title: Dimethyl fumarate induces ferroptosis and impairs NF-κB/STAT3 signaling in DLBCL

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

summary: Multi-agent chemotherapy still represents the first-line standard-of-care treatment for diffuse large B-cell lymphoma (DLBCL), the most common form of lymphoma in adults. However, the clinicopathological and molecular heterogeneity of DLBCLs poses a major challenge in their successful therapy. At least two major subtypes, i.e. germinal center B-cell-like (GCB) and the aggressive activated B-cell-like (ABC) DLBCL, which differ both in their gene expression profile and in their mutation patterns, have been identified. Here we demonstrate a broad inhibitory effect of dimethyl fumarate (DMF) on the outgrowth of both DLBCL subtypes, even though the molecular basis for its efficacy differs between GCB and ABC DLBCL. Due to high expression of arachidonate 5-lipoxygenase in concert with low glutathione and glutathione peroxidase 4 levels, DMF induced lipid peroxidation and thus ferroptotic cell death in GCB DLBCL. In contrast, in ABC DLBCL inhibition of NF-κB and STAT3 activity essentially contributed to DMF-dependent cytotoxicity. Interestingly, the BCL-2 specific BH3 mimetic ABT-199 or an inhibitor of the ferroptosis suppressor protein 1 synergized with DMF treatment in inducing cell death in DLBCL cell lines. Collectively, our findings identify the established and approved drug DMF as a promising novel therapeutic option in the treatment of both GCB and ABC DLBCL.

overall_design: Gene expression profiling was performed in HBL-1 cells after 6, 12, 24 and 48h of treatment with 20µM DMF, compared to control. Each time point was measured in triplicate, resulting in 24 samples in total.

first: Stephan

last: Hailfinger

first: Georg

last: Lenz


title: Examine the impact of insulin suppression on embryo H3K27 trimethylation.

status: Public on Jul 01 2021

city: Dallas

first: Matt

last: Sieber

state: Texas

address: 5323 Harry Hines blvd, MC 9040 ND12.214

country: USA

institute: UT Southwestern Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: These expeirments compare the H3L27-trimethylation ChIP profiles for embryonic progeny of  GFP expressing (control) and InR-DN expressing stage 14 oocytes.

overall_design: In this experiment we collected 16 hr embryonic progeny of GFP expressing oocytes and InR-DN expressing oocytes and conducted  H3K27-me3 sequencing analysis

first: Matthew


title: PD-1-stimulated T cell subsets are transcriptionally and functionally distinct

city: NYC

first: Adam

last: Mor

state: NY

department: Medicine

institute: CUIMC

type: Expression profiling by high throughput sequencing

summary: Analysis of 3 subsets of primary human CD4+ T cells (naive, CM, EM) stimulated with anti-CD3, anti-CD28 and PD-L1/PD-L2 for 18 hours. we show that naive, EM, and CM T cell subsets had distinct gene expression profiles following PD-1 ligation.

overall_design: 3x donors;  3x CD4+ T cell subsets from each donor (naïve, CM, EM);  4x treatments - unstimulated, aCD3/28, aCD3/28+PDL1, aCD3/28+PDL2;  35 samples it total (the sample of CM cells of donor#2 treated with aCD3/28 did not pass QC and was excluded from all RNA-seq analyses)

first: Shalom

last: Lerrer


title: Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation

city: Gif-sur-Yvette

first: Stéphanie

middle: Germaine

last: Bury-Moné

address: 1 Avenue de la Terrasse

country: France

institute: Institute for Integrative Biology of the Cell

summary: Streptomyces are among the most prolific bacterial producers of specialized metabolites, including antibiotics. The linear genome is partitioned into a central region harboring core genes and two extremities enriched in specialized metabolite biosynthetic gene clusters (SMBGCs). The molecular mechanisms governing structure and function of these compartmentalized genomes remain mostly unknown. Here we show that in exponential phase, chromosome structure correlates with genetics compartmentalization: conserved, large and highly transcribed genes form boundaries that segment the central part of the genome into domains, whereas the terminal ends are transcriptionally, largely quiescent compartments with different structural features. Onset of metabolic differentiation is accompanied by remodeling of chromosome architecture from an ‘open’ to a rather ‘closed’ conformation, in which the SMBGCs are expressed forming new boundaries. Altogether, our results reveal that S. ambofacien's linear chromosome is partitioned into structurally distinct entities, indicating a link between chromosome folding, gene expression and genome evolution

overall_design: Analysis of chromosome conformation and transcriptome of Streptomyces ambofaciens ATCC 23877 during metabolic differentiation

first: Virginia

last: Lioy

first: Jean-Noël

last: Lorenzi

first: Soumaya

last: Najah

first: Thibault

last: Poinsignon

first: Hervé

last: Leh

first: Corinne

last: Saulnier

first: Bertrand

last: Aigle

first: Sylvie

last: Lautru

first: Annabelle

last: Thibessard

first: Olivier

last: Lespinet

first: Pierre

last: Leblond

first: Yan

last: Jaszczyszyn

first: Kevin

last: Gorrichon

first: Nelle

last: Varoquaux

first: Ivan

last: Junier

first: Frédéric

last: Boccard

first: Jean-Luc

last: Pernodet


title: Transcriptomic analysis of Resp18mutant rat kidneys reveals up-regulation of Renin-Angiotensin system

city: Toledo

first: Sivarajan

last: Kumarasamy

state: OH

address: 3000 Arlington Ave

department: Physiology Pharmacology

institute: University of Toledo College of Medicine and Life Sciences

summary: Regulated endocrine specific protein 18 (Resp18), expression has been specifically located in a series of tissues and cell types however the exact cellular function is unknown. In previous studies we have showed that a targeted disruption of Resp18 in Dahl SS rats (Resp18mutant) resulted in higher blood pressure (BP), increased renal fibrosis, and decreased survival rate on a long term (6-week) 2% high salt (HS) diet treatment compared with wild type SS rats. In the current study we studied whether a short term (1 week) exposure to HS diet shows a similar effect in Resp18mutant rats. Furthermore, previously we have shown that in addition to BP phenotype Resp18mutant rats have demonstrated deteriorative kidney phenotype evident through renal fibrosis, protein urea and protein cast formation. Based on this background we conducted BP study and performed transcriptomic profiling of the kidney after one-week exposure to HS diet treatment. Through radio-telemetry procedure, we found that the systolic BP was increased in the Resp18mutant rats compared with SS rats even with short term HS diet exposure. Therefore, we sought out to investigate if there was any alteration in the transcriptomic response by HS diet treatment in the Resp18mutant rat kidneys. Using RNA sequencing approach, we found that Resp18mutant rats showed a differential expression of 25 genes of which one was an upregulation of Ren. We confirmed the upregulation of Ren and other differentially expressed genes via qRT-PCR analysis. Upon KEGG pathway enrichment we found that the Resp18mutant rat showed upregulation in the renin angiotensin system (RAAS), and renin secretion pathway. Furthermore, the renin activity is found to be higher in Resp18mutant rats serum compared with SS rats. Therefore, these observations demonstrate that upon disruption of Resp18 gene in SS rats associated with the increase in renin secretion and thus increase BP.

overall_design: RNA sequencing of Kidneys from control and Resp18 mutant rat RNA samples in triplicate, using Illumina.

first: Kumarasamy

last: Sivarajan

first: Ashraf

last: Usman


title: Tracing colonic embryonic transcriptional programs and their reactivation in inflammatory disease at single cell level

city: Zürich

first: Michael

middle: David

last: Brügger

address: Winterthurerstrasse 190

department: Molecular Life Sciences

country: Switzerland

institute: University of Zürich

summary: Purpose: determine transcriptional programs active during hindgut development and their reactivation in inflammatory disease; Summary: Our analyses reveal that most adult cell lineages are established by the late embryonic stage. In addition we find reactivation of embryonic features in inflammatory disease.

overall_design: All embryonic (E14.5, E15.5, E18.5) and adult (DSS treatment) cells were sorted using FACS (using EpCAM and CD45 antibodies). Single cell RNA sequencing was perfomed (for details see Fazilaty et al, in prep)

first: Hassan

last: Fazilaty

first: Tomas

last: Valenta


title: Examine the impact of insulin suppression on embryo H3K27-ac

first: Matt

last: Sieber

summary: These expeirments compare the H3k27-ac ChIP profiles for embryonic progeny of  GFP expressing (control) and InR-DN expressing stage 14 oocytes.

overall_design: In this experiment we collected 16 hr embryonic progeny of GFP expressing oocytes and InR-DN expressing oocytes and conducted  H3K27-ac sequencing analysis

first: Matthew


title: Tumor transcriptomes profiling of SS18-SSX, Smarcb1-/- and combination of SS18-SSX and Smarcb1-/- driven tumor

city: Beijing

first: Jinxiu

last: Li

state: Beijing

address: Yuanmingyuan west road 2#

department: College of biological sciences

country: China

institute: China Agricutural University

summary: We generated mouse tumors of each combination of genotypes that included either presence or absence of heterozygosity for hSS2 in Rosa26 and homozygosity for wildtype or floxed alleles of Smarcb1. In order to test how these different tumor genotypes impacted BAF distribution across the genome, we performed ChIPseq in tumors of each genotype for member components shared by all BAF subtypes, SMARCC1 (also named BAF155) and SMARCA4 (also named BRG1.) We also performed ChIPseq for RNAPOLII to determine the BAF relationship with transcription in each genotype. The length of peaks is extended in fusion-expressing tumors, regardless of Smarcb1 status. The heatmaps of SMARCC1 enrichments at transcription start sites (TSSs) across the genome in fusion-only tumors demonstrate a very similar overall pattern with that in combination genotype tumors, which suggested that the fusion plays a deterministic role in the distribution of BAF complexes across the genome. Specifically around each TSS across the genome was a striking absence of BAF enrichment in both groups that bore genetic silencing of Smarcb1, not present in the fusion-only group. This suggests that some SMARCB1-retaining BAF complex is necessary to permit binding to the TSS or the +1 nucleosome position. Fusion expression and Smarcb1 silencing have different impacts on BAF genomic locations.

overall_design: BAF genomic locations of SS18-SSX, Smarcb1-/- and combination of SS18-SSX and Smarcb1-/- driven tumor

first: J

first: L

first: A

last: Pozner

first: K

middle: B

last: Jones


title: OCT4 cooperates with distinct chromatin remodelers in naive and primed pluripotent states in human [ChIP-Seq]

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: Understanding the molecular underpinnings of pluripotency is a prerequisite for optimal maintenance and application of embryonic stem cells (ESCs). We mapped the protein-protein interactions of OCT4 in naive and primed hESCs, revealing extensive connections to ATP-dependent nucleosome remodeling complexes. In naive hESCs, OCT4 is associated with both BRG1 and BRM, the two mutually exclusive ATPase subunits of the BAF complex. Genome-wide location analyses and genetic deletion studies reveal that these two enzymes exert a functionally redundant role in transcriptional regulation of blastocyst-specific genes. In contrast, OCT4 cooperates with BRG1 and the transcription factor SOX2 to create an open chromatin architecture at neural lineage-associated genes in primed hESCs. This work offers insight into the regulation of human stem cell identity and reveals how a common transcription factor utilizes differential compositions of the BAF complex in controlling distinct transcriptional programs governing naive vs. primed human pluripotent states.

overall_design: Genome binding/occupancy profiling of chromatin remodelers BAF155, BRG1, BRM, and transcription factors SOX2 in naive and primed hESCs by ChIP sequencing. Transcriptomes of naive and primed hESCs upon knockdown of either BRG1 or BRM by RNA sequencing.

first: Xin

last: Huang

first: Thorold

middle: W

last: Theunissen


title: Effects of cannabidiol on the inflammation-stimulated keratinocytes

city: Chengdu

first: Quan

last: Yuan

state: Sichuan

address: 14 Third section, Renmin Nan Road

institute: West China Hospital of Stomatology, Sichuan University

summary: Cannabidiol (CBD) oral spray on murine oral ulcer significantly inhibited inflammation, relieved pain and accelerated healing process. To gain insight into transcriptional regulation of CBD on cells related to healing progress of oral ulcer, we performed RNA-Seq on the immortalized human oral keratinocyte HOK-16B cell lines stimulated with LPS and ATP, after 10μM CBD or vehicle excipient pretreatment.

overall_design: Comparison of gene expression between inflammation-stimulated HOK-16B cell lines pretreated with CBD or vehicle

first: Xingying

last: Qi


title: RNA sequencing of isolated murine basal and suprabasal hair follicle bulge stem cells

city: Cologne

first: Catherin

last: Niemann

address: Robert-Koch-Str. 21

country: Germany

institute: Center for Molecular Medicine Cologne (CMMC)

summary: In most tissues, stem cells (SCs) comprise a heterogeneous cell population. Previous reports showed that slow cycling label-retaining cells (LRCs) are present in two prominent hair follicle SC populations, basal and suprabasal bulge SCs (bBSCs, sbBSCs). CD34+/itga6low sbBSC and neighbouring CD34+/itga6high bBSCs seem similar with both SC populations able to self-renew in vitro and to generate new hair follicles when grafted. Until now, functional differences have not been reported and molecular mechanisms underlying a positional encoded, intrinsic bulge SC heterogeneity and the relations to SC plasticity and tissue function are not well understood. Following fluorescence activated cell sorting for CD34 and integrin alpha6 of keratinocytes from 7 weeks old mice, we provide sequencing data for two prominent hair follicle SC populations, bBSC and sbBSC, suggesting distinct and overlapping functions in skin homeostasis.

overall_design: mRNA profiles of non-stem cells, basal bulge stem cells and suprabasal bulge stem cells of second telogen backskin from wild-type mice

first: Anna

last: Geueke

first: Prerana

last: Wagle

first: Giada

last: Mantellato


title: Examination of H3k27-me3, H3k27-ac, and H3k9-me3  in recurrent MCF7 cells

summary: These expeirments compare the chnages in h3K27-me3, H3k27-ac, and H3K9-me3 levels that occur in recurrent MCF7 cells.

overall_design: In this experiment we collected actively growing MCF7 cells and recurrent MCF7 cells that survied cysplatin treatment.


title: Cytomegalovirus Late Transcription Factor Target Sequence Diversity Orchestrates Viral Early to Late Transcription

city: Iowa City

first: Jeffery

middle: L

last: Meier

state: IA

address: SW34 GH, Department of Internal Medicine, University of Iowa. 200 Hawkins Drive

department: Departments of Internal Medicine and Epidemiology

institute: University of Iowa and Iowa City Veterans Affairs Health Care System

summary: Herpesviruses have a group of genes earmarked for expression late in the infection. Beta- and gammaherpesviruses utilize a six-member set of viral late transcription factors to selectively activate these genes by binding to a DNA sequence signature in gene promoters. We made an unexpected discovery that differences in sequence signature configures the late gene expression program for human cytomegalovirus, a beta-herpesvirus of global public health importance. Diversity in signature patterns expands promoter targets and pre-sets amount of individual promoter output. A unique palindromic sequence signature is linked to the activation of back-to-back promoters at multiple locations in the viral genome. We deduce that diversity in late transcription factor targets functionally orchestrates the productive rollout of the late-stage infection. This may be a generalizable feature adopted by beta- and gammaherpesvirus  subfamilies.

overall_design: In this study, we assessed the effects of LTF (UL87 and UL79) depletion in late HCMV infection. We analyzed 20 PRO-Seq datasets and 4 ChIP-seq datasets from HFF that were infected with HCMV strains Towne or TB40/E. We show that the effects LTF depletion on viral gene transcription are reproduced in the content of infection with different HCMV strains. Replicate analyses of the effects of LTF depletion were performed.

first: Ming

first: Qiaolin

last: Hu

first: Geoffrey

last: Collins

first: Mrutyunjaya

last: Parida

first: Christopher

last: Ball

first: David

middle: H

last: Price


title: Expression patterns of Plasmodium falciparum clonally variant genes at the onset of a blood infection in non-immune humans

city: Barcelona

first: Anastasia

last: Pickford

state: Barcelona

address: Carrer Rosselló 153

country: Spain

institute: ISGlobal

summary: Clonally variant genes (CVGs) play fundamental roles in the adaptation of Plasmodium falciparum parasites to the fluctuating conditions of the human host, but their expression patterns under the natural conditions of the blood circulation have been characterized in detail only for a few specific gene families. Here we provide a detailed characterization of the full P. falciparum transcriptome across the full intraerythrocytic development cycle (IDC) at the onset of a blood infection in non-immune human volunteers. We found that the vast majority of transcriptional differences between parasites obtained from the volunteers and the parental parasite line maintained in culture occur for CVGs. Specifically, we observed a major increase in the transcript levels of most members of the pfmc-2tm and gbp families and of specific genes of other families, in addition to previously reported changes in var and clag3 genes. The expression patterns were almost identical between parasites obtained from the different volunteers. Large transcriptional differences correlate with changes in the distribution of histone modifications associated with heterochromatin, confirming their epigenetic nature. The analysis of parasites collected at different points along the infection indicates that when parasites pass through transmission stages, the epigenetic memory at CVG loci is lost, resulting in a reset of their expression state and reestablishment of new epigenetic patterns.

overall_design: Time-course transcriptomic analysis of parental NF54 line (two biological replicates: NF54 I and NF54 II) and of parasites obtained from four different volunteers who participated in a CHMI (V18, V35, V48, V63). Parasites were tightly synchronized to a 5h age window and samples for transcriptomic analysis were collected every 10h at four different time points (10-15h, 20-25h, 30-35h and 40-45h). The reference pool consisted of RNA from NF54 cultures throughout the asexual blood cycle. Total RNA was harvested using the Trizol method. A total number of 24 individual samples were analysed using the microarray design AMADID-085763 (GEO ID: GPL26985).

first: Lucas

last: Michel-Todó

first: Alfred

last: Cortés


title: Long-term treatment with senolytic drugs Dasatinib and Quercetin ameliorates age-dependent intervertebral disc degeneration in mice

city: Philadelphia

first: Emanuel

middle: José

last: Novais

state: PA

address: 1025 Walnut St., Suite 511 College Bldg.

department: Department of Orthopaedic Surgery

institute: Thomas Jefferson

summary:
Intervertebral disc degeneration is highly prevalent in the elderly population and is a leading cause of chronic back pain and disability. Studies have linked degenration with increased disc cell senescence. Likewise, senolytics such as Dasatinib + Quercetin combination may provide a novel approach to mitigate age-dependnt disc degeneration.
We used microarrays to explore the transcriptomics of differentially expressed genes between aged disc compartments: AF vs NP at 23M, AF: D+Q vs Veh and NP: D+Q vs Veh.

overall_design:
NP and AF tissue were dissected from lumbar discs from BL6 mice Vehicle (n=5) and D+Q treated mice (n=4). Mice were treated weekly with intraperitoneal injections of either Vehicle (1:2 PBS and 1:2 DMSO) or Dasatinib, 5 mg/kg (Sigma-Aldrich, CDS023389) plus Quercetin, 50 mg/kg (Sigma-Aldrich, Q4951) until they became 23-months-old. RNA extraction and hybridization on Affymetrix microarrays.
disc compartment, treatment

middle: J


title: Expression patterns of Plasmodium falciparum clonally variant genes at the onset of a blood infection in non-immune humans [ChIP-seq]

overall_design: Samples from the NF54 parental line and V63 (parasites obtained from a volunteer who participated in a  controlled human malaria infection trial) were processed to perform a ChIP-Seq experiment against H3K9me3.


title: Expression data from NR2F2(COUP-TFII) depleted mouse MA-10 Leydig cells

city: Québec City

first: Jacques J.

last: Tremblay

state: Quebec

address: 2705 Laurier Blvd.

department: Reproduction, Mother and Child Health

country: Canada

institute: Centre de recherche du CHU de Québec

summary:
In males, Leydig cells are the main producers of testosterone and insulin-like 3, hormones which are both essential for sex differentiation and reproductive functions. Nuclear receptor chicken ovalbumin upstream promoter-transcription factors II  (COUP-TFII) is expressed in the cells committed to give rise to the fully functional steroidogenic adult Leydig cells and has a major role in their function and differentiation. Up to date, only handful of COUP-TFII gene targets have been reported.
A transcriptomic approach  was used to identify additional genes affected by depletion of COUP-TFII in mouse MA-10 Leydig cell line.

overall_design: MA-10 Leydig cells were depleted in COUP-TFII by use targeting siRNAs. Total RNA was extracted and subjected to microarray analysis.

first: Jacques

first: Samir

last: Mehanovic

first: Raifish

middle: E

last: Mendoza-Villarroel


title: ZEB1 Promotes Pathogenic Th1 and Th17 Cells Differentiation in Autoimmune Disease

status: Public on Jul 12 2021

city: Chicago

first: Yuan

last: Qian

state: ILLINOIS

address: 303 E Superior St

institute: Northwestern University

type: Non-coding RNA profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: ACKR1 favors transcellular over paracellular T-cell diapedesis across the blood-brain barrier during neuroinflammation

city: Bern

first: Britta

last: Engelhardt

address: Freiestrasse 1

department: Theodor Kocher Institute

institute: University of Bern

summary: The migration of CD4+ effector/memory T cells across the blood-brain barrier (BBB) is a critical step in multiple sclerosis or its animal model, experimental autoimmune encephalomyelitis (EAE). T-cell diapedesis across the BBB can occur paracellular, via the complex BBB tight junctions or transcellular via a pore through the brain endothelial cell body. Making use of primary mouse brain microvascular endothelial cells (pMBMECs) as in vitro model of the BBB we here directly compared the transcriptome profile of pMBMECs favoring transcellular or paracellular T-cell diapedesis by RNA sequencing (RNA-seq).  We identified the atypical chemokine receptor 1 (Ackr1) as one of the main candidate genes upregulated in pMBMECs favoring transcellular T-cell diapedesis. We confirmed upregulation of ACKR1 protein in pMBMECs favoring transcellular T-cell diapedesis and in venular endothelial cells in the CNS during EAE. Lack of endothelial ACKR1 reduced transcellular T-cell diapedesis across pMBMECs under physiological flow in vitro. Combining our previous observation that endothelial ACKR1 contributes to EAE pathogenesis by shuttling chemokines across the BBB, the present data supports that ACKR1 mediated chemokine shuttling across the BBB enhances transcellular T-cell diapedesis during autoimmune neuroinflammation.

overall_design: Non-stimulated, TNFalpha or IL1beta-stimulated pMBMECs were sequenced using Illumina Hiseq 2500 and differential expression was assesed between the 3 groups using DESeq2

first: Luca

last: Marchetti

middle: M

last: Francisco


title: Maternal multi-generational high fat diet (HFD) exposure increases the offspring HCC incidence

city: Wuhan

first: Yu

last: Sun

address: Luojiashan Street

institute: Wuhan University

summary:
Purpose: To investiagte why maternal obesity induces the susceptibility of offspring to diethylnitrosamine (DEN)-induced hepatocellular carcinoma (HCC) over generations upon over nutrition.The goals of this study are to find over-generationally altered genes and miRNAs which may contribute the accumulative progeny susceptibility to HCC under over nutrition.
Methods: C57BL/6 female mice (F0 generation) were fed with either normal chow (NC) or HFD (60% kcal fat) from 1-month to 3-month old, and mated with NC-fed male mice to produce F1 generation. The F2 generation was similarly created. Male offspring of the F0, F1 and F2 generations were intraperitoneally injected with DEN at 2-weeks-old, and kept inmaintained on HFD and named as H1D, H2D and H3D groups, respectively. Male offspring of the F0 generation injected with PBS (Nor group) or DEN (NCD group) at the same age and kept inmaintained on NC. All groups were sacrificed at 40-weeks-old. Liver mRNA profiles and miRNA profiles from the different offspring groups were generated by LncRNA sequencing and small RNA sequencing.
Results: We identified many over-generationally changed genes and miRNAs in the offspring by RNA-sequencing.
Conclusions: The study revealed an important role of miRNA and targeting genes in regulating the incidence of HCC in the offspring of maternal-lineage under multi-generational HFD exposure, which has a profound effect on exploring the link between maternal obesity and the development of diseases in offspring.

overall_design: 10 samples (Nor rep1, Nor rep2, NCD rep1, NCD rep2, H1D rep1, H1D rep2, H2D rep1, H2D rep2, H3D rep1, H3D rep2) for lncRNA sequencing and 5 samples (Nor, NCD, H1D, H2D, H3D) for small RNA sequencing.

first: Ling

last: Zheng

first: Kun

last: Huang


title: RNAseq analysis of synovial sarcoma (SS), Smarcb1-/- and combined genotype of SS18-SSX and Smarcb1-/- mouse tumors

first: Jinxiu

last: Li

summary: Transcriptomic data were generated for mouse tumors of each combination of genotypes that included either presence or absence of heterozygosity for hSS2 in Rosa26 and homozygosity for wildtype or floxed alleles of Smarcb1. Each genotype clustered most closely with itself in pairwise comparisons of whole transcriptomes and principal component analysis. Overall Principal component analysis, K-mean cluster and KEGG Pathway analysis all demonstrated that tumors generated by genetically disrupted Smarcb1 are different from tumors with SS18-SSX expression only.

overall_design: Tumor transcriptomes profiling of SS18-SSX, Smarcb1-/- and combination of SS18-SSX and Smarcb1-/- driven tumor

first: J

first: L

first: K

last: Jones


title: Niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica

status: Public on Jun 30 2021

city: Hinxton

first: Alexander

last: Predeus

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: Wellcome Sanger Institute

summary: Salmonella enterica serovar Typhimurium (S. Typhimurium) is a zoonotic pathogen that causes diarrheal disease in humans and animals. During salmonellosis, S. Typhimurium colonizes epithelial cells lining the gastrointestinal tract. S. Typhimurium has an unusual lifestyle in epithelial cells that begins within an endocytic-derived Salmonella-containing vacuole (SCV), followed by escape into the cytosol, epithelial cell lysis and bacterial release. The cytosol is a more permissive environment than the SCV and supports rapid bacterial growth. The physicochemical conditions encountered by S. Typhimurium within the cytosol, and the bacterial genes required for cytosolic colonization, remain unknown. Here we have exploited the parallel colonization strategies of S. Typhimurium in epithelial cells to decipher the two niche-specific bacterial virulence programs. By combining a population-based RNA-seq approach with single-cell microscopic analysis, we identified bacterial genes/sRNAs with cytosol-specific or vacuole-specific expression signatures. Using these genes/sRNAs as environmental biosensors, we defined that Salmonella is exposed to iron and manganese deprivation and oxidative stress in the cytosol and zinc and magnesium deprivation in the SCV. Furthermore, iron availability was critical for optimal S. Typhimurium replication in the cytosol, as well as entC, fepB, soxS and sitA-mntH. Virulence genes that are typically associated with extracellular bacteria, namely Salmonella pathogenicity island 1 (SPI1) and SPI4, had a cytosolic-specific expression profile. Our study reveals that the cytosolic and vacuolar S. Typhimurium virulence gene programs are unique to, and tailored for, residence within distinct intracellular compartments. Therefore, this archetypical vacuole-adapted pathogen requires extensive transcriptional reprogramming to successfully colonize the mammalian cytosol.

overall_design: HeLa cells were pre-treated with either with Earle's Balanced Salt Solution (EBSS) to induce authphagy, or with wortmannin (WTM) to inhibit autophagy, then infected with Salmonella enterica servary Typhimurium strain SL1344. Intracellular bacteria were then isolated at 8 h post-infection, bacterial RNA was extracted, and RNA sequencing performed. Two replicates of each experiment were performed. Four samples were sequenced overall.

first: TuShun

middle: R

last: Powers

first: Amanda

last: Haeberle

first: Disa

last: Hammarlöf

first: Jennifer

middle: A

last: Cundiff

middle: V

first: Karsten

last: Hokamp

first: Jay

middle: C

last: Hinton

first: Leigh

last: Knodler


title: High-throughput single-cell RNA-Seq profiling of DMSO-differentiated Huh7.5.1 undergoing or not long-term HCV infection

city: Strasbourg

first: Thomas

middle: F

last: Baumert

address: 3, rue Koeberlé

department: University of Strasbourg

institute: Inserm U1110

summary: Hepatocellular carcinoma (HCC) is the second leading cause of cancer death worldwide, indicating urgent need for novel preventive strategies. Cancer chemoprevention discovery has been challenging due to the absence of tractable and clinically relevant model systems. Here, we developed a simple and robust human liver cell-based system, in which persistent hepatitis C virus (HCV) infection induces a HCC risk signature robustly predicting long-term HCC risk in cirrhotic patients. Using single-cell RNA-Seq analysis we observed a virus-dependent induction of the HCC high-risk gene signature and EGFR/MAPK signaling in HCV-infected liver cells. Our system, modeling the cell circuits encoded in the clinical HCC risk signature, enables investigation of the mechanisms of hepatocarcinogenesis and the discovery of cancer preventive strategies for HCC.

sample_organism:
Homo sapiens
Hepacivirus hominis

platform_organism:
Homo sapiens
Hepacivirus hominis

overall_design: DMSO-differentiated Huh7.5.1 cells were infected or not using HCV cell-culture derived (HCVcc) Jc1E2FLAG. On day 7 post-infection, single-cells were isolated, total cellular RNA was purified, and subjected to RNA-Seq. The modulation of specific gene signatures in association with the normalized HCV copy number in single cell RNA-Seq data was determined using the pre-ranked GSEA module implemented in GenePattern with Pearson correlation as the rank metric.

first: Simonetta

last: Bandiera

first: Sophie

last: Pernot

first: Sarah

last: Durand

first: Magalie

last: Soumillon

first: Karun

last: Kiani

first: Tom

last: Croonenborghs

first: Alex

middle: K

last: Shalek

first: Orit

last: Rozenblatt-Rosen

first: Aviv

last: Regev

first: Mirjam

last: Zeisel

first: Nathalie

last: Pochet


title: OCT4 cooperates with distinct chromatin remodelers in naive and primed pluripotent states in human

first: Jianlong

last: Wang


title: Transcriptomics analysis during the transient ceftazidime tolerance of Burkholderia pseudomallei

city: Khon Kaen

first: Supaksorn

last: Chattagul

state: Khon Kaen

address: 123 Moo 16 Mittraphap Rd., Nai-Muang

department: Biochemistry

country: Thailand

institute: Khon Kaen University

summary: B. pseudomallei strain K96243 is sensitive to the drug ceftazidime (CAZ), but has been shown to exhibit transient CAZ tolerance when in a biofilm form. To investigate an observed shift in gene expression profile during ceftazidime (CAZ) tolerance and to better understand the mechanistic aspects of this transient tolerance, RNA-sequencing was performed on B. pseudomallei K96243 from the following three growth states: planktonic-free, biofilm, and planktonic shedding cells. Results indicated that the expression of 651 genes (10.97%) were significantly changed in both biofilm (resistant) and planktonic shedding (sensitive) cells in comparison to the planktonic state. Burkholderia biofilm shifts its transcriptome in response to ceftazidime exposure by regulating iron-sulfur stabilizing and metabolic-related genes.

overall_design: To confirm the transient tolerance condition. The B. pseudomallei strain K96243 was grown under biofilm and the control by growing in an enrichment planktonic cells and then observed for their ceftazidime (CAZ) susceptibility by evaluating the minimum inhibitory concentration (MIC) in planktonic (MIC), biofilm (MBEC) and planktonic shedding (P-MIC) forms. The total RNA was extracted from B. pseudomallei K96243 that grew under transient tolerance condition without CAZ exposure including planktonic-free, biofilm, and planktonic shedding cells. Each sample was generated from three biological replicates of bacterial growth state.

first: Alison

last: Scott

first: Rasana

last: Sermswan


title: Examine the impact of insulin suppression on oocyte and embryo gene expression

city: Dallas

first: Matt

last: Sieber

address: 5323 Harry Hines blvd, MC 9040 ND12.214

institute: UT Southwestern Medical Center


title: Expression data of the livers of male C57Bl6/N mice after partial (two-third) hepatectomy

city: Heidelberg

first: Christian

middle: H.

last: Holland

address: Im Neuenheimer Feld 267

department: Institute for Computational Biomedicine

institute: Heidelberg University

summary: After surgical removal of approximately two-thirds of liver tissue the liver mass restors within ~2 weeks.

overall_design: Partial hepatectomy (two-third resection) was performed as described in Mitchell and Willenbring (2008). Mice were sacrificed 1 hour, 6 hours, 12 hours, 1 day, 2 days, 3 days, 4 days, 1 week, 2 weeks, 1 month, and 3 months after surgery. Male C57BL6/N mice (8-12 weeks old) were used. The animals received standard diet ad libitum before and after partial hepatectomy. Reference: Mitchell C, Willenbring H. A reproducible and well-tolerated method for 2/3 partial hepatectomy in mice. Nat Protoc 2008;3:1167–1170.

first: Ahmed

last: Ghallab

first: Jan

middle: G

last: Hengstler


title: Interplay between CTCF boundaries and a super enhancer controls cohesin extrusion trajectories and gene expression

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: To understand how chromatin domains coordinate gene expression, we dissected select genetic elements organizing topology and transcription around the Prdm14 super enhancer in mouse embryonic stem cells. Taking advantage of allelic polymorphisms, we developed methods to sensitively analyze changes in chromatin topology, gene expression, and protein recruitment. We show that enhancer insulation does not strictly rely on loop formation between its flanking boundaries, that the enhancer activates the Slco5a1 gene beyond its prominent domain boundary, and that it recruits cohesin for loop extrusion. Upon boundary inversion, we find that oppositely-oriented CTCF terminates extrusion trajectories but does not stall cohesin, while deleted or mutated CTCF sites allow cohesin to extend its trajectory. Enhancer-mediated gene activation occurs independent of paused loop extrusion near the gene promoter. We expand upon the loop extrusion model to propose that cohesin loading and extrusion trajectories originating at an enhancer contribute to gene activation.

overall_design: Allele-specific 129 4C profiles (Illumina, 19 files), 129/cas cHiC heat maps (Illumina, 4+4 files), and 129 MC-4C plots (Nanopore, 4 files) for WT and mutant 129/castaneous F1 hybrid mESCs

first: Erica

last: Vos

last: Valdes-Quezada

first: Yike

last: Huang

first: Amin

last: Allahyar

first: Marjon

last: Verstegen

first: Anna-Karina

last: Felder

first: Floor

last: van der Vegt

first: Esther

last: Uijttewaal

first: Wouter

last: de Laat


title: Examine the impact of insulin suppression on oocyte gene expression.

summary: These expeirments compare the polyA selected RNA isolated from GFP expressing (control) and InR-DN expressing stage 14 oocytes.

overall_design: In this experiment we collected GFP expressing oocytes and InR-DN expressing oocytes and conducted mRNA seq to indentify gene differentailly regulate by insulin suppression

first: Matthew


title: Expression data of the livers of male C57Bl6/N mice after i.p. injection of paracetamol (APAP)

summary:
Male C57BL6/N mice were obtained from Janvier Labs (France). Mice were starved overnight before APAP administration and were fed ad libitum afterward. A single dose of 300 mg APAP/kg b.w. was intraperitoneally injected in warm phosphate-buffered saline (PBS; Table 3). The used APAP was obtained from Sigma-Aldrich (A7085-500G, Germany). The mice were sacrificed at 1, 6, and 12 hours, and on days 1, 2, 4, 6, and 8 after APAP administration.
Expression data of the livers of male C57Bl6/N mice after intoxication with paracetamol (APAP)

overall_design: Male C57BL6/N mice were obtained from Janvier Labs (France). Mice were starved overnight before APAP administration and were fed ad libitum afterward. A single dose of 300 mg APAP/kg b.w. was intraperitoneally injected in warm phosphate-buffered saline (PBS). APAP was obtained from Sigma-Aldrich (A7085-500G, Germany). The mice were sacrificed at 1, 6, and 12 hours, and on days 1, 2, 4, 6, and 8 after APAP administration.


title: Expression data of the livers of male C57Bl6/N mice after bile duct ligation

summary: Bile duct ligation is a commonly used technique to induce obstructive cholestasis in mice.

overall_design: 8 to 10 week-old C57BL/6N mice (male) were used. The extrahepatic common bile duct was ligated. Mice received standard diet ad libitum before and after the surgery. Liver tissue was harvested on days 1, 3, 7, and 21 after bile duct ligation. Sham operated mice were used as controls.

first: Verena

last: Keitel


title: OCT4 cooperates with distinct chromatin remodelers in naive and primed pluripotent states in human [RNA-Seq]

first: Jianlong

last: Wang

summary: Understanding the molecular underpinnings of pluripotency is a prerequisite for optimal maintenance and application of embryonic stem cells (ESCs). We mapped the protein-protein interactions of OCT4 in naive and primed hESCs, revealing extensive connections to ATP-dependent nucleosome remodeling complexes. In naive hESCs, OCT4 is associated with both BRG1 and BRM, the two mutually exclusive ATPase subunits of the BAF complex. Genome-wide location analyses and genetic deletion studies reveal that these two enzymes exert a functionally redundant role in transcriptional regulation of blastocyst-specific genes. In contrast, OCT4 cooperates with BRG1 and the transcription factor SOX2 to create an open chromatin architecture at neural lineage-associated genes in primed hESCs. This work offers insight into the regulation of human stem cell identity and reveals how a common transcription factor utilizes differential compositions of the BAF complex in controlling distinct transcriptional programs governing naive vs. primed human pluripotent states.

overall_design: Genome binding/occupancy profiling of chromatin remodelers BAF155, BRG1, BRM, and transcription factors SOX2 in naive and primed hESCs by ChIP sequencing. Transcriptomes of naive and primed hESCs upon knockdown of either BRG1 or BRM by RNA sequencing.

first: Xin

first: Thorold

last: Theunissen


title: IL13Rα2 promotes the proliferative switch required for outgrowth of breast cancer brain metastases

city: Aurora

first: Diana

last: Cittelly

state: CO

department: Pathology

institute: University of Colorado AMC

summary:
The survival of women with brain metastases (BM) from breast cancer remains very poor, and more than 80% will die within a year of their diagnosis. Here we define the function of IL13Rα2 in outgrowth of breast cancer brain metastases (BCBM) in vitro and in vivo, and postulate IL13Rα2 as a suitable therapeutic target for BM.
Experimental design: We performed IHC staining of IL13Rα2 in BCBM to define its prognostic value. Using inducible-shRNAs in TNBC and HER2+ breast-brain metastatic models we assessed IL13Rα2 function in vitro and in vivo. We performed RNAseq and functional studies to define the molecular mechanisms underlying IL13Rα2 function in BCBM.
Results: High IL13Rα2 expression in BCBM predicted worse survival after BM diagnoses. IL13Rα2 was essential for cancer-cell survival, promoting proliferation while repressing invasion. IL13Rα2 KD resulted in repression of cell cycle and proliferation mediator Cyclin D2 and upregulation of Ephrin B1 signaling. Ephrin-B1 (i) promoted invasion of BC cells in vitro, (ii) marked micrometastasis and invasive fronts in BCBM, (iii) predicted shorter disease-free survival (DFS) and BM-free survival (BMFS) in breast primary tumors known to metastasize to the brain. In experimental metastases models, which bypass early tumor invasion, downregulation of IL13Rα2 prior or after tumor seeding and brain intravasation decreased BMs, suggesting that IL13Rα2 and a switch to a more proliferative phenotype is critical to BM outgrowth.

overall_design: RNA-seq profiling of 231BR treated with either shEV or shIL13RA2.

first: Alejandor

last: Marquez


title: H2AK119ub1 native ChIP-seq upon Xist indution

city: Oxford

first: Joseph

middle: S

last: Bowness

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

summary: Native ChIP-seq for H2AK119ub1 upon Xist induction in iXist-ChrX mouse embryonic stem cells. Comparison of WT with Spen RRM deletion and SPOC domain mutants for two timepoints of Xist induction, 3h and 24h.

overall_design: ChIP-seq for H2AK119ub1 was performed on native chromatin extract from WT and biological replicate clones for Spen RRM deletion and SPOC mutation cell lines derived from parental iXist-ChrX cells. For the purposes of this report H2AK119ub1 distribution acts a surrogate marker for Xist RNA distribution across the Xi chromosome, and its pattern is clearly abnormal in Spen RRM deletion but not SPOC mutant cells. Two time points of Xist induction, 3h and 24h were profiled for comparison. Whereas all samples for the 3h experiment were processed in parallel on the same day, for the 24h experiment the Spen RRM deletion lines, SPOC mutant lines, and each of the three WT replicates were processed on separate occasions. For 24h data sets (WT Reps1&2, SpenRRM, SPOCmut), Drosophila SG4 cells were carefully added as a spike in (40 million mES cells with 10 million SG4 cells) upon collection and prior to chromatin extraction. Although spike-in normalisation was not performed for this study, input samples are provided here for this analysis.


title: Molecular profiles and urinary biomarkers of upper tract urothelial carcinomas associated with aristolochic acid exposure [miRNA_tissue]

city: Lyon

first: Jiri

last: Zavadil

address: 150 cours Albert Thomas

institute: International Agency for Research on Cancer (IARC)

summary:
This study presents a comprehensive multi-omic analysis of upper urinary tract urothelial tumours (UTUC) and urines of patients with past exposure to carcinogenic aristolochic acid (AA). We determined complex miRNA:mRNA tumor networks and their key protein components. Tumor exome and transcriptome sequencing revealed a burden of AA-specific mutations in UTUC and identified deleteriously mutated genes and their mRNA transcripts. A subset of identified urinary miRNAs presents potential biomarkers of UTUC development or presence.
Recurrent upper urinary tract carcinomas (UTUC) arise in the context of nephropathy linked to exposure to the herbal carcinogen aristolochic acid (AA). We aimed to delineate the detailed biological programs underlying UTUC tumorigenesis in patients from endemic aristolochic acid nephropathy (AAN) regions in Southern Europe, by using an integrative multi-omics analysis of UTUCs, corresponding unaffected tissues and of patient urines. Quantitative miRNA and mRNA expression profiling, immunohistochemical analysis by tissue microarrays, and exome and transcriptome sequencing were performed in UTUC and non-tumor tissues. Urinary miRNAsof cases undergoing surgery were profiled before and after UTUC resection. RNA and protein levels were analyzed using appropriate statistical tests and trend assessment. Dedicated bioinformatic tools were used for analysis of pathways, mutational signatures and result visualization. The results delineate UTUC-specific miRNA:mRNA networks comprising 89 miRNAs associated with 1862 target mRNAs and involving deregulation of cell cycle, DNA damage response, DNA repair, bladder cancer, oncogenes, tumor suppressors, chromatin structure regulators and developmental signaling pathways. Key UTUC-specific transcriptome components were confirmed at the protein level. Exome and transcriptome sequencing of UTUC revealed AA-specific COSMIC mutational signature 22, with 68-76% AA-specific, deleterious mutations propagated at the mRNA level. We next identified a signature of UTUC-specific miRNAs consistently more abundant in the patients’ urine prior to tumor resection. The gene regulation programs of AAN-associated UTUC tumors are highly complex and involve regulatory miRNAs prospectively applicable to non-invasive urine-based screening of AAN patients for cancer recurrence.

overall_design: Gene expression profiles from UTUC tumors and matched normal urothelium of 12 patients with aristolochic acid nephropathy related cancers were determined by using the Affymetrix Human Genome U133 Plus 2.0 Arrays, matched with upstream regulatory miRNAs determined by Applied Biosystems TaqMan Human MicroRNA A Cards v2.1 + B Cards v3.0  on the ABI 7900HT Sequence Detection System (Applied Biosystems, CA, USA). Modulation of gene products (proteins) were validated by tissue microarray-based immunohistochemistry analysis. The study was complemented by exome and transcriptome sequencing of a UTUC subset, and a temporal screen of cell-free miRNAs in urine samples of 5 UTUC patients, collected before and after surgery.

first: Sandra

last: Karanović

first: Maude

last: Ardin

first: Zuojian

last: Tang

first: Karla

last: Tomić

first: Stephanie

last: Villar

first: Claire

last: Renard

first: Elisa

last: Venturini

first: Adam

last: Lorch

first: Daniel

last: Lee

first: Želimir

last: Stipančić

first: Neda

last: Slade

first: Ivana

last: Brinar

first: Damir

last: Dittrich

first: Krešimir

last: Karlović

first: Fran

last: Borovečki

first: Kathleen

last: Dickman

first: Magali

last: Olivier

first: Arthur

middle: P

last: Grollman

first: Bojan

last: Jelaković


title: Single Cell RNA Sequencing of mouse kidneys

city: Rochester

first: Lilach

middle: O

last: O Lerman

state: Minnesota

address: 200 First St. SW

department: Division of Nephrology & Hypertension

institute: Mayo Clinic

summary: Unbiased single-cell RNA-sequencing in freshly-dissociated cells from healthy and stenotic mouse kidneys identified stenotic-kidneys epithelial cells undergoing both mesenchymal transition and senescence.

overall_design: Chronic renal ischemia or sham was induced in mice by unilateral renal artery stenosis (RAS; n=4 each).

last: Lerman

first: Amrutesh

last: Puranik


title: CXCR6 Positions Cytotoxic T Cells to Receive Critical Survival Signals in the Tumor Microenvironment

city: Boston

first: Thorsten

last: Mempel

state: Massachusetts

address: Charlestown Navy Yard Building 149

department: Center for Immunology and Inflammatory Diseases

institute: Massachusetts General Hospital

summary: Cytotoxic T lymphocyte (CTL) responses against tumors are maintained by stem-like memory cells that self-renew, but also give rise to effector-like cells. The latter gradually lose their anti-tumor activity and acquire an epigenetically fixed, hypofunctional state, leading to tumor tolerance. Here, we show that the conversion of stem-like into effector-like CTL involves a major chemotactic reprogramming that includes the upregulation of chemokine receptor CXCR6. This receptor positions effector-like CTL in a discrete perivascular niche of the tumor stroma that is densely occupied by CCR7+ dendritic cells (DC) expressing the CXCR6 ligand CXCL16. CCR7+ DC also express and trans-present the survival cytokine IL-15. CXCR6 expression and IL-15 trans-presentation are critical for the survival and local expansion of effector-like CTL in the tumor microenvironment to maximize their anti-tumor activity before progressing to irreversible dysfunction. These observations reveal a cellular and molecular checkpoint that determines the magnitude and outcome of anti-tumor immune responses.

overall_design: We analyzed the single cell transcriptomes of subcutaneous D4M.3A-pOVA, an immunogenic mouse melanoma model (Di Pilato et al., 2019, Nature). Tumor single cell suspensions were enriched for immune cells and rapidly processed for analysis on the inDrops scRNA-seq platform (Klein et al., 2015, Cell). After filtering to exclude putative cell doublets and stressed or dead cells, a total of 8,757 cell transcriptomes from 2 animals were retained for analysis

first: Mauro

last: Di Pilato

first: Raphael

last: Kfuri-Rubens

first: Jasper

middle: N

last: Pruessmann

first: Aleksandra

last: Ozga

first: Marius

last: Messemaker

first: Bruno

middle: L

last: Cadilha

first: Ramya

last: Sivakumar

first: Chiara

last: Cianciaruso

first: Ross

middle: D

last: Warner

first: Francesco

last: Marangoni

first: Esteban

last: Carrizosa

first: Stefanie

last: Lesch

first: James

last: Billingsley

last: Perez-Ramos

first: Fidel

last: Zavala

first: Esther

last: Rheinbay

first: Andrew

last: Luster

first: Michael

middle: Y

last: Gerner

first: Sebastian

last: Kobold

first: Mikael

last: Pittet


title: RNA-seq of NIC AXL KO in hypoxia

first: Marie-Anne

last: Goyette

address: 450 Brookline avenue

institute: DFCI

summary: RNA-seq of MMTV-NIC WT and AXL KO cells in normoxia and hypoxia (1% O2)

overall_design: Differential gene expression profile between AXL WT and AXL KO cells in hypoxia by RNA sequencing (Illumina HiSEq 2000)

first: Jean-François

last: Côté


title: Genome wide transcriptional profiling of RBMXDRGG human induced poluripotent stem cells and neural progenitor cells

city: montreal

first: stephane

last: Richard

address: 3755 Cote ste catherine, LDI Room 420

institute: McGill

summary:
Purpose: investigate Shashi XLID patient mutation (RBMX-RGG motif deletion) caused gene expression and splicing alteration during neural differentiation
Methods: hiPSCs with Shashi XLID patient mutation(RBMX-DRGG) were generated by CRISPR-Cas9.  hiPSCs were differentiated to NPCs using STEMdiff SMADi Neuronal Induction Kit. A patient-mutation iPS cell line (DRGG1) and a non-edited clone (CTRL) and the derived NPCs were selected for characterization by mRNA profiling. iPSC and NPC RNA samples were purified using GenElute™ Mammalian Total RNA Miniprep Kit (RTN70, Sigma Aldrich).  Total RNA was assessed for quality using an Agilent Tapestation 4200, and RNA sequencing libraries were generated using TruSeq Stranded mRNA Sample Prep Kit with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, starting with 50 ng of RNA and modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 base pair (bp) paired-end reads (PE100) to a depth of approximately 60 million reads per sample on an Illumina HiSeq 4000.
Results:Gene expression was quantified by HOMER and differential expression was analyzed by DESeq2. Comparing with CTRL, we identified 1914 and 1028 differentially expressed genes in DRGG1 iPSCs and NPCs respectively with a threshold of |FC|>1.5 and FDR<0.05. Alternative splicing analysis was carried out using rMATs ,  which revealed 369 and 111 altered splicing events in iPSCs and NPCs respectively.

overall_design: mRNA profiles of CTRL and DRGG iPSCs and derived NPCs

first: Oscar

last: Villarreal

first: Ting

last: Cai

first: Stéphane


title: De novo generation of macrophage from placenta-derived hemogenic endothelium

city: Shanghai

first: Zhixin

last: Kang

address: 320 Yue Yang Road, Shanghai

institute: Shanghai Institute of Biochemistry and Cell Biology

summary: We profile the transcriptional landscape of mouse fetal placenta and identify four distinct types of haematopoietic stem/progenitor cells (HSPCs) during mid-gestation using single-cell RNA sequencing. We  experimentally validate and uncover that a subpopulation of placental endothelial cells exhibits hemogenic endothelial (HE) potential and shares transcriptional features with HE cells in the aorta-gonad-mesonephros (AGM) region.

overall_design: Examination of gene expressive levels in sorting placental cells, placental HE cells, AGM HE cells, placental ECs, AGM ECs and yolk sac ECs from pregnant mice.

first: Guixian

last: Liang

first: Chunyu

last: Zhou

first: Xiangxiang

last: Jiang

first: Hongmei

last: Wang

first: Jingdong

last: Han

first: Feng

last: Liu


title: Next Generation Sequencing Analysis of Wild Type intestine(Control), RelishE20 mutant intestine, intestine with tumor (Shn-RNAi ) and intestine with tumor in RelishE20 mutant background(Shn-RNAi plus Relish mutation)  Transcriptomes

first: Erica

last: Valentini

address: Im Neuenheimer Feld 580

institute: DKFZ

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived intestinal transcriptome profiling between control, immune deficienct, tumor and immune deficient tumor condition and using a Drosophila inducible intestinal tumor model to identify signaling cascades that involved in tumorigenesis downstream of immune signaling pathway
Methods: intestine mRNA profiles of 7-day old  control (esgts>w1118), immune deficient (esgts>RelishE20), Shn-RNAi (esgts>Shn-RNAi_KK) and Shn-RNAi plus immune deficient (esgts>Shn-RNAi,RelishE20) Drosophila were generated by deep sequencing, Shn-RNAi in triplicate, Control, and RelishE20 or Shn-RNAi plus RelishE20 in duplicate, using Illumina GAIIx.
Results: Using an optimized data analysis workflow, we mapped about 21 million sequence reads per sample to the Drosophila genome (ENSEMBL BDGP6.22) and identified a total of 146,391 million counts in the Drosophila midgut of  control, immune deficienct, tumor and immune deficient tumor condition. Salmon was used to map and quantify the transcript abundance and DESeq2 was used for the gene expression analysis. DAVID GO term analysis for biological processes clustering of differentially expressed genes enriched for certain known pathays.
Conclusions: Our study represents the detailed analysis of intestinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The data analysis revealled that pro-apoptotic gene signature is governed by immune signaling pathway that are required for intestinal tumorigenesis in Drosophila

overall_design: Midgut mRNA profiles of 7-day old control (esgts>w1118), Relish mutant (esgts>RelishE20) and Shn-RNAi (esgts>Shn-RNAi) and Shn-RNAi plus Relish mutation (esgts>Shn-RNAi,RelishE20) Drosophila were generated by deep sequencing, RNAi samples in triplicate and Control, Relish mutant or RNAi plus Relish mutant samples in duplicates, using Illumina GAIIx.

first: Jun


title: Expression data of the livers of male C57Bl6/N mice after i.p. injection of lipopolysaccharide (LPS)

first: Christian

last: Holland

summary: Lipopolysaccharides (LPS) are found in the outer membrane of Gram-negative bacteria. The intraperitoneal (i.p.) application of LPS into mice represents a frequently applied experimental model to induce hepatic and systemic inflammation.

overall_design: C57BL6/N mice (8-10 weeks old, male) received intraperitoneal injections of lipopolysaccharide (LPS), 750 µg/kg b.w. in PBS. LPS from Escherichia coli O55:B5 was used (Sigma-Aldrich, L2880-25mg, Germany). Liver tissue was harvested 24 hours after LPS injection. The mice received standard diet ad libitum before and after LPS administration. This data set contains 5 mice injected with LPS and 3 control mice that received injections of PBS.

first: Patricio

last: Godoy

first: Ahmed

last: Ghallab

middle: H

first: Jan

last: Hengstler


title: Molecular profiles and urinary biomarkers of upper tract urothelial carcinomas associated with aristolochic acid exposure [miRNA_urine]

first: Jiri

last: Zavadil

overall_design: Gene expression profiles from UTUC tumors and matched normal urothelium of 12 patients with aristolochic acid nephropathy related cancers were determined by using the Affymetrix Human Genome U133 Plus 2.0 Arrays, matched with upstream regulatory miRNAs determined by Applied Biosystems TaqMan Human MicroRNA A Cards v2.1 + B Cards v3.0 on the ABI 7900HT Sequence Detection System (Applied Biosystems, CA, USA). Modulation of gene products (proteins) were validated by tissue microarray-based immunohistochemistry analysis. The study was complemented by exome and transcriptome sequencing of a UTUC subset, and a temporal screen of cell-free miRNAs in urine samples of 5 UTUC patients, collected before and after surgery.

first: Sandra

last: Karanović

first: Maude

last: Ardin

first: Zuojian

last: Tang

first: Karla

last: Tomić

first: Stephanie

last: Villar

first: Claire

last: Renard

first: Elisa

last: Venturini

first: Adam

last: Lorch

first: Daniel

last: Lee

first: Želimir

last: Stipančić

first: Neda

last: Slade

first: Ivana

last: Brinar

first: Damir

last: Dittrich

first: Krešimir

last: Karlović

first: Fran

last: Borovečki

first: Kathleen

last: Dickman

first: Magali

last: Olivier

first: Arthur

last: Grollman

first: Bojan

last: Jelaković


title: Molecular profiles and urinary biomarkers of upper tract urothelial carcinomas associated with aristolochic acid exposure

first: Jiri

last: Zavadil

type:
Expression profiling by array
Expression profiling by RT-PCR

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

overall_design: Refer to individual Series


title: Molecular profiles and urinary biomarkers of upper tract urothelial carcinomas associated with aristolochic acid exposure [mRNA]

summary:
This study presents a comprehensive multi-omic analysis of upper urinary tract urothelial tumours (UTUC) and urines of patients with past exposure to carcinogenic aristolochic acid (AA). We determined complex miRNA:mRNA tumor networks and their key protein components. Tumor exome and transcriptome sequencing revealed a burden of AA-specific mutations in UTUC and identified deleteriously mutated genes and their mRNA transcripts. A subset of identified urinary miRNAs presents potential biomarkers of UTUC development or presence.
Recurrent upper urinary tract carcinomas (UTUC) arise in the context of nephropathy linked to exposure to the herbal carcinogen aristolochic acid (AA). We aimed to delineate the detailed biological programs underlying UTUC tumorigenesis in patients from endemic aristolochic acid nephropathy (AAN) regions in Southern Europe, by using an  integrative multi-omics analysis of UTUCs, corresponding unaffected tissues and of patient urines. Quantitative miRNA and mRNA expression profiling, immunohistochemical analysis by tissue microarrays, and exome and transcriptome sequencing were performed in UTUC and non-tumor tissues. Urinary miRNAsof cases undergoing surgery were profiled before and after UTUC resection. RNA and protein levels were analyzed using appropriate statistical tests and trend assessment. Dedicated bioinformatic tools were used for analysis of pathways, mutational signatures and result visualization. The results delineate UTUC-specific miRNA:mRNA networks comprising 89 miRNAs associated with 1862 target mRNAs and involving deregulation of cell cycle, DNA damage response, DNA repair, bladder cancer, oncogenes, tumor suppressors, chromatin structure regulators and developmental signaling pathways. Key UTUC-specific transcriptome components were confirmed at the protein level. Exome and transcriptome sequencing of UTUC revealed AA-specific COSMIC mutational signature 22, with 68-76% AA-specific, deleterious mutations propagated at the mRNA level. We next identified a signature of UTUC-specific miRNAs consistently more abundant in the patients’ urine prior to tumor resection. The gene regulation programs of AAN-associated UTUC tumors are highly complex and involve regulatory miRNAs prospectively applicable to non-invasive urine-based screening of AAN patients for cancer recurrence.

overall_design: Gene expression profiles from UTUC tumors and matched normal urothelium of 12 patients with aristolochic acid nephropathy related cancers were determined by using the Affymetrix Human Genome U133 Plus 2.0 Arrays, matched with upstream regulatory miRNAs determined by Applied Biosystems TaqMan Low Density Arrays (TaqMan Array Human MicroRNA Panel A and B) on the ABI 7900HT Sequence Detection System (Applied Biosystems, CA, USA). Modulation of gene products (proteins) were validated by tissue microarray-based immunohistochemistry analysis. The study was complemented by exome and transcriptome sequencing of a UTUC subset, and a temporal screen of cell-free miRNAs in urine samples of 5 UTUC patients, collected before and after surgery.

first: Sandra

last: Karanović

first: Maude

last: Ardin

first: Zuojian

last: Tang

first: Karla

last: Tomić


title: The naturally occurring ∆40p53 isoform inhibits eRNA transcription and enables context-specific regulatory inputs during p53 activation.

city: Boulder

first: Dylan

middle: J

last: Taatjes

address: Campus Box 596

institute: University of Colorado Boulder


title: RNA-seq profiling of Ewing sarcoma cells after TRIM8 knockout and EWS/FLI over-expression

first: Neekesh

middle: V.

last: Dharia

state: MA

address: 350 Brookline Ave

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: Fusion-transcription factors (fusion-TFs) represent a class of driver oncoproteins that are difficult to therapeutically target. Recently, protein degradation has emerged as a strategy to target these challenging oncoproteins. The mechanisms that regulate fusion-TF stability, however, are generally unknown. Using CRISPR-Cas9 screening, we discovered tripartite motif- containing 8 (TRIM8) as an E3 ubiquitin ligase that ubiquitinates and degrades EWS/FLI, a driver fusion-TF in Ewing sarcoma. Moreover, we identified TRIM8 as a selective dependency in Ewing sarcoma compared to >700 other cancer cell lines. Mechanistically, TRIM8 knockout led to an increase in EWS/FLI protein levels that was not tolerated. EWS/FLI acts as a neomorphic substrate for TRIM8, defining the selective nature of the dependency. Our results demonstrate that fusion-TF protein stability is tightly regulated and highlight fusion-oncoprotein specific regulators as selective therapeutic targets. This study provides a tractable strategy to therapeutically exploit oncogene overdose in Ewing sarcoma and potentially other fusion-TF driven cancers.

overall_design: TC71 Ewing sarcoma cells engineered to express FKBP12F36V-HA-TRIM8 was treated with either DMSO control or dTAGV-1 for 24 hours to induce TRIM8 degradation. In addition, TC71 Ewing sarcoma cells engineered to express doxycycline-inducible EWS/FLI-HA was treated with either water control or doxycycline (500ng/mL) for 8 hours. Triplicates for all groups were used for paired-end RNA-sequencing.

first: Bo Kyung

last: Seong

first: Shan

last: Lin

first: Katherine

last: Donovan

first: Sasha

last: Chong

first: Amanda

last: Robichaud

first: Amy

last: Conway

last: Hamze

first: Linda

last: Ross

first: Gabriela

last: Alexe

first: Biniam

last: Adane

first: Behnam

last: Nabet

first: Fleur

last: Ferguson

first: Björn

last: Stolte

first: Emily

last: Wang

first: Jialin

last: Sun

first: Xavier

last: Darzacq

first: Federica

last: Piccioni

first: Nathaniel

last: Gray

first: Eric

last: Fischer

first: Kimberly

last: Stegmaier


title: Expression data of the livers of male C57Bl6/N mice after i.p. injection of CCl4

first: Christian

last: Holland

summary: Intoxication with CCl4 is a frequently used technique to induce liver damage in mice. The compound induces cell death of hepatocytes in the pericentral region of the liver lobule.

overall_design: Male 8-10 weeks old C57BL/6N mice were obtained from Janvier Labs (France). Mice received a single intraperitoneal injection of CCl4 (1.6 g/kg b.w. in olive oil). The used CCl4 was obtained from Sigma-Aldrich (289116-1L, Germany). The liver tissue was collected after 2 and 8 hours and 1, 2, 4, 6, 8, and 16 days following CCl4 administration. The control liver (time point zero) was collected from untreated mice. The mice received standard diet ad libitum before and after CCl4 administration.

first: Patricio

last: Godoy

first: Ahmed

last: Ghallab

first: Jan

last: Hengstler


title: Targeting trisomy 12 in chronic lymphocytic leukemia using molecular networks identified from pluripotent stem cells

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

summary: Chronic lymphocytic leukemia (CLL) is the most common hematologic malignancy in adults. While B cell-targeted therapies have revolutionized treatment, the underlying molecular targets of disease have not been addressed. A quarter of CLL patients have somatic trisomy 12 (tri12) which confers intermediate risk, and is otherwise embryonically lethal. Here, we report human pluripotent stem cells (PSC) harboring tri12 uniquely genocopy and phenocopy tri12 CLL. Using unbiased machine learning and transcriptomics, combined with chemical genomics, we reveal candidate tri12 gene networks and targets. These targets were validated to specifically reduce leukemic growth of tri12 CLL patient samples. Our study establishes a paradigm for using PSC to overcome barriers in revealing molecular networks involved in complex genetic abnormalities of human cancers such as tri12 CLL.

overall_design: Human embryonic stem cell (hESC) research received Canadian Stem Cell Oversight Committee (SCOC; Canadian Institutes of Health Research, CIHR) approval, and Research Ethics and Biohazard Utilization Protocols approval at McMaster University, following the principles of the 2016 ISSCR Guidelines for Stem Cell Research and Clinical Applications of Stem Cells. Human iPSC and ESC were cultured in feeder-free conditions in mouse embryonic feeder-conditioned media with 8 ng/mL basic fibroblast growth factor, with daily media changes. Cells were passaged as clumps every seven days on to matrigel-coated tissue culture plates.

first: Jennifer

last: Reid

first: Diana

last: Golubeva

first: Luca

last: Orlando

first: Allison

last: Boyd


title: PTX3 secreted by human adipose-derived stem cells promotes dopaminergic neuron repair in Parkinson's disease via inhibiting apoptosis.

city: Guangzhou City,

first: Changlin

last: Lian

state: Guangdong Province

address: 253 Industrial Avenue Middle, Haizhu District

institute: Southern medical University Zhujiang Hospital

summary: Adipose-derived human mesenchymal stem cells (hADSCs) transplantation has recently emerged as a promising method in the treatment of Parkinson's disease (PD), however, the mechanism underlying has not been fully illustrated.  In this study, we discovered that hADSCs protected the dopaminergic (DA) neurons in a 6-hydroxydopamine(6-OHDA) induced PD mice model. Using a transwell co-culture system, we reported that, in 6-OHDA brain slice cultures, hADSCs significantly promoted host DA neuronal viability. Within the analysis of hADSCs' exocrine proteins through RNA-seq, Human protein cytokine arrays and label-free quantitative proteomics, we identified Pentraxin3 (PTX3) as a key extracellular factor in hADSCs secretion environment. Moreover, we found that human recombinant Pentraxin3 (rhPTX3) treatment could rescue the physiological behaviour of the PD mice in-vivo, as well as prevent DA neurons from death and increase the neuronal terminals in the Ventral tegmental area(VTA)+ substantia nigra pars compacta (SNc) and striatum (STR) on the PD brain slices in-vitro. Furthermore, within testing on the pro-apoptotic markers of PD mice brain following the treatment of rhPTX3, we found that rhPTX3 can prevent the apoptosis and degeneration of DA neurons.  Overall, the current study investigated that PTX3, a hADSCs secreted protein, played a potential role in protecting the DA neurons from apoptosis and degeneration in PD progression and improving the motor performances in PD mice to give a possible mechanism of how hADSCs works in the cell replacement therapy in PD. Importantly, our study also provided a potential translational implications for the development of PTX3-based therapeutics in PD.

overall_design: mRNA profiles of hADSCs(ASC) and hADSCs-PD(ASC-PD)

first: Qiongzhen

last: Huang


title: The naturally occurring ∆40p53 isoform inhibits eRNA transcription and enables context-specific regulatory inputs during p53 activation [PRO-seq]

first: Dylan

last: Taatjes

summary: The naturally occurring p53 isoform ∆40p53 lacks the first N-terminal transactivation domain of WTp53 and is implicated in mammalian aging. ∆40p53 is preferentially translated during cell stress. The ∆40p53 isoform oligomerizes with WTp53 to form hetero-tetramers with altered function compared to WTp53 tetramers. Co-expression of ∆40p53 and WTp53 results in the formation of a mixed population ∆40p53:WTp53 tetramers, including “contaminating” WTp53 tetramers. Here we implemented a strategy—based upon the native p53 tetramer structure—in which ∆40p53 was tethered to WTp53 (∆40p53:WTp53) as a single transcript, resulting in tetramers with a defined 2:2 ratio of Δ40p53 to WTp53. Using CRISPR/Cas9, human cell lines were generated in which ∆40p53:WTp53 (and controls) was inserted at the native TP53 locus. This enabled ∆40p53:WTp53 expression and induction in a physiologically relevant manner. As with WTp53, activation of ∆40p53:WTp53 with Nutlin-3a causes increased genome occupancy. However, unlike WTp53, precision run-on nuclear sequencing (PRO-seq) showed that increased ∆40p53:WTp53 occupancy does not correlate with robust transcriptional activation. Activated ∆40p53:WTp53 only induces transcription of a small subset of WTp53 enhancer RNAs (eRNAs) and other annotated regions. Defective eRNA production correlates with loss of downstream mature mRNA and p53-dependent cell-cycle arrest. Pathway analysis of ∆40p53:WTp53 induced transcriptional changes identified increased activation of stress and aging related pathways in ∆40p53:WTp53 compared to WTp53. However, these pathways never mature to full activation under Nutlin-3a treatment. Therefore, we propose a model where activation of ∆40p53 results in the transcription of a subset of WTp53 targets, setting the stage for synergistic pathway activation with other stress specific transcription factors driving cellular response in ways that differ from WTp53. Implications of these results provide an additional mechanistic layer of p53 regulation, in which expression of ∆40p53 isoform allows for modulation of WTp53 activities in a context dependent manner, tipping the scales towards activation of aging-associated pathways.

overall_design:
CRISPR/Cas9 edited MCF10A cells were treated with 10uM nutlin3a and 0.01% DMSO (control) for 3 hours with a total of 2 biological replicates. Nuclei were isolated and PRO-seq libraries were constructed and sequenced.
nascent RNA (PRO-seq) from MCF10A cells

first: Cecilia

middle: B

last: Levandowski

first: Margaret

last: Gruca


title: Transcriptome sequencing of human lung cancer cell line NCI-H838 treated with LINC00472 overexpression

city: Cheongju-si

first: Wanyeon

last: Kim

state: Chungbuk

address: Taeseongtabyeonro 250, Gangnaemyeon, Heungdeokgu

department: Biology Education

country: South Korea

institute: Korea National University of Education

summary: To evaluate the changes in the expression of genes in lung cancer cells due to LINC00472, we performed transcriptome sequencing of LINC00472 overexpressing cells and control cells.  First, raw reads were obtained through sequencing of control cells not treated with LINC00472 and cells treated with overexpression of LINC00472.  Thereafter, genes differentially expressed in the two groups were selected through pretreatment, mapping to the reference genome, trascripts assaembly, and transcript quantification.  The sequencing result provides quantitative and qualitative information of total RNAs whose expression is changed by LINC00472.  This information will facilitate analysis of the signaling network of LINC00472 in lung cancer cells.

overall_design: mRNA profiles of NCI-H838 (H838_cont) not treated with LINC00472 and NCI-H838 (H838_LINC00472) overexpressed with LINC00472

first: Danbi

last: Seo

first: Jungwook

last: Roh

first: Yeonsoo

last: Chae


title: Analysis of the transcriptomic changes in murine small and large intestinal organoids after the sudden expression of BRAFV600E and/or p53R172H

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: BRAFV600E confers poor prognosis and a distinct molecular type of colorectal cancer, which is often associated with TP53 alterations. In order to understand how BRAFV600E and p53R172H promote tumorigenesis in the intestinal epithelium, we generated murine organoids harboring conditional BraffloxV600E and/or Trp53LSL-R172H alleles and conducted RNA sequencing analysis after sudden oncogene induction. As expected from their phenotypes, organoids expressing BRAFV600E, either singly or in combination with p53R172H, displayed strong changes in their transcriptome, while induction of mutant p53 alone had only little impact on gene expression. Our transcriptome analyses revealed there are profound differences in the transcriptomes of SI and COL organoids, in their oncogene naïve ground state and upon BRAFV600E expression. We observed many transcripts positively associated with proliferation, invasion and metastasis to be upregulated in both organoid types expressing BRAFV600E or BRAFV600E together with p53R172H. However, several of them were only differentially regulated in COL organoids, or displayed a more pronounced fold change in COL than in SI organoids. Interestingly, COL organoids more closely recapitulate human CRC patterns and p53R172H cooperates with mutant BRAFV600E in the regulation of several transcripts.

overall_design: Small intestinal (SI) and colonic (COL) organoids of three donor mice per tissue (Trp53LSL-R172H/+;Villin::CreERT2, BraffloxV600E/+;Villin::CreERT2, BraffloxV600E/+;Trp53LSL-R172H/+;Villin::CreERT2) were cultured. Cre recombination was induced with 4-Hydroxytamoxifen (0.5 µM for SI organoids, 3.5 µM for COL organoids) or organoids were treated with ethanol as controls in duplicates in-vitro for 24 hours. Isolated mRNA (for SI organoids 8 days after Cre recombination, for COL organoids 3 days after Cre recombination) was sequenced on an Illumina HiSeq4000.

first: Nadine

last: Reischmann

first: Tilman

last: Brummer

first: Melanie

last: Börries


title: Polyomic analyses of dopaminergic neurons isolated from human substantia nigra in Parkinson’s disease: An exploratory study.

city: Geneva 14

first: PIerre

last: Burkhard

address: 4 rue Gabrielle-Perret-Gentil

department: Department of Clinical Neurosciences

institute: HUG

summary: In this exploratory study, we used laser microdissection to extract dopaminergic neurons from 10 human SNpc samples obtained at autopsy in Parkinson’s disease patients and control subjects. Extracted RNA and proteins were identified by RNA sequencing and nano-LC-MS/MS, respectively, and the differential expression between Parkinson’s disease and control group was assessed.

overall_design: 2 groups of samples: Parkinson's disease and Control. 3 replicated samples per group. 6 analyses per group. 12 analyses for the study

first: Paola

last: Antinori

first: Natacha

last: Civic

first: Didier

last: Chollet

first: Affif

last: Zaccaria

first: Pierre


title: The effect of doxorubicin treatment on variant rs22297749/S427L)-dependent transcriptome changes in patient-derived human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs).

city: Shreveport

first: Tarek Magdy

last: Mohamed

state: LA

address: 1501 Kings Highway, BRI F3-15/22

institute: LSU Health Shreveport

summary: We investigate transcriptome changes of variant S427L and control hiPSC–CMs in response to 1 µM doxorubicin for 24 h, using an unbiased approach

overall_design: Day 30 hiPSC–CMs from 6 patients (3 Control and 3 S427L) were treated with 1 mM doxorubicin or vehicle for 24 h. We have previously determined that this is a physiologically relevant dose (Burridge et al., 2016)

first: Tarek

last: Magdy

first: Zhengxin

last: Jiang

first: Paul

last: Burridge


title: KDM4B-CCAR1-Mediator axis is a critical regulator of osteoclast differentiation and bone homeostasis

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

institute: Chungbuk National University

summary: Bone undergoes a constant and continuous remodeling process which is tightly regulated by the coordinated and the sequential action of bone-resorbing osteoclasts and bone-forming osteoblasts. Recent studies have shown that histone demethylases are implicated in osteoblastogenesis. However, little is known about the role of histone demethylases in osteoclast formation. Here, we identify KDM4B as an epigenetic regulator of osteoclast differentiation.Our biochemical analysis revealed that KDM4B physically and functionally associates with CCAR1 and Med complex. Using chromatin immunoprecipitation (ChIP) with sequencing, we revealed that KDM4B-CCAR1-Med1 is localized at the promoters of several osteoclast-related genes after RANKL stimulation. We demonstrated that KDM4B-CCAR1-MED1 axis is required for p65 localization at the promoters of osteoclast-related genes through a direct interaction between KDM4B and p65 and changes in chromatin structures (euchromatinization). Finally, small-molecular inhibition of KDM4B impedes bone loss in the ovariectomized mouse model. Taken together, our findings establish KDM4B as a critical regulator of osteoclastogenesis, providing a potential therapeutic target of osteoporosis.

overall_design: ChIP-sequencing of KDM4B, CCAR1, MED1 and p65 in BMM cells with RANKL treatment. High-throughput sequencing was performed as single read 75bp sequencing using HigSeq 2500.


title: Next Generation Sequencing Analysis of Wild Type intestine(Control),  intestine with tumor (Shn-RNAi ) and intestine with severe tumor (Shn-RNAi plus Puc mutation) Transcriptomes

city: Heidelberg

first: Erica

last: Valentini

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived intestinal transcriptome profiling between control, tumor and severe tumor condition and using a Drosophila inducible intestinal tumor model to identify signaling cascades involved in tumorigenesis
Methods: intestine mRNA profiles of 7-day old  control (esgts>w1118), Shn-RNAi (esgts>Shn-RNAi_KK) and Shn-RNAi plus Puc mutaion (esgts>Shn-RNAi,PucE69/+) Drosophila were generated by deep sequencing, Control in triplicate, and Shn-RNAi or Shno-RNAi in duplicate, using Illumina GAIIx.
Results: Using an optimized data analysis workflow, we mapped about 19 million sequence reads per sample to the Drosophila genome (ENSEMBL BDGP6.22) and identified a total of 105,674 million counts in the midgut of control, Shn-RNAi and Shn-RNAi plus puc mutation Drosophila. Salmon was used to map and quantify the transcript abundance and DESeq2 was used for the gene expression analysis. DAVID GO term analysis for biological processes clustering of differentially expressed genes enriched for certain known pathays.
Conclusions: Our study represents the detailed analysis of Drosophila intestinal transcriptomes with control and 2 tumor conditions, with biologic replicates, generated by RNA-seq technology. The data analysis showed that signaling pathways are enriched in tumor conditions such as EGFR, NFkB, JAK/STAT and JNK.

overall_design: Midgut mRNA profiles of 7-day old control (esgts>w1118) and Shn-RNAi (esgts>Shn-RNAi) and Shn-RNAi plus Puc mutation (esgts>Shn-RNAi,PucE69/+) Drosophila were generated by deep sequencing, Control samples in triplicate and RNAi or RNAi plus Puc mutation samples in duplicates, using Illumina GAIIx.

first: Jun

last: Zhou


title: The naturally occurring ∆40p53 isoform inhibits eRNA transcription and enables context-specific regulatory inputs during p53 activation [RNA_Nutlin]

first: Dylan

last: Taatjes

overall_design: CRISPR/Cas9 edited MCF10A cells were treated with 10uM nutlin3a and 0.1% DMSO (control) for 20 hours with a total of 2 biological replicates. Total RNA was isolated and enriched for mRNA and directional RNA-seq libraries were constructed and sequenced.

first: Cecilia

last: Levandowski

first: Margaret

last: Gruca

first: Taylor

last: Jones


title: Ribosomal profiling in single cells reveals cell-cycle dependent translational pausing

city: Utrecht

first: Michael

last: VanInsberghe

state: Utrecht

address: Uppsalalaan 8

institute: Hubrecht Institute

summary: In recent years novel single-cell sequencing methods have allowed an in-depth analysis of the diversity of cell types and cell states in a wide range of organisms. These novel tools predominantly focus on sequencing the genomes, epigenomes, and transcriptomes of single cells. However, despite recent progress in detecting proteins by mass spectrometry with single-cell resolution, it remains a major challenge to measure translation in individual cells. Building upon existing ribosome profiling protocols, we majorly increased the sensitivity of these assays allowing ribosome profiling in single cells. Integrated with a machine learning approach, this technology achieves single codon resolution in individual cells. We validate this method by demonstrating that limitation for a particular amino acid causes ribosome pausing at a subset of the codons representing this amino acid. Interestingly, this pausing is only observed in a sub-population of cells correlating to its cell-cycle state. We further corroborate this phenomenon in non-limiting conditions and detect pronounced GAA pausing during mitosis. Finally, we demonstrate the applicability of this technique to rare primary enteroendocrine cells. This new technology provides the first steps towards determining the contribution of the translational process to the astonishing diversity between seemingly identical cells.

overall_design: Ribosome profiling in single HEK293T and hTERT-RPE1 FUCCI cells.

first: Jeroen

last: van den Berg

first: Amanda

last: Andersson-Rolf

first: Hans

last: Clevers

first: Alexander

last: van Oudenaarden


title: Immune modulation underpins the anti-cancer activity of HDAC inhibitors

city: St. Petersburg

last: Kanapin

address: 7/9 University Emb.

department: Institute for Translational Biomedicine

country: Russia

institute: St Petersburg Universoty

summary: We have explored at the genome-wide expression level the effects of the novel HDAC inhibitor CXD101. In human CRC cell lines, a diverse set of differentially expressed genes were up- and down-regulated. Functional profiling of the expression data highlighted immune-relevant concepts related to antigen processing and natural killer (NK) cell mediated cytotoxicity. Similar gene profiles were apparent when global gene expression was investigated in murine CT26 cells treated with CXD101, which were also apparent in syngeneic CT26 tumours growing in vivo. The ability of CXD101 to affect immune-relevant gene expression coincided with changes in the tumour micro-environment (TME), especially in the sub-groups of tumour-infiltrating lymphocytes which occurred upon CXD101 treatment. The altered TME reflected synergistic anti-tumour activity apparent when CXD101 was combined with immune oncology (IO) agents, like anti-PD1 and anti-CTLA4.The ability of CXD101 to instate antigen presentation and augment NK activity in the TME, combined with the synergy between HDAC inhibitors and IO agents, provides a powerful rationale for exploring the combination effect in human cancers.

overall_design: Examination of expresion profile of human and murine colorectal cancer cells treated with HDAC inhibitor

first: Wiktoria

last: Blaszczak

first: Hong

last: Zhu

first: Geng

last: Liu

first: Shunsheng

last: Zheng

first: Wojciech

last: Barczak

first: Anastasia

last: Samsonova

first: Nicholas

last: La Thangue


title: The naturally occurring ∆40p53 isoform inhibits eRNA transcription and enables context-specific regulatory inputs during p53 activation [ChIP-seq]

last: Taatjes

overall_design:
CRISPR/Cas9 edited MCF10A cells were treated with 10uM nutlin3a and 0.01% DMSO (control) for 6 hours with a total of 2 biological replicates. P53 bound DNA was immunoprecipitated using DO-1 antibody (BS Biosciences: BD554293 lot number 8254872) (6ug/25uL Protein G Dynabeads for 100ug Chromotin/15 million nuclei; BD Biosciences: BD554293).

DNA bound by p53 immunoprecipitated from MCF10A cells 6hr after treatment with DO-1 antibody (BS Biosciences: BD554293 lot number 8254872)

Please note that each processed data was generated from both input and ChIP replicates, and is linked to the corresponding '*input replicate 1' sample records.


title: Preformed aerenchyma determines the differential tolerance response under partial submergence imposed by fresh and saline water flooding in rice

city: Cuttack

first: Koushik

last: Chakraborty

address: Bidyadharpur

country: India

institute: ICAR-National Rice Research Institute

summary: In this project we are investigating the differential mechanism of tolerance in rice under combined stresses of salinity and partial submergence as encountered during saline water flooding by looking into expression profile of DEGs and uniquely expressed genes.

overall_design: 12 Rice plants were grown under fresh and saline water flooding conditions.


title: Amyotrophic Lateral Sclerosis Transcriptomics Reveals Immunological Effects of Low-Dose Interleukin-2.

city: Sheffield

first: Ilaria

last: Giovannelli

address: 385a Glossop Road

department: Sheffield Institute for Translational Neuroscience

institute: University of Sheffield

summary: Neuroinflammation is one of the hallmarks of ALS. Regulatory T cells (Tregs) are immune-suppressive cells which physiologically regulate the immune system preventing the onset of autoimmune disorders. These cells are dramatically and progressive reduced in ALS patients, with lower levels correlated with shorter survival. Low-dose interleukin-2 (IL-2) has been roposed as an immune-modulatory strategy to boost Tres in ALS patient and to dampen neuroinflammation. Thirty-six patient were included in the IMODALS clinical trial and randomly assigned to three treatment arms: 1MIU IL-2, 2MIU IL-2 and placebo. They underwent subcutaneous injections once daily for 5 days every 28 days for a total of three administration cycles. The aim of this study was to assess transcriptomic changes occurring in the blood of ALS patients following low-dose IL-2 administration.

overall_design:
Peripheral blood was collected and, using LeukoLOCK TM filters, white blood cells were isolated at different time points (day(D)1 or baseline; D8 three days after the first injection cycle; D64 three days after the last treatment cycle; D85 24 days after the last treatment). Total RNA was extracted using LeukoLOCK TM Total RNA isolation kit (AmbionTM). This was hybridized to Affymetrix Clariom D human microarrays and data was analysed using Transcriptome Analysis Console (TAC) software or Linear Models for Microarray Data (Limma) software package in R. Genes were considered differentially expressed if they showed a 1.2-fold changes (1.2≤FC≤-1.2) and if their p-value was less than 0.05. A total of 107 microarrays were generated: 24 arrays from samples at D1 (12 placebo and 12 2MIU-IL-2-treated patients), 23 from D8 (12 placebo and 11 2MIU-IL-2), 36 from D64 (12 placebo, 12 1MIU and 12 2MIU-IL-2) and 24 from D85 (12 placebo and 12 2MIU-IL-2).
Peripheral blood transcriptomic profiling of ALS patient included in the IMODALS clinical trial by microarrays

first: Nadhim

last: Bayatti

first: Abigail

last: Brown

first: Dennis

last: Wang

first: Marius

last: Mickunas

first: William

last: Camu

first: Jean-Luc

last: Veryune

first: Christine

last: Payan

last: Garlanda

first: Massimo

last: Locati

first: Raul

last: Juntas-Morales

first: Nicolas

last: Pageot

first: Andrea

last: Malaspina

first: Ulf

last: Andreasson

first: Carey

last: Suehs

first: Safa

last: Saker

first: Christophe

last: Massegiun

first: John

last: de Vos

first: Henrik

last: Zetterberg

first: Ammar

last: Al-Chalabi

first: P

last: Leigh

first: Timothy

last: Tree

first: Gilbert

last: Bensimon

first: Paul

middle: R

last: Heath

first: Pamela

last: Shaw

first: Janine

last: Kirby


title: RNA-seq of murine tibialis anterior muscle treated with AAV expressing AR isoform 2 (AR45) or AAV-GFP

status: Public on Jun 29 2021

city: Oxford

first: Thomas

middle: C

last: Roberts

address: Paediatrics, University of Oxford, Le Gros Clark Building, South Parks Road

institute: University of Oxford

summary: The goal of this study was to determine the transcriptomic response of AR-2 (AR45) overexpression in the TA muscles of the AR100Q murine model of SBMA (spinal and bulbar muscular atrophy). Conclusion: AAV-AR45 therapy resulted in a partial restoration of the SBMA-like expression signature compared with mock-treated controls.

overall_design: RNA-seq was performed on tibialis anterior muscles from SBMA (spinal and bulbar muscular atrophy) AR100Q mice treated with AAV vectors expressing either AR-2 (AR45) or GFP mock control. Untreated wild-type mice (C57BL/6) were analysed in parallel as additional controls.

first: Wooi

last: Lim

first: Carlo

last: Rinaldi


title: Targeting tumor-macrophage interaction via the Notch2-Jag1 axis reverses tumor resistance to paclitaxel

city: Hefei

first: Fazhi

last: Yu

address: huangshan road 443

institute: USTC

summary: Taxanes are widely used in chemotherapy, but intrinsic and acquired resistance limit the clinical outcomes. Studies showed tumor interaction with suppressive macrophages plays a key role in taxane resistance, yet therapeutic strategies that deplete or repolarize macrophages are challenging. Here we uncovered a novel tumor-macrophage interaction via Notch2-Jag1 justacrine signaling that can be targeted to sensitize paclitaxel response without affecting the broad macrophage functions. Using translatome profiling, we identified Notch2 upregulation during taxol-induced prolonged mitosis. Notch2 was subsequently activated in the post-mitotic G1 phase by Jag1 expressed on neighboring macrophages, which promoted tumor cell survival by upregulating p38 and anti-apoptotic proteins. Notch2 also upregulated cytokines that further recruited Jag1-expressing macrophages. By targeting this Notch2-Jag1 interaction with a pan-Notch inhibitor, RO4929097, taxol resistance was significantly attenuated in multiple mouse tumor models. Our results point to combining Notch inhibitor with taxane as an effective strategy to selectively disrupt tumor-macrophage interaction underlying chemoresistance.

overall_design:
For ribosome profiling, HeLa cells were synchronized by double thymidine (2 mM, Sigma). Then the dishes were washed three times with PBS to release the cells in complete DMEM again. 9h later, DMSO and 5nM Taxol were added to each group, respectively. The mitosis cells were collected by shake-off. And the mitosis cells from DMSO and Taxol treatment were defined as mitosis(M) and prolonged mitosis(pM) cells, respectively. Mitotic (M) and prolonged mitotic (pM) HeLa cells were lysed in lysis buffer (20 mM Tris pH 7.5, 150 mM KCl, 5 mM MgCl2, 1 mM dithiothreitol, 8% glycerol) supplemented with 0.5% Triton X-100, 30 U/ml Turbo DNase (Ambion, Life Technologies, CA, United States) and 100 μg/ml cycloheximide (Sigma Aldrich, MO, United States). Ribosome protected fragments were then isolated and sequenced as previously described (PMID: 22056041). The resulting mRNAs were modestly fragmented by partial hydrolysis in bicarbonate buffer so that the average size of fragments was ∼80 bp. The fragmented mRNAs were separated by denaturing PAGE and fragments of 26–34 nt were selected. The sequencing libraries were prepared and sequenced as previously described (PMID: 22056041).The differential gene translation profile between M and pM were analyzed.
The differential gene expression profile between wild type and Notch2 knockdown OVCAR8 cell lines were analyzed. RNA was extracted from OVCAR8 cells using Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. Subsequently, total RNA was quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA). The Beijing Genomics Institute (BGI, Shenzhen, China) performed the RNA integrity checking, library preparation and sequencing.Each group was performed in two replicates. Notch2 knockdown OVCAR8 cells were established using plko.1 lentivirus system and two shRNAs target different sequences on Notch2 mRNA were used. Subsequently, we confirmed the RNAseq result in ovarian cancer cells by qPCR (data not included).

first: Jing

last: Guo

first: Zhenye

last: Yang


title: Oncogenic mutations select and sculpt conditional cooperative networks in breast cancer

city: Toronto

first: Sean

last: Egan

state: ON

address: 555 University Ave

institute: Hospital for Sick Children

summary: Many cancers show recurrent copy number aberrations (CNA) affecting large regions of the genome. To identify genes responsible for this we performed Sleeping Beauty (SB) screens in eight different mouse models of breast cancer. Transposon insertion site analysis identified ~1000 cancer genes, most of which are driver- and/or histotype-specific and appear to have sustained loss-of-function insertions in a single allele. This list greatly exceeds the number identified through searches for recurrent focal mutations.  Many SB-targeted genes were identified that function on the same driver-specific pathway responsible for tumor initiation.  Some pairs of genes were co-targeted in tumors, and when tested, two such pairs of hemizygous loss-of-function mutations showed significant cooperative interaction with respect to mammary tumor induction. Thus, oncogenic mutations, including haploinsufficient tumor suppressors located in common regions of CNA, form conditional cooperative networks that select and sculpt “just enough and just right” levels of oncogenic signaling in transformation.

overall_design: Sleeping Beauty (SB) screens in multiple models of breast cancer


title: The corepressor of Topless-related 1 (TPR1): Transcript analysis of TPR1-GFP lines

city: Cologne

last: Griebel

address: Carl-von-Linne-Weg 10

department: Department of Plant Microbe Interactions

institute: Max-Planck Institute for Plant Breeding Research

summary: Transcriptional corepressors of the Topless family are important regulators of plant hormone and immunity signaling. We present here the transcriptome of Arabidopsis thaliana Col-0 plants expressing GFP-tagged TPR1 (Topless-related 1). Expression of TPR1 driven by its own promoter (pTPR1:TPR1-GFP) in Arabidopsis results in EDS1-dependent defense activation and dwarfed growth affected by the plant immune regulator EDS1 but not by accumulation of salicylic acid. We used total RNA sequencing to characterize the transcriptional status of TPR1-GFP expressing lines in Col, eds1-2 and sid2-1 mutant backgrounds.

overall_design: mRNA transcripts of Col-0, pTPR1:TPR1-GFP, pTPR1:TPR1-GFP sid2-1, pTPR1:TPR1-GFP eds1-2 were deep sequenced in triplicates using illumina. In three independent experiments, we harvested untreated leaf material of 5-week-old plants.

first: Jane

middle: E

last: Parker

first: Dmitry

last: Lapin

first: Barbara

last: Kracher


title: Chromatin-associated RNAchIP and transcriptome analyses of the relationship between HP1g/CBX3 and RNA [RNA-seq]

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

summary: RNA-seq and RNAchIP-seq experiments were performed on MEF-derived cell lines knock-out for the expression of HP1g/CBX3 (R cell line) or recomplemented for the expression of HP1g (HPg cell line). Cells were tested under normal growth or conditions of stress (p samples) by treatment with the phorbol ester PMA. Each experiment was performed in biological triplicates.

first: C

last: Rachez

first: R

first: H

last: Varet

last: Proux

last: Muchardt