the MSC to give a stable complex lacking the two enzymes (MSCΔRQ). Protein synthesis, under a variety of stress conditions, was unchanged in MSCΔRQ cells. Most strikingly, levels of charged tRNAGln and tRNAArg remained unchanged and no ribosome pausing was observed at codons for Arg and Gln. Thus, increasing or regulating protein synthesis efficiency is not dependent on ArgRS and GlnRS in the MSC. Alternatively, and consistent with previously reported ex-translational roles, we found manipulations that do not affect protein synthesis but instead MSC cellular localization.

overall_design: Ribosome footprints of wildtype, ArgRS deltaLZ, and delta LZ + LZ mCer HEK 293T cells.

first: Haissi

last: Cui

first: Mridu

last: Kapur

first: Susan

last: Ackerman


title: Plasma cells are enriched in localized prostate cancer in black men and are associated with improved outcomes  [Discovery Cohort]

summary:
Black men die more often of prostate cancer (PC) yet, interestingly, may derive greater survival benefits from immunotherapy. Since no signatures of immune-responsiveness exist for PC, we explored race-based immune-profiles to identify vulnerabilities.
Black men have increases in plasma cell infiltrate and associated augmented NK cell and IgG activity. These findings are associated with improved survival and nominate plasma cells as drivers of PC immune-responsiveness.

overall_design: This discovery cohort was comprised of two groups of patients who underwent radical prostatectomy and no additional treatment until metastatic recurrence at Johns Hopkins Medical Institute (JHMI). The first group consisted of 355 intermediate- or high-risk patients treated between 1995 and 2005, of which 33 were Black.1 The second group consisted 143 Black men treated from 2006 to 20102 for a total of 355 White men and 176 Black men. To prepare for matching, 6 (1%) men were excluded due to missing data on pathological stage. All men with grade group 1 disease were excluded given the disproportionate numbers among Black men (24 vs 6; 30 total, 6%). Finally, the cohort was randomly sorted before using the “matchit” function from the “Matchit” R package to derive a final grade- and stage-matched cohort of 300 men, 150 each of Black and White men. Race was defined by self-identification in this cohort.

first: Adam

last: Weiner

first: Thiago

last: Vidotto

first: Yang

last: Liu

first: Adrianna

last: Mendes

first: Daniela

middle: C

last: Salles

first: Farzana

last: Faisal

first: Sanjana

last: Murali

last: McFarlane

first: Eddie

last: Imada

first: Xin

last: Zhao

first: Ziwen

last: Li

first: Luigi

last: Marchionni

first: Arul

last: Chinnaiyan

first: Stephen

last: Freedland

first: Daniel

last: Spratt

first: Jennifer

last: Wu

first: Tamara

last: Lotan

first: Edward

last: Schaeffer


title: The INO80 complex regulates epigenetic inheritance of heterochromatin

first: Songtao

last: Jia

address: 116th & Broadway

department: Biological Sciences

institute: Columbia University


title: Microglial RNA sequencing from humanized mouse model expressing schizophrenia susceptibility factor C4A

status: Public on Nov 17 2020

city: Boston

first: Melis

last: Yilmaz

state: MA

address: 300 Longwood Avenue

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

summary: Human C4A gene locus is associated with increased schizophrenia risk. In order to investigate this genetic link, we constructed two mouse models that express human C4A or C4B, and one that overexpresses C4A. To investigate whether the isotypic effects of human-C4 gene is observed in the microglial transcriptional profile during adolescence in mice (postnatal day 40) in the medial prefrontal cortex, we conducted a bulk RNA sequencing of microglia. Our analyses showed no significant differentially expressed genes between any two groups.

overall_design: Microglial mRNA profiles of P40 humanized-transgenic mice containing human C4A and C4B sequences

first: Jessy

last: Presumey

first: Ernest

last: Aw

first: Michael

last: Carroll


title: The INO80 complex regulates epigenetic inheritance of heterochromatin (RNA-seq)

summary: One key aspect of epigenetic inheritance is that chromatin structure can be stably inherited through generations even after removal of the initial signal that establishes such structure. In fission yeast, the RNA interference (RNAi) machinery is critical for the targeting of histone methyltransferase Clr4 to repetitive DNA elements to establish a large domain of heterochromatin marked with histone H3 lysine 9 methylation (H3K9me). Subsequently during DNA replication, the deposition of parental histones containing H3K9me into daughter DNA strands is expected to recruit Clr4 to modify neighboring new histones, resulting in the inheritance of heterochromatin in both daughter cells. However, pericentric heterochromatin cannot be properly inherited in the absence of RNAi, suggesting the existence of mechanisms that counteract chromatin-based inheritance. Here we show that in the absence of certain components of the INO80 chromatin remodeling complex, pericentric heterochromatin can be properly inherited in RNAi mutants. The ability of INO80 to counter heterochromatin inheritance is attributed to one accessory subunit Iec5, which promotes histone turn over at heterochromatin regions, but has little effects on the ability of INO80 in regulating nucleosome positioning at heterochromatin, gene expression, or the DNA damage response. Slow histone turnover preserves parental histones at repeat regions to enhance epigenetic inheritance of heterochromatin not only in RNAi mutants but also in wild type cells. Our analyses identified a separation-of-function mutation of INO80 in regulating histone turnover at heterochromatin and demonstrate the important role of histone turnover in controlling heterochromatin inheritance and maintaining the proper heterochromatin landscape of the genome.

overall_design: RNA-seq analysis of three ino80 mutants

first: Chun-min

last: Shan

first: Kehan

last: Bao

first: Jolene

last: Diedrich

first: Xiao

last: Chen

first: Chao

last: Lu

first: John

last: Yates


title: NOP10 predicts NSCLC prognosis and its associated small nucleolar RNAs drive proliferation and migration [PSI-seq]

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

country: Germany

institute: Heidelberg University

summary: Non-coding RNAs are critical players in non-small cell lung cancer (NSCLC). In the present study, we investigate the role of H/ACA box snoRNA and snoRNA-bound ribonucleoproteins (RNP) in the tumorigenesis of NSCLC.

overall_design: We used Psi-Seq to determine the pseudouridylation modification profile of ribosomal RNA in 7 matched tumor and normal samples from parafﬁn-embedded tissue from non-small cell lung cancer (NSCLC) patients. To further investigate the role of NOP10 we analyzed A549 cell line with CRISPR Cas9 knock out of NOP10.

first: Schraga

last: Schwartz

first: Carsten

last: Müller-Tidow


title: Gain-of-Function p53 Protein Transferred via Small Extracellular Vesicles Promotes Conversion of Fibroblasts to a Cancer-Associated Phenotype

city: Houston

first: Shaolin

last: Ma

state: Tx

address: 1881 East Road

institute: MD Anderson Cancer Center

summary: Crosstalk between tumor and stromal cells is essential for tumor pathogenesis. Tumor and stromal interactions consist of reciprocal signaling through cytokines, growth factors, direct cell-cell interactions, and extracellular vesicles (EVs), among others. Small EVs (≤200 nm) have been considered critical messengers of cellular communication during tumor development. Here, we demonstrated that gain-of-function (GOF) p53 protein can be packaged into small EVs and transferred to stromal cells. In this study, we performed RNA sequencing to explore the gene signature alterations in small EVs after knockdown GOF p53 expression.

overall_design: Small EVs were isolated from HT29-nontargeting control sequence (ntsh) cells (ntsh-sEVs) and HT29-p53 shRNA cells (shp53-sEVs). RNA samples from small EVs were extracted using an exoRNeasy Midi and Maxi Kit (Qiagen, Hilden, Germany; Cat. # 77144) following the manufacturer’s instructions. The library construction for small RNA and the sequencing were performed by Novogene Corporation Inc. (Sacramento, CA).

first: Anil

last: Sood


title: Sequence- and structure-specific cytosine-5 methylation in mRNAs by NSUN6

status: Public on Nov 20 2020

city: Cambridge

first: Susanne

last: Bornelöv

address: Tennis Court Road

department: WT-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

summary: Methylation is the most common internal modification in mRNA. While the highly abundant N6-methyladonsine (m6A) modification affects most aspects of mRNA function, the precise functions of the rarer 5-methylcytosine (m5C) remains largely unknown. Here, we map m5C in the human transcriptome using methylation-dependent individual-nucleotide resolution cross-linking and immunoprecipitation (miCLIP) combined with RNA bisulfite sequencing. We identify NSUN6 as a methyltransferase with strong substrate specificity towards mRNA. NSUN6 primarily targeted three prime untranslated regions (3’UTR) at the consensus sequence motif CTCCA. Knockout and rescue experiments revealed that only mRNA methylation sites containing the consensus motif depended on the presence of NSUN6. Furthermore, ribosome profiling demonstrated that NSUN6-specific consensus motifs marked translation termination. However, even though NSUN6-methylated mRNAs were reduced in NSUN6 knockout cells, NSUN6 was dispensable for mouse embryonic development. Thus, our study identifies NSUN6 as methyltransferase targeting mRNA in a sequence- and structure-specific manner.

overall_design:
Ribosome profiling and total RNA-seq from human H9 and HEK293 cells. Control or NSUN6-knockout samples.
Identification of NSUN6 methylation targets by miCLIP in human HEK293 cells.

first: Tommaso

last: Selmi

first: Shobbir

last: Hussain

first: Sabine

last: Dietmann

first: Matthias

last: Heiss

first: Jean-Michel

last: Carter

first: Rebecca

last: Lantaff

first: Sophia

last: Flad

first: Ya-Lin

last: Huang

first: Stefanie

last: Kellner

first: Michaela

last: Frye


title: Transcriptional profiling of naïve and in vitro activated B cells from WT and DOT1L KO mice

first: Fred

last: van Leeuwen

summary: We studied the role of the histone methyltransferase DOT1L in B cell development and differentiation. Here we generated RNA-seq data naive B cells from (WT) MB1+/-;Dot1L+/+ and Dot1L KO (MB1+/-;Dot1Lfl/fl) mice. This data was to define tissue specific expression signatures and it was compared with H3K79me2 ChIP-seq data from the same subsets.

overall_design: RNA-seq from MACS sorted CD19+ naïve and actiavted B cells WT and Dot1L KO mice

first: Teun

last: van den Brand

first: Muhammad

last: Aslam

first: Tibor

last: van Welsem


title: Expression data from differently treated mouse cardiomyocytes

city: ZhengZhou

first: Chen

last: Ni

state: Henan

address: NO.1 Jianshe East Road

department: Midical Research Center

institute: The First Affiliated Hospital of Zhengzhou University

summary:
We wanted to analyze the global gene expression to unravel molecular mechanisms underlying the combined action of DOX and IFNγ in mouse cardiomyocytes.
We treated the cardiomyocytes respectively with PBS, DOX and DOX plus IFN-γ, and the differentially expressed genes and the gene expression patterns were supposed to be analyzed.

overall_design: Mouse cardiomyocytes were treated with PBS, 0.3μm DOX, 0.3μm DOX plus 20ng/ml IFN-γ respectively, then the cells were harvested for RNA extraction and hybridization on Affymetrix microarrays. We have three repetitions in each group: PBS treated control group (Con); DOX treated group (DOX); DOX plus IFN γ group (DOX+IFN-γ).

first: Pan

last: Ma


title: Distinct populations of crypt-associated fibroblasts act as signaling hubs to control colon homeostasis

city: Zürich

first: Michael

middle: David

last: Brügger

address: Winterthurerstrasse 190

department: Molecular Life Sciences

institute: University of Zürich

summary: Purpose: to determine cellular heterogeneity of the murine colonic epithelium and mesenchyme; Summary: We determined 16 disctinct sub-populations of colonic epithelial and mesenchymal cells. Further we found 3 distinct sub-populations of colonic PdgfraEGFP-positive fibroblasts.

overall_design: Wildtype murine colon cells were sorted using FACS (using EpCAM and CD45 antibodies). PdgfraEGFP intestinal mesenchymal cells were sorted using FACS (GFP positvity). Single cell RNA sequencing was perfomed (for details see Brügger et al, in prep)

middle: D

first: Tomas

last: Valenta

first: Hassan

last: Fazilaty


title: Low-dose decitabine priming endows CAR T cells with enhanced and persistent anti-tumor potential by epigenetic reprogramming in vivo and in vitro.

status: Public on Nov 16 2020

city: Beijing

first: Wang

last: Yao

address: No. 28, fuxing street

institute: Chinese general PLA hospital

type: Methylation profiling by genome tiling array

summary: Chimeric antigen receptor T (CAR T) cells targeting CD19 have achieved breakthroughs in the treatment of haematological malignancies, but many clinical studies have also shown that a proportion of patients relapse after remission.In this study, we designed CART treatment by DNMTi（dCART) inhibitor and found that dCAR T cells retained relatively potent antitumour activity compared with CAR T cell upon target antigen recognition. It may be associated with memory and anti-exhausion. Our transcriptional analysis underscores the potential of  dCAR T cells.

overall_design: In order to assess the different phenotypic and functional patterns of CARs between dCAR T and CAR T, we compared the DNA-methylation profiles of dCAR and CAR T cell before and after cocultured with Raji cells for 24 h.

first: Han

last: Weidong


title: A phosphorylation-regulated eIF3d translation switch mediates cellular adaptation to metabolic stress

first: Amy

middle: Si-Ying

last: Lee

address: 450 Brookline Ave SM520

department: Cancer Immunology and Virology

institute: DFCI

summary: Shutoff of global protein synthesis is a conserved response to cellular stresses. This general phenomenon is accompanied by induction of distinct gene programs tailored to each stress condition. Although the mechanisms that lead to general repression of protein synthesis are well characterized, how cells reprogram the translation machinery for selective gene expression remains poorly understood. Here we show that the noncanonical 5′ cap-binding protein eIF3d is specifically activated in response to metabolic stress, due to loss of CK2-mediated phosphorylation near the eIF3d cap-binding pocket. Activated eIF3d controls a gene program enriched in factors important for glucose homeostasis, including members of the mTOR pathway, and eIF3d-mediated translation adaptation is essential for cell survival during chronic glucose deprivation. Our findings reveal a new mechanism of translation reprogramming engaged in response to metabolic stress.

overall_design: eIF3dTEV-293T cells were grown in complete or glucose-free media for 48 h prior to harvest. Cells were crosslinked with UV 254 nm light, and eIF3d was isolated using anti-HA magnetic beads. eIF3d was released from the eIF3 complex by TEV protease digestion.

middle: S


title: bZIP dimers CREB1, ATF2, Zta, ATF3|cJun, and cFos|cJun prefer binding some DNA sequences containing 5-formylcytosine and 5-carboxylcytosine

city: Bethesda

first: Desiree

last: Tillo

state: MD

address: 41 Center Dr, Room D310

institute: NIH/NCI

summary: In mammalian cells, 5-methylcytosine (5mC) occurs in genomic double-stranded DNA (dsDNA) and is enzymatically oxidized to 5-hydroxymethylcytosine (5hmC), then to 5-formylcytosine (5fC), and finally to 5-carboxylcytosine (5caC). These cytosine modifications are enriched in regulatory regions of the genome. The effect of these oxidative products on five bZIP dimers (CREB1, ATF2, Zta, ATF3|cJun, and cFos|cJun) binding to five types of dsDNA was measured using protein binding microarrays. The five dsDNAs contain either cytosine in both DNA strands or cytosine in one strand and either 5mC, 5hmC, 5fC, or 5caC in the second strand. Some sequences containing the CEBP half-site GCAA are bound more strongly by all five bZIP domains when dsDNA contains 5mC, 5hmC, or 5fC. dsDNA containing 5caC in some TRE (AP-1)-like sequences, e.g., TGACTAA, is better bound by Zta, ATF3|cJun, and cFos|cJun.

overall_design: Protein binding microarray (PBM) experiments were performed for a set of bZIP transcription factors: Atf2, Creb1, and Zta homodimers, and cJun-cFos and Atf3-cJun heterodimers. Briefly, the PBMs involved binding GST-tagged DNA-binding proteins to double-stranded 44K Agilent microarrays (Berger et al., Nature Biotechnology 2006) in order to determine their binding preferences to sequences containing modified cytosines. We modified the double stranding step of the PBM protocol in which the nucleotide mixture contained 5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxymethylcytosine. Details of the modified cytosine PBM protocol are described in Khund-Sayeed S et al., Integrative Biology, 2016.


title: The m6A reader Ythdf restricts axonal growth in Drosophila through target selection modulation of the Fragile X mental retardation protein

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

institute: University of Lausanne

summary: The abundant mRNA modification N6-methyladenosine (m6A) regulates a variety of physiological processes through modulation of RNA metabolism. m6A is particularly enriched in the nervous system of several species and its dysregulation has been associated with neurodevelopmental defects as well as neural dysfunctions. In Drosophila, the loss of m6A alters fly behavior but the underlying mechanism and the role of m6A during nervous system development have remained elusive. Here we found that impairment of the m6A pathway leads to axonal overgrowth and misguidance at larval neuromuscular junctions as well as in the adult mushroom bodies. We identify the RNA binding protein Ythdf as the main m6A reader in the nervous system required for limiting axonal growth. Mechanistically, we show that Ythdf interacts directly with Fragile X mental retardation protein (Fmr1) to inhibit the translation of key transcripts involved in axonal growth regulation. Altogether, this study demonstrates that the m6A pathway controls development of the nervous system by modulating Fmr1 target selection.

overall_design: identification of methylated transcripts in Drosophila S2R+ cells. The experiment was performed in quadruplicates (IP), one non-crosslinked IP control and one input control sample.

first: Tina

last: Lence

first: F

middle: X

last: Sutandy

first: Hans-Hermann

last: Wessels

first: Anke

last: Busch

first: Julian

last: König


title: The ELAV/Hu protein Found in neurons regulates cytoskeletal and ECM adhesion inputs for space-filling dendrite growth

city: Princeton

first: Wei

last: Wang

state: NJ

address: 135 Icahn Lab

institute: Princeton University

summary: RNA-binding proteins play important roles in neuronal development and function. We sought to understand the role of the RNA-binding protein Found in neurons (Fne) in regulating the development of Drosophila larval class IV dendritic arborization neurons, in part by identifying its transcript targets using TRIBE. We were able to identify many cell adhesion proteins and cytoskeletal regulators as targets of Fne, which is consistent with our genetic and phenotypic analysis of the role of Fne in class IV da neurons.

overall_design: To identify targets of Fne in Drosophila S2 cells, we used the TRIBE method, which makes use of the RNA-editing enzyme ADAR. ADAR deaminates adenosine to inosine, which is read by reverse transcriptase as guanosine. By generating a fusion protein consisting of the RNA-binding domains of Fne fused to the catalytic domain of ADAR, we were able to identify Fne targets using RNA-seq to detect A-to-G edits in the transcriptome.

first: E

last: Gavis

first: R

last: Alizzi

first: W


title: Loss of Fas-signaling in pro-fibrotic fibroblasts impairs homeostatic fibrosis resolution and promotes persistent pulmonary fibrosis

city: Denver

first: Satria

last: Sajuthi

state: Colorado

address: 1400 Jackson St.

institute: National Jewish Health

summary: Idiopathic pulmonary fibrosis (IPF) is a progressive, irreversible fibrotic disease of the distal lung alveoli that culminates in respiratory failure and reduced lifespan. Unlike normal lung repair in response to injury, IPF is associated with the accumulation and persistence of fibroblasts and myofibroblasts and continued production of collagen and other extracellular matrix (ECM) components. Prior in vitro studies have led to the hypothesis that the development of resistance to Fas-induced apoptosis by lung fibroblasts and myofibroblasts contibributes to their accumulation in the distal lung tissues of IPF patients. Here, we test this hypothesis in vivo in the resolving model of bleomycin-induced pulmonary fibrosis in mice. Using genetic loss-of-function approaches to inhibit Fas signaling in fibroblasts, novel flow cytometry strategies to quantify lung fibroblast subsets and transcriptional profiling of lung fibroblasts by bulk and single cell RNA-sequencing, we show that Fas is necessary for lung fibroblast apoptosis during homeostatic resolution of bleomycin-induced pulmonary fibrosis in vivo. Furthermore, we show that loss of Fas signaling leads to the persistence and continued pro-fibrotic functions of lung fibroblasts. Our studies provide novel insights into the mechanisms that contribute to fibroblast survival, persistence and continued ECM deposition in the context of IPF and how failure to undergo Fas-induced apoptosis prevents fibrosis resolution.

overall_design: Bulk RNA-seq,: Naïve(4 reps) + 3wk_Fas-- (4 reps) + 3wk_Fas++ (4 reps) + 6wk_Fas-- (4 reps) + 6wk_Fas++ (4 reps)  scRNA-seq: paired Naive, 3wk_Fas--, 3wk_Fas++, 6wk_Fas--, 6wk_Fas++

first: Elizabeth

last: Redente

first: Sangeeta

last: Chakraborty

middle: P

first: Bart

last: Black

first: Ben

last: Edelman

first: Max

last: Seibold

first: David

middle: W

last: Riches


title: SWI/SNF inhibition leads to epigenetic reprogramming in rhabdoid tumor [ChIP-seq]

city: Philadelphia

first: Patrick

last: Grohar

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

summary: Rhabdoid tumor is a pediatric cancer characterized by the biallelic inactivation of SMARCB1, a subunit of the SWI/SNF chromatin remodeling complex. SMARCB1 inactivation leads to SWI/SNF redistribution to favor a proliferative dedifferentiated cellular state. Although this deletion is the known oncogenic driver, SWI/SNF therapeutic targeting remains a challenge. Here we show mithramycin and a second-generation analogue EC-8042 are effective in this tumor type. Mithramycin evicts SWI/SNF from chromatin triggering a cellular response characterized by chromatin compartment remodeling and promoter reprogramming. These effects lead to differentiation and marked xenograft tumor regressions in vivo. This study provides a therapeutic candidate for rhabdoid tumor and an approach that may be applicable to the more than 20% of cancers characterized by mutated SWI/SNF.

overall_design: Three biological replicates per treatment and time point were sequenced; ChIP libraries were isolated from individual replicates.

first: Maggie

middle: H

last: Chasse

first: Benjamin

middle: K

last: Johnson

first: Timothy

last: TricheJr


title: Plasma cells are enriched in localized prostate cancer in black men and are associated with improved outcomes [Validation Cohort]

first: Elai

last: Davicioni

overall_design: This validation cohort was comprised of a large retrospective cohort with whole transcriptomic data (DVA; n=538). Race was patient-identified in this cohort (236 White and 302 Black). This group was comprised of genome-wide expression profiles from formalin-fixed paraffin-embedded prostate tumors from radical prostatectomy between 1989 and 2016.

first: Adam

middle: B

last: Weiner

first: Thiago

last: Vidotto

first: Yang

last: Liu

first: Adriana

last: Mendes

first: Daniela

last: Salles

first: Farzana

last: Faisal

first: Sanjana

last: Murali

first: Matthew

last: McFarlane

first: Eddie

middle: L

last: Imada

first: Xin

last: Zhao

first: Ziwen

last: Li

last: Elai

first: Luigi

last: Marchionni

first: Arul

last: Chinnaiyan

first: Stephen

last: Freedland

first: Daniel

last: Spratt

first: Jennifer

last: Wu

first: Tamara

last: Lotan

first: Edward

last: Edward


title: Global gene expression analysis of enveloping layer (EVL) and non-EVL cells from 6 hpf zebrafish embryos

city: London

first: Christopher

middle: Douglas Robert

last: Wyatt

address: Gower street

institute: UCL

summary: RNA-seq data of EVL and non-EVL cells FACS sorted by the expression of GFP from the krt18 promoter (EVL cells). The analysis was performed with the aim to understand the global gene expression pattern of EVL cells in the context of their phagocytic activity detected in the accompanying manuscript

overall_design: Cells from 6hpf Tg(krt18:krt18-GFP) embryos were sorted in GFP+ (EVL) and GFP- (non-EVL) expressing cells and RNA sequencing performed

first: Esteban

last: Hoijman

first: Manuel

last: Irimia

first: Verena

last: Ruprecht


title: NOP10 predicts NSCLC prognosis and its associated small nucleolar RNAs drive proliferation and migration

first: Christian

last: Rohde

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

overall_design: Refer to individual Series


title: NOP10 predicts NSCLC prognosis and its associated small nucleolar RNAs drive proliferation and migration [ncRNA-seq]

overall_design: We used small RNA-Seq to determine the expression profile of small nucleolar RNA (snoRNA) in 7 matched tumor and normal samples from parafﬁn-embedded tissue from non-small cell lung cancer (NSCLC) patients. To further investigate the role of NOP10, we analyzed A549 cell line with CRISPR Cas9 knock out of NOP10.

first: Carsten

last: Müller-Tidow

first: Marcel

last: Köhn


title: mRNA-seq in human 293T HEK cells in the presence (shScr) or absence of HSF1 (shHSF1) or CTCF (shCTCF).

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH Royal Institute of Technology

summary: Profiling the mRNA content in 293T human embryonic kidney (HEK) cells in the presence and absence of HSF1 or CTCF. The mRNA was enriched from total cellular RNA using using polyadenyltion-selection. HSF1 (shHSF1) or CTCF (shCTCF) was downregulated using shRNA for 48hours. Scrambled RNA (shScr) was used as a negative control.

overall_design: Paired-end sequencing of mRNA content in 293T human embryonic kidney (HEK) cells. The mRNA was enriched from total cellular RNA of 293T HEK after transfecting the cells with shRNA against either a scrambled RNA (shScr; negative control), HSF1 (shHSF1; HSF1down-regulation), or CTCF (shCTCF; CTCF downregulation). The samples were prepared in four biological replicates.

first: Eileen

last: Burchfiel

first: Dennis

middle: J

last: Thiele


title: Heart failure impairs the mechanotransduction properties of human cardiac pericytes

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

country: Italy

institute: Università degli Studi di Udine

summary: Aim of this work is to verify if pericytes (Pc) residing in ischemic failing human hearts display altered mechano-transduction properties and to assess which alterations of the mechano-sensing machinery are associated with the observed impaired response to mechanical cues.  Results: microvascular rarefaction and defects of YAP/TAZ activation characterize failing human hearts. Although both donor (D-) and explanted (E-) heart derived cardiac pericytes (CPc) support angiogenesis, D-CPc exert this effect significantly better than E-CPc. The latter are characterized by reduced focal adhesion density, decreased activation of the focal adhesion kinase (FAK)/ Crk-associated substrate(CAS) pathway, low expression of caveolin-1, and defective transduction of extracellular stiffness into cytoskeletal stiffening, together with an impaired response to both fibronectin and lysophosphatidic acid. Importantly, Mitogen-activated protein kinase kinase inhibition restores YAP/TAZ nuclear translocation.

overall_design: Comparison of the transcriptome of human cardiac stromal cells with pericyte features obtained from normal vs ischemic, failing hearts.

first: A

last: Zanello

first: E

last: Mazzega

first: I

last: Crivellari

first: M

last: Bulfoni

last: Avolio

last: Battistella

last: Lazzarino

middle: G

last: Rolle

first: C

last: Cervellin

first: S

last: Sponga

first: U

last: Livi

first: N

last: Finato

first: G

last: Sinagra

last: Aleksova

first: D

last: Cesselli

last: Beltrami


title: Mouse Olfactory Epithelium, Lineage-Traced Injury timecourse K5-Cre ER^T2 > Rosa YFP

city: Berkeley

first: Rebecca

middle: K.

last: Chance

state: CA

department: Molecular and Cell Biology

institute: UC Berkeley

summary: The lineage of wild-type horizontal basal cells (HBC) stem cells  from the olfactory epithelium were profiled by single-cell RNA-Seq (10X v2 chemistry) to identify differentiated cells types, intermediate stages, transition states, and to infer the lineage trajectories.

overall_design: Following methimazole injury (IP) K5-Cre lineage traced cells are FACS-purified via YFP reporter expression over a time series: 24 Hours Post Injury (HPI); 48HPI; 96HPI; 7DPI; 14DPI. A minimum of two biological replicates were collected for each time-point/experimental condition.

first: Russell

last: Fletcher

first: Yoon

last: Choi


title: Single-cell sequencing of cortical cells following murine traumatic brain injury [scRNA-seq]

status: Public on Nov 15 2020

city: Columbus

first: Kristina

middle: Grace

last: Witcher

state: OH

address: 460 Medical Center Dr

department: Neuroscience

institute: Ohio State University

summary: Traumatic brain injury (TBI) can lead to significant neuropsychiatric problemsand neurodegenerative pathologies, which develop and persist years after injury. Neuroinflammatory processes evolve over this same period. Cortical mRNA analysis  showed a  robust contribution of  microglia  to  neuroinflammatory  pathways that persisted  over  time post-injury. These data also indicate that inflammation persists in the subacute and chronic time points after TBI, which may affect surrounding neurons, oligodendrocytes and astrocytes. To investigate this hypothesis, a single-cell sequencing approach was used to determine cell-type specific gene expression within the cortex 7 dpi with and without microglial depletion.

overall_design: Mice were subjected to midline fluid percussion injury (TBI) or kept as naïve controls. Half of the mice were fed PLX5622 (colony stimulating factor 1-receptor antagonist) in the chow prior to injury and up until the 7 dpi endpoint; the other half were fed AIN-7 vehicle chow. PLX5622 and CSF1R antagonism were used to deplete microglia. Therefore there were four experimental groups: Control, Control+PLX5622, TBI, and TBI+PLX5622. Cortex was dissociated and single cell suspensions from 3 mice per group were pooled into a single sample. This experiment was completed in two replicates (6 mice per group total; 2 experimental replicates per group).

first: Jonathan

last: Godbout


title: SWI/SNF inhibition leads to epigenetic reprogramming in rhabdoid tumor

first: Patrick

last: Grohar


title: Biparental contributions of the H2A.B histone variant control embryonic development in mice

status: Public on Nov 14 2020

city: Seattle

first: Jorja

last: Henikoff

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

summary: H2A.B KO were generated by CRISPR-editing in B6;SJLF1/J mouse zygotes which were backcrossed to C57BL/6, haploid spermatids were isolated using Hoechst dye, according to Bastos et al., Cytometry Part A, 2005

overall_design: We used Automated Cleavage Under Targets and Release Using Nuclease (AutoCUT&RUN), a chromatin profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing.

first: Antoine

last: Molaro

first: Anna

last: Wood

first: Derek

last: Janssens

first: Selina

middle: M

last: Kindelay

first: Michael

middle: T

last: Eickbush

first: Steven

last: Wu

first: Charles

last: Muller

first: Harmit

last: Malik


title: RNA-Seq of distal colonic homogenates from intestinal epithelial-specific Sprouty2-deleted mice versus littermate controls

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

institute: The University of Chicago

summary: We asked whether Sprouty2 controls secretory cell differentiation in the distal colon. Loss of Sprouty2 leads to expansion of tuft and goblet cell populations. Sprouty2 loss induced PI3K/Akt signaling, leading to GSK3β inhibition and epithelial IL-33 expression

overall_design: Comparing the profiles of distal colonic gene expression from VillinCre/Sprouty2-floxxed and littermate Sprouty2-floxxed controls

middle: A

last: Schumacher

middle: Y

first: Mark

middle: R

last: Frey


title: Ror2-mediated non-canonical Wnt signaling regulates Cdc42 and cell proliferation during root development

status: Public on Nov 13 2020

city: LA

first: Yuanyuan

last: Ma

address: 2250 Alcazar Street

department: CCMB

institute: USC

summary: We show that Ror2 mediated non-canonical Wnt signaling in the dental mesenchyme plays a critical role in cell proliferation and thereby regulates root development size in mouse molars. Furthermore, Cdc42 acts as a potential downstream mediator of Ror2 signaling in root formation.

overall_design: we detected the tooth development in in Ror2 conditional knockout mouse models

first: Yang

last: Chai


title: SWI/SNF inhibition leads to epigenetic reprogramming in rhabdoid tumor [RNA-seq]

overall_design: Three biological replicates per treatment and time point were sequenced; mRNA was isolated individually from each replicate.

first: Maggie

last: Chasse

first: Benjamin

last: Johnson

first: Timothy

last: TricheJr


title: DUSP11-mediated Control of 5’-Triphosphate RNA Regulates RIG-I Sensitivity

city: Austin

last: Battenhouse

state: TX

address: 100 East 24th St., Stop A5000

department: Center for Biomedical Research Support

institute: The University of Texas at Austin

summary: Mice lacking DUSP11 display enhanced interferon signaling signature

overall_design: RNA extracted from liver (n=24) or spleen (n=6) of wild-type (n=15) and DUSP11-deficient (n=15) mice subjected to immune-stimulatory 5'-ppp RNA treatment (n=12 liver, 8 male/4 female), mock treatment (n=6 liver, 2 male/4 female;  n=6 spleen, 2 male/4 female), or untreated (n=6 liver, 4 male/2 female). Mice were age/sex pair-matched within each treatment.

first: Joon

last: Choi

first: James

last: Burke

first: Kayla

last: Szymanik

first: Upasana

last: Nepal

first: Justin

last: Lau

first: Aaron

last: Stark

first: Victor

last: Lam

first: Christopher

middle: S

last: Sullivan


title: The effects of METTL3 on islet β-cell function

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

summary:
Purpose: The goal of this study is to investigate how METTL3 regulates islet β-cell function.
Methods:  Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from pancreatic islets of Mettl3flox/flox and β-Mettl3-KO mice at 8 weeks old. Each RNA sample was pooled from four Mettl3flox/flox and β-Mettl3-KO mice, respectively. Three independent biological replicates for each group were used for RNA-seq. RNA-seq was performed by deep sequencing using an Illumina Novaseq 6000 platform. Paired-end clean reads were aligned to the mouse reference genome(GRCm38.p6) with Hisat2 v2.0.5, and the aligned reads were used to quantify mRNA expression by using featureCounts v1.5.0-p3.
Conclusion: Our study represents the first detailed analysis of islet transcriptomes from Mettl3flox/flox and β-Mettl3-KO mice, generated by RNA-seq technology. The RNA-seq analysis showed that 2560 genes were downregulated and 3408 genes were upregulated in the pancreatic islets of β-Mettl3-KO mice. GO analysis showed that the downregulated genes were primarily related to insulin secretion, SNARE binding, and mitochondrial respiratory chain, whereas the upregulated genes were associated with the immune response, B cell activation, and antigen binding.

overall_design: mRNA profiles in pancreatic islets of Mettl3flox/flox and β-Mettl3-KO mice were generated by deep sequencing using Illumina Novaseq 6000 platform (n=3 for each group).

first: Xinzhi

last: Li


title: MeRIP-Seq of pancreatic islets in Mettl3flox/flox and islet β cell-specific Mettl3 knockout (β-Mettl3-KO) mice

summary:
Purpose: Through mRNA m6A-profiling, we aim to characterize the mRNA m6A changes in pancreatic islets obtained from Mettl3flox/flox and β-Mettl3-KO mice.
Methods: Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from pancreatic islets of Mettl3flox/flox and β-Mettl3-KO mice at 8 weeks old. A total of 2-3 μg RNAs were pooled from nine Mettl3flox/flox mice and twelve β-Mettl3-KO mice, respectively. Three independent biological replicates of each group were used for MeRIP-seq. Fragmented RNA (~100 nt) was incubated for 2 hr at 4oC with anti-m6A polyclonal antibody (Merk Millipore) in the immunoprecipitation experiment. Then, immunoprecipitated RNAs or Input was used for library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN). The library preparations were sequenced on an Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols. After mapping reads to the reference genome, exomePeak R package (version 2.16.0) was used for the m6A peak identification in each anti-m6A immunoprecipitation group with the corresponding input samples serving as a control, and q-value threshold of enrichment of 0.05 was used for all data sets. The m6A-enriched motifs of each group were identified by HOMER (version 4.9.1).
Conclusion: The islet mRNA m6A profiles in Mettl3flox/flox and β-Mettl3-KO mice were characterized.

overall_design: To map the mRNA m6A modification caused by METTL3 in pancreatic islets, MeRIP-seq was performed in pancreatic islets obtained from Mettl3flox/flox and β-Mettl3-KO mice.


title: Controlled hydroxylations of diterpenoids allow for plant chemical defense without autotoxicity

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

summary: Disturbing the biosynthetic pathway of 17-hydroxylgeranyllinalool diterpene glycosides (HGL-DTGs), including silencing NaCYP736A, caused severe plant autotoxicity. This autotoxicity can be restored by co-silencing the upstream biosynthetic genes, like geranyllinalool synthase (GLS). Through comparing the transcriptome data of EV, VIGS-GLS, VIGS-CYP736A and VIGS-GLS&CYP736A, we tried to figure out the potential mechanism of this autotoxicity.

overall_design: Virus-induced gene silencing (VIGS) was performed on Nicotiana attenauta plants, in which NaCYP736A and NaGLS were silenced individually or together, with empty vector (EV) in as controls. Leaves of rossete stage plants were harvested after treated by 150 µg MeJA per leaf for 3 days. Four replicate samples per genotype were used for the analysis. Total RNA was extracted from 30 mg leaf samples using the Plant RNeasy kit (Qiagen) and quality checked by spectrophotometry (NanoDrop). Genomic DNA was removed by DNAse treatment (Ambion) following manufacturer instructions. RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent) in the Agilent 2100 Bioanalyzer (Agilent). RNA was labeled with Cyanine-3 (Cy3) with the Quick Amp labeling kit (Agilent) according to manufacturer instructions and followed by RNAeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with a NanoDrop ND-1000 Spectrophotometer. Samples were hybridized in a N. attenuata whole genome single color array (Agilent 8×60K; GPL19764). Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting. Probe feature extraction was performed with the feature extraction software (Agilent). Quality control, data filtering and normalization were performed in Genespring GX (Agilent). Probe filtering was performed in Genespring GX using the flag (gIswellAboveBG). Probes that did not pass the condition in all replicates for one of the conditions were filtered out. Probe signals were tressholded to 1, log2 transformed and normalized to the 75th percentile. Differential expression analysis between peduncles of EV and irZTL-314 plants at ZT0 was performed with a moderated t-test in Genespring GX (Agilent). Probe to gene association and gene annotations were based in the N. attenuata genome assembly v2.5.

first: Jiancai

first: Ian

last: Baldwin


title: A gateway for SARS-CoV-2 infection in the human olfactory neuroepithelium

city: Geneva

first: Ivan

last: Rodriguez

address: 30 quai Ernest Anrsermet

department: Genetics and Evolution

institute: University of Geneva

summary: Various reports indicate an association between COVID-19 and anosmia, suggesting an infection of the olfactory sensory epithelium, and thus a possible direct virus access to the brain. To test this hypothesis, we generated RNA-seq libraries from human olfactory neuroepithelia, in which we found substantial expression of the genes coding for the virus receptor angiotensin-converting enzyme-2 (ACE2), and for the virus internalization enhancer TMPRSS2. We analyzed a human olfactory single-cell RNA-seq dataset and determined that sustentacular cells, which maintain the integrity of olfactory sensory neurons, express ACE2 and TMPRSS2. We then observed that the ACE2 protein was highly expressed in a subset of sustentacular cells in human and mouse olfactory tissues. Finally, we found ACE2 transcripts in specific brain cell types, both in mice and humans. Sustentacular cells thus represent a potential entry door for SARS-CoV-2 in a neuronal sensory system that is in direct connection with the brain.

overall_design: With the aim of exploring the potential expression of ACE2 and TMPRSS2 in olfactory sensory tissue, we collected biopsies via nasal endoscopic surgery from 4 adult patients. Samples of both nasal respiratory and olfactory sensory epithelia were harvested. Bulk tissue RNA was extracted, libraries generated, and sequenced

first: Leon

last: Fodoulian

first: Joel

last: Tuberosa

first: Daniel

last: Rossier

first: Madlaina

last: Boillat

first: Chenda

last: Kan

first: Véronique

last: Pauli

first: Kristof

last: Egervari

first: Johannes

last: Lobrinus

first: Basile

first: Alan

last: Carleton


title: SWI/SNF inhibition leads to epigenetic reprogramming in rhabdoid tumor [ATAC-seq]

first: Patrick

last: Grohar

overall_design: Three biological replicates per treatment and time point were sequenced; ATAC libraries were isolated from individual replicates.

first: Maggie

last: Chasse

first: Benjamin

last: Johnson

first: Timothy

last: TricheJr


title: Gene expression-based prediction of neodjuvant chemotherapy response in early breast cancer

city: Dortmund

first: Jan

middle: G.

last: Hengstler

address: Ardeystrasse 67

institute: Leibniz Research Centre for Working Environment and Human Factors

summary: Prospective, non-comparative Phase II multicenter trial (EXPRESSION EudraCT: 2008-006381-29) where the patients received three 3-week cycles of docetaxel (100 mg/m2) followed by three 3-week cycles of 5-fluorouracil (500 mg/m2), epirubicin (100 mg/m2), and cyclophosphamide (500 mg/m2) (FEC). The primary end point was the identification of a gene expression signature predictive of pathological complete response (pCR). In this trial, pCR was defined as absence of invasive or non-invasive cancer in the breast. External validation of the predictive performance was performed using publicly available data.

overall_design: Pre-treatment core needle biopsies were obtained from primary tumors and stored at -80°C until analysis. RNA was isolated and hybridized to Affymetrix HG U133 plus 2.0 microarrays.

first: Marcus

last: Schmidt


title: A ubiquitin ligase mediates target-directed microRNA decay independently of tailing and trimming [TDMD]

city: Dallas

first: Joshua

last: Mendell

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: MicroRNAs (miRNAs) act in concert with Argonaute (AGO) proteins to broadly repress mRNA targets. After AGO loading, miRNAs generally exhibit slow turnover. An important exception occurs when miRNAs encounter targets with extensive complementarity, which can trigger a process termed target-directed microRNA degradation (TDMD). Prevailing models of TDMD invoke miRNA tailing and trimming as an essential step in the decay mechanism. Here, a genome-wide screen revealed a novel cullin-RING ubiquitin ligase, which we named the DECAY complex, that mediates TDMD. The DECAY complex interacts with AGO proteins, mediates TDMD induced by multiple transcripts, and does not require tailing and trimming to elicit miRNA turnover. Based upon these findings, we propose a model in which the DECAY complex mediates TDMD by promoting proteasomal decay of miRNA-containing complexes.

overall_design: Total RNA was isolated from biological triplicates of each cell line using the miRNeasy Mini RNA isolation kit (QIAGEN). Library preparation and next generation sequencing were performed by DNA Link using NEB Next Small RNA Library Prep for Illumina (New England BioLabs).

first: Jaeil

last: Han

first: Collette

last: LaVigne

first: Benjamine

last: Jones

first: He

last: Zhang


title: A ubiquitin ligase mediates target-directed microRNA decay independently of tailing and trimming [miRNA-seq]


title: Identification and characterization of distinct brown adipocyte subtypes in C57BL/6J mice

city: Neuherberg

first: Matthias

last: Heinig

address: Ingolstädter Landstrasse

institute: Helmholtz-Zentrum München

summary: Here we provide scRNAseq data from the stromal vascular fraction of adult (8 weeks) murine brown adipose tissue. This allows studying cellular composition and cellular heterogeneity within brown fat.

overall_design: We utilize the stromal vascular fraction of brown adipose tissue of an adult (8 weeks) old male C57Bl/6J mouse

first: Ruth

last: Karlina

first: Dominik

last: Lutter

first: Viktorian

last: Miok

first: David

last: Fischer

first: Irem

last: Altun

first: Theresa

last: Schöttl

first: Kenji

last: Schorpp

first: Andreas

last: Israel

first: Cheryl

last: Cero

first: James

middle: W

first: Ingrid

last: Kapser-Fischer

first: Anika

last: Böttcher

first: Susanne

last: Keipert

first: Annette

last: Feuchtinger

first: Elisabeth

last: Graf

first: Tim

last: Strom

first: Axel

last: Walch

first: Heiko

last: Lickert

first: Thomas

last: Walzthoeni

first: Fabian

last: Theis

first: Christina

last: García-Cáceres

first: Aaron

last: Cypess

first: Siegfried

last: Ussar


title: Live imaging in freely behaving mice reveals that adult neural stem cell activation is regulated by the day/night cycle and intracellular Ca2+ dynamic

status: Public on Nov 12 2020

city: Planegg

first: Jovica

last: Ninkovic

address: Grosshaderner strasse 9

institute: LMU Munich

summary: We compared transcriptome of qNSCs and aNSCs

overall_design: quiscent neural stem cells were isolated 3 days after intraventricular injection of either aCSF or miR204 specific antagomers using described protocol (Fischer et al., 2011) and their transcriptome was analyzed

first: Archana

last: Gengatharan

first: Armen

last: Saghatelyan


city: Baltimore

first: Saraswati

last: Sukumar

address: 1650 Orleans St, CRB 1, Rm 132

department: Breast Cancer Program

institute: Johns Hopkins School of Medicine

summary:
HEYL regulates neoangiogenesis in both breast tumor epithelium and endothelium
We used Affymetrix microarrays to interrogate time-dependent transcriptomic change upon HEYL induction.

overall_design: Expression data from time series induction of HEYL from a HEYL-inducible HS578T cell line. Cells were induced for 0, 6, and 24 hours.

first: Soonweng

last: Cho

first: Liangfen

last: Han


title: Results from analysis of microarray data from clinical trial NCT00805389

city: Rixensart

first: Robbert

middle: Gerrit

last: van der Most

address: 89, rue de l'Institut

country: Belgium

institute: GSK

summary: The analysis was performed in 2 parts: a descriptive analysis of the response within each adjuvant group and an analysis at the individual subject level. We used blood transcriptional modules to perform interpretation of the results.

overall_design: There are 924 samples from 112 subjects, divided into 5 adjuvant groups: respectively 18, 23, 28, 22 and 21 in the AS01B, AS01E, AS03A, AS04 and Alum groups, respectively. Subjects were injected with 2 doses of Hepatitis B + adjuvant at Day 0 (D0) and Day 30 (D30). Whole blood samples were collected at the following time points: D0 pre-vaccination (D0_pre), D0 3 to 6 hours post-vaccination (D0_post), D1, D14, D30 pre-vaccination (D30_pre), D30 3 to 6 hours post-vaccination (D0_post), D31, D33 and D37.

first: Laurane

last: De Mot

first: Viviane

last: Bechtold

first: Wivine

last: Burny

first: Dicle

last: Hasdemir

first: Andrea

last: Callegaro

first: Emilio

last: Siena

first: Margherita

last: Coccia

first: Vanesa

last: Bol

first: Catherine

last: Legrand

first: Cheikh

last: Ndour

first: Ahmed

last: Essaghir

first: Fernando

middle: U

last: Montoya

first: Robert

last: van den Berg

first: Age

last: Smilde

first: Arnaud

last: Didierlaurent


title: CTLA-4 expression by B-1a B cells is essential for immune tolerance

city: Cleveland

first: Xiao

last: Li

address: W123, Wood building

institute: CWRU

summary: The importance of CTLA-4 regulation of T cell function is well recognized. Studies here report the expression of this immune-regulator in murine B-1a cells, and demonstrate the critical roles CTLA-4 plays in maintaining self-tolerance through regulating these early-developing B cells that express a repertoire enriched for auto-reactivity. By selectively deleting CTLA-4 from B cells, we show that the conditional knockout mice spontaneously generate T follicular helper (Tfh) cells and germinal centers (GC) in spleen; produce autoantibodies; and, later in life, develop autoimmune pathologies. This impaired immune homeostasis results from B-1a dysfunction when they lose CTLA-4. Thus, CTLA-4-deficient B-1a cells up-regulate epigenetic and transcriptional activation programs and show increased self-replenishment. These activated cells further internalize surface IgM, differentiate to antigen-presenting cells and, when reconstituted in normal congenic recipients, induce GC responses and Tfh cells expressing a highly selected repertoire. These findings introduce CTLA-4 regulation of B-1a as a crucial immune-regulatory mechanism.

overall_design: mRNA profile of sorted B-1a cells derived from CTLA-4 B cell conditional knockout (CKO) mice and the control mice

first: Yang

last: Yang

first: Zhihai

last: Ma

first: Chunlin

last: Wang

first: Qunying

first: Miranda

last: Byrne-Steele

first: Rongjian

last: Hong

first: Qing

last: Min

first: Gao

last: Zhou

first: Yong

last: Cheng

first: Guang

last: Qin

first: Justin

middle: V

last: Youngyunpipatkul

first: James

middle: B

last: Wing

first: Shimon

last: Sakaguchi

first: Christian

last: Toonstra

first: Lai-Xi

first: Jose

last: Vilches-Moure

first: Denong

first: Michael

middle: P

last: Snyder

first: Ji-Yang

first: Jian

last: Han

first: Leonore

last: Herzenberg


title: Next generation sequencing (NGS) allows identification of differentially regulated genes during Bacteroides growth on xylose:arabinose and insoluble wheat arabinoxylan

city: Ann Arbor

first: Gabriel

last: Vasconcelos Pereira

state: MI

address: 1150 West Medical Center Drive

institute: University of Michigan

summary:
Purpose: Identify differentially regulated genes in three Bacteroides species (B. intestinalis, B. cellulosylitycus, and B. oleiciplenus) under xylose:arabinose growth compared to insoluble wheat arabinoxylan
Methods: Bacterial mRNA profiles of mid-log cultures were generated by deep sequencing using Illumina 4000, in duplicates. The sequences were trimmed based on quality scores using Trimmomatic.

sample_organism:
Bacteroides cellulosilyticus
Bacteroides intestinalis
Bacteroides oleiciplenus

overall_design: Bacterial mRNA profiles of three Bacteroides species were generated after growth on two different substrates (monosaccharides and insoluble wheat arabinoxylan)

first: Isaac

last: Cann


title: Genomic basis of rice geographic adaptation to soil nitrogen

city: Beijing

first: Yongqiang

last: Liu

address: 1# West Beichen Road, Chaoyang Dist

department: Center for Genome Biology

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: Intensive application of inorganic nitrogen underlies marked increase in crop production yet imposes detrimental impact on ecosystems, hence it is crucial for future sustainable agriculture to improve nitrogen-use efficiency (NUE). Here we report the genetic basis of NUE associated with the local soil adaptation in rice. With a diverse rice germplasm panel collected from different ecogeographic regions, we performed genome-wide association study on tillering response to nitrogen (TRN), the most correlated trait with NUE of rice, and identified OsTCP19 as a modulator of TRN via transcriptionally responding to nitrogen and targeting to Dwarf and Low-Tillering (DLT), a tiller-promoting gene. A 29-bp InDel in OsTCP19 promoter confers differential transcription response to nitrogen and TRN variation among rice varieties. The high-TRN allele of OsTCP19 (OsTCP19-H) is prevalent in wild rice population, but largely lost in modern cultivars correlating with increased local soil nitrogen content, suggesting that it might have contributed to geographic adaptation in rice. Introgression of OsTCP19-H into modern rice cultivars boosts grain yield and NUE under low or moderate nitrogen levels, demonstrating its enormous potential for rice breeding and environment amelioration through reducing nitrogen application.

overall_design: mRNA profiles of rice seedling roots (14-day-old) in wild-type (ZH11) and OsTCP19 overexpression lines were generated by high throughput sequencing using BGISEQ-500 platform, each line was sequenced with three biologically independent repeats.

first: Chengcai

last: Chu


title: No detectable alloreactive transcriptional responses under standard sample preparation conditions during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells

city: San Francisco

first: Christopher

last: McGinnis

address: 600 16th Street

department: Pharmaceutical Chemistry

institute: University of California, San Francisco

summary: We employed an experimental design where PBMCs from a single donor was sequenced with or without mixing with PBMCs from other healthy unrelated donors in order to determine whether PBMCs engage in an allogeneic response under standard scRNA-seq sample preparation conditions (e.g., 30 minute co-incubation at 4C)

overall_design: Single-cell gene expression profiles of PBMCs from unrelated healthy donors tagged with MULTI-seq LMOs and/or antibody-DNA conjugates from the BD Single-Cell Multiplexing Kit (SCMK)

first: Nadia

last: Roan


title: LSM12-EPAC1 Defines a Neuroprotective Pathway that Sustains the Nucleocytoplasmic RAN Gradient

city: Ulsan

first: Chunghun

last: Lim

address: 50 UNIST-gil

country: South Korea

institute: UNIST

summary: We performed gene expression analyses using total RNA-seq and TRAP-seq

overall_design: GFP-RPL10A TRAP-seq under control vs. LSM12-depleted SH-SY5Y cells

first: Jongbo

last: Lee


title: RNA-seq on human muscle progenitor cells cultured with (1000 uM) or without serine and glycine

city: Birmingham

first: Anna

middle: E

last: Thalacker-Merc er

state: Alabama

address: 1720 University Blvd

institute: University of Alabama at Birmingham

type: Genome variation profiling by high throughput sequencing

summary: To determine the transcriptional response to serine and glycine deprivation in human muscle progenitor cells

overall_design: RNA was harvested from human muscle progenitor cells (n = 5 separate donors) after 5 days of culture with or without 1000uM serine/glycine

last: Thalacker-Mercer

first: Brandon

middle: J

last: Gheller

first: Jamie

last: Blum

first: Esther

first: Michal

middle: K

last: Handzlik

first: Ern

middle: H

last: Fong

first: Anthony

middle: C

last: Ko

first: Shray

last: Khanna

first: Molly

first: Erica

middle: L

last: Bender

first: Matthew

last: Alexander

first: Patrick

last: Stover

first: Martha

last: Field

first: Benjamin

middle: D

last: Cosgrove

last: Metallo


title: A CRISPR Screen Reveals Resistance Mechanisms to CD3-Bispecific Antibody Therapy

city: Cambridge

first: Tony

last: D'Alessio

address: 250 Massachusetts Avenue

institute: Novartis Institutes for BioMedical Research

summary: CD3-bispecific antibodies represent an important therapeutic strategy in oncology. These molecules work by redirecting cytotoxic T cells to antigen-bearing tumor cells. Although CD3-bispecific antibodies have been developed for several clinical indications, cases of cancer-derived resistance are an emerging limitation to the more generalized application of these molecules. Here, we devised whole-genome CRISPR screens to identify cancer resistance mechanisms to CD3-bispecific antibodies across multiple targets and cancer types. By validating the screen hits, we found that deficiency in IFNγ signaling has a prominent role in cancer resistance. Interestingly, IFNγ functions by stimulating the expression of T cell killing-related molecules in a cell type-specific manner. Additionally, by assessing resistance to the clinical CD3-bispecific antibody flotetuzumab, we identified core fucosylation as a novel and critical pathway to regulate flotetuzumab binding to the CD123 antigen. Disruption of this pathway resulted in significant resistance to flotetuzumab treatment. Moreover, proper fucosylation of CD123 is required for its normal biological functions. In order to treat the resistance associated with fucosylation loss, flotetuzumab in combination with an alternative targeting CD3-bispecific antibody demonstrated superior efficacy. Together, our study reveals multiple mechanisms that can be targeted to enhance the clinical potential of current and future T cell engaging CD3-bispecific antibody therapies.

overall_design: Using RNA-seq to analyze the effects of interferon-gamma (IFNg) treatment on three cancer cell lines (MOLM13, SEM, HCC827) at three time points (0, 6, and 24 hours of IFN-g) in biological triplicates.

first: Si-Qi

last: Liu

first: Alyssa

last: Grantham

first: Casey

last: Landry

first: Brian

last: Granda

first: Rajiv

last: Chopra

first: Srinivas

last: Chakravarthy

first: Sabine

last: Deutsch

first: Markus

last: Vogel

first: Katie

last: Russo

first: Katherine

last: Seiss

first: William

last: Tschantz

first: Tomas

last: Rejtar

first: David

middle: A

last: Ruddy

first: Tiancen

last: Hu

first: Kimberly

last: Aardalen

first: Joel

last: Wagner

first: Glenn

last: Dranoff

first: Joseph


title: BMP signaling: at the gate between activated melanocyte stem cells and differentiation [ATAC-seq]

city: New York City

last: Stewart

state: NY

address: 1230 York Avenue

department: Laboratory of Mammalian Cell Biology and Development

institute: The Rockefeller University

summary: Through recurrent bouts synchronous with the hair cycle, quiescent melanocyte stem cells (McSCs) become activated to generate proliferative progeny that differentiate into pigment-producing melanocytes. The signaling factors orchestrating these events remain incompletely understood. Here, we use single cell RNA-sequencing with comparative gene expression analysis to elucidate the transcriptional dynamics of McSCs through quiescence, activation, and melanocyte maturation. Unearthing signs of increased WNT and BMP signaling along this progression, we endeavored to understand how these pathways are integrated during differentiation. Employing conditional lineage-specific genetic ablation studies in mice, we find that loss of BMP signaling in the lineage leads to hair graying due to a block in melanocyte maturation.  We show that interestingly, BMP signaling functions downstream of activated McSCs and maintains WNT effector, transcription factor LEF1. Employing pseudotime analysis, genetics, and promoter analyses, and chromatin landscaping, we show that following WNT-mediated activation of McSCs, BMP and WNT pathways collaborate to trigger the commitment of proliferative progeny by fueling LEF1 and MITF-dependent differentiation. Our findings shed light upon the signaling interplay and timing of cues that orchestrate melanocyte lineage progression in the hair follicle and underscore a key role for BMP signaling in driving complete differentiation.

overall_design: For ATAC-sequencing, cells were FACS purified using an 85 uM nozzle. qMcSCs (p60-80) were isolated as described in Fig. S2A; differentiating progeny were isolated form Dct-eGFP+ anagen skin at P9 (Dump-, Sca-1-, CD34-, eGFPhigh, CD117+ cells). Library preparation was performed as described (Buenrostro et al., 2013) with some modifications. After sorting, cells were washed with 1X PBS, pelleted, and resuspended in cold lysis buffer  (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Lysis buffer was removed by centrifugation, and samples were incubated in the transposition reaction at 37C for 30 minutes (Illumina Nextera DNA Preparation Kit; TDE1 enzyme, 10uL). The reaction was terminated by addition of Tagmentaion Clean Up buffer (300 mM EDTA, 900 mM NaCl) and purified with the Qiagen MiniElue PCR purification kit. The DNA was then PCR amplified for 12-18 cycles, and the products were tested by D1000 Tape Station (Agilent) at 3 cycling conditions. Optimal samples were then pooled and bead purified before sequencing on NextSeq High Output 75 single read (40 x 40 bp paired end).

first: Nicole

middle: R

last: Infarinato

first: Thomas

last: Carroll

first: Elaine

last: Fuchs


title: Early adaptation of colorectal cancer cells to the peritoneal cavity depends on activation of ‘stemness’ programs and local inflammation.

city: Manchester

first: Jorge

last: Barriuso

state: Please Select

address: Wilmslow Road

department: Division of Cancer Sciences

institute: University of Manchester

summary: Purpose: At diagnosis, colorectal cancer presents with synchronous peritoneal metastasis in up to 10% of patients. The peritoneum is poorly characterized with respect to its super-specialised microenvironment. Our aim was to describe the differences between peritoneal metastases and their matched primary tumours excised simultaneously at the time of surgery. Also, we tested the hypothesis of these differences being present in primary colorectal tumours and having prognostic capacity. Experimental design: We report a comprehensive analysis of thirty samples from peritoneal metastasis with their matched colorectal cancer primaries obtained during cytoreductive surgery. We tested and validated the prognostic value of our findings in a pooled series of 660 colorectal cancer primary samples with overall survival (OS) information and 743 samples with disease free survival (DFS) information from publicly available databases. Results: We identified 20 genes dysregulated in peritoneal metastasis that promote an early increasing role of ‘stemness’ in conjunction with tumour favorable inflammatory changes. When adjusted for age, gender and stage, the 20-gene peritoneal signature proved to have prognostic value for both OS (adjusted-hazard ratio (HR) for the high-risk group (vs low-risk) 2.32 (95% confidence interval (CI) 1.69-3.19; p-value < 0.0001)) and for DFS (adjusted-HR 2.08 (95%CI 1.50-2.91; p-value < 0.0001)).  Conclusions: Our findings indicated that the activation of “stemness” pathways and adaptation to the peritoneal specific environment are key to early stages of peritoneal carcinomatosis. The in-silico analysis suggested that this 20-gene peritoneal signature may hold prognostic information with potential for development of new precision medicine strategies in this setting.

overall_design: Fifteen sample from primary colorectal cancers and fifteen paired peritoneal metastaes (n=15+15)


title: RNA secondary structome of SARS-CoV-2 and other 6 virus structures in the UTR regions

city: Qingdao

first: Lei

last: Sun

state: Shandong

address: Shandong street

institute: Shandong University

summary: we resolved the RNA secondary structure of SARS-CoV-2 infected in Huh7.5.1 cells, in vitro structure of SARS-CoV-2 RNA purified from infected cells and refolded in test tube and viral RNA fragments of 7 coronaviruses including SARS-CoV-2, SARS-CoV and MERS-CoV based on  in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). We built RNA structural model of SARS-CoV-2, found some functional structural elements, analysed the RNA structure conservation among different coronavirus. Also, we predicted RBP binding sites and identified some potential drug for CoVID-19 therapy.

sample_organism: Middle East respiratory syndrome-related coronavirus

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: RNA secondary structure of SARS-CoV-2 infected in Huh7.5.1 cells, in vitro structure of SARS-CoV-2 RNA purified from infected cells and refolded in test tube and iral RNA fragments of 7 coronaviruses including SARS-CoV-2, SARS-CoV and MERS-CoV were resolved based on icSHAPE. The RNA structure in vivo and in vitro of SARS-CoV-2 was calculated based on DMSO samples (D), in vivo NAI-N3 treatment samples (N) and in vitro NAI-N3 treatment samples (T).

first: Qiangfeng

last: Zhang


title: Corneal Nonmyelinating Schwann Cells Illuminated by Single Cell Transcriptomics and Visualized by Protein Biomarkers

city: Farmington

first: Royce

last: Mohan

state: Connecticut

address: 263 Farmington Avenue

institute: University of Connecticut Health Center

summary: The cornea is the most innervated tissue in the human body. Myelinated axons upon inserting into the peripheral corneal stroma lose their myelin sheaths and continue into the central cornea wrapped by only nonmyelinating corneal SCs (nm-cSCs). This anatomical organization is believed to be important for central vision. Here we employed single-cell RNA sequencing (scRNA-seq), microscopy, and transgenics to characterize these nm-cSCs of the central cornea. Using principal component analysis, uniform manifold approximation and projection, and unsupervised hierarchal cell clustering of scRNA-seq data derived from central corneal cells of male rabbits, we successfully identified several clusters representing different corneal cell types, including a unique cell cluster representing nm-cSCs. To confirm protein expression of cSC genes, we performed cross-species validation, employing corneal whole mount immunostaining with confocal microscopy in mouse corneas. We expect that our results will advance the future study of nm-cSCs in applications of nerve repair, and provide a resource for the study of corneal sensory function.

overall_design: Examination of non-myelinating Coreneal Schwann Cells through single cell RNA sequencing

first: Paola

last: Bargagna-Mohan

first: Gwendolyn

last: Schultz

first: Bruce

last: Rheaume

first: Ephraim

last: Trakhtenberg

first: Paul

last: Robson

first: Sonali

last: Pal-Ghosh

first: Mary-Ann

last: Stepp

middle: S

last: Given

first: Wendy

last: Macklin


title: A ubiquitin ligase mediates target-directed microRNA decay independently of tailing and trimming

first: Joshua

last: Mendell

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: A ubiquitin ligase mediates target-directed microRNA decay independently of tailing and trimming [small RNA-seq]

summary: MicroRNAs (miRNAs) act in concert with Argonaute (AGO) proteins to broadly repress mRNA targets. After AGO loading, miRNAs generally exhibit slow turnover. An important exception occurs when miRNAs encounter targets with extensive complementarity, which can trigger a process termed target-directed microRNA degradation (TDMD). Prevailing models of TDMD invoke miRNA tailing and trimming as an essential step in the decay mechanism. Here, a genome-wide screen revealed a novel cullin-RING ubiquitin ligase, which we named the DECAY complex, that mediates TDMD. The DECAY complex interacts with AGO proteins, mediates TDMD induced by multiple transcripts, and does not require tailing and trimming to elicit miRNA turnover. Based upon these findings, we propose a model in which the DECAY complex mediates TDMD by promoting proteasomal decay of miRNA-containing complexes.

overall_design: Total RNA was isolated from biological triplicates of each cell line using the miRNeasy Mini RNA isolation kit (QIAGEN). Library preparation and next generation sequencing were performed by DNA Link using NEB Next Small RNA Library Prep for Illumina (New England BioLabs).

first: Jaeil

last: Han

first: Collette

last: LaVigne

first: Benjamine

middle: T

last: Jones

first: He

first: Frank

last: Gillett


title: Ribosomal protein S7 ubiquitination during ER stress in yeast is associated with selective mRNA translation and stress outcome.

city: Tokyo

first: Yoshitaka

last: Matsuo

address: 4-6-1, Shirokanedai, Minato-Ku

department: IMSUT

country: Japan

institute: The University of Tokyo,

summary: eIF2α phosphorylation-mediated translational regulation is crucial for global translation repression by various stresses, including the unfolded protein response (UPR). However, translational control during UPR has not been demonstrated in yeast. This study investigated ribosome ubiquitination-mediated translational controls during UPR. Tunicamycin-induced ER stress enhanced the levels of ubiquitination of the ribosomal proteins uS10, uS3 and eS7. Not4-mediated monoubiquitination of eS7A was required for resistance to tunicamycin, whereas E3 ligase Hel2-mediated ubiquitination of uS10 was not. Ribosome profiling showed that the monoubiquitination of eS7A was crucial for translational regulation, including the upregulation of the spliced form of HAC1 (HAC1i) mRNA and the downregulation of Histidine triad NucleoTide-binding 1 (HNT1) mRNA. Downregulation of the deubiquitinating enzyme complex Upb3-Bre5 increased the levels of ubiquitinated eS7A during UPR in an Ire1-independent manner. These findings suggest that the monoubiquitination of ribosomal protein eS7A plays a crucial role in translational controls during the ER stress response in yeast.

overall_design:
2~4 different Tm treatment in 3 different strains.
1µg/ml Tunicamycin (Tm) was added into the growing cell culture at log phase, and harvested the cell at the following time points.
WT cells were harvested at 0, 1, 2, 4 hour after Tunicamycin treatment.
eS7-WT and eS7-4KR cells were harvested at 0 and 4 hour after Tunicamycin treatment.

first: Yasuko

last: Matsuki

first: Shintaro

last: Iwasaki

first: Yasushi

last: Saeki

first: Hideyuki

last: Yoko

first: Yu

last: Nakano

first: Tsuyoshi

last: Udagawa

first: Tohru

last: Yoshihisa

first: Keiji

last: Tanaka

first: Nicholas

last: Ingolia

first: Toshifumi

last: Inada


title: Genome-wide identification of enhancer domains in the healthy and post-stroke mouse cortices

city: Edison

first: Ashutosh

last: Dharap

address: 65 James st

institute: HackensackMeridian Health JFK Medical Center

summary: We report the identification of enhancer domains in sham and stroke mouse cerebral cortices by high-throughput profiling of H3K27Ac chromatin modification. A total of 35.4, 28.8 and 29.6 million reads were generated from chromatin immunoprecipitated DNA from sham, stroke and pooled input samples. This resulted in 55,571 peaks in sham and 56,110 peaks in stroke samples representing 50408 and 51,292 active regions, respectively. These active regions represent putative enhancer domains.

overall_design: Examination of H3K27Ac histone modifications in sham and stroked mouse cerebral cortices

first: Sunil

last: Bhattarai


title: A Phase 1b Randomized Single-Center Trial of Topical Cerdulatinib (DMVT-502) in Patients with Mild-to-Moderate Atopic Dermatitis

city: New York

first: Ana

last: Pavel

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

summary: This phase 1b, single-center, double-blind study evaluated safety, efficacy, and effect on molecular profiles of a topical Janus kinase/spleen tyrosine kinase (JAK/Syk) inhibitor, cerdulatinib gel 0.37%, in ten adults with mild-to-moderate atopic dermatitis (AD).

overall_design: Patients were randomized to cerdulatinib gel 0.37% (n=8) or vehicle (n=2) twice daily (BID) for 14 days. Lesional skin biopsies on days 1 and 14 evaluated change in AD-related biomarkers. Cellular infiltrates were assessed by immunohistochemistry and gene expression was analyzed using RNA-sequencing (RNA-seq) and quantitative real-time polymerase chain reaction (qRT-PCR).

first: Steve

last: Piscitelli

first: Kimberly

last: McHale

first: John

last: Jett

first: Jon

last: Collins

first: Dawn

last: Gillmor

first: Glenn

last: Tabolt

first: Randall

last: Li

first: Teresa

last: Song

first: Ning

last: Zhang

first: Anna

last: Tallman

first: Emma

last: Guttman-Yassky


title: Expression matrices of circRNAs and coding genes from siFOXA1 and control group in the HepG2 cells

status: Public on Nov 11 2020

city: Daqing

first: Xuecang

address: 39 Xinyang Road

institute: School of Medical Informatics, Daqing Campus, Harbin Medical University

summary: NOT PROVIDED; REQESTED

overall_design:
The Agilent Human circRNA Microrray V6 (4*180K,Design ID:084410) was used in this experiment and data analysis of the  2  samples have been completed.
Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C(Agilent Technologies).

first: Li

last: Peng

first: De-Chen

last: Lin


title: Mettl3-/Mettl14-mediated mRNA N6-methyladenosine modulates murine spermatogenesis

city: Shanghai

first: Zhen

state: Shanghai

address: 320 Yue Yang Road

department: Shanghai  Institute of Biochemistry and Cell Biology

institute: University of Chinese Academy of Sciences

summary: Spermatogenesis is precisely controlled at the transcriptional, posttranscriptional, and translational levels. Here we report that N6-methyladenosine (m6A), an epitranscriptomic mark regulating gene expression, plays essential roles during spermatogenesis. We present comprehensive m6A mRNA methylomes of mouse spermatogenic cells from five developmental stages: undifferentiated spermatogonia, type A1 spermatogonia, preleptotene spermatocytes, pachytene/diplotene spermatocytes, and round spermatids. Germ cell-specific inactiva- tion of the m6A RNA methyltransferase Mettl3 or Mettl14 with Vasa-Cre causes loss of m6A and depletion of SSCs. m6A depletion dysregulates translation of transcripts that are required for SSC proliferation/differentiation. Com- bined deletion of Mettl3 and Mettl14 in advanced germ cells with Stra8-GFPCre disrupts spermiogenesis, whereas mice with single deletion of either Mettl3 or Mettl14 in advanced germ cells show normal spermatogenesis. The sper- matids from double-mutant mice exhibit impaired translation of haploid-specific genes that are essential for spermio- genesis. This study highlights crucial roles of mRNA m6A modification in germline development, potentially ensuring coordinated translation at different stages of spermatogenesis.

overall_design: Undifferentiated spermatogonia, type A1 spermatogonia, preleptotene spermatocytes, pachytene/diplotene spermatocytes, and round spermatids were isolated from wild-type mice (B6 background ) to perform m6A-seq. Undifferentiated spermatogonia from 5-day-old wild-type, Mettl3-vKO and Mettl14-vKO mice were isolated to perform ribosome profiling and RNA-seq. Pachytene spermatocytes and round spermatids from wild-type and Mettl3/14-sKO were isolated to perform ribosome profiling and RNA-seq.

first: Phillip

last: Hsu

first: Xudong

last: Xing

first: Jianhuo

last: Fang

first: Zhike

last: Lu

first: Qin

last: Zou

first: Ke-Jia

first: Xiao

first: Yuchuan

last: Zhou

first: Teng

first: Youcheng

first: Wanlu

first: Guifang

last: Jia

first: Xuerui

last: Yang

first: Chuan

last: He

first: Ming-Han

last: Tong


title: BMP signaling: at the gate between activated melanocyte stem cells and differentiation

first: Katherine

last: Stewart


title: Circadian Profiling of the Bone Marrow Derived Macrophage Transcriptome

city: Troy

first: Jennifer

middle: Marie

last: Hurley

institute: Rensselaer Polytechnic Institute

summary: Investigation of Circadianly Expressed Transcripts in Murine BMDMs

overall_design: Triplicate time courses sampling for RNA-seq every 2 hours over 48 hours, starting at 16 hours post serum shock

middle: M

first: Emily

last: Collins


title: RNA sequencing analyses of fused heterokaryons between mouse embryonic stem cells and human B lymphocytes collected at early timepoints after fusion

city: Barcelona

first: Karthik

last: Arumugam

state: Barcelona

address: C/Dr.Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

summary: Tcf3 is an effector of Wnt canonical pathway and deletion of Tcf3 in mouse embryonic stem cells (mESCs) strongly enhances reprogramming efficiency after fusion.  We fused murine Tcf3-/- mESCs with human B-lymphocytes using the Polyethylene glycol (PEG) reagent and isolated heterokaryons at different time points to analyze early reprogramming events starting from 4 hours after fusion.  We performed a genome-wide expression profile of the heterokaryons by RNA-sequencing at a high resolution.

overall_design: Tc3-/- mESCs and human B lymphocytes labeled with distinct dyes were fused and hybrids were sorted at 4h, 12h, 48h and 120h after fusion. Human B lymphocytes mock treated with PEG were used as reference. The experiments were done in triplicates for each timepoint

first: William

last: Shin

first: Neus

last: Romo

first: Maria

last: Cosma

first: Andrea

last: Califano


title: Single cell profiling of human hematopoietic cells

summary: We demonstrated that the induction of BAZ2B expression in human CD34+ cells or Lineage-CD34+CD38+ cells, enhanced the stemness of clonogenicity of the cells in in vitro assays. In order to confirm the stemness mRNA expression signature of the progenitors we performed single-cell sequencing of the BAZ2B-treated CD34+ or Lineage-CD34+CD38+ progenitors and used the luciferase-treated progenitors as a control.

overall_design: To assess the stemness of the reprogrammed progenitor population at the molecular level, we proceeded to perform transcriptional profiling of single cells before and after treatment with the BAZ2B. To establish a positive control for the stemness signature, we sorted hematopoietic multipotent stem fractions of HSCs (Lin-CD34+CD38-CD45RA-CD90+), MPPs (Lin-CD34+CD38-CD45RA-CD90-), MLPs (Lin-CD34+CD38-CD45RA+) and the lineage-committed progenitor populations (Lin-CD34+CD38+) and performed single-cell RNA sequencing.  Then, to investigate BAZ2B-mediated induction toward an HSC-like state we induced Luciferase or BAZ2B cDNA ectopic expression in CD34+ cells for 14 days and sorted Lineage-GFP+ cells for single cell expression profiling. To specifically test reprogramming of lineage committed hematopoietic progenitors we induced BAZ2B/Luciferase expression in Lineage-CD34+CD38+ cells for 14 days and sequenced the Lineage-GFP+ single cells.

first: Valentina

last: Schiavone

first: Jeremy

last: Worley

first: Evan

last: Paull

first: Lukas

last: Vlahos


title: The Master Regulator protein BAZ2B can reprogram human hematopoietic lineage-committed progenitors into a multipotent state


title: Single Cell Transcriptional Profile of Col1a1GFP+ cells in health and EAE

city: La Jolla

first: Cayce

last: Dorrier

address: 9500 Gilman Drive

institute: UCSD

summary: Col1a1GFP+ cells from the spinal cords of healthy mice or mice in the early stages of EAE symptoms were transcriptionally profiled at the single cell level to determine subtypes of Col1+ CNS cells in health and disease

overall_design: Spinal cords from Col1a1GFP mice with or without EAE were dissociated into a single cell suspension, GFP+ cells enriched using FACS sorting and sequenced using the 10x genomics v2 pipeline

first: Richard

last: Daneman


title: Single cell transcriptional profile of mouse spinal cord in EAE

summary: Single cell RNA sequencing of a whole spinal cord homogenate from a mouse with EAE 4 days after symptom onset

overall_design: A spinal cord from a wild type mouse with EAE 4 days after symptom onset was digested and single cells were separated using FACS sorting. The resulting single cell suspension was run through the 10x Genomics v2 pipeline.


title: BMP signaling: at the gate between activated melanocyte stem cells and differentiation [RNA-Seq]

summary: Adult tissue stem cells protect their long-term potential by exerting precise control over their transitions between quiescence, activation, and differentiation. Through cyclic bouts synchronous with the hair cycle, quiescent melanocyte stem cells (McSCs) become activated to generate proliferative progeny that differentiate to produce and transfer pigment to hair cells.  The signaling factors orchestrating this process are still poorly understood. Here, we use single cell RNA-sequencing with pseudotime analysis to elucidate the transcriptional trajectory of McSCs through quiescence, activation, and differentiation into mature melanocytes. Unearthing signs of increased WNT and BMP signaling along this progression, we lineage-ablate either pathway and see hair graying.  We show that BMP signaling functions downstream of McSCs but upstream of WNT signaling through LEF1. After stem cell activation, the two pathways trigger committed, proliferative progeny to fuel MITF-dependent differentiation. Analyses of the promoters required for melanosome maturation suggest a specific reliance upon MITF and LEF1 transcription factors, which  we show are dampened without BMP signaling. Our findings shed light upon the signaling interplay that orchestrates the melanocyte lineage. Moreover, the block in differentiation and enhanced proliferation observed in the absence of BMP signaling raises the disconcerting possibility that BMP may harbor not only tumor promoting but also tumor suppressing activity in melanoma.

overall_design: RNA-sequencing was performed on FACS-sorted second telogen (~P60) quiescent melanocyte stem cells (2 biological replicates) and full anagen (P10) melanocytes (3 biological replicates). Cells were FACS purified into TRI Reagent LS, and total RNA was purified using the Direct-zol RNA MicroPrep kit (Zymo Research) according to the kit protocol.  RNA quality was determined by Agilent 2100 Bioanalyzer, and cDNA libraries were prepared using the Illumina TrueSeq mRNA sample preparation kit (non-stranded, poly-A selection) and sequenced on an Illumina HiSeq 4000 instrument.

first: Nicole

last: Infarinato

first: Tom

last: Carroll

first: Nicholas

last: Gomez

first: Elaine

last: Fuchs