title: Long-range Pitx2c Enhancer Promoter Interactions Prevent Predisposition to Atrial Fibrillation [RNA-seq]

summary: Genome-wide association studies (GWAS) have found that increased risk for atrial fibrillation (AF), the most common type of arrhythmia in humans, is associated with non-coding sequence variants located in proximity to the PITX2 homeobox gene. Using cardiomyocyte-specific epigenomic and comparative genomic analyses, we identified two AF-associated enhancers neighboring PITX2 with varying degrees of conservation in mice. Pitx2c promoter directly contacted the AF-associated enhancer regions. CRISPR/Cas9 mediated deletion of a 20 kb long topologically engaged enhancer lead to reduced Pitx2c transcription and AF predisposition. Allele-specific ChIP-seq and CUT&RUN experiments showed that long-range interaction of this AF-associated region with the Pitx2c promoter was required for maintenance of the Pitx2c promoter chromatin state. Moreover, long-range looping was mediated by CTCF, as the genetic disruption of an intronic CTCF binding site caused decreased Pitx2c cardiac expression, AF predisposition, and reduced active chromatin marks on Pitx2. Our findings reveal that AF risk variants located at 4q25 reside in genomic regions possessing long-range transcriptional regulatory functions directed at PITX2

overall_design: Epigenetic and transcriptomic analyses were performed on left ventricular tissue of FVB control and Pitx2 Enh20k Deletion mice.

first: Matthew

last: Hill

first: Zachary

last: Kadow

first: James

middle: F

last: Martin


title: Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo

status: Public on Oct 07 2019

city: Boston

first: Bradley

middle: E

last: Bernstein

state: MA

address: 185 Cambridge Street

department: Pathology

country: USA

institute: Massachusetts General Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Here, we developed mouse models expressing inducible lysine to methionine mutants of histone H3, which function as dominant negative inhibitors of methylation at their respective sites. Upon induction of H3K9M or H3K36M, we observed potent differentiation defects in stem cells and regenerative tissues. This work covers ChIP-seq in this model system for H3K9me3, H3K36me3, and H3K27me3.

overall_design: Examination of H3K9me3 in hemaotpoietic stem and progenitor cells expressing H3K9M.Examination of H3K27me3 and H3K36me3 in hemaotpoietic stem and progenitor cells expressing H3K36M.H3K9M.Examination of H3K9me3, H3K27me3, and H3K36me3 in hemaotpoietic stem and progenitor cells expressing WT H3.

first: Justin

last: Brumbaugh

first: Ik-Soo

last: Kim


title: Induction of human hemogenesis in adult fibroblasts by defined factors and hematopoietic co-culture

city: NEW YORK

first: MICHAEL

last: DANIEL

state: NY

address: 1 GUSTAVE L LEVY PL # 1496

institute: ICAHN SCHOOL OF MEDICINE OF MOUNT S

type: Expression profiling by high throughput sequencing

summary: Previous work demonstrates an induction of definitive hematopoiesis from human dermal fibroblasts (HDFs) after transduction with the transcription factors (TFs) GATA2, GFI1B, and FOS. To improve the yield and function of the derived hematopoietic cells, TF screening identified GFI1 as a causative factor in hematopoietic cell expansion with in vitro and in vivo functional capacity.

overall_design: mRNAseq profiling of adult human dermal fibroblasts (HDFs) at the population level after transduction with GATA2, GFI1, GFI1B and FOS at days 15 and 25

first: Michael

middle: G

last: Daniel

first: David

last: Sachs

first: Kateri

middle: A

last: Moore


title: RNA-sequencing of the female adult fly guts with enterocyte-specific overexpression  and silencing of lark  in control and Pseudomonas entomophila infected states.

city: Lausanne

first: Maroun

last: Bou Sleiman

state: Vaud

address: Rue Cantonale

department: IBI

country: Switzerland

institute: EPFL

summary: The lark gene was either overexpressed or silenced in adult enterocytes. Flies were fed sucrose or Pseudomonas entomophila (Pe).

overall_design: The lark gene was either overexpressed or silenced in adult enterocytes. Flies were fed sucrose or Pseudomonas entomophila (Pe), Total RNA was extracted and paired-end sequencing was performed. The experiment was performed three times ( three biological replicates)

middle: S

first: Bart

last: Deplancke


title: Long-range Pitx2c Enhancer Promoter Interactions Prevent Predisposition to Atrial Fibrillation [ChIP-seq]

status: Public on Oct 08 2019

city: Houston

first: Min

last: Zhang

state: Texas

address: One Baylor Plaza Room 504E

department: Department of Molecular Physiology

institute: Baylor College of Medicine

middle: C


title: Genome-wide map of DNA Polymerase II binding in the adult Drosophila melanogaster gut in control and infected conditions

summary: In order to gain insight into gene regulation in the Drosophila gut following oral infection, we performed the genome-wide DNA Polymerase II binding data for Polymerase II in the fly gut.

overall_design: There are three conditions: Control, Pseudomonas entomophila infection, and Erwinia carotovora carotovora 15 infection. One replicate of each with input and chipped samples.

last: Frochaux


title: Gene expression profile of rice shoot in response to nitrogen deficiency condition

status: Public on Oct 06 2019

city: Tsukuba

first: Hinako

last: Takehisa

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences (NIAS)

summary: Nitrogen (N) are pivotal element for proper plant growth and development. We performed microarray analysis of rice shoot under nitrogen deficiency (-N) to obtain a global view of gene regulations associated with plant response to -N.

overall_design: We performed microarray analysis of rice shoot at 6 hours after -N and control treatments. We collected a total of 6 microarray data corresponding to 2 samples with 3 replicates.

first: Yutaka

last: Sato

first: Baltazar

last: Antonio

first: Yoshiaki

last: Nagamura


title: Gene expression profile of rice root in response to macronutrient deficiency

summary: Macronutrients are pivotal elements for proper plant growth and development. We performed microarray analysis of rice root under nitrogen (N), phosphorus (P), and potassium (K) deficiency conditions to obtain a global view of gene regulations associated with plant response to essential nutrients.

overall_design: We performed microarray analysis of rice root at 6 and 24 hours after N, P and K deficiency and control treatments, respectively. We collected a total of 24 microarray data corresponding to 8 samples with 3 replicates.


title: RNA-sequencing of the female adult fly guts from 38 DGRP lines with and without oral infection with Pseudomonas entomophila

summary: In order to gain insights into gut immunocompetence and its variation in a population, we performed RNA-sequencing of whole guts of 38 Drosophila Genetic Reference Panel strains.

overall_design: 76 gut samples profiled from 38 DGRP strains under two conditions: control and infected with Pseudomonas entomophila.

first: Dani

last: Osman


title: Methylation levels in H3.3 mutant hematopoietic stem cells.

city: Cambridge

first: Jocelyn

last: Charlton

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

type: Methylation profiling by high throughput sequencing

summary: Reduced Representation Bisulfite Sequencing for mouse in vivo hematopoietic stem cells, 3 conditions: wildtype, expressing dominant negative mutant H3.3 at lysine 9 (K9M) or dominant negative H3.3 at lysine 36 (K36M).

overall_design: DNA was extracted, digested with Msp1, bisulfite-converted and sequenced to assess DNA methylation levels.

first: Alex

last: Meissner

first: Konrad

last: Hochedlinger


title: Gene expression profiling study by RNA-seq in Arabidopsis thaliana infected by Vibrio vulnificus

city: Daejeon

first: Seon-Kyu

last: Kim

address: 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea

department: Personalized Genomic Medicine Research Center

country: South Korea

institute: Korea Research Institutue of Bioscience & Biotechnology

summary: The objective of this study is to assess gene expression changes in Arabidopsis thaliana as time passed after Vibrio vulnificus 96-11-17M infection. We performed transcript profiling using 10 RNA-seq samples of Arabidopsis obtained at 0h, 12h, 24h, 48h, and 72h after 96-11-17M treatment. Through various statistical tests, differentially expressed genes at each time point were obtained and enriched biological functions were compared across infection time points. Many enriched functions associated with immune or defence systems of plant were common in all infection times. Compared with other gene expression data sets infected by several plant pathogens, common activated genes were small, but similar biological functions were shared between Vibrio and plant pathogen infections.

overall_design: RNA-seq data of 10 samples were generated at 5 time points. Two samples were replicated at each time point. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x100 bp) using Hiseq-2000 (Illumina).

first: Jeong-Hwan

first: Seon-Young

first: Yong-Soon

last: Park

first: Choong-Min

last: Ryu


title: Enteric infection induces extensive Lark-mediated 5' retention of exon-like introns in Drosophila

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

overall_design: Refer to individual Series


title: Gene expression profile of rice shoot and root in response to nitrogen deficiency treatment under phosphorus deficiency condition.

summary: Nitrogen (N) and phosphorus (P) are pivotal element for proper plant growth and development. We performed microarray analysis of rice shoot and root after nitrogen deficiency (-N) treatment under phosphorus deficiency (-P) condition to obtain a global view of gene regulations associated with plant response to -N under -P condition.

overall_design: We performed microarray analysis of rice shoot and root treated with both phosphorus and nitrogen deficiencies (-P/-N) and only phosphorus deficiency (-P) for 6 hours after a 5-day P deficiency (-P) treatment, respectively.  We collected a total of 12 microarray data corresponding to 4 samples with 3 replicates.


title: Gene expression profile of rice shoot in response to macronutrient excess conditions

summary: Macronutrients are pivotal elements for proper plant growth and development. We performed microarray analysis of rice shoot under nitrogen (N), phosphorus (P), and potassium (K) excess to obtain a global view of gene regulations associated with plant response to essential nutrients.

overall_design: We performed microarray analysis of rice shoot under N, P and K excess conditions (x64, x16, and x4 of normal concentration) and control. We collected a total of 36 microarray data corresponding to 12 samples with 3 replicates.


title: RNA-sequencing of the adult female fly guts (w1118) with and without oral infection with Pseudomonas entomophila (Pe) or Erwinia carotovora carotovora 15 (Ecc15)

overall_design: Adult female Drosophila melanogaster flies from the w1118 background were fed sucrose, Pseudomonas entomophila (Pe), or Erwinia carotovora carotovora 15 (Ecc15). Whole guts were dissected after 4 hours and 16 hours. Total RNA was extracted and paired-end sequencing was performed. The experiment was performed twice (two biological replicates)


title: Gene expression profile of leaf in rice grown under paddy field with macronutrient deficiencies

summary: Macronutrients are pivotal elements for proper plant growth and development. We performed microarray analysis of rice leaves under nitrogen (N), phosphorus (P), and potassium (K) deficiency conditions in paddy field to obtain a global view of gene regulations associated with plant response to essential nutrients.

overall_design: We performed microarray analysis of rice grown under N, P and K deficiency and control conditions in the paddy field, respectively. Leaf samples were collected at 1 week-interval under nutrient deficiency and control conditions, and obtained a total of 36 microarray data. For the gene expression profile, the uppermost fully-expanded leaf in the main stem was sampled at 12:00 PM.


title: In vitro and in vivo antitumor activity of cucurbitacin C, a novel natural product from cucumber

status: Public on Oct 05 2019

city: Shenzhen

first: zhang

last: xiantong

address: Xinan Road

country: China

institute: Southern Medical University Shenzhen Hospital

summary: Cucurbitacin C (CuC), a novel analogue of triterpenoids cucurbitacins, confers a bitter taste in cucumber. Genes and signaling pathways responsive for biosynthesis of CuC have been identified in the recent years. In the present study, we explored the anti-cancer effects of CuC against human cancers in vitro and in vivo. CuC inhibited proliferation and clonogenic potential of multiple cancer cells in a dose dependent manner. Low dose CuC treatment induced cell cycle arrest at G1 or G2/M stage in different cancer lines, whereas high dose treatment of CuC caused apoptosis in cancer cells. PI3K-Akt signaling pathway was found to be one of the major pathways involved in CuC-induced cell growth arrest and apoptosis by RNA-Seq and western blotting. Mechanistic dissection further confirmed that CuC effectively inhibited the Akt signaling by inhibition of Akt phosphorylation at Ser473. In vivo CuC treatment (0.1 mg/kg body weight) effectively inhibited growth of cancer cells derived xenograft tumors in athymic nude mice and caused significant apoptosis. Our findings for the first time demonstrated the potential therapeutic significance of CuC against human cancers.

overall_design: Experiment the antitumor activity of cucurbitacin C In vitro and in vivo

first: Dinglan

last: Wu

first: Zhu

last: Wang

first: Muqi

last: Lin

first: Yi

last: Shang

first: Fei

first: JiaYi

last: Zhou

first: Xiaomin

last: Luo

first: Weiren

last: Huang


title: Transcriptomic analysis and high dimensional phenotypic mapping of mononuclear phagocytes in mesenteric lymph nodes reveal differences between ulcerative colitis and Crohn’s disease

status: Public on Oct 04 2019

city: Montreal

first: Marika

last: Sarfati

state: Quebec

address: 900 rue St Denis

country: Canada

institute: CRCHUM

summary: Background and Aims: Crohn’s disease [CD] and ulcerative colitis [UC] are distinct forms of  inflammatory bowel disease. Heterogeneity of HLA-DR+SIRPα + mononuclear phagocytes [MNPs],  including macrophages [MΦ], monocyte-derived [Mono] cells, and dendritic cells [DCs], was  reported in gut tissue but not yet investigated in mesenteric lymph nodes [MLNs] of IBD patients.  We here compared the phenotype, function, and molecular profile of HLA-DR+SIRPα+ MNPs in CD  and UC MLNs.  Methods: Cell distribution, morphology, immune function, and transcriptomic [bulk RNAseq] and  high-dimensional protein expression profiles [CyTOF] of HLA-DR+SIRPα+ MNPs were examined in  MLNs of UC [n = 14], CD [n = 35], and non-IBD [n = 12] patients.  Results: Elevated frequencies of CD14+CD64+CD163+ [Mono/MΦ-like] MNPs displaying monocyte/  MΦ morphology and phagocytic function were a distinct feature of UC MLNs. In CD, the proportion  of CD14-CD64-CD163- [DC-like] cells was augmented relative to Mono/MΦ-like cells; DC-like cells  drove naïve T cell proliferation, Th1 polarisation, and Th17 TCM plasticity. Gene expression profile  corroborated the nature of DC-like cells, best represented by BTLA, SERPINF, IGJ and, of Mono/MΦ-  like cells, defined by CD163, MARCO, MAFB, CD300E, S100A9 expression. CyTOF analysis showed   that CD123+ plasmacytoid cells predominated over conventional DCs in DC-like cells. Four CD163+  clusters were revealed in Mono/MΦ-like cells, two of which were enriched in MARCO-CD68dimHLA-DRdim  monocyte-like cells and MARCOhiCD68hiHLA-DRhi Mɸ, whose proportion increased in UC relative to CD.  Conclusions: Defining the landscape of MNPs in MLNs provided evidence for expansion of  CD163+ Mono/MΦ-like cells in UC only, highlighting a distinction between UC and CD, and thus the  potential contribution of monocyte-like cells in driving colitis.

overall_design: Bulk RNA sequencing of FACS-sorted CD14+CD64+CD163+ and CD14-CD64-CD163- populations from MLNs of 5 UC and 7 CD patients

first: Laurence

last: Chapuy

first: Alexandra-Chloé

last: Villani

first: Nir

last: Hacohen


title: Early Life Programming of Mesenteric Lymph Node Stromal Cell Identity by the Lymphotoxin Pathway Regulates Mucosal Immune Responses in the Adult (B cells)

city: Toronto

first: Jennifer

last: Gommerman

state: Ontario

address: 1 King's College Circle, MSB 7310

department: Immunology

institute: University of Toronto

summary: Redundant mechanisms support IgA responses to intestinal antigens. These include multiple priming sites (mesenteric lymph nodes (MLN), Peyer's patches and isolated lymphoid follicles) and various cytokines that promote class switch to IgA, even in the absence of T cells. In spite of these back-up mechanisms, vaccination against enteric pathogens such as Rotavirus has limited success in some populations.Genetic and environmental signals experienced during early life are known to influence mucosal immunity, yet the mechanisms for how these exposures operate remain unclear. Here we used Rotavirus infection to follow antigen-specific IgA responses through time and in different gut compartments. Using genetic and pharmacological approaches, we tested the role of a pathway known to support IgA responses (Lymphotoxin - LT) at different developmental stages. We found that LT-beta receptor (LTβR) signalling in early life programs intestinal IgA responses in adulthood by affecting antibody class switch recombination to IgA and subsequent generation of IgA antibody-secreting cells within an intact MLN. In addition, early life LTβR signalling dictates the phenotype and function of MLN stromal cells in order to support IgA responses in the adult. Collectively, our studies uncover new mechanistic insights into how early life LTβR signalling impacts mucosal immune responses during adulthood.

overall_design: RNA profiles of MLN B220low vs B220high Blimp-1 YFPhigh cells sorted from day 8 rotavirus infected Blimp-1 YFP -> WT mice were generated by deep sequencing, in triplicate, using Illumina NextSeq500

first: Conglei

last: Li

first: Musaddeque

last: Ahmed

first: Housheng

middle: H

last: He

middle: L


title: Propranolol exhibits activity against hemangiomas independent of beta blockade

city: Atlanta

first: Jack

last: Arbiser

state: GA

address: 101 Woodruff Circle WMB 5309

department: Dermatology

institute: Emory School of Medicine

summary: Propranolol is a widely used beta blocker that consists of a racemic mixture of R and S stereoisomers. Only the S stereoisomer has significant activity against the beta-adrenergic receptor. A fortuitous clinical observation was made in an infant who received propranolol for cardiac disease, and regression of a hemangioma of infancy was noted. order to gain further insights in the mechanisms of action of R-propranolol in vivo, we subjected vehicle- and R-propranolol-treated tumors to RNAseq analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that choline metabolism was the pathway most affected by R-propranolol treatment. Consistent with this, the most highly regulated gene by R-propranolol treatment was Betaine-Homocysteine Methyl Transferase (Bhmt). Other genes that are involved in tumor suppressive activities such as Early Growth Response 1 (Egr1) and AP-1 subunit, which are both transcription factors implicated in tumor suppression.  Egr1 regulates important tumor suppressors such as PTEN and p53, and upregulates tumor necrosis factor α (TNF-α).  Fos, which has been known to be rearranged and expressed frequently in epithelioid hemangioma, was also upregulated in R-propranolol-treated samples.  The genes identified in the RNAseq analysis pose as interesting targets for further investigations.

overall_design: Analysis of transcriptome regulation in R-propranolol treated tumors

first: Maiko

last: Sasaki

first: Paula

last: North

first: Justin

last: Elsey

first: Jeffrey

last: Bubley

first: Shikha

last: Rao

first: Yoonhee

last: Jung

first: Shengnan

first: Ming-Hui

last: Zou

first: Brian

middle: P

last: Pollack

first: Jayanth

last: Kumar

first: Hartej

last: Singh


title: Early Life Programming of Mesenteric Lymph Node Stromal Cell Identity by the Lymphotoxin Pathway Regulates Mucosal Immune Responses in the Adult


title: Characterization of the transcriptional response to Orsay RNA1

city: La Jolla

first: Emily

last: Troemel

state: CA

department: Cell and Developmental Biology

institute: University of California, San Diego

summary: We used RNA-seq to identify gene expression changes in C. elegans ectopically expressing Orsay virus RNA1(wt) or RNA1(RDRP defective mutant), in both wt and drh-1 mutant backgrounds

overall_design: Whole synchronized L4 stage worms ectopically expressing Orsay virus RNA1 were collected in biological triplicate

first: Jessica

middle: N

last: Sowa

first: Hongbing

last: Jiang

first: Lakshmi

last: Somasundaram

first: Eillen

last: Tecle

first: Guorong

last: Xu

first: David

last: Wang

middle: R


title: RNA-seq analysis of control and CDK12-depleted ovarian cancer cells

status: Public on Oct 03 2019

city: Rochester

first: Daniel

middle: Rothschild

last: OBrien

state: MN

address: 200 First St. SW

institute: The Mayo Clinic

summary: We report the differential gene expression in control versus CDK12-depleted OVCAR-8 cells

overall_design: Examination of mRNA profiles in two-independent CDK12 siRNA-transfected OVCAR-8 cells compared to control luciferase siRNA transfected cells. Three technical replicates per sample.

first: Larry

last: Karnitz

first: Arun

last: Kanakkanthara


title: Early Life Programming of Mesenteric Lymph Node Stromal Cell Identity by the Lymphotoxin Pathway Regulates Mucosal Immune Responses in the Adult (Stromal cells)

first: Jennifer

last: Gommerman

overall_design: RNA profiles of MLN stromal cells sorted from of day8-rotavirus infected WT mice that were treated at E14/E17 with LTbR-Ig (labeled as “PPless” in the sample names) or control Ig (labeled as “WT”), were generated by deep sequencing, in quadruplicate, using Illumina NextSeq500

first: Conglei

last: Li

first: Musaddeque

last: Ahmed

first: Housheng

last: He


title: Gene expression profile of rice root in response to phosphorus deficiency condition

first: Hinako

last: Takehisa

summary: Phosphorus (P) are pivotal element for proper plant growth and development. We performed microarray analysis of rice root under phosphorus deficiency (-P) to obtain a global view of gene regulations associated with plant response to -P.

overall_design: We performed microarray analysis of rice root at 5 days after -P and control treatments, respectively. We collected a total of 6 microarray data corresponding to 2 samples with 3 replicates.

first: Yutaka

last: Sato

first: Baltazar

last: Antonio

first: Yoshiaki

last: Nagamura


title: Sour Sensing from the Tongue to the Brain

city: New York

first: Jin

last: Zhang

address: 3227 Broadway

institute: Columbia University

summary: The ability to sense sour provides an important sensory signal to prevent the ingestion of unripe, spoiled or fermented foods. Taste and somatosensory receptors in the oral cavity trigger aversive behaviors in response to acid stimuli. Here we show that the ion channel Otopetrin-1, a proton-selective channel normally involved in the sensation of gravity in the vestibular system, is essential for sour-sensing in the taste system. We demonstrate that a knockout of Otop1 eliminates acid responses from sour-sensing taste-receptor-cells (TRCs). In addition, we show that mice engineered to express otopetrin-1 in sweet TRCs now have sweet cells that also respond to sour stimuli. Next, we genetically identified the taste ganglion neurons mediating each of the five basic taste qualities, and demonstrate that sour taste uses its own dedicated labeled line from TRCs in the tongue to finely tuned taste neurons in the brain to trigger aversive behaviors.

overall_design: (1) Geniculate ganglion single cell sequencing.   Previously our lab showed that the different taste qualities are mediated by dedicated TRCs tuned to individual tastes and innervated by dedicated ganglion neurons tuned to matching taste qualities (Barretto et al., 2015; Lee et al., 2017). We performed single cell RNA-seq on 800 neurons from the geniculate ganglion of P2rx3-tdTomato animals. We classified 454 neurons as expressing Phox2b, a marker for sensory neurons (D'Autreaux et al., 2011).  From this dataset, we performed t-distributed stochastic neighboring embedding analysis (tSNE) to identify and visualize their distribution into different neuronal groups.  Our results revealed 5 distinct clusters each potentially defining one of the five basic taste qualities, and 2 putative somatosensory clusters characterized by high levels of expression of the mechanosensory channel Piezo2.  (2) Sour taste receptor cell bulk and single cell sequencing.  To identify candidate sour taste receptors, we molecularly characterized the repertoire of genes expressed in sour (Pkd2l1-expressing) taste cells using a combination of bulk and single-cell RNA sequencing. We performed these sequencing experiments from animals expressing the tdTomato reporter in Pkd2l1-expressing taste cells and also carried out bulk RNA sequencing from “non-sour” TRCs and surrounding tongue epithelia to search for genes preferentially expressed in sour versus other classes of cells in the tongue.

first: Charles

last: Zuker


title: The gene expression signatures for Huh7 cell lines with HCC-associated HBV variants in small S proteins transfection

city: Tainan

first: Wen-Chun

last: Liu

address: 138 Sheng-Li Road

country: Taiwan

institute: National Cheng Kung University

summary: To further investigating the novel NGS-defined HCC-associated SNVs in small S region involve hepatocarcinogenesis pathways, the plasmid pEGFP-N1-HBVS-genoB was used as the template for mutagenesis to create mutations T216C, A273G, and double mutant T216C/A273G at small surface (S) region, with the QuikChange site-directed mutagenesis kit (Stratagene, La Jolla, CA). The plasmid pEGFP-N1-HBVS-genoC was used as the template for mutagenesis to create mutations A293G, C446G, A456G, A293G/C446G, C446G/A456G, A293G/A456G, and triple mutant A293G/C446G/A456G at small S region. Wild-type or mutant envelope expression vectors were transfected into Huh7 cells by using lipofectamine 3000 (Thermo Fisher Scientific) according to the manual of the manufacturer. All mutants were confirmed by DNA sequencing. all the novel NGS-defined HCC-associated SNVs in small S region could involve hepatocarcinogenesis pathways with inducing cell apoptosis, regulating cell death and survival, affecting DNA replication, recombination, and repair.

overall_design: The plasmid pEGFP-N1-HBVS-genoB was used as the template for mutagenesis to create mutations T216C, A273G, and double mutant T216C/A273G at small surface (S) region, with the QuikChange site-directed mutagenesis kit (Stratagene, La Jolla, CA). The plasmid pEGFP-N1-HBVS-genoC was used as the template for mutagenesis to create mutations A293G, C446G, A456G, A293G/C446G, C446G/A456G, A293G/A456G, and triple mutant A293G/C446G/A456G at small S region. Wild-type or mutant envelope expression vectors were transfected into Huh7 cells by using lipofectamine 3000 (Thermo Fisher Scientific) according to the manual of the manufacturer. The gene expression were compared between each group.

first: Ting-Tsung

last: Chang


title: Dinucleotide regulation by REXO2 maintains promoter specificity in mammalian mitochondria

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

summary: Oligoribonucleases are conserved enzymes that degrade short RNA molecules of up to 5 nt in length, and are assumed to constitute the final stage of RNA turnover. We have investigated the function of the mammalian oligoribonuclease REXO2 through a combination of biochemical, structural and animal model studies. We find that REXO2 is a specialised dinucleotide degrading enzyme that shows no preference between RNA and DNA dinucleotide substrates. This specialisation is explained by crystal structures of REXO2 bound to RNA or DNA substrates. REXO2 is an essential gene, while a heart and skeletal muscle-specific knockout mouse displays elevated dinucleotide levels and alterations in gene expression patterns indicative of aberrant dinucleotide-primed transcription initiation. We find that dinucleotides act as potent stimulators of mitochondrial transcription initiation in vitro, and conclude that efficient RNA turnover is required to maintain the promoter specificity of transcription in mammalian mitochondria.

overall_design: Total RNA was isolated from heart tissue from 52 week old control (Rexo2loxP/loxP) and Rexo2 knockout mice (Rexo2loxP/loxP, +/Ckmm), TruSeq libraries produced in triplicate, sequenced and analysed for differential expression. Mitochondrial RNA was isolated from heart tissue from 52 week old control (Rexo2loxP/loxP) and Rexo2 knockout mice (Rexo2loxP/loxP, +/Ckmm), PARE libraries produced  in triplicate and sequenced for analysis of mitochondrial RNA processing.

first: Thomas

last: Nicholls

first: Henrik

last: Spahr

first: Shan

last: Jiang

first: Camilla

last: Koolmeister

first: Volkhard

last: Kaever

first: Oliver

last: Rackham

first: Maria

last: Falkenberg

first: Aleksandra

last: Filipovska

first: Nils-Goran

last: Larsson

first: Claes

last: Gustafsson


title: Control iPSC lines with clinically annotated genetic variants for versatile multi-lineage differentiation

first: James

last: Ellis

state: ON

address: 686 Bay Street

institute: Hospital for Sick Children

summary: Induced Pluripotent Stem Cells (iPSC) derived from healthy individuals are important controls for disease modeling studies. To create a resource of genetically annotated iPSCs, we reprogrammed footprint-free lines from four volunteers in the Personal Genome Project Canada (PGPC). Multilineage directed differentiation efficiently produced functional cortical neurons, cardiomyocytes and hepatocytes. Pilot users further demonstrated line versatility by generating kidney organoids, T-lymphocytes and sensory neurons. A frameshift knockout was introduced into MYBPC3 and these cardiomyocytes exhibited the expected hypertrophic phenotype. Whole genome sequencing (WGS) based annotation of PGPC lines revealed on average 20 coding variants. Importantly, nearly all annotated PGPC and HipSci lines harboured at least one pre-existing or acquired variant with cardiac, neurological or other disease associations. Overall, PGPC lines were efficiently differentiated by multiple users into cell types found in six tissues for disease modeling, and clinical annotation highlighted variant-preferred lines for use as unaffected controls in specific disease settings.

overall_design: RNAseq of 4 control induced pluripotent stem cell lines for submission to Pluritest to analyze pluripotency status.

first: M

last: Hildebrandt

first: R

last: Mok

first: J


title: Cellular recruitment by podocyte-derived pro-migratory factors in assembly of the human renal filter

first: Kun

last: Zhang

state: California

address: 9500 Gilman Drive

institute: UCSD

summary: Analysis of monogenic kidney disease-causing genes, and secondary pathology resulting from systemic diseases including diabetes and hypertension, highlight the importance of the kidney’s filtering system, the renal corpuscles. To elucidate the developmental processes that establish the renal corpuscle, we employed single-nucleus droplet-based sequencing to capture single nuclei from the human fetal kidney. This enabled the identification of distinct cell types of the nephron (podocytes), interstitial (mesangial cells) and vascular (glomerulus) lineages that together generate the renal corpuscles. Computational trajectory analysis identified transient gene expression in the development of these cell types, predicting early precursors or mature podocytes express FBLN2, BMP4 or NTN4, in conjunction with recruitment, differentiation, and modeling of vascular and mesangial cell types into a functional filter. In vitro studies provide evidence these factors exhibit angiogenic or mesangial recruiting and inductive properties consistent with a key organizing role for podocyte precursors in kidney development. Together these studies define a spatiotemporal developmental program for the primary filtration unit of the human kidney and provide novel insights into cell interactions regulating co-assembly of constituent cell types.

overall_design: With the goal of defining the developmental processes of nephron development, we used snDrop-seq to process human fetal kidney samples (n = 4) that included fetal nephrogenic cortex (14.4 and 16.5 week) and renal corpuscles (13 and 15 week). Altogether, we generated 7,018 single-nucleus data sets.

first: Albert

middle: D

last: Kim

first: Blue

middle: B

last: Lake

first: Song

last: Chen

first: Andrew

last: McMahon


title: Grady Kids Saliva Methylation

status: Public on Oct 02 2019

city: Munich

first: Binder

last: Elisabeth

address: Kraepelinstr. 2+10

country: Germany

institute: Max-Planck-Institute Psychiatry

type: Methylation profiling by genome tiling array

summary:
DNA methylation from Grady Trauma Project
Parental and childhood exposure to trauma increases an individual's lifetime risk for psychiatric and stress-related disorders. This study evaluates DNA methylation in saliva from children, with the goal of identifying associations between peripheral DNA methylation and psychiatric symptoms.

overall_design: DNA methylation was assessed in saliva samples from participants of the Grady Trauma Project. Saliva was collected in DNA Genotek kits prior to extraction. DNA methylation was interrogated for each sample using the Methylation450k BeadChip (Illumina).

first: K

last: Ressler

first: E

last: Binder

first: A

middle: K

last: Smith

first: T

last: Jovanovic


title: scRNASeq analysis of cycling cardiomyocytes

city: Grand Rapids

first: Eric

last: Kort

state: MI

address: 333 Bostwick NE

institute: Van Andel Research Institute

summary: Cardiomyocytes with true mitotic potential were enriched by means of CDC20 and SPG20 molecular beacons and analyzed by scRNASeq using the inDrops droplet based encapsulation platform

overall_design: 766 cells from three different populations: G1/M (n=329 cells), G2M-CDC20-/SPG20- (n=62), G2M-CDC20+/SPG20- (n=213), G2M-CDC20+/SPG20+ (n=162),

first: Stefan

last: Jovinge


title: Emergent gene expression responses to drug combinations predict higher-order drug interactions

city: Köln

first: Martin

last: Lukačišin

state: Deutschland

address: Zülpicher Straße 47a

department: Institute for Biological Physics

institute: Universität zu Köln

summary: Effective design of combination therapies requires understanding the changes in cell physiology resulting from drug interactions. Here, we show that the genome-wide transcriptional response to combinations of two drugs, measured at a rigorously controlled growth rate, can predict higher-order antagonism with a third drug in Saccharomyces cerevisiae. Using isogrowth profiling, over 90% of the variation in cellular response can be decomposed into three principal components (PCs) that have clear biological interpretations. We demonstrate that the third PC captures emergent transcriptional programs that are dependent on both drugs and can predict antagonism with a third drug targeting the emergent pathway.  We further show that emergent gene expression patterns are most pronounced at a drug ratio where the drug interaction is strongest, providing a guideline for future measurements. Our results provide a readily applicable recipe for uncovering emergent responses in other systems and for higher-order drug combinations.

overall_design: Sequencing of polyA RNA from yeast cells grown in 2D discretised gradients of all pairwise combinations of four growth inhibitors using automated reinoculation system to ensure control of cell density and a detailed sampling of conditions with varied growth rate. No drug controls as well as single drug controls at various drug concentrations were also included.

first: Tobias

last: Bollenbach


title: mRNA sequencing of highly and lowly metastatic human colorectal cancer PDXs

first: Norihiro

last: Yamaguchi

state: Ny

address: 1230 York Avenue, Box 16

department: Systems Cancer Biology

institute: The Rockefeller University

summary: We performed in-vivo selection of human patient derived colorectal cancer xenografts. 4 independent highly-liver metastatic sub-lines (lvm PDXs) were generated. Those lvm PDXs were harvested with the corresponding parental PDX tumors from mice and then we performed MACS mice cell depletion followed by FACS sorting to obtain human EpCAM positive and mice MHC negatitve populations. total RNA was extracted from those ex-vivo tumors and high-throuput sequencing was performed

overall_design: Differential gene expression study between 4 independent highly-liver metastatic PDXs and their corresponding parental PDXs

first: Ethan

last: Weinberg


title: Inflammation induced by incomplete radiofrequency ablation accelerates tumor progression and hinders PD-1 immunotherapy

city: Changsha

first: Liangrong

last: Shi

state: Hunan

address: No. 87 Xiangya Rd.

department: Interventional Radilology Center

institute: Xiangya Hospital, Central South University

summary: High-throughput RNA-seq analysis was performed using fresh residual CT26 tumors 3 days after incomplete radiofrequency abaltion (iRFA) as well as control tumors.   We ound genes encoding damage-associated molecular patterns molecules (DAMPs), proinflammatory cytokines, chemokines, and genes associated with immunosuppression were overexpressed in the iRFA-treated tumor, indicating iRFA  elicits inflammation and induces immunosuppression in residual tumors.

overall_design: Tumor mRNA profiles of CT26 colon cancer in Balc/c mice in two different groups (control and iRFA ) were generated by deep sequencing, in triplicate.

first: L

first: W

last: Liao


title: Expression data in TDEC obtained from irradiated GBM stem cell

city: Toulouse

first: Solene

middle: Marie

last: Evrard

address: 1 avenue Irène Joliot Curie

country: France

institute: CHU toulouse IUCT

summary: Glioblastomas (GBM) are brain tumors which display a bad prognosis despite conventional treatment associating surgical resection and subsequent radio-chemotherapy. These tumors are defined by an abundant and abnormal vascularization as well as by an important cellular heterogeneity. GBM notably contain a subpopulation of GBM stem-like cells (GSC) which contribute to tumor aggressiveness, resistance, and recurrence. Moreover, GSC directly take part in the formation of new vessels via their transdifferentiation into tumor derived endothelial cells (TDEC). Considering the importance of the vascularization in the GBM, we postulate that radiation could enhance the transdifferentiation of GSC into TDEC. Here, we show that ionizing radiation potentiates endothelial features of TDEC obtained from 3 patient-derived primocultures of GSC. Indeed, TDEC obtained from irradiated GSC (TDEC IR+) migrate more towards VEGF, form more pseudotubes in Matrigel in vitro and develop more functional blood vessel in Matrigel plugs implanted in Nude mice than TDEC obtained from non-irradiated GSC. Transcriptomic analysis allows us to highlight an overexpression of Tie2 in TDEC IR+ which is associated with the activation of AKT signaling pathway. All radiation-induced effects on TDEC IR+ were abolished by using a Tie2 kinase inhibitor, confirming the role of Tie2 signaling pathway in this process. Finally, the number of Tie2+ vessels is increased in recurrent GBM compared with matched untreated tumors. In conclusion, we show that irradiation potentiates proangiogenic features of TDEC throught Tie2/AKT signaling pathway. New therapeutic stategies associating standard teatment and an inhibitor of Tie2 signaling pathway should be considered for forthcoming trials.

overall_design: 12 samples were analyzed: 3 replicates of 4 different condition: GBM stem cells (GSC) (line SRC3), GBM differentiated cells (GDC) obtained from SRC3 GSC and Tumor Derived endothelial cells (TDEC) obtained from irradiated or not SRC3 GSC

middle: M

first: Pauline

last: Deshors

first: Monique

last: Courtade-Saidi


title: The regulation of ferroptosis by TAZ in epithelial ovarian cancer

city: Durham

first: Jen-Tsan

last: Chi

state: NC

address: 101 Science Drive

institute: Duke University

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

overall_design: Refer to individual Series


title: Transcriptional profile of CAOV2 ovarian cancer cells with TAZ silencing

summary: We performed RNAseq to study the transcriptional changes of human CAOV2 ovarian cancer cells with or without TAZ silencing by siRNAs to understand the genetic determinants of ferroptosis response

overall_design: Human ovarian cancer cell line CAOV2 were transfected by siRNA targeting TAZ (siTAZ) and compared to the control with non-targeting siRNA (siNT).

first: Wen-Hsuan

last: Yang


title: Response to extended drought stress and recovery involve epigenetic control of stress adaptation and flowering regulation in Zea mays

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan

summary: During their lifespan, plants continuously respond to a multitude of stressful factors that affects their development and reproductive fitness through a sophisticated variety of physiological, biochemical, transcriptional, and epigenetic mechanisms.  Dynamic changes in chromatin structure and concomitant transcriptional variations play an important role in both stress response and adaptation. Epigenetic memory mechanisms seem to be involved because chromatin and expression patterns can be indeed stably maintained during cell division, once the triggering stimulus has been removed. In this study we performed transcriptome and genome-wide analysis of histone modifications of maize plants subjected to a mild and prolonged drought stress followed by a complete recovery phase. Results led to the identification of stress-responsive genes in which variations in transcript and/or histone modification levels persist after stress removal. Genes not showing an immediate response to stress, but perceiving and storing stress signal for a delayed response were also identified. This provides valuable information about genes and mechanisms utilized by plants to adapt to stressful environment and potentially involved in stress memory. We also report that drought stress alters flowering and inflorescences patterning, possibly by affecting expression and chromatin of flowering regulatory genes.

overall_design: ChIP-Seq analysis of three histone modifications (H3K4me3, H3K9ac and H3K27me3) on maize young leaves collected from drought stressed (WS) and control (NS) plants after 10 days of progressive mild drought stress (WST0 and NST0) and subsequent 7 days of recovery period (WST7 and NST7)

first: Cristian

last: Forestan

first: Silvia

last: Farinati

first: Giulio

last: Pavesi

first: Vincenzo

last: Rossi

first: Serena

last: Varotto


title: Sacharomyces cerevisiae Transcript Isoform mapping (set2)

city: Heidelberg

first: Wu

last: Wei

address: EMBL Heidelberg,Meyerhofstraße 1

department: Genome Biology Unit

institute: EMBL Heidelberg

summary: Application of TIF-Seq to mutants of the molecular components involved in transcription process.

overall_design: Application of TIF-Seq (Transcript IsoForm Sequencing) to S.cerevisiae. The method was applied to simultaneously identify the 5’ capped mRNA transcription start site and the 3’polyadenylation site in delta set2 mutant strain grown in glucose media [set2, 2 biological replicates (bio)].


title: Expression data from E0771 mouse mammary tumor cell line and its derivative with high metastatic potential

status: Public on Oct 01 2019

city: Edinburgh

first: Takanori

last: Kitamura

state: State...

address: 47 Little France Crescent

country: United Kingdom

institute: University of Edinburgh

summary:
A distinct type of macrophages helps breast cancer cells to overcome rate-limiting steps in the metastatic process and establish lethal metastatic tumors. Since only a minor population of cancer cells can establish macroscopic metastatic tumors, we hypothesized that this metastatic cancer cell population have higher expression of receptors for macrophage-derived ligands compared to their parental cells.
We used microarrays to investigate this hypothesis, and identified that a selected population of mouse mammary tumor cells with high metastatic potential had higher expression of Met, a gene encoding hepatocyte growth factor receptor.

overall_design: To obtain cancer cell subpopulations with high metastatic potential, we injected E0771 mouse mammary tumor cells into the mammary fat pad of syngeneic C57BL/6 mice and retrieved the metastasized cells from the lung. We repeated this in vivo selection and established second-generation populations (named E0771-HML2). Total RNA was extracted from E0771-HML2 and their parental cells (E0771-parental) in culture, and hybridized on Affymetrix GeneChip Mouse Genome 430 2.0 Array.

first: Yu

last: Kato

first: Jeffrey

middle: W

last: Pollard


title: Genome wide analysis of H4K16Ac distribution in WT and nhp6ab cells

summary: We report genome wide distribution of H4K16 acetylation in nhp6ab cells compared to WT

overall_design: examination of  WT or nhp6ab

first: G

last: Camilloni


title: Single-cell gene expression in CD19-specific and GD2-specific CAR T cells on day 10 in culture.

city: Stanford

first: Zinaida

last: Good

address: 265 Campus Drive, Room G2105

department: Stanford Cancer Institute, Department of Biomedical Data Science

institute: Stanford University School of Medicine

summary:
Purpose: To compare cell states between CD19-28z and GD2-28z human CAR T cells on day 10 of cell culture.
Methods: Human T cells were activated and lentivirally transduced with CD19-28z or GD2-28z CAR constructs and maintained in culture for 10 days, and then delivered to the Stanford Functional Genomics Facility for 3' single-cell RNA-sequencing on the 10X Genomics platform.
Results: Comparison of transcription factor profiles by single cell RNA-seq analysis of CD8+ T cells expressing CD19-28z vs. GD2-28z CAR confirmed that the bZIP family members JUN, JUNB, JUND, and ATF4 were among the most differentially expressed and broadly connected in exhausted GD2-28z CAR T cells.
Conclusions: This study provides insights into cell states that could explain the underlying differences between highly functional CD19-28z CAR T cells and exhaustion-prone GD2-28z CAR T cells on day 10 in culture.

overall_design: A total of 1,530 CAR T cells were sequenced. 804 CD19-28z CAR T cells were sequenced to an average of 350,587 reads per cell capturing a median of 12,675 unique molecular identifier (UMI) counts per cell mapping to a median of 2,990 unique genes per cell. 726 GD2-28z CAR T cells were sequenced to an average of 405,585 reads per cell capturing a median of 15,708 unique molecular identifier (UMI) counts per cell mapping to a median of 3,446 unique genes per cell.

first: Crystal

last: Mackall


title: RNA-seq WT and nhp6ab

summary: Transcriptome analysis of WT and nhp6ab cells of S. cerevisiae

overall_design: examination of two different yeast strains


title: Syndromic immune disorder caused by a viable hypomorphic allele of spliceosome component Snrnp40

city: Dallas

first: Sara

last: Hildebrand

state: TX

address: 5323 Harry Hines blvd

department: Center for the Genetics of Host Defense

institute: UT Southwestern Medical Center

summary: We report a new immunodeficiency disorder in mice caused by a viable hypomorphic mutation of Snrnp40, an essential gene encoding a subunit of the U5 small nuclear ribonucleoprotein (snRNP) complex of the spliceosome. Snrnp40 is ubiquitous but strongly expressed in lymphoid tissue. Homozygous mutant mice showed hypersusceptibility to infection by murine cytomegalovirus and multiple defects of lymphoid development, stability and function. Cell-intrinsic defects of hematopoietic stem cell differentiation also affected homozygous mutants. SNRNP40 deficiency in primary hematopoietic stem cells or T cells or the EL4 cell line increased the frequency of splicing errors, mostly intron retention, in several hundred messenger RNAs. Altered expression of proteins associated with immune cell function was also observed in Snrnp40-mutant cells. The immunological consequences of SNRNP40 deficiency presumably result from cumulative, moderate effects on processing of many different mRNA molecules and secondary reductions in the expression of critical immune proteins, yielding a syndromic immune disorder.

overall_design: For EL4 cells: examination of splicing and transcript abundance in two Snrnp40-KO clonal EL4 cell lines, one wild-type clonal EL4 cell line, and one pool of polyclonal wild-type EL4 cells that were untreated or treated with PMA/ionomycin. For primary cells: examination of splicing and transcript abundance in HSPCs and T cells from three wild-type (WT), three heterozygous (HET), and three compound heterozygous (CMPDHET) mice.

first: Duanwu

last: Zhang


title: WT and nhp6ab


title: Characterization of Npas4 and heterodimer DNA binding in stimulated and silenced rat neurons

first: Michael

last: Hayes

address: UCSD Campus Direct, Room 105H/GPL, 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

summary: We evaluated genome-wide DNA binding of NPAS4, ARNT1, ARNT2, H3K27ac, and RNAPII by chromatin immunoprecipitation sequencing (ChIP-seq) in mature primary hippocampal neurons (rat, DIV 28) that were pharmacologically silenced (“–”; 24 hours in TTX, CPP, and NBQX) or silenced and then treated with PTX for two hours (“+”) to trigger the production of AP- and EPSP-induced NPAS4.

overall_design: ChIP-seq for Npas4, Arnt1, Arnt2, H3K27ac, and RNAPII were performed in stimulated and silenced cultured rat neurons, with 2 biological replicated of each ChIP.

last: Brigidi

middle: G

last: B Hayes

first: Nathaniel

last: Delos Santos

first: Andrea

last: Hartzell

first: Lorane

last: Texari

first: Pei-Ann

last: Lin

first: Anna

last: Bartlett

first: Joseph

last: Ecker

first: Christopher

last: Benner

first: Sven

last: Heinz

first: Brenda

last: Bloodgood


title: CAR T cells Overexpressing cJun Are Exhaustion-Resistant and Mediate Enhanced Antitumor Activity

first: Michelle

last: Monje

address: 265 Campus Drive, SIM1 G3035

institute: Stanford University

summary: CAR T cells mediate antitumor effects in a small subset of cancer patients, but dysfunction due to T cell exhaustion is an important barrier to progress. To investigate the biology of exhaustion in human T cells expressing CAR receptors, we used a model system employing a tonically signaling CAR, which induces hallmarks of exhaustion described in other settings. Exhaustion was associated with a profound defect in IL-2 production alongside increased chromatin accessibility of AP-1 transcription factor motifs, and overexpression of numerous bZIP and IRF transcription factors that have been implicated in inhibitory activity. Here we demonstrate that engineering CAR T cells to overexpress c-Jun, a canonical AP-1 factor, enhanced expansion potential, increased functional capacity, diminished terminal differentiation and improved antitumor potency in numerous in vivo tumor models. We conclude that a functional deficiency in c-Jun mediates dysfunction in exhausted human T cells and that engineering CAR T cells to overexpress c-Jun renders them exhaustion-resistant, thereby addressing a major barrier to progress for this emerging class of therapeutics.

overall_design: ChIP-seq or input controls from CAR-T cells overexpressing either JUN-HA or HA tag alone from two distinct viral transductions.

first: Surya

last: Nagaraja


first: David

last: Gennert

address: 269 Campus Drive

department: Genetics

summary: CAR T cells mediate antitumor effects in a small subset of cancer patients, but dysfunction due to T cell exhaustion is an important barrier to progress.  To investigate the biology of exhaustion in human T cells expressing CAR receptors, we used a model system employing a tonically signaling CAR, which induces hallmarks of exhaustion described in other settings.  Exhaustion was associated with a profound defect in IL-2 production alongside increased chromatin accessibility of AP-1 transcription factor motifs, and overexpression of numerous bZIP and IRF transcription factors that have been implicated in inhibitory activity. Here we demonstrate that engineering CAR T cells to overexpress c-Jun, a canonical AP-1 factor, enhanced expansion potential, increased functional capacity, diminished terminal differentiation and improved antitumor potency in numerous in vivo tumor models. We conclude that a functional deficiency in c-Jun mediates dysfunction in exhausted human T cells and that engineering CAR T cells to overexpress c-Jun renders them exhaustion-resistant, thereby addressing a major barrier to progress for this emerging class of therapeutics.

overall_design: ATAC-seq profiles of CAR T cells expressing either the CD19-28z or HA-28z CAR were generated by sequencing on the Illumina NextSeq.  CAR T cells were first sorted by CD4+/CD8+ expression and Naïve/Central Memory surface marker expression and processed in duplicate.

first: Jeffrey

last: Granja

first: Rachel

last: Lynn

first: Evan

last: Weber

first: Ansuman

middle: T

last: Satpaty

last: Mackall

first: Howard

middle: Y

last: Chang


title: Ketone body signaling mediates intestinal stem cell homeostasis and adaptation to diet

city: Houston

first: Kunal

last: Rai

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

summary: Little is known about how metabolites couple tissue stem function with physiology. Here we show that in the mammalian small intestine, the expression of Hmgcs2 (3-hydroxy-3-methylglutaryl-CoA synthetase 2)—the gene encoding the rate-limiting enzyme in the production of ketone bodies, including beta-hydroxybutyrate (ßOHB)—distinguishes the self-renewing Lgr5+ stem cells (ISCs) from differentiated cell types. Hmgcs2 loss depletes ßOHB levels in Lgr5+ ISCs and skews their differentiation towards secretory cell fates, which can be rescued by exogenous ßOHB and class I histone deacetylases (HDACs) inhibitor treatment. Mechanistically, ßOHB acts by inhibiting HDACs to reinforce Notch signaling in ISCs, thereby instructing self-renewal and lineage decisions. Notably, while a low glucose ketogenic diet elevates ISC function and post-injury regeneration through ßOHB-mediated Notch signaling, a glucose supplemented diet has the opposite effects. These findings reveal how control of ßOHB-activated signaling in ISCs by diet helps to fine-tune stem cell adaptation in homeostasis and injury.

overall_design: Examination of H3K27ac in FED and FASTED mice replicates

first: Kristina

last: Stemler

last: Terranova


title: Timecourse of gene expression in HeLa cells (parental cells and clonal knockouts of MED12 and MED24) following induction by TNFa or IL-1b

city: Cambridge

first: Paul

last: Blainey

state: MA

address: 415 Main Street

institute: Broad Institute

summary: Activation of nuclear factor kappa B (NF-kB) by inflammatory signals results in nuclear translocation of the transcription factor p65 and induction of gene expression. We identified MED12 and MED24 in an optical pooled CRISPR knockout screen in HeLa-Cas9 cells for genes affecting the activation and/or relaxation of p65 to the cytoplasm following induction by either TNFa or IL-1b. We generated isogenic clonal knockout HeLa-Cas9 lines using crRNA transfection and confirmed that loss of MED12 or MED24 results in delayed relaxation of p65, assayed by live-cell imaging of a p65-mNeonGreen fluorescent fusion.

overall_design: Biological replicates were defined as replicate clonal knockout cell lines (for MED12 and MED24 knockouts) or replicate stimulations (for parental control cells) (n = 3 or 4 biological replicates).

first: Jonathan

last: Schmid-Burgk

last: Feldman

first: Feng

last: Zhang


title: Single-cell gene expression in Her2-specific CAR T cells in osteosarcoma mouse model.

first: Zinaida

last: Good

summary:
Purpose: To compare cell states between control Her2-BBz and JUN-overexpression Her2-BBz human CAR T cells in a mouse model of osteosarcoma.
Methods: 8-week old NSG mice were implanted with 1 million 143B osteosarcoma tumor cells intramuscularly in the right leg. 14 days post tumor implantation, mice were infused intravenously with 10 million human CAR+ T cells via tail vein injection. Before T cell transfer, mice were randomized for tumor size and treated with either control Her2-BBz or JUN-overexpressing Her2-BBz CAR T cells. T cells were 70% CAR+ at infusion for both groups. 14 days post T cell treatment (day 28 post tumor engraftment), 6 mice per group were euthanized, solid tumor tissue was collected, mechanically dissociated, and single cell suspensions were labeled with human-CD45 antibody and viability dye. Live hCD45+ tumor-infiltrating lymphocytes were sorted from each tumor and 6 samples were pooled for each group. ~35,000-40,000 sorted live cells (counted post sort) for each group were delivered to the Stanford Functional Genomics Facility for 3' single-cell RNA-sequencing on the 10X Genomics platform.
Results: We found that substantially more JUN-overexpressing Her2-BBz CAR T cells were within the G2/M and S phases of the cell cycle than control Her2-BBz CAR T cells, consistent with increased in vivo proliferation of JUN-Her2-BBz CAR T cells. Furthermore, JUN-Her2-BBz CAR T cells also demonstrated a more activated transcriptional program (as measured by IL2RA and CD38), while many exhaustion-associated genes were downregulated (PDCD1, BTLA, TIGIT, CD200, ENTPD1, NR4A2) compared to control Her2-BBz CAR T cells. Finally, a small cluster of cells characterized by high IL7R expression (IL7R+ KLF2+ CD27+ TCF7+ SELL+) was apparent in JUN-overexpressing but not in control Her2-BBz CAR T cells, consistent with maintenance of a memory-like population capable of self-renewal.
Conclusions: This study provides insights into cell states that could explain the improved efficacy of JUN-overexpression Her2-BBz CAR T cells compared to control Her2-BBz CAR T cells in a mouse model of osteosarcoma.

overall_design: A total of 17,931 Her2-BBz CAR T cells (control: 6,946, JUN-overexpressing: 10,985) were sequenced to an average of 49,542 post-normalization reads per cell capturing a median of 4,281 unique molecular identifier (UMI) counts per cell mapping to a median of 1,599 unique genes per cell.

first: Crystal


title: Molecular signature of hepatitis B virus regulation by IFN-γ in primary human hepatocyte

city: Yoshida-gun

first: Takuto

last: Nosaka

state: Fukui

address: 23-3 Matsuoka, Eiheiji-cho

department: Second Department of Internal Medicine

institute: University of Fukui

summary: Hepatitis B virus (HBV) infection is a risk of developing fibrosis, cirrhosis, liver failure, and hepatocellular carcinoma. Although HBV elimination requires complete elimination of covalently closed circular DNA (cccDNA), its treatment has not been established. Interferon (IFN) -γ, a type ⅠⅠ IFN, is produced by intrahepatic cytotoxic T lymphocytes and has the noncytolytic antiviral potential. However, the mechanism by which IFN-γ regulates HBV infection in hepatocytes has not been fully elucidated. In this study, to replicate the HBV infection and monitor the amount of cccDNA, we developed an in vitro HBV infection assay system with primary hepatocytes and examined the molecules and signaling pathways. IFN-γ suppressed both HBV propagation and transcription to the same extent as IFN-α. RNA microarray analysis revealed that IFN-γ stimulation induced not only IFN-γ but also IFN-α signaling activation and regulated HBV cccDNA. Moreover, the HBV production was reduced by IFN-γ through JAK-STAT signaling and interferon stimulated genes such as OAS2 and APOBEC3G. Taken together, these results demonstrate that IFN-γ suppresses both HBV propagation and transcription by activating specific intracellular signaling pathways in hepatocytes and suggests the future application of this particular signaling pathways or genes for the complete elimination of HBV.

overall_design: The comprehensive gene expression profiles were investigated in the primary human hepatocytes derived from chimeric mice with human liver (PXB cells). PXB cells were infected with HBV at Day 0 and IFN-γ or IFN-α was added to each medium from day 4 after the infection. PXB cells were harvested at 22 days after the infection. The comparison combinations used in this analysis were the ratios Control/ IFN-γ or Control/ IFN-α.

first: Tatsushi

last: Naito

first: Hidetaka

last: Matsuda

first: Katsushi

last: Hiramatsu

first: Masahiro

last: Ohtani

first: Tomoyuki

last: Nemoto

first: Tsutomu

last: Nishizawa

first: Hiroaki

last: Okamoto

first: Yasunari

last: Nakamoto


title: YAP1 oncogene is a context-specific driver for pancreatic ductal adenocarcinoma

city: HOUSTON

first: HAOQIANG

last: YING

address: 1515 Holcombe Blvd

department: Molecular and Cellular Oncology

summary: Transcriptomic profiling classifies pancreatic ductal adenocarcinoma (PDAC) into several molecular subtypes with distinctive histological and clinical characteristics. However, little is known about the molecular mechanisms that define each subtype and how this correlates with clinical outcome. Mutant KRAS is the most prominent driver in PDAC, present in over 90% of tumors, but the dependence of tumors on oncogenic KRAS signaling varies between subtypes. In particular, squamous subtype PDACs are relatively independent of oncogenic KRAS signaling and typically display much more aggressive clinical behavior versus progenitor subtype PDACs. Here, we identified that YAP1 activation is enriched in the squamous subtype and associated with poor prognosis. Activation of YAP1 in progenitor subtype cancer cells profoundly enhanced malignant phenotypes and transformed progenitor subtype cells into squamous subtype. Conversely, depletion of YAP1 specifically suppressed tumorigenicity of squamous subtype PDAC tumors. Mechanistically, we uncovered a significant positive correlation between WNT5A expression and the YAP activation signature, and we demonstrated that WNT5A overexpression led to YAP activation and recapitulated YAP1-dependent but but Kras-independent phenotype of tumor progression and maintenance. Thus, our study identifies YAP1 oncogene as a major driver of squamous subtype PDAC and uncovers the role of WNT5A to drive PDAC malignancy via activation of the YAP pathway.

overall_design: Total RNA were obtained from PDAC cell line Pa04C expressing constitutive active Yap1 (S127A) or from a control vector

first: Bo

last: Tu

first: Jun

last: Yao

first: Sammy

last: Ferri-Borgogno

last: Zhao

first: Shujuan

last: Chen

first: Qiuyun

last: Wang

first: Liang

last: Yan

first: Xin

last: Zhou

first: Cihui

last: Zhu

first: Seungmin

last: Bang

first: Qing

last: Chang

first: Christopher

middle: A

last: Bristow

first: Ya’an

last: Kang

first: Hongwu

last: Zheng

first: Huamin

first: Jason

last: Fleming

first: Michael

last: Kim

first: Giulio

middle: F

last: Draetta

first: Duojia

last: Pan

first: Anirban

last: Maitra

first: Wantong

first: Sonal

last: Gupta

first: Haoqiang

last: Ying


title: Effect of cycloheximide in the co-translation mRNA degradation pattern in  set2D and rrp6D strains

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

summary: We investigated cryptic transcription start site usage, chromatin organization and post-transcriptional consequences in Saccharomyces cerevisiae. We used 5PSeq approach, which measures ribosome dynamics by sequencing the presence of co-translation mRNA degradation intermediates, to assess if cryptic transcripts are engaged in active translation. Here we assay the effect of Cycloheximide treatment (CHX) in the co-translational degradation profile of using strains where cryptic transcription is enhanced. We study the profiles in set2D and rrp6D, enhanced for the presence of chromatin-sensitive and RNA degradation-sensitive cryptic transcripts respectively.

overall_design: We performed 2 biologically independent 5PSeq experiments. All cells were grown in YPD. CHX treated samples were incubated for 10 min and flash frozen in N2.

first: Yerma

last: Sanchez

first: Yujie

last: Zhang

first: Jingwen


title: Detection of carbohydrate-active enzyme genes in the rumen of young lambs

city: Saint Genes Champanelle

first: Evelyne

last: Forano

state: France

address: INRA Centre ARA

department: UMR MEDIS

institute: INRA

summary: In this study, we studied the fibrolytic potential of the rumen microbiota in the rumen of 6 lambs separated from their dams from 12h of age and artificially fed with milk replacer (MR) and starter feed from d8, in absence (3 lambs) or presence (3 lambs) of a combination of the live yeast Saccharomyces cerevisiae CNCM I-1077 and selected yeast metabolites. The fibrolytic potential of the rumen microbiota of the lambs at 56 days of age was analyzed with a DNA microarray (FibroChip) targeting genes coding for 8 glycoside hydrolase (GH) families.

platform_organism:
Bacteroides fragilis
Bacteroides thetaiotaomicron
Butyrivibrio fibrisolvens
Fibrobacter succinogenes
Xylanibacter ruminicola
Selenomonas ruminantium
Ruminococcus albus
Ruminococcus flavefaciens
Enterococcus faecium
Lactococcus lactis
Clostridium acetobutylicum
Clostridium cellulovorans
Clostridioides difficile
Acetivibrio thermocellus
Clostridium beijerinckii
Ruminiclostridium cellulolyticum
Levilactobacillus brevis
Limosilactobacillus fermentum
Bifidobacterium adolescentis
Cellulomonas fimi
Cellulomonas flavigena
Neocallimastix frontalis
Neocallimastix patriciarum
Piromyces communis
Bifidobacterium animalis
Bacteroides ovatus
Fibrobacter intestinalis
[Eubacterium] cellulosolvens
Bacteroides sp.
Pseudobacteroides cellulosolvens
Lachnospira eligens
Agathobacter rectalis
Ruminococcus sp.
Enterobacter sp.
Piromyces sp.
Epidinium caudatum
Eudiplodinium maggii
Polyplastron multivesiculatum
Orpinomyces joyonii
Piromyces rhizinflatus
Segatella bryantii
Piromyces sp. 'equi'
Roseburia intestinalis
Pseudobutyrivibrio xylanivorans
Butyrivibrio hungatei
Bifidobacterium longum
Acetivibrio clariflavus
Epidinium ecaudatum
Roseburia hominis
uncultured Neocallimastigales
Bacteroides xylanisolvens
Cellulosilyticum ruminicola
Ruminococcus champanellensis
Orpinomyces sp.

overall_design: We analysed two groups of lambs, with or without the feed supplement. These represented six samples (3 control and 3 supplemented lambs).

first: Frederique

last: Chaucheyras-Durand


title: Transcriptional profile of CAOV2 primary and CAOV2 recurrent cells

first: Jen-Tsan

last: Chi

summary: We performed RNAseq to study the transcriptional changes of human CAOV2 recurrent vs CAOV2 primary ovarian cancer cells to understand the genetic determinants of ferroptosis response

overall_design: CAOV2-GFP/LUC cells (3.5x10^5 per mouse) were injected intraperitoneally into female nude mice with tumor formation monitored weekly using the IVIS in vivo imaging system. Once tumor formation was evident, we initiated treatment with carboplatin (60mg/kg intraperitoneally twice a week for two weeks) and monitored for changes in tumor flux. In this model, tumor signal was reduced following carboplatin treatment but then recurred approximately 2-4 weeks after carboplatin treatment had stopped. Therefore, we refer to the residual tumor cells that eventually emerged as CAOV2R (recurrent). Both CAOV2 primary and CAOV2 recurrent cells are cultured in DMEM+10%FBS before submitting for RNAseq.

first: Wen-Hsuan

last: Yang

first: Zhiqing

last: Huang

first: Susan

last: Murphy


title: Global transcriptional profiling changes upon knockout of USP22 in human Non-small cell lung cancer cells

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: The experiment was designed to display differential gene expression profiling changes in two human non-small cell lung cancer cells A549 and H1299 upon knockout of USP22 gene, by using RNAseq technology.

overall_design: USP22 was knocked out in Non-small cancer cell lines A549 and H1299 by two individual Crispr/Cas9 sgRNAs. Total RNA was extracted from each USP22 knockout clone and control parental cells for RNAseq analysis. Differentially expressed genes in USP22 knockout NSCLC cells were identified in comparison to that in parental NSCLC cells.

first: Keqiang

first: Jinghan

last: Wang

first: Lu

first: Dan

last: Raz


title: Single cell sequencing of hypothalamus tissues in IDOL KO

city: Los Angeles

first: Douglas

last: Arneson

address: 2000 Terasaki Life Sciences Bldg 610 Charles E Young Drive East

department: Integrative Biology and Physiology

institute: UCLA

summary: A single cell suspension was generated from IDOL KO and Control mouse hypothalami, and single-cell mRNAseq libraries were generated with Drop-Seq.

overall_design: Drop-Seq was performed on two separate days mixing experimental groups using the same age (8 week) and strain (C57BL/6J) mice.

first: P

last: Tontonoz

first: S

last: Lee


title: Transcriptional dysregulation by a nucleus-localized aminoacyl-tRNA synthetase is associated with Charcot-Marie-Tooth neuropathy

city: Antwerp

first: Ligia

middle: Monica

last: Mateiu

address: Universiteitsplein 1

department: Center for Molecular Neurology

country: Belgium

institute: VIB

summary: Charcot-Marie-Tooth disease (CMT) is a length-dependent peripheral neuropathy. The aminoacyl-tRNA synthetases constitute the largest protein family implicated in CMT. Aminoacyl-tRNA synthetases are predominantly cytoplasmic, but are also present in the nucleus. Here we show that a nuclear function of tyrosyl-tRNA synthetase (TyrRS) is implicated in a Drosophila model of CMT. CMT-causing mutations in TyrRS induce unique conformational changes, which confer capacity for aberrant interactions with transcriptional regulators in the nucleus, leading to transcription factor E2F1 hyperactivation. Using neuronal tissues, we reveal a broad transcriptional regulation network associated with wild-type TyrRS expression, which is disturbed when a CMT-mutant is expressed. Pharmacological inhibition of TyrRS nuclear entry with embelin reduces, whereas genetic nuclear exclusion of mutant TyrRS prevents hallmark phenotypes of CMT in the Drosophila model. These data highlight that this translation factor may contribute to transcriptional regulation in neurons, and suggest a therapeutic target for CMT.

overall_design: To assess the full spectrum of downstream effects triggered by mutant TyrRS, we performed expression profiling on whole brains of controls: nSyb-Gal4>+, TyrRS-WT, TyrRS-WT-NLS, TyrRS-E196K-NLS and the affected condition: TyrRS-E196K flies that were aged for 10 days

first: Sven

last: Bervoets

last: Wei

first: Maria-Luise

last: Erfurth

first: Shazie

last: Yusein-Myashkova

first: Biljana

last: Ermanoska

first: Bob

last: Asselbergh

first: David

last: Bloquel

first: Priyanka

last: Kakad

first: Tyrone

last: Penserga

first: Florian

last: Thomas

first: Velina

last: Guergueltcheva

first: Ivailo

last: Tournev

first: Tanja

last: Godenschwege

first: Albena

last: Jordanova

first: Xiang-Lei


title: Zebrafish larvae aryl hydrocarbon receptor ligands and inhibitor

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: Wild type zebrafish (AB strain, https://zfin.org/action/genotype/view/ZDB-GENO-960809-7) were set up for mating overnight, in 3:2 ratios, females and males, respectively. Fertilized embryos from wildtype zebrafish AB strain were used for all experiments and kept in Embryo medium (E3, 5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4) in an incubator at 28ºC. At 1dpf, larvae were manually dechorionated under a stereomicroscope. At 2dpf, zebrafish larvae were divided randomly into the different experimental groups, at a density of 12 larvae per well of a 12 well plate (Corning) in 1.5mL of E3. Three biological replicates of 12 larvae per condition were exposed to different conditions for 4 hours at 28 ºC: DMSO; DMSO + CH223191 (5mM); 3-o-C12-L-HSL (50mM); 3-o-C12-L-HSL (50mM) + CH223191 (5 mM ); 1-hydroxyphenazine (1-HP, 5mM); 1-HP (5mM) + CH223191(5mM) and 1-HP (5mM) + 3-o-C12-L-HSL (50mM).To mention, in experiments using the Aryl hydrocarbon Receptor inhibitor CH223191, larvae were pre-exposed to 5uM of the inhibitor for 2h prior to the start of the experiment and the inhibitor was kept during the experiment. After the desired exposure to diverse ligands, larvae were euthanized with Tricaine (MS-222, 300 µg/mL) and placed in Trizol for RNA isolation. The same experimental layout was performed 5 times, and samples were subjected to microarray hybridization and analysis.

overall_design: Microarray experiments were performed as single-color hybridizations. Quality control and quantification of total RNA amount was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies) and a NanoDrop 1000 spectrophotometer (Kisker).

first: Pedro

last: Moura-Alves

first: January

last: Weiner

first: Stefan

middle: E

last: Kaufmann


title: Detection of cryptic start codons in set2D by 5PSeq

first: Vicent

last: Pelechano

summary: We investigated cryptic transcription start site usage, chromatin organization and post-transcriptional consequences in Saccharomyces cerevisiae. We used 5PSeq approach, which measures ribosome dynamics by sequencing the presence of co-translation mRNA degradation intermediates, to assess if cryptic transcripts are engaged in active translation. We show that chromatin-dependent cryptic transcripts can be recognized by ribosomes and have the potential to produce truncated polypeptides by using downs-stream, in-frame start codons. Our work suggests that a significant fraction of chromatin-dependent internal cryptic promoters are in fact alternative truncated mRNA isoforms.

overall_design: We performed 2 biologically independent 5PSeq experiments.

first: Yujie

last: Zhang

first: Jingwen

last: Wang


title: Nannochloropsis metabolism during transition from quiescence to autotrophy.

city: Goettingen

first: Agnieszka

last: Zienkiewicz

address: Justus-von-Liebig Weg 11

department: Department of Plant Biochemistry

institute: University of Goettingen

summary:
Purpose: The marine microalgae Nannochloropsis oceanica (CCMP1779) is a  prolific producer of oil and is considered a viable and sustainable  resource for biofuel feedstocks. Nitrogen (N) availability has a strong impact on the physiological status and metabolism of microalgal cells. However the exact nature of this response is poorly understood. To fill this gap we performed transcriptomic profiling combined with cellular and molecular analyses of N. oceanica CCMP1779 during the transition from quiescence to autotrophy.
Methods: Nannochloropsis cells (50 ml per sample) were harvested for RNA isolation during nitrogen deprivation (N-) and after nitrogen resupply (NR) at the following time points: 6, 12, 24, 48 and 72 h. For each time point two biological replicates were harvested. RNA was extracted using the E.Z.N.A® Plant RNA kit (OMEGA) according to the manufacturer’s instructions. RNA quality was verified using the Bioanalyzer (Agilent). Single-end, 50 bp nucleotide sequences were acquired for each sample using an Illumina HiSeq 2500 (MSU-Research Technology Support Facility). RNA-Seq reads were trimmed using Trimmomatic (v0.32) with removal of leading and trailing low quality bases (below quality score 10 with a 4-base wide sliding window) as well as TruSeq Single End adaptors. The resulting reads were aligned to the N. oceanica CCMP1779 genome assembly (GSE36959) using STAR (2.3.0e) (Dobin et al., 2013) by only allowing unique mapping, a maximum of 4 mismatches per pair and a maximum intron length of 10,000 bp. The HTSeq (0.6.1) was used to generate a count table for all genes using the exon as the feature type as well as the intersect-nonempty mode so that only reads that were completely aligned to two genes are considered ambiguous. HTSeq count tables were used for differential expression analysis using DEseq2. Differential gene expression was examined using DESeq2. A generalized linear model was fit, and we tested on condition (deprivation or recovery) and the time:condition interaction with log2-fold changes greater than 1. Significant differentially expressed genes with p-values less than 0.01 were identified after Benjamini-Hochberg (BH) multiple testing correction. Differentially expressed genes were clustered based on expression using K-means clustering (k = 4) with the Pearsons correlation distance metric within MeV (4.8.1).
Results: We showed that N deprivation-induced quiescence is accompanied by a strong reorganization of the photosynthetic apparatus and changes in the lipid homeostasis leading to accumulation of triacylglycerol (TAG). Cell cycle activation and re-establishment of photosynthetic activity observed in response to resupply of the growth medium with N were accompanied by a rapid degradation of TAG stored in lipid droplets (LDs). Beside observing  LD translocation into vacuoles we also provide  evidence for direct interaction between the lipid droplet surface protein (NoLDSP) and autophagy-related 8 (NoATG8) protein and show a role of microlipophagy in LD turnover in N. oceanica CCMP1779.
Conclusions: This knowledge  is crucial not only for understanding the fundamental mechanisms controlling the cellular energy homeostasis in microalgal cells but also for the development of efficient strategies to achieve higher algal biomass and better microalgal lipid productivity.

overall_design: Nannochloropsis mRNA profiles during during nitrogen deprivation (N-) and after nitrogen resupply (NR) at the following time points: 6, 12, 24, 48 and 72 h were generated by deep sequencing, in duplicate, using Illumina HiSeq 2500.

first: Krzysztof

first: Eric

last: Poliner

first: Jane

last: Pulman

first: Zhi-Yan

last: Du

first: Chia-Hong

last: Tsai

first: Patrick

last: Horn

first: Ivo

last: Feussner

first: Eva

last: Farre

first: Kevin

last: Childs

first: Christoph

last: Benning


title: Detection of cryptic unstable transcripts associated with ribosomes in yeast

summary: We investigated the association of cryptic unstable transcripts (CUTs) to ribosomes in Saccharomyces cerevisiae.   We used 5’cap-sequence followed by sucrose gradient fractionation of polyribosome fractions after ultracentrifugation to assess the relative association of transcripts to the ribosomes.  We used 5PSeq approach, which measures ribosome dynamics by sequencing the presence of co-translation mRNA degradation intermediates, to assess if cryptic transcripts are engaged in active translation. We performed 5PSeq after glucose depletion to increase the number of ribosomes stop at the 5’UTR and start codon.

overall_design: We performed 2 biologically independent experiments for polyribosome fractionation and for 5PSeq.

first: Wu

last: Wei

first: Lars

last: Steinmetz


title: Pretransplant transcriptomic signature in peripheral blood predicts acute rejection and renal allograft loss

city: New York

first: Weijia

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

summary: Early development of acute rejection after kidney transplantation is associated with diminished long-term graft survival. Predicting early acute rejection (EAR) at the time of transplant is important to risk-stratify patients and titrate immunosuppression accordingly. We performed whole-blood RNA sequencing at the time of transplant in 235 kidney transplant recipients enrolled in a prospective-cohort study [one discovery set (N=81), two validation sets (N=74 and N=80)] and evaluated the relationship with EAR and graft loss. We identified a blood based 23-gene set in recipients at the time of transplant that predicts the risk of EAR and is associated with late AR and allograft loss. This gene set is an important new tool to risk-stratify recipients before kidney transplantation and help guide immunosuppressive therapy accordingly.

overall_design: The transcriptomic profiles of discovery set (N=81) was used for identification of gene signatures associated with early acute rejection. The early acute rejection prediction with the gene signatures was validated on validation set V1 (N=74) and late acute rejection and graft loss was validated on combined datasets of V1 (N=74) and V2 (N=80).

first: Zhengzi

last: Yi

first: Paolo

last: Cravedi

first: Barbara

last: Murphy


title: Pancreatic ductal adenocarcinoma

city: Tokushima

first: Toshihito

last: Tanahashi

address: Kuramotocho 3-18-5

institute: Tokushima University

summary: We sought to determine whether certain miRNAs could serve as a biomarker for the prognosis of pancreatic ductal adenocarcinoma (PDAC) and uncover the uncharacterized miRNAs function in the pancreatic carcinogenesis

overall_design: Eexpressions of 2042 miRNAs were comprehensively profiled in 13 micro tissues of PDAC by endoscopic ultrasonography-guided fine needle aspirate (EUS-FNA), and compared to the survival periods of 13 PDAC patients

first: Jun

last: Okazaki


title: Chromatin-dependent cryptic promoters encode alternative  protein isoforms in yeast

first: Vicent

last: Pelechano

summary: Cryptic transcription is widespread and generates a heterogeneous group of RNA molecules of unknown function. To improve our understanding of cryptic transcription, we investigated their transcription start site usage, chromatin organization and post-transcriptional consequences in Saccharomyces cerevisiae. We show that  transcription start sites of chromatin-dependent internal cryptic transcripts resemble those of protein coding genes in terms of DNA sequence, directionality and chromatin accessibility. We define the 5’ and 3’ boundaries of cryptic transcripts and show that, contrary to RNA degradation-dependent ones , they often overlap with the end of the gene thereby using the canonical polyadenylation site and associate to polyribosomes. In fact, we show that chromatin-dependent cryptic transcripts can be recognized by ribosomes and may produce truncated polypeptides from downstream, in-frame start codons. Our work suggests that a significant fraction of chromatin-dependent internal cryptic promoters are in fact alternative truncated mRNA isoforms. The expression of these chromatin-dependent isoforms is conserved from yeast to human expanding the functional consequences of cryptic transcription and proteome complexity.

overall_design: We identify 5' transcription start sites applying our 5'cap -sequencing approach as previously described (Pelechano et al. Nat Protocols. 2016  PMID: 26820793). To measue polyribosome association we applied the 5'cap -sequencing approach to either total RNA extracts or polyribosome-associated fraction after ultracentrifugation in sucrose gradient. We performed 2 biologically independent experiments.

first: Bianca

middle: P

last: Hennig

first: Jingwen

last: Wang

first: Yujie

last: Zhang

first: Christophe

last: Chabbert

first: Sophie

middle: H

last: Adjalley


title: Tumor microenvironment-activated angiotensin blockers enhance cancer immunotherapy

city: Charlestown

first: Kamila

last: Naxerova

address: 149 13th Street

department: Center For Systems Biology

institute: Massachusetts General Hospital / Harvard Medical School

summary: Cancer-associated fibroblasts (CAFs) suppress anti-tumor immunity mediated by T-lymphocytes – making CAFs tempting targets for enhancing cancer immunotherapy. Unfortunately, the signaling mechanisms driving CAF activity in tumors have crucial functions outside tumors. Consequently, agents like angiotensin receptor blockers (ARBs) that inhibit CAF activity are limited by systemic adverse effects such as hypotension. To address this challenge, we developed tumor microenvironment-activated ARBs (TMA-ARBs) by chemically linking ARBs to novel polymeric materials that selectively degrade in the tumor microenvironment. TMA-ARBs remain in an inactive, material-bound state until they reach tumors, wherein the ARBs become active as the materials break apart. This tumor-selective activity enhances the CAF-inhibiting effects of ARBs while eliminating blood pressure-lowering effects. By reducing CAF activity, TMA-ARBs induce a comprehensive immunostimulatory shift in the tumor microenvironment with improved T-lymphocyte activity and distribution. Accordingly, TMA-ARBs dramatically increase animal survival when combined with immunotherapy in mice with metastatic breast cancer.

overall_design: 5 control samples, 5 TMA-ARB treated samples

first: Vikash

last: Chauhan

first: Ivy

middle: X

last: Chen


title: Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

institute: University of Georgia

type: Non-coding RNA profiling by high throughput sequencing

summary: Tissue culture is a major method for plant regeneration and for production of transgenic plants. Thus far, our knowledge of the dynamic epigenomic during tissue culture is limited. In this study, we generated epigenomes from nine different stages throughout the tissue culture process and found significant genome-wide increases of DNA methylation throughout the soybean genome. This change mostly happens in CHH (H = A, T, C) context and targets transposable elements (TEs). Subsequent analyses of corresponding transcriptomes and small RNA distributions indicate that it is associated with high activity of the RNA-directed DNA methylation (RdDM) pathway. These results provide important insights into the function of a dynamic epigenome throughout tissue culture and extends our understanding of epigenome-wide reprogramming of the DNA methylome in plants.

overall_design: Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance


title: Dual modulation of neuron specific microRNAs and the REST complex promotes functional maturation of induced human adult neurons

city: Lund

first: Johan

last: Jakobsson

address: Solvegatan 17

institute: Lund University

summary: Direct neural reprogramming can be achieved using different approaches, including by expressing neuronal transcription factors or microRNAs, and by knocking down neuronal repressive elements. However, there still exists a high variability in terms of the quality and maturity of the induced neurons (iNs) obtained, depending on the reprogramming strategy employed. Here, we evaluate different long-term culture conditions and study the effect of expressing the neuronal-specific microRNAs miR124 and miR9/9* while reprogramming with Ascl1, Brn2 and knockdown of the neuronal repressor REST. We show that addition of microRNA supports neuronal maturation both in terms of gene and protein expression, as well as promotes the development of active ion channels and the ability of iNs to generate current induced and spontaneous action potentials.

overall_design: RNA sequencing of induced human neurons from fibroblasts with two different conditions. Three replicatess were used for each condition.

first: Yogita

last: Sharma


title: Hi-C during mitotic release and G1 entry

status: Public on Sep 30 2019

city: Worcester

first: Kristin

last: Abramo

address: 368 Plantation Street

institute: University of Massachusetts Medical School

summary: DpnII Hi-C libraries for samples synchronized to G2/M using single 24h thymidine, 3h release, and 12h nocodazole--these samples are then released for x amount of time

overall_design: Hi-C

first: Anne-Laure

last: Valton

first: Sergey

middle: V

last: Venev

first: Hakan

last: Ozadam

first: A

middle: N

last: Fox

first: Job

last: Dekker


title: Repression of Ect2 induces cytokinesis failure and decreases heart muscle cell proliferation in congenital heart disease

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

summary: Proliferation of heart muscle cells (cardiomyocytes) is the basis for heart development and regeneration. In mammals, cardiomyocytes become binucleated, which is thought to limit their proliferative capacity, but mechanisms are unknown. Here, we show the detailed mechanisms of formation of binucleated cardiomyocytes and how these mechanisms are dysregulated in congenital heart disease (CHD). Cardiomyocytes become binucleated by failing the last stage of cytokinesis, abscission. We identified the underlying molecular mechanism with single-cell transcriptional profiling, which showed repression of the cytokinesis gene Ect2, a Rho-guanine-nucleotide exchange factor. Inactivating Ect2 tripled the proportion of binucleated cardiomyocytes and reduced the number of cardiomyocytes by 34% in newborn mice, which was lethal. Cardiomyocyte-specific overexpression of Ect2 in transgenic mice decreased cytokinesis failure. We demonstrate that the Ect2 gene is regulated by the Hippo tumor suppressor pathway, and upstream of that, by β-adrenergic receptor signaling. In neonatal mice, stimulating β-adrenergic signaling pathway output with forskolin decreased the number of cardiomyocytes, and administration of β-blockers increased the number of cardiomyocytes. Finally, we show that patients with tetralogy of Fallot with pulmonary stenosis (ToF/PS), a common type of CHD, develop a 2.2-fold increase in bi- and multi-nucleated cardiomyocytes. Using in vivo labeling of one ToF/PS patient with 15N-thymidine, followed by imaging mass spectrometry, we demonstrate that this increase happens after birth. Organotypic cultures of myocardium from infants with ToF/PS showed that cardiomyocyte binucleation could be reduced with β-blockers. These results demonstrate how cardiomyocyte proliferation stops and provide the basis for new therapeutic strategies to increase cardiomyocyte proliferation in patients with CHD.

overall_design: The cardiomyocytes were isolated from embryonic (E14.5) and postnatal (P5) mouse (FUCCI) hearts, then the single cardiomyocytes were collected through FACS. The cycling cardiomyocytes were identified through Azami Green-Geminin (mAG-hGem) signal. The mRNA was amplified using the antisense RNA (aRNA) amplification method.

first: Honghai

last: Liu

first: Cheng-Hai

first: Sangita

last: Suresh

first: Niyatie

last: Ammanamanchi

first: Christopher

last: Lewarchik

first: Krithika

last: Rao

first: Gerrida

last: Uys

first: Lu

last: Han

first: Maryline

last: Abrial

first: Balakrishnan

last: Ganapathy

first: Christelle

last: Guillermier

first: Nathalie

first: Mugdha

last: Khaladkar

first: Jennifer

last: Spaethling

first: James

last: Eberwine

first: Stuart

last: Walsh

last: Choudhury

first: Kathryn

last: Little

first: Kimberly

last: Francis

first: Mahesh

first: Melita

last: Viegas

first: Matthew

middle: L

last: Steinhauser

first: Bernhard

last: Kühn


title: Porcine macrophages: ASFV-infected vs. mock-infected

city: Orient

middle: J.

last: Zhu

department: Foreign Animal Disease Research Unit

institute: USDA-ARS

summary: Transcriptional profiling of porcine macrophages infected with Afraican swine fever virus (ASFV) infected cells and mock infection was conducted in this experiment.

overall_design: Two-condition experiment: ASFV infected vs. mock infected cells. Biological replicates: three. Macrophages were prepared from 3 pigs. Macrophages from each pig were infected and mock-infected with ASFV. The total RNA samples were prepared at six time points, 3, 6, 9, 12, 15 and 18 hours post infection. Array hybridization was based on a dye-swap design in which each array contained a Cy5 or Cy3 labeled infected and a Cy3 or Cy5 labeled mock-infected sample of the same time point, respectively.

first: Palaniappan

last: Ramanathan

first: Elizabeth

last: Bishop

first: Vivian

last: O’Donnell

first: Douglas

last: Gladue

first: Manuel

last: Borca


title: Acute effects of high pCO2 and hypoxia on gene expression in blue rockfish (Sebastes mystinus)

city: Seaside

first: Andrew

middle: Jacob

last: Cline

state: CA

address: 100 Campus Center

department: School of Natural Sciences

institute: California State University, Monterey Bay

summary: We sequenced complementary DNA created from white muscle messenger RNA in juvenile blue rockfish and performed a differential gene expression analysis to describe the fishes' responses to the global change-related stressors of high pCO2 (low pH) and hypoxia (low dissolved oxygen, DO). To examine gene expression over ecologically realistic timescales that emulate the duration of spring upwelling events in the California Current ecosystem, we collected and sequenced samples after 12 h, 24 h and two weeks of exposure to four treatments: control (pH≈8.0, pCO2≈400μatm, DO≈8 mg/L), high pCO2 (pH≈7.6, pCO2≈1200μatm, DO≈8 mg/L), hypoxic (pH≈8.0, pCO2≈400μatm, DO≈4 mg/L), and combined high pCO2/hypoxic (pH≈7.6, pCO2≈1200μatm, DO≈4 mg/L).

overall_design: Differential gene expression analysis performed on blue rockfish muscle tissue after 12 h, 24 h and two weeks of exposure to high pCO2 and hypoxia

first: A

first: Cheryl

last: Logan


title: Genomics analysis of L-DOPA exposure in Drosophila sechellia

status: Public on Sep 28 2019

city: Middletown

first: Joseph

last: Coolon

state: CT

address: 52 Lawn Avenue Biology Department

institute: Wesleyan University

summary: The dietary specialist fruit fly Drosophila sechellia evolved to feed primarily on the toxic fruit of Morinda citrifolia. Seeking the basis of adaptations to the unique chemistry of its host plant, we profiled genome-wide gene expression response to L-DOPA because it is highly abundant in M. citrifolia, critical for reproductive success of D. sechellia, and may influence toxin resistance in this species. Here we used a combination of functional genetics and genomics to identify a new gene, Esterase 6 (Est6) that is important for D. sechellia ecological adaptation to this new niche.

sample_organism:
Drosophila melanogaster
Drosophila sechellia
Drosophila simulans

overall_design: Differential gene expression analysis of D. sechellia, D. simulans, and D. melanogaster flies exposed to control food and food supplemented with L-DOPA using RNA-sequencing.

first: Stephen

middle: M

last: Lanno

first: Ivy

last: Lam

first: Zachary

last: Drum

first: Samuel

middle: C

last: Linde

first: Sara

last: Gregory

first: Serena

last: Shimshak

first: Mariel

last: Becker

first: Kerry

last: Brew

first: Aashli

last: Budhiraja

first: Eliza

last: Carter

first: Lorecia

last: Chigweshe

first: Keagan

last: Collins

first: Timothy

last: Earley

first: Hannah

last: Einstein

first: Angela

last: Fan

first: Sarah

middle: S

last: Goss

first: Eric

middle: R

last: Hagen

middle: B

last: Hutcheon

last: Kim

first: Mackenzie

last: Mitchell

first: Nola

last: Neri

first: Sean

last: Patterson

first: Gregory

last: Ransom

first: Guadalupe

last: Sanchez

first: Bella

last: Wiener

first: Dacheng

last: Zhao

middle: D


title: Tregs deltaDC mice vs. wt mice

status: Public on Sep 27 2019

city: Erlangen

first: David

last: Vöhringer

state: Bavaria

address: Wassersturmstr 3-5

department: Microbiology

institute: University Hospital Erlangen

summary: Tregs from spleen and thymus of naive Wild-type mice and mice lacking Dendritic Cells (deltaDC) were analyzed. Thymus derived Tregs of both strains show similar expression patterns, peripheral splenic Tregs from deltaDC mice differ from Tregs of WT mice.

overall_design: There are 4 samples in total. The following conditions were analyzed: Wild-type Tregs from Spleen (WT_Spleen), Wild-type Tregs from Thymus (WT_Thy), deltaDC Tregs from Spleen (dDC_Spleen), and deltaDC Tregs from Thymus (dDC_Thy).

last: Voehringer


title: Translational dynamics during seed maturation

city: Wageningen

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

summary:
We analysed the polysomal mRNA and total mRNA during Col-0 seed maturation
The aim was to investigate the translational dynamics during seed maturation.

overall_design: Transcript level on both total mRNA and polysomal mRNA of Col-0 seeds were eveluated. For each RNA fraction, three replicates were used.

first: Bing

last: Bai

first: Sjors

last: van der Horst

first: Johannes

last: Hanson