title: A Non-genetic Mechanism Involving the Integrin b4/Paxillin Axis Contributes to Chemoresistance in Lung Cancer

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary: Tumor heterogeneity and cisplatin resistance are major causes of tumor relapse and poor survival. Here, we show that in lung cancer, interaction between paxillin (PXN) and integrin b4 (ITGB4), components of the focal adhesion (FA) complex, contributes to cisplatin resistance. Knocking down PXN and ITGB4 attenuated cell growth and improved cisplatin sensitivity, both in 2D and 3D cultures. PXN and ITGB4 independently regulated expression of several genes. In addition, they also regulated expression of common genes including USP1 and VDAC1 that are required for maintaining genomic stability and mitochondrial function, respectively. Mathematical modelling suggested that bistability could lead to stochastic phenotypic switching between cisplatin-sensitive and resistant states in these cells. Consistently, purified subpopulations of sensitive and resistant cells recreated the mixed parental population when cultured separately. Altogether, these data point to an unexpected role of the FA complex in cisplatin resistance, and highlight a novel non-genetic mechanism.

overall_design: Knockdown of ITGB4 (Cat #: SR302473C) at the mRNA level was executed using siRNAs purchased from OriGene Technologies (Rockville, MD, USA). Knockdown of PXN was achieved by siRNA purchased from Life Technologies Corporation (Cat #: 4392421). JetPRIME transfection reagent (Polyplus Transfection, Illkirch, France) was used to transfect the siRNAs according to the manufacturer’s protocol. Cells were seeded in 6-well plates (200,000 cells/well) and allowed to adhere overnight. Next day, 10 nM siRNA was transfected with 4 μl jetPRIME reagent in complete growth medium for each well. Cell growth medium was changed the next day and expression was detected 72 h post-transfection by qPCR and immunoblot. The RNA extracted at 72hr of transfection was sent to the core for RNA sequencing. The experiments were repeated two times with SiRNA ITGB4 or SiRNA PXN or both SiRNA ITGB4 and PXN.

first: Atish

last: Mohanty

first: Arin

last: Nam

first: Ravi

last: Salgia


title: Expression data from Min6 cells overexpressing control or SPARC adenovirus

status: Public on Aug 01 2020

city: Changsha

first: Yan-Shan

last: Dai

state: Hunan

address: Furong District People's road, No. 139

country: China

institute: Central South University

summary:
SPARC-deficient mice have been shown to exhibit impaired glucose tolerance and insulin secretion, but the underlying mechanism remains unknown.
We used microarrays to detail the global programme of gene expression and identified distinct classes of up-regulated and down-regulated genes changed by overexpressing SPARC.

overall_design: Min6 cells were infected with AdV-EGFP or AdV-SPARC for 48 hours.

first: Li

last: Hu


title: Gonadal white adipose tissue gene expression changes in response to adipose-specific Med19 knockout

city: St Louis

first: Irfan

middle: J

last: Lodhi

state: MO

address: 660 S Euclid Ave Campus box 8127

country: USA

institute: Washington University School of Medicine in St. Louis

type: Expression profiling by high throughput sequencing

summary: We report the gene expression changes in the gWAT tissue of adipose-specific Med19 knockout mice

overall_design: 12-week old MED19-iAKO mice were injected with 100mg/kg of tamoxifen for 5 days. 14 days post tamoxifen gWAT was harvested for RNA-sequencing.

first: John

middle: M

last: Dean

first: Anyuan

last: He

first: Jun

last: Wang

first: Babak

last: Razani


title: Profiling of histone modification H3K27me3 in Norway spruce embryonic calli and non-embryonic calli

city: Uppsala

first: Miyuki

last: Nakamura

address: Ulls Grand1

country: Sweden

institute: Swedish University of Agricultural Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Histone modification H3K27me3 profilings by the CUT&RUN method (Skene et al., 2017) were performed using embryonic callus and non-embryonic callus of Picea abies to identify genes related to somatic embryogenesis capacity.

overall_design: 2 different calli with 2 different conditions and seedlings.


title: Depicting the battle between nectarine and Monilinia laxa: the fruit developmental stage dictates the effectiveness of the host defenses and the pathogen’s infection strategies

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: One Shields Avenue

department: Plant Sciences

institute: University of California, Davis

summary: Infections by the fungus Monilinia laxa, the main cause of brown rot in Europe, result in considerable losses of stone fruit. Herein, we present a comprehensive transcriptomic approach to unravel strategies deployed by nectarine fruit and M. laxa during their interaction. We used M. laxa-inoculated immature and mature fruit, which were resistant and susceptible to brown rot, respectively, to perform a dual RNA-seq analysis. In immature fruit, host responses, pathogen biomass, and pathogen transcriptional activity peaked at 14 – 24 hours post inoculation (hpi), at which point M. laxa appeared to switch its transcriptional response to either quiescence or death. Mature fruit experienced an exponential increase in host and pathogen activity beginning at 6 hpi. Functional analyses in both host and pathogen highlighted differences in stage-dependent strategies. For example, in immature fruit, M. laxa unsuccessfully employed carbohydrate-active enzymes (CAZymes) for penetration, which the fruit was able to combat with tightly regulated hormone responses and an oxidative burst that challenged the pathogen’s survival at later time points. In contrast, in mature fruit, M. laxa was more dependent on proteolytic effectors than CAZymes and was able to invest in filamentous growth early during the interaction. Hormone analyses of mature fruit infected with M. laxa indicated that, while jasmonic acid activity was likely useful for defense, high ethylene activity may have promoted susceptibility through induction of ripening processes. Lastly, we identified M. laxa genes that were highly induced in both quiescent and active infections and may serve as targets for control of brown rot.

first: Marta

last: Balsells-Llauradó

first: Christian

last: Silva

first: Josep

last: Usall

first: Núria

last: Vall-Ilaura

first: Sandra

last: Serrano-Prieto

first: Neus

last: Teixidó

first: Saskia

middle: D

last: Mesquida-Pesci

first: Antonieta

last: de Cal

first: Rosario

last: Torres


title: BCL6 mediates Chemoresistance in Acute Myeloid Leukemia

city: New York

first: Cem

last: Meydan

state: New York

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

summary: BCL6 is a transcription repressor that plays a crucial role in germinal center formation and lymphomagenesis. However, its role in myeloid malignancies remains unclear. Here, we explored the role of BCL6 in acute myeloid leukemia (AML). Heterogeneous levels of BCL6 were found across AML cell lines and primary AML samples. Cells with higher levels of BCL6 were indeed sensitive to treatment with BCL6 inhibitors. Gene expression profiling of AML cells treated with BCL6 inhibitor revealed a subset of target genes that are common with lymphoma cells. Ex vivo treatment of primary AML cells with BCL6 peptide inhibitor (BPI) induced apoptosis and decrease colony forming capacity which correlated with the levels of BCL6 expression . Importantly, inhibition of BCL6 in primary AML cells with either BPI or BCL6 siRNA resulted in significant reduction of leukemia initiating capacity using immunodeficient mice, suggesting ablation of leukemia stem cells (LSC). Such anti-LSC activity was also observed as downregulation of LSC gene signatures using gene expression analyses of cells treated with a BCL6 inhibitor. Importantly, treatment with cytarabine (AraC) induced BCL6 expression, and the levels of BCL6 induction were correlated with resistance to AraC. Treatment of AML primary derived xenografts (PDX) revealed that when AraC was combined with BCL6 inhibitor, inhibition of BCL6 significantly potentiated the efficacy of AraC and improved cytotoxic effects by interfering with the leukemia initiating capacity of AML cells. This suggests that pharmacological inhibition of BCL6 might provide a novel therapeutic strategy for ablation of LSCs and overcome chemoresistance in AML.

overall_design: Nine samples total: AML37 primary cell (three experimental replicates) treated with FX1, DMSO, and untreated for 12 hours after CD34 positive selection using FACS. Cells were treated for 12 hours using EC50 concentration for the same primary cell.

first: Kimihito

last: Kawabata

first: Monica

last: Guzman

first: Ari

last: Melnick


title: Chromatin architecture landscape in hierarchical hematopoietic cells

city: Kunming

first: Chao

last: Zhang

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

institute: Chinese Academy of Sciences

summary: The spatiotemporal chromatin reorganization during hematopoietic differentiation has not been well characterized, which partly limited by the large amounts of starting cells for the current high-throughput chromatin conformation capture approaches. Here, we introduce a low-input Hi-C method, tagHi-C, to capture the chromatin structures in hundreds of cells. We proved tagHi-C was a feasible and reproducible approach.

overall_design: We applied tagHi-C in 10 mouse adult hematopoietic cell populations at different stages to comprehensively map the 3D chromatin landscape during normal hematopoiesis.

first: Hui

last: Cheng

first: Cheng

last: Li

first: Tao


title: RNA-Seq of UXT KO in Primary Sertoli cells

status: Public on Jul 31 2020

first: Susan

last: Logan

state: NY

address: 450 East 29th St

department: Urology

institute: NYU School of Medicine

summary: We created a knockout model of ART-27(UXT) specially in the Sertoli cells of the mouse testes. In order to see how loss of ART-27 effects the Sertoli cell transcriptome we isolated Sertoli cells from WT and KO animals. The WT cells were infected with a vector only construct, and the KO cells were infected with CRE producing construct.

overall_design: examination of transcriptional changes in WT primary Sertoli cells and KO Primary Sertoli cells. Each condition was done in triplicate

first: Phillip

middle: A

last: Thomas

first: Sophie

middle: E

last: Ruff

last: Ha


title: Transcriptome and epigenome analyses of vernalization in Arabidopsis thaliana

city: Austin

first: Sibum

last: Sung

state: Texas

address: 2506 SPEEDWAY, Stop A5000

department: Molecular Biosciences

institute: University fo Texas at Austin

summary: In this work, we present the first comprehensive analyses of transcriptomic and epigenomic dynamics during the vernalization process in Arabidopsis thaliana. Six major clusters of genes exhibiting distinctive features were identified. Temporary changes in histone H3K4me3 levels were observed that likely coordinate photosynthesis and prevent oxidative damage during cold. In addition, vernalization induced a stable accumulation of H3K27me3 over genes encoding many development-related transcription factors, resulting in either inhibition of transcription or a bivalent status of the genes. Lastly, FLC-like and VIN3-like genes were identified that appear to be novel components of the vernalization pathway.

overall_design: ChIP-seq of H3K27me3, H3K4me3, H3K36me3, each from 3 vernalization time points and 2  replicates; RNA-seq from 7 vernalization time points and 2 replicates

first: Xi

last: Yanpeng

first: Sung

last: Sibum


title: Functional genomic landscape of cancer-intrinsic immune evasion to cytotoxic T lymphocyte killing [CRISPRseq]

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: The genetic circuits that allow cancer cells to evade destruction by the host immune system remain poorly understood. To identify a phenotypically robust core set of genes and pathways that facilitate cancer cell-intrinsic evasion to cytotoxic T lymphocyte (CTL)-mediated killing, we performed genome-wide CRISPR screens across a panel of genetically diverse cancer models cultured in the presence of CTLs. We uncovered a core set of 182 genes whose individual perturbation leads to either cancer cell sensitivity or resistance to CTL toxicity. Systematic exploration of our dataset using genetic co-similarity reveals the hierarchical and coordinated nature by which genes and pathways act to orchestrate intrinsic CTL evasion, with discrete functional modules controlling the interferon response and tumor necrosis factor alpha (TNFa)-induced cytotoxicity emerging as dominant sub-phenotypes. Our data establish a central role for previously identified negative regulators of the Type II interferon response (e.g. Ptpn2, Socs1, Adar1) in mediating intrinsic CTL evasion and demonstrate a requirement for the lipid droplet related gene Fitm2 for maintaining cell fitness upon exposure to interferon gamma (IFNg). Additionally, we identify the autophagy pathway as a conserved mediator of cancer intrinsic CTL evasion, required to resist cytokine-mediated cytotoxicity caused by IFNg and TNFa. By mapping cytokine- and CTL-based genetic interactions, as well as in vivo CRISPR screens, we illuminate the pleiotropic nature by which autophagy acts to orchestrate intrinsic CTL evasion and highlight the importance of our observed effects within the tumor microenvironment. Collectively, our data expands our appreciation of the genetic circuits that contribute to cancer intrinsic immune evasion, highlighting the importance of leveraging systematic functional genomics approaches for furthering our understanding of this biology.

overall_design: CRISPR screens in Renca (wild-type vs. Atg12-KO vs. Fitm2-KO), Renca-HA (wild-type vs. Atg12-KO vs. Fitm2-KO), EMT6-HA, CT26-HA, 4T1-HA, B16-Ova, MC38-Ova cultured in the presence or absence of IFNg, TNFa or cytotoxic T-lymphocytes

first: Keith

last: Lawson

first: Cristovão

last: Sousa

first: Xiaoyu

first: Eiru

last: Kim

first: Rummy

last: Akthar

first: Joseph

last: Caumanns

first: Yuxi

last: Yao

first: Nicholas

last: Mikolajewicz

first: Abdelrahman

last: Zid

first: Zi

middle: P

last: Fan

first: Shirley

last: Hui

first: Jordan

last: Krall

first: Donald

last: Simons

first: Chloe

last: Slater

first: Victor

last: De Jesus

first: Lujia

last: Tang

first: Richa

last: Singh

first: Joshua

last: Goldford

first: Sarah

last: Martin

first: Qian

last: Huang

first: Elizabeth

last: Francis

first: Andrea

last: Habsid

first: Ryan

last: Climie

first: David

last: Tieu

first: Jiarun

last: Wei

first: Ren

first: Amy

middle: H

last: Tong

first: Kevin

middle: R

last: Brown

first: Catherine

last: Ross

first: Michael

last: Aregger

first: Katherine

middle: S

last: Chan

first: Hong

last: Han

first: Xiaowei

last: Wang

first: Patricia

last: Mero

first: John

last: Brumell

first: Antonio

last: Finelli

first: Laurie

last: Ailles

first: Gary

last: Bader


title: Single-cell RNA-sequencing analysis of the IL-10 dependent response of human CD14+ monocytes to LPS

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

country: United Kingdom

institute: Kennedy Institute of Rheumatology

summary: Inflammatory bowel diseases (IBD) involve dysregulated immune responses. Understanding the cellular specificity and compartmentalisation of cytokine responses may help to target cytokine therapies. Intestinal inflammation involves influx of CD14+ monocytes into the lamina propria of the gut where they can adopt pro-inflammatory phenotypes. In the healthy intestine, IL-10 plays a key role in controlling inflammation and promoting homeostasis. This data was generated to investigate the phenotypes that CD14+ monocytes can adopt following LPS stimulation with or without concominant IL-10 signaling blockade.

overall_design: CD14+ monocytes were isolated from a healthy human donor and subject to droplet based single-cell RNA-sequencing after exposure to conditions of (i) no stimulation, (ii) stimulation with LPS or (iii) stimulation with LPS + anti-IL-10R antibody. The stimulation with LPS + anti-IL10R antibody was repeated with cells from a second healthy donor.

first: Dominik

last: Aschenbrenner

first: Maria

last: Quaranta

first: Moustafa

last: Attar

first: Holm

last: Uhlig

middle: N


title: REQUIREMENT FOR PKC EPSILON IN KRAS-DRIVEN LUNG TUMORIGENESIS

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

summary: Non-small cell lung cancer (NSCLC), the most frequent subtype of lung cancer, remains a highly lethal malignancy and one of the leading causes of cancer deaths worldwide. Mutant KRAS is the prevailing oncogenic driver of lung adenocarcinoma, the most common histological form of NSCLC. In this study, we examined the role of PKCe, an oncogenic kinase highly expressed in NSCLC and other cancers, in KRAS-driven tumorigenesis. Notably, database analysis revealed an association between PKCe expression and poor outcome in lung adenocarcinoma patients specifically having KRAS mutation. By generating a PKCe-deficient, conditionally activatable allele of oncogenic Kras (LSL-Kras G12D ;PKCe -/- mice) we were able to demonstrate the requirement of PKCe for Kras-driven lung tumorigenesis in vivo, which is consistent with the impaired transformed growth observed in PKCe-deficient KRAS-dependent NSCLC cells. Moreover, PKCe-knockout mice were found to be less susceptible to lung tumorigenesis induced by benzo[a]pyrene, a carcinogen that induces mutations in Kras. Mechanistic analysis using RNA-Seq revealed little overlapping for PKCe and KRAS in the control of genes/biological pathways relevant in NSCLC, suggesting that a permissive role of PKCe in KRAS-driven lung tumorigenesis may involve non-redundant mechanisms. Our results thus highlight the relevance and potential of targeting PKCe for lung cancer therapeutics.

overall_design: H2009 cells were subjected to PKCe RNAi (e1 or e3 duplexes) or KRAS RNAi (K1 or K3 duplexes). As controls we used NTC RNAi and parental cells. Three replicates were done for each condition. Forty-eight h later, total RNA was isolated from subconfluent plates.

first: Marcelo

middle: G

last: Kazanietz

middle: C


title: Functional genomic landscape of cancer-intrinsic immune evasion to cytotoxic T lymphocyte killing [RNA-seq II]

first: Jason

last: Moffat

overall_design: RNAsequencing was performed in wild type versus Atg12 or Fitm2 knockout Renca, Renca-HA, MC38-Ova or B16-Ova cells cultured in the presence or absence of IFNg of TNFa (performed in biological triplicate)

first: Keith

last: Lawson

first: Cristovão

last: Sousa

first: Xiaoyu

last: Zhang

first: Eiru

last: Kim

first: Rummy

last: Akthar

first: Joseph

last: Caumanns

first: Yuxi

last: Yao

first: Nicholas

last: Mikolajewicz

first: Abdelrahman

last: Zid

first: Zi

last: Fan

first: Shirley

last: Hui

first: Jordan

last: Krall

first: Donald

last: Simons

first: Chloe

last: Slater

first: Victor

last: De Jesus

first: Lujia

last: Tang

first: Richa

last: Singh

first: Joshua

last: Goldford

first: Sarah

last: Martin

first: Qian

last: Huang

first: Elizabeth

last: Francis

first: Andrea

last: Habsid

first: Ryan

last: Climie

first: David

last: Tieu

first: Jiarun

last: Wei

first: Ren

last: Li

first: Amy

last: Tong

first: Kevin

last: Brown

first: Catherine

last: Ross


title: Single cell RNA-seq reveals high heterogeneity among human γδ T cells.

city: Hamburg

first: Immo

last: Prinz

address: Falkenried 94

department: Institute of Systems Immunology

country: Germany

institute: University medical center Hamburg Eppendorf

summary: Human γδ T cells take a small but important part in the immune system. Human γδ T cells are usually categorized by the V gene of their T cell receptor (TCR) δ chain; most of which are Vδ1+ or Vδ2+. Naive γδ T cells are often found from neonates and cytotoxic γδ T cells (γδCTLs) are frequent in adults. However, phenotypes and the developmental programs of human γδ T cells are not fully clear. Here, by single-cell RNA sequencing (sc-RNAseq) of transcriptome and T cell receptor (sc-TCRseq) on γδ T cells from neonates and adults, we revealed human γδ T cells can be divided as naïve T cells, γδCTLs, and γδNKT cells which are featured by pro-Vδ1, Vδ1, and Vδ2 TCR repertoire, respectively. γδNKT cells can be further described as γδNKT-1, γδNKT-2, and γδNKT-17 cells.

overall_design: Sort  ϒδT cells from neonatal cord blood and adult peripheral blood, then do 5'-RNA single cell transcriptome and TCR sequening (10x genomics).

first: Likai

last: Tan

first: Alina

last: Fichtner

first: Sarina

last: Ravens


title: Functional genomic landscape of cancer-intrinsic immune evasion to cytotoxic T lymphocyte killing [RNA-seq I]

first: Jason

last: Moffat

overall_design: RNAsequencing was performed in Renca-HA, MC38-Ova, B16-Ova, EMT6-HA, CT26-HA, 4T1-HA cells cultured for 48hrs (using biological duplicates)

first: Keith

last: Lawson

first: Cristovão

last: Sousa

first: Xiaoyu

last: Zhang

first: Eiru

last: Kim

first: Rummy

last: Akthar

first: Joseph

last: Caumanns

first: Yuxi

last: Yao

first: Nicholas

last: Mikolajewicz

first: Abdelrahman

last: Zid

first: Zi

last: Fan

first: Shirley

last: Hui

first: Jordan

last: Krall

first: Donald

last: Simons

first: Chloe

last: Slater

first: Victor

last: De Jesus

first: Lujia

last: Tang

first: Richa

last: Singh

first: Michael

last: Aregger

first: Katherine

last: Chan

first: Hong

last: Han

first: Xiaowei

last: Wang

first: Patricia

last: Mero

first: John

last: Brumell

first: Antonio

last: Finelli

first: Laurie

last: Ailles

first: Gary

last: Bader


title: Functional genomic landscape of cancer-intrinsic immune evasion to cytotoxic T lymphocyte killing

first: Jason

last: Moffat

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

overall_design: Refer to individual Series


city: Subang Jaya

first: Aimi Syamima

last: Abdul Manap

state: Selangor

address: No. 1, Jalan Taylor's

country: Malaysia

institute: Taylor's University

summary:
Whole transcript analysis of amyloid beta 42 (Aβ42)-induced SH-SY5Y cells in control and treated groups (curcumin, piperine and combination therapy) were assessed using microarray profiling. A number of up-regulated and down-regulated genes were altered in sample-specific group.
In this study, an optimized concentration of 35 µM of curcumin and piperine in combination was used to treat Aβ42 fibril and then high-throughput microarray profiling (Clariom S assay) was performed on the extracted RNA from pelleted cells.

overall_design: Twelve total RNA samples were submitted to UMBI ("the service lab"). All the RNA samples passed initial QC checks and were determined to be of good quality to continue with whole transcripts analysis. All samples were processed according to Applied Biosystems™ recommended protocols, and the service lab Standard Operating Procedures (SOP). With the consent from the customer, all 12 samples which passed the assay quality control (QC) check points were selected and hybridized to Human Clariom S Array. The data generated passed all our quality metrics with POS vs NEG AUC of values of above 0.9.

first: Aimi-Syamima

first: Priya

last: Madhavan

first: Adeline

last: Yoke Yin

first: Shantini

last: Vijayabalan


title: The NTP Generating Activity of Pyruvate Kinase II is Critical for Apicoplast Maintenance in Plasmodium falciparum

city: Baltimore

first: Anne

middle: E.

last: Jedlicka

state: MD

address: 615 N. Wolfe street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins University, School of Public Health

summary: The apicoplast of Plasmodium falciparum parasites is believed to rely on the import of three-carbon phosphate compounds for use in organelle anabolic pathways, in addition to the generation of energy and reducing power within the organelle. We generated a series of genetic deletions in an apicoplast metabolic bypass line to determine which genes involved in apicoplast carbon metabolism are required for blood-stage parasite survival and organelle maintenance. We were able to demonstrate that pyruvate kinase II (PyrKII), the sole predicted source of pyruvate and NTPs within the apicoplast, is essential for organelle maintenance. However, deletions within apicoplast pathways that metabolize pyruvate did not result in organelle disruption, indicating that NTPs generated by PyrKII are the products required for this process. Enzymatic characterization of PyrKII revealed that it was active against all NDPs and dNDPs tested with broad substrate specificity, suggesting that it may be capable of generating any and all NTPs and dNTPs within the organelle. Conditional mislocalization of PyrKII resulted in a decrease in transcript levels within the apicoplast that preceded organelle disruption, suggesting that PyrKII is required for organelle maintenance due to its role in nucleotide triphosphate generation within the apicoplast.

overall_design: PyrKII CLD parasites were cultured for 48 hours with samples taken every eight hours for transcriptomics and processed in triplicate. Nf54 attB parasites without treatment were cultures for 48 hours with samples taken every eight hours and processed in quadruplicate, except for Time 48 Control which is in triplicate. Time 8 for the PyrKII CLD dataset corresponds to the same parasite developmental stage as Time 0 of the Nf54 attB dataset. PyrKII CLD timepoints 8-56 were compared to Nf54 attB timepoints 0-48 for analysis.

first: Russel

last: Swift

first: Cyrianne

last: Keutcha

first: Hans

last: Liu

first: Krithika

last: Rajaram

first: Amanda

last: Dziedzic

first: Sean

last: Prigge


title: Haploinsufficiency of RREB1 causes a Noonan-like RASopathy via epigentic regulation of RAS-MAPK pathway genes.

first: Rob

last: Rottapel

address: 101 College Street, Room 12-704

department: Medical Biophysics

institute: University Health Network

summary: Whole genome analysis of mRNA transcripts regulated by RRBE1 in HEK293 cells.

overall_design: RNAseq analysis of HEK293 cells expressing shRNA control versus shRNA targeting RREB1.

first: Oliver

last: Kent

first: Kevin

last: Brown

first: Robert


title: Maternal exposure to a mitochondrial toxicant results in life-long alterations in DNA methylation and gene expression in the offspring

city: RTP

first: Janine

last: Santos

state: NC

address: 111 TW Alexander drive

department: GISBL

institute: NIEHS

type: Methylation profiling by high throughput sequencing

summary: We exposed dams to rotenone starting 2 weeks prior to conception all the way to the end of lactation to determine its effects on the DNA methylation landscape of the offspring. We find that this treatment not only affects the DNA methylation status in one locus in the skin (both doses were studied here) but the entire DNA methylome of the liver is also changed (only lower dose was analyzed). The effects last throughout the lifespan of the animals and are accompanied by changes in the transcriptome.

overall_design: Whole genome bisulfite sequencing (WGBS) and RNA-seq were performed using livers from animals in the control group or exposed perinatally to rotenone at PND22, 6, 12 and 18 months of age. WGBS and RNA-seq Samples with the same title and replicate number are derived from the same liver sample.

first: Oswaldo

last: Lozoya

first: Fuhua

last: Xu

first: Richard

last: Woychik


title: Single-nucleus characterization of spinal dynorphin-lineage cells and identification of persistent transcriptional effects of neonatal hindpaw incision

city: Cincinnati

first: Mark

middle: L

last: Baccei

state: OH

address: 231 Albert Sabin Way

department: Anesthesiology

institute: University of Cincinnati

summary: Neonatal tissue damage can have long-lasting effects on nociceptive processing in the central nervous system, which may be partially due to persistent injury-evoked alteration of the normal balance between synaptic inhibition and excitation in the spinal dorsal horn. Spinal dynorphin-lineage (pDyn) neurons are part of an inhibitory circuit which limits the flow of nociceptive input from the periphery to the brain and is disrupted by neonatal tissue damage. To identify the potential molecular underpinnings of this disruption, an unbiased single-nucleus RNAseq analysis of adult spinal pDyn cells characterized this population in depth, then identified changes in gene expression evoked by neonatal hindpaw incision. The analysis revealed twelve transcriptionally distinct subpopulations (i.e., clusters) of dynorphin-lineage cells, including both inhibitory and excitatory neurons as well as oligodendrocytes and astrocytes. Investigation of injury-evoked differential gene expression identified genes which were significantly up- or downregulated in adult pDyn neurons from neonatally incised mice compared to naïve littermate controls. Some of these injury-evoked changes appeared to be cluster-specific while others were similar across all pDyn neuron clusters, and many of the identified genes were related to the cellular stress response. However, the relatively low number of injury-evoked differentially expressed genes also suggests that post-transcriptional regulation within pDyn neurons may play a key role in the priming of developing nociceptive circuits by early life injury.  Overall, the findings reveal novel insight into the molecular heterogeneity of a key population of dorsal horn interneurons that has previously been implicated in the suppression of mechanical pain and itch.

overall_design: Prodynorphin (Pdyn)-lineage spinal nuclei were collected from 8 naïve adult mice and 8 adult mice with prior neonatal (P3) hindpaw incision. Single-cell RNA sequencing data was obtained from each injured and naïve sample using 10X Chromium 3v3.

first: Elizabeth

middle: K

last: Serafin

first: Aditi

last: Paranjpe

first: Chelsie

last: Brewer


title: Ependymoma subpopulation lineages underlie clinical classification and outcome (microarray data set)

city: Aurora

first: Andrew

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

summary:
Introduction: single-cell RNA sequencing identified multiple subpopulations in childhood posterior fossa ependymoma. The contribution of individual neoplastic subpopulations to bulk tumor transcriptome-based molecular classification and patient outcome was estimated by deconvolution in a cohort of clinically-annotated primary and recurrent EPN samples.
The abundance of EPN subpopulations was estimated in primary EPN samples and showed that the ratio of subpopulation fractions dictated assignment to the two main transcriptomic classification subgroups in childhood posterior fossa ependymoma. Longitudinal analysis revealed that subpopulation fractions changed between presentation and recurrence. Outcome analyses demonstrated that a different proportions of subpopulations were associated with differential survival.

overall_design: Gene expression profiles were generated from primary and recurrent surgical tumor  samples (n=69) using Affymetrix HG-U133plus2 chips (Platform GPL570).


title: RNA-seq from monocytes derived dendritic cells (MoDC) samples purified from spleen of C57BL/6 mice to evaluate their gene expression during Plasmodium berguei ANKA (PbA) infection

city: Worcester

first: Ricardo

middle: Tostes

last: Gazzinelli

state: Massachusetts

address: 364 Plantation Street

department: Medicine

institute: University of Massachusetts Medical School

summary: Dendritic cells have an important role in immune surveillance. After being exposed to microbial components, they migrate to secondary lymphoid organs and activate T lymphocytes. During mouse model malaria, splenic inflammatory monocytes differentiate into monocyte-derived dendritic cells (MO-DCs), which are CD11b+F4/80+CD11c+MHCIIhighDC-SIGNhighLy6c+ and express high levels of CCR5, CXCL9 and CXCL10 (CCR5+CXCL9/10+ MO-DCs). We intend to use these malaria-induced splenic MO-DCs gene expression data to understand more about the migratory route taken by these cells as well the most important genes/pathways involved on this cell differentiation in the spleen, allowing them to migrate to the brain where they develop an important role in cerebral malaria.

overall_design: RNA-seq was performed in biological replicates (3 mice per group). Monocytes (CD11b+F4/80+CD11c-DC-Sign-MHC II-from spleen and bone marrow); inflammatory monocytes (CD11b+F4/80+Ly6ChighCD11c-DC-Sign-MHC II- from bone marrow) and MO-DCs (CD11b+F4/80+CD11c+DC-Sign+MHC II+) from splenocytes were purified using a cell sorting ARIA (BD). Monocytes were collected from non-infected mice and MO-DCs from PbA-infected C57BL/6 mice at day 5 post-infection with PbA.


title: Change in translation efficiency by RNG140-GFP overexpression in CHO cells

city: Okazaki

first: Kaori

last: Nakazawa

address: Nishigonaka 38, Myodaiji

country: Japan

institute: National Institute for Basic Biology

summary: RNG140 is an RNA binding protein involved in the regulation of various cell differentiation and functional processes. Although RNG140 has been shown to inhibit translation in rabbit reticulocyte lysates, it is not known what kind of mRNAs were regulated their translation by RNG140. Comprehensive ribosome profiling revealed that overexpression of RNG140 in cultured CHO cells reduces translation of long mRNAs, including those associated with cell proliferation.

overall_design: Ribosome profiling and RNA-seq in RNG140-GFP-expressing CHO cells and control CHO cells

first: Yuichi

last: Shichino

first: Shintaro

last: Iwasaki

first: Nobuyuki

last: Shiina


title: A cellular mechanism to detect and alleviate reductive stress

status: Public on Jul 30 2020

city: Berkeley

first: Michael

last: Rape

address: 1951 Oxford St Li Ka Shing Center, 330A

institute: University of California, Berkeley

summary: Metazoan organisms rely on conserved stress response pathways to detect and  alleviate adverse conditions and preserve their cellular integrity. Stress responses are  particularly important in stem cells that provide lifetime support for tissue formation and  repair, yet how these protective systems are integrated into developmental programs is  poorly understood. Here, we have used myoblast differentiation to identify the E3  ligase CUL2FEM1B and its substrate FNIP1 as core components of the reductive  stress response. Reductive stress, as caused by prolonged antioxidant signaling or  mitochondrial inactivity, reverts the oxidation of invariant Cys residues in FNIP1 and  thereby allows CUL2FEM1B to recognize its target. The ensuing proteasomal  degradation of FNIP1 restores mitochondrial activity to preserve both redox  homeostasis and stem cell integrity. The reductive stress response is therefore built  around a ubiquitin-dependent rheostat that tunes mitochondrial activity to cellular redox  needs and implicates metabolic control in the coordination of stress and developmental  signaling.

overall_design: RNA-seq analysis was perfomred on undiffernitataed myoblasts cells seeded at subcondluent densities, and treated with ON-TARGETplus Non-targeting Control (Horizon Discovery; D-001810-03 UGGUUUACAUGUUUUCUGA), or ON-TARGET plus siRNA siKeap1 #1 mouse (Horizon Discovery; J-041104-09 GCGCCAAUGUUGACACGGA), or ON-TARGET plus siRNA siFem1b #1 mouse (Horizon Discover;y J-065205-08 GAAGAUCAGUGCAGAAUUA, or codepletion with siKeap/siFem1b

first: Fernando

last: Rodriguez Perez


title: Kidney tertiary lymphoid structures in Lupus Nephritis develop into large interconnected networks and resembles lymph nodes in gene signature.

city: TROMSØ

first: Kristin

middle: Andreassen

last: Fenton

state: Troms

address: MH Building

department: Medical Biology

country: Norway

institute: UiT Norges arktiske universitet

summary: Immune aggregates organized as tertiary lymphoid structures (TLS) are observed within kidneys of systemic lupus erythematosus (SLE) patients with lupus nephritis (LN). We characterized renal TLS in lupus-prone (NZBxNZW) F1 mice with respect to cell composition and vessel formation. Ribonucleic acid (RNA) sequencing was performed on transcriptomes isolated from Lymph nodes (LyN), macro-dissected TLS from kidneys, and total kidneys of mice at different disease stages by using Ion Torrent Personal Genome Machine (Ion PGM) and RNAseq from Illumina. Formation of TLS was found in anti-dsDNA antibody positive mice and the structures were organized as interconnected large networks with distinct T and B cell zones with adjacent dendritic cells, macrophages, plasma cells, high endothelial venules, supporting follicular dendritic cells network, and functional germinal centers. Comparison of gene profiles of whole kidney, renal TLS and LyN revealed a similar gene signature of TLS and LyN. The upregulated genes within the kidneys of lupus-prone mice during the development of LN reflected the TLS formation, while the downregulated genes were involved in metabolic processes of the kidney cells. A comparison with human LN gene expression revealed similar upregulated genes as observed during the development of murine LN and TLS.  We conclude that kidney TLS have a similar cell composition, structure and gene signature as LyN, and therefore may function as a kidney specific type of LyN.

overall_design: Total RNA

first: Esmaeil

last: Dorraji

first: Chris

first: Mikael

last: Stenersrød

first: Premasany

last: Kanapathippillai

first: Aud-Malin

last: Hovd

first: Anita

last: Ursvik

first: Kjersti

last: Horvei

first: Dhivya

last: Thiagyaran

first: Stine

last: Figenschau

first: Hege

last: Pedersen


title: Functional genomic landscape of cancer-intrinsic immune evasion to cytotoxic T lymphocyte killing [CRISPR screen]

first: Jason

last: Moffat

overall_design: CRISPR screens in Renca (wild-type vs. Atg12-KO vs. Fitm2-KO), Renca-HA (wild-type vs. Atg12-KO vs. Fitm2-KO), EMT6-HA, CT26-HA, 4T1-HA, B16-Ova, MC38-Ova cultured in the presence or absence of IFNg, TNFa or cytotoxic T-lymphocytes

first: Keith

last: Lawson

first: Cristovão

middle: M

last: Sousa

first: Xiaoyu

last: Zhang

first: Eiru

last: Kim

first: Rummy

last: Akthar

first: Joseph

middle: J

last: Caumanns

first: Yuxi

last: Yao

first: Nicholas

last: Mikolajewicz

first: Abdelrahman

last: Zid

first: Zi

last: Fan

first: Shirley

last: Hui

first: Jordan

last: Krall

first: Donald

last: Simons

first: Chloe

last: Slater

first: Victor

last: De Jesus

first: Lujia

last: Tang

first: Richa

last: Singh

first: Joshua

last: Goldford

first: Sarah

last: Martin

first: Qian

last: Huang

first: Elizabeth

last: Francis

first: Andrea

last: Habsid

first: Ryan

last: Climie

first: David

last: Tieu

first: Jiarun

last: Wei

first: Ren

last: Li

first: Amy

last: Tong

first: Kevin

last: Brown

first: Catherine

last: Ross

last: Aregger

first: Katherine

last: Chan

first: Hong

last: Han

first: Xiaowei

last: Wang

first: Patricia

last: Mero

first: John

last: Brumell

first: Antonio

last: Finelli

first: Laurie

last: Ailles

first: Gary

last: Bader


title: Change in translation efficiency in mouse eyes at P0.5 by RNG140 knockout

first: Kaori

last: Nakazawa

summary: RNG140 is an RNA-binding protein that increases in expression during eye lens differentiation and is involved in lens formation. However, the relevance of RNG140-mediated translational regulation to differentiation is not well understood. RNG140-mediated translational regulation operates in the mouse eye, where RNG140 knockout increased the translation of long mRNAs. mRNAs involved in lens differentiation, such as crystallin mRNAs, are short, and can escape translational inhibition by RNG140 and be translated in differentiating lenses.

overall_design: Ribosome profiling and RNA-seq in the eye from P0.5 RNG140 knockout mice and control mice

first: Yuichi

last: Shichino

first: Shintaro

last: Iwasaki

first: Nobuyuki

last: Shiina


title: Charaterization of function of ST2 receptor on macrophages function during Club cell regeneration after naphthalene injury in WT mice

city: Gaithersburg

first: Jingya

state: Maryland

address: 1 Medimmune Way

department: Early respiratory and immunology

institute: Astrazeneca

summary: During repair phase after naphathalene injury 3 subsets of myeloid cells accumulate at the site of injury including P1 (monoyte), P2 (monocyte-derived macrophages and P3 (resident alternatively activated airway macrophages). ST2 receptor was found to be expressed by P2 and P3 subsets. To understand which biological processes in lung macrophages were regulated by ST2, myeloid cell subsets were flow-sorted from Naphthalene-treated WT and ST2-/- mice on d6 and their transcriptome analyzed using RNA-seq

overall_design: ST2Ko and C57Bl/6J female mice (9-10 weeks) were treatment with naphthalene at a dose of 200-250 mg/kg. On day 6, mice were euthanized and their lungs were collected and digested for myeloid cell sorting of P1 (CD11b+ ly6c+ cells), P2 (CD11b+ CD11c+ F4/80+ cells) and P3 (Siglrc-F+ CD206+ CD11c+ F4/80+ cells). then P1-P3 were RNAseq analysis.

first: Rania

last: Dagher


title: Mitochondrial - Y Chromosome Epistasis in Drosophila melanogaster

city: Ithaca

first: Andrew

last: Clark

address: 215 Tower Road

institute: Cornell University

summary: We generate 36 otherwise isogenic Drosophila melanogaster strains differing only in the geographical origin of their mitochondrial genome and Y chromosome to experimentally examine the effects of the uniparentaly inherited parts of the genome, as well as their interaction, in males. We assay gene expression through RNA-sequencing and detect an important role for both mitochondrial and Y-linked genes, as well as extensive mitochondrial-Y chromosome epistasis.

overall_design: We used a 6x6 crossing design, crossing females from six mitochondrial replacement lines with males from six Y chromosome replacement lines, resulting in male offspring with 36 mito-Y combinations. Mitochondrial and Y Replacement lines share the same 4361 nuclear background, which means our 36 mitochondrial-Y replacement lines are isogenic outside of their mitochondrial haplogroup and Y haplotype. Mitochondrial genomes came from Beijing, China (2 lines; B38 and B39), Ithaca, NY, USA (1 line; I02), and the Netherlands (3 lines; N01, N02, and N23), and the Y chromosomes from Beijing, China (2 lines; B04 and B11), the Netherlands (2 lines; N03 and N07), and Zimbabwe (2 lines ; ZWH123 and YZW139). These populations represent deeply divergent mitochondrial and Y chromosome clades chosen from the Global Diversity Lines. We performed RNA sequencing on 10 3-5 day old males from each of the 36 mitochondrial-Y combinations. We used two biological replicates for each combination, with individuals for each replicate being collected from separate crosses between females from the mitochondrial-replacement and males from the Y-replacement parental lines performed on the same day.

first: J

middle: A

last: Ågren

first: Manisha

last: Munasinghe


title: Expression data from embryonic mouse spinal cords from NFIX knockout and wild-type mice.

city: Brisbane

first: Michael

last: Piper

state: QLD

address: Building 81, University of Queensland, St Lucia

department: School of Biomedical Science

country: Australia

institute: University of Queensland

summary:
The generation of cellular identity and diversity within the developing spinal cord is critically dependent on networks of gene expression controlled by transcription factors, such as Nuclear Factor One X (NFIX). NFIX has been identified as an important factor in promoting astrocyte formation during embryonic mouse spinal cord development.
To gain a more comprehensive understanding of the transcriptional landscape controlled by NFIX within the developing spinal cord, here we performed microarray analysis on E14.5 wild-type and Nfix-/- mouse spinal cords, the age at which the expression of NFIX by neural progenitor cells lining the spinal central canal is strongest.

overall_design: Whole spinal cords from Nfix-/- mouse embryos at E14.5 (and wild-type littermate controls; n=4) were dissected for RNA extraction and hybridization on an Affymetrix Mouse Transcriptome Analysis microarray.

first: Elise

last: Matuzelski


title: Transcriptional profiling of human monocytes treated with indoxyl sulfate (IS) or p-cresyl sulfate (PCS)

city: Seoul

first: Hee Young

last: Kim

address: 103 Daehak-ro, Jongno-gu,

department: Department of Microbiology and Immunology

country: South Korea

institute: Seoul National University College of Medicine

summary:
End-stage renal disease (ESRD) is the final stage of chronic kidney disease, which is increasingly prevalent worldwide and is associated with the progression of cardiovascular disease (CVD). Indoxyl sulfate (IS) and p-cresyl sulfate (PCS), major uremic toxins, are major risk factors involved in the pathology of CVD via adverse effects on endothelial cells and immune cells. Thus, transcriptomic overview of uremic toxin-mediated genes in immune cells of ESRD patients is critical, but not yet fully known. We investigated the alteration of gene expressions and biological pathways mediated by major uremic toxins, in ESRD patients monocytes, via microarray analysis.
To explore uremic toxin-related transcriptional profiling in ESRD patient-derived monocytes, purified monocytes from healthy controls were treated with IS or PCS for 24 hr, followed by conducting microarray on these samples.

overall_design: Purified monocytes of healthy controls were treated with IS or PCS for 24 hr and then were subjected to microarray

first: Hee

middle: Y

first: Won-Woo

last: Lee


title: Charaterization of monocytes/macrophages function in Club cell regeneration after naphthalene injury in WT mice

last: Wang

summary: During repair phase after naphathalene injury 3 subsets of myeloid cells accumulate at the site of injury including P1 (monoyte), P2 (monocyte-derived macrophages and P3 (resident alternatively activated airway macrophages). To better understand the function of each subset in epithelial repair, myeloid cell subsets were flow-sorted from lungs of WT mice treated with naphtahelen for 6 days and RNA-seq analysis was performed

overall_design: C57Bl/6J female mice (9-10 weeks) were treatment with naphthalene at a dose of 200-250 mg/kg. On day 6, mice were euthanized and their lungs were collected and digested for myeloid cell sorting of P1 (CD11b+ ly6c+ cells), P2 (CD11b+ CD11c+ F4/80+ cells) and P3 (Siglrc-F+ CD206+ CD11c+ F4/80+ cells). then P1-P3 were RNAseq analysis.


title: IL-33-ST2 axis regulates myeloid cell differentiation and activation facilitating effective club cell regeneration

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

overall_design: Refer to individual Series


title: Global gene expression profiling in human cervical fibroblasts in the absence or presence of progesterone and/or interleukin-1 beta.

city: Columbus

first: Douglas

last: Kniss

state: Ohio

address: 395 W. 12th Ave

department: Obstetrics and Gynecology

institute: Ohio State University

summary: Preterm birth is an important unsolved clinical problem.  Despite advanced treatments, infants who survive prematurity remain at increased risk for permanent disabilities.  In approximately one-third of cases, prematurity is related to infection and/or inflammation, which renders hostile the normally receptive intrauterine environment.  Proinflammatory cytokines provoke up-regulation of genes that promote uterine contractions.  Using monolayer cultures of human cervical fibroblast cells as a model, we profiled the global pattern of gene expression in response to cytokine challenge.

overall_design: Using monolayer cultures of human cervical fibroblasts as a model, we profiled the global pattern of gene expression in response to progesterone in the absense or presence of cytokine (interleukin-1 beta) challenge. The cells were subjected to total RNA extraction, quantification, and evaluation, followed by hybridization on Affymetrix Human Transcriptome 2.0 arrays (Platform GPL17586). Three biological replicates were used (12 total samples).

first: William

middle: E

last: Ackerman

first: Taryn

last: Summerfield


title: pAgo-induced DNA interference protects bacteria from invader DNA [smDNA]

city: Moscow

first: Anton

last: Kuzmenko

email: dr.ant.kuz@gmail.com, antonk@img.ras.ru

address: Akademika Kurchatova square 2

country: Russia

institute: Institute of Molecular Genetics, Russian Academy of Sciences

summary: Members of the conserved Argonaute protein family use small RNA guides to find their mRNA targets to regulate gene expression and suppress mobile genetic elements in eukaryotes. Argonautes are also present in many bacterial and archaeal  species. Unlike eukaryotic proteins, several studied prokaryotic Argonautes use small DNA guides to cleave DNA, a process dubbed DNA interference. However, the natural functions and targets of DNA interference are poorly understood and the  mechanisms of DNA guide generation and target discrimination remain unknown. Here, we studied the in vivo activities of a bacterial Argonaute nuclease CbAgo and demonstrated that it induces cleavage of multicopy genetic elements, including plasmids, transposons and repetitive chromosomal loci. Generation of small DNA guides employed by CbAgo requires cooperation between its intrinsic endonuclease activity and the cellular double-strand break repair machinery. The mechanism of guide generation ensures that small DNA guides are enriched in sequences that target foreign DNA and endows CbAgo with capacity to eliminate plasmids and fight phage infection. Similar principles may underlie the specificity of self-nonself discrimination by diverse defense systems in prokaryotes.

overall_design: Investigation of the factors that influence loading of small DNA into CbAgo in Escherichia coli by NGS profiling of CbAgo-associated smDNA.

first: Anastasiya

last: Oguienko

first: Daria

last: Esyunina

first: Denis

last: Yudin

first: Mayya

last: Petrova

first: Alina

last: Kudinova

first: Olga

last: Maslova

first: Maria

last: Ninova

first: Sergei

last: Ryazansky

first: David

last: Leach

first: Alexei

last: Aravin

first: Andrey

last: Kulbachinskiy


title: pAgo-induced DNA interference protects bacteria from invader DNA [gDNA]

overall_design: The study was designed to explore the role of the cellular double-strand break repair machinery in CbAgo small DNA biogenesis process.


title: pAgo-induced DNA interference protects bacteria from invader DNA


title: FGFR4 is a regulator of tumor subtype differentiation in luminal breast cancer and metastatic disease

city: Chapel Hill

first: Charles

middle: M.

last: Perou

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Mechanisms driving tumor progression from less aggressive subtypes to more aggressive states represent key targets for breast cancer therapy. We identified a subset of Luminal A primary breast tumors to give rise to HER2-enriched (HER2E) subtype metastases, but remain clinically HER2 negative (cHER2-). By testing the unique genetic and transcriptomic features of these cases, we developed the hypothesis that fibroblast growth factor receptor 4 (FGFR4) drives this subtype switching. To evaluate this, we developed two FGFR4 genomic signatures using a PDX model treated with a FGFR4 inhibitor (BLU9931), which inhibited PDX growth in vivo. Examining patient outcomes in the METABRIC breast cancer cohort showed that the FGFR4-induced and FGFR4-repressed signatures each predicted overall survival (OS) (HR=6.30, P<0.0001; HR=0.33; P<0.0001, respectively). Multivariate analysis showed that the FGFR4-induced signature was also an independent prognostic factor beyond subtype and stage for OS (HR=2.34, P=0.014). Supervised analysis of 77 primary tumors with paired metastasis revealed that the FGFR4-induced signature was significantly higher in luminal/ER+ tumor metastases compared with their primaries. Finally, multivariate analysis demonstrated that the FGFR4-induced signature also predicted site-specific metastasis for lung, liver and brain, but not for bone or lymph nodes. These data identify a link between FGFR4-regulated genes and metastasis, suggesting a treatment options for FGFR4-positive patients, whose high expression is non-genetically determined.

overall_design: Single-Cell RNA-seq profiling WHIM11 PDX (patient-derived xenograft) tumor under three different experimental conditions. For therapeutic testing, tumors were allowed to progress to a diameter of 0.5-0.7 cm and tumor-bearing mice were assigned at random to one of three groups: untreated or control (WHIM11_SG334, WHIM11_SG362), BLU9931 treatment  (WHIM11_SG334, WHIM11_SG362) or BLU9931 treatment and drug released group (WHIM11_SG329, WHIM11_SG363). BLU9931 was administered at 0.6g of drug/Kg/day. The untreated group were sacrificed if tumors reached 1.5 mm in any direction and the tumors were collected and processed for single cell RNA sequencing (scRNAseq). Once tumors were established to be growing in the presence of BLU9931 (18 days) the tumors were also collected for scRNAseq. Finally, the third group of BLU9931 treatment was ceased for 14 days and processed in the same way for scRNAseq.

first: Susana

last: Garcia-Recio


title: Transcriptomic analysis of Nicotiana benthamiana plants infected with a plum pox virus (PPV) deletion mutant (P1Pro) that lacks the self-cleavage inhibitory domain of the P1 leader protease

city: Mutilva Baja

first: Junkal

last: Garmendia

address: Pamplona, 123

country: Spain

institute: Instituto de Agrobiotecnologia, Consejop Superior de Investigaciones Científicas

summary: Transcriptomes of wild-type Nicotiana benthamiana plants inoculated with plum pox virus (PPV) or the P1Pro clone, a PPV deletion mutant that lacks the self-cleavage inhibitory domain of the P1 leader protease; in addition, N. benthamiana nahG-expressing plants inoculated with P1Pro were analyzed to identify genes whose expression is altered by P1Pro infections but does not depend on salicylic acid signaling.

overall_design: Wild-type Nicotiana benthamiana plants and the N. benthamiana nahG-expressing line were inoculated with plum pox virus (PPV) or the P1Pro clone, a PPV deletion mutant that lacks the self-cleavage inhibitory domain of the P1 leader protease. Viral clones were delivered by Agrobacterium-mediated infection, and upper uninoculated leaves were collected at 14 days post-agroinoculation. For each experimental condition, three biological replicates (each sample was a pool of ≥ 2 infected plants) were used for transcriptomic analysis (RNA-seq).

first: Fabio

last: Pasin

last: San León

first: Juan

last: García


title: Transcriptomics analysis of FAM122A knockout and NC K562 cells

city: Shanghai

first: Jing

last: Chen

address: 280 South Chongqing Road

institute: Shanghai Jiao-Tong University School of Medicine

summary: To understand the molecular mechanism associated with increased erythroid differentiation upon FAM122A deletion, we performed RNA sequencing to examine the global gene expression profiling of FAM122A KO and NC K562 cells.

overall_design: The mRNA profiles of FAM122A knockout and NC K562 cells were generated by deep sequencing, in duplicate, using Illumina HiSeq platform.

first: Ying

last: Huang


title: The Hepatocyte Clock and Feeding Interdependently Control Chrono-Homeostasis of Multiple Liver Cell Types (single nuclei RNA-seq)

city: Houston

first: Dongyin

last: Guan

state: TX

address: 1 Baylor Plaza, ABBR

institute: Baylor College of Medicine

summary: Most cells in the body contain a cell autonomous molecular clock, but the requirement of peripheral clocks for circadian rhythmicity, and their effects on physiology, are not well understood. Here we show that deletion of core clock components REV-ERBa and b in adult mouse hepatocytes caused the loss of circadian rhythmicity of many liver genes, as expected, but also led to maintained and even gained rhythmicity of other genes without altering feeding behavior. The loss of REV-ERBs from hepatocytes leads to an exaggerated circadian rhythm of de novo lipogenesis and serum triglyceride levels. It is increasingly recognized that liver function is also influenced by non-hepatocytic cells, and remarkably the loss of REV-ERBs in hepatocytes remodeled the circadian transcriptomes of multiple cell types within the liver without altering their core clocks, indicating that hepatocytes communicated time signals to the non-hepatocytic cells. Finally, alteration of food availability, which is the dominant zeitgeber in the liver, demonstrated strong interdependence of the cell-autonomous hepatocyte clock mechanism and non-cell-autonomous environmental change. Together these studies reveal the interdependence of endogenous hepatocyte clocks and feeding entrainment on the regulation of circadian rhythms of multiple cell types in the liver.

overall_design: RNA sequencing in livers, isolated EC and KC of control and adult hepatocytes REV-ERB a/b double knockout cell, ATAC-seq in isolated EC and KC of control and adult hepatocytes REV-ERB a/b double knockout cell, single nuclei RNA-seq in control and adult hepatocytes REV-ERB a/b double knockout cell

last: Xiong

first: Trang

last: Trin

first: Yang

last: Xiao

first: Wenxiang

last: Hu

first: Chunjie

last: Jiang

first: Pieterjan

last: Dierickx

first: Cholsoon

last: Jang

first: Joshua

middle: D

last: Rabinowit

first: Mitchell

last: Lazar


title: The Hepatocyte Clock and Feeding Interdependently Control Chrono-Homeostasis of Multiple Liver Cell Types (ATAC-seq)


title: Charaterization club cell lineages in small airways of naïve WT mice

status: Public on Jul 29 2020

city: gaithersburg

first: Xiaotao

last: Qu

state: md

address: 1 medimmune way

summary: Mouse small airways are populated by different epithelial lineages that generate from club cell progenitors that can express IL-33 as alarmin which could be released after epithelial injury

overall_design: Small airways were dissected from the lungs of naïve mouse, After enzymatic digestion, immune cells were depleted and cells were analyzed by single cell RNAseq by focusing on epithelial lineages EpCaM+ Scgb1a1+ cells

first: Rania

last: Dagher


title: Next Generation Sequencing Analysis of Maize Wild Type (WT) and thk1 Mutants Transcriptomes

first: Hao

last: Wu

state: NY

address: 236 Tower Rd, Plant Science Building Room #236

summary: The thk1 mutant, causing multiple aleurone layers, disrupts the NOT1 scaffolding subunit of the CCR4-NOT regulatory complex and dysregulates genes involved in cell division, signaling, differentiation and metabolism.

overall_design: Transcriptomes of 19 DAP endosperm from WT (as reference) and mutants of two thk1 alleles, thk1-iso15 and thk1-iso17 were profiled and analyzed.  All were in a B73 inbred genetic background and 3 biological replicates were conducted for each.

first: Bryan

last: Gontarek

first: Gibum

last: Yi

first: Brandon

last: Beall

first: Anjanasree

last: Neelakandan

first: Bibechana

last: Adhikari

first: Rumei

first: Donald

middle: R

last: McCarty

first: Andrew

last: Severin

first: Philip

middle: W

last: Becraft


title: RNA sequencing analysis of anti-CD3/CD28 stimulated wild type-OT1 (WT) and Lrch1-/- -OT1 (KO) CD8+ T cells

first: Chang

last: Liu

address: 301, Yanchang Road

institute: Shanghai Tenth People's Hospital

summary: We report the differential gene expression between anti-CD3/CD28 stimulated WT and LRCH1-deficient CD8+ T cells. Improving cytotoxicity, proliferation and infiltration ability of CD8+ T cells is critical in T cell immunotherapies against tumors. This study has identified LRCH1 as a negative regulator of LAT-mediated TCR signal transduction, as LRCH1 inhibits LAT signalosome formation and facilitates the endocytosis of LAT on the plasma membrane. LRCH1-deficient CD8+ T cells are more proliferative and effective at pathogen control and tumor elimination. Importantly, CRISPR/Cas9-mediated knockout of LRCH1 in human T cells also increases IFN-γ production, cell proliferation and migration ability in vitro. These data suggest LRCH1 as a potential target to improve CD8+ T cell responses against tumor and pathogens.

overall_design: Splenic naïve CD8+ T cells from WT and Lrch1 KO mice were cultured with plate-bound anti-CD3 (2μg/ml) plus anti-CD28 (2μg/ml) for 12 hours. Total RNA was isolated with Trizol and subjected to RNA sequencing using an Illumina HiSeq-X-Ten sequencer.

first: Hongyan

last: Wang


title: Transcriptomic profiling of bovine ovarian cortical tissue cultured with FSH

city: Utrecht

first: Maria

middle: Belen

last: Rabaglino

address: Yalelaan 7

department: Population Health Science

country: Netherlands

institute: Utrecht University

summary: The objective of this study was to determine the transcriptomic effects of FSH stimulation in the bovine ovarian cortical tissue, including responses elicited by the preantral follicles within. Genes whose change in expression between groups was associated with FDR < 0.05 were considered differentially expressed genes (DEG). Results showed after 4 days of culture, there were 34 DEG between FSH- and vehicle-treated ovary; of those, 28 genes were upregulated and 6 were down-regulated in response to FSH. Time-course gene expression analysis identified 252 genes that changed over time in FSH- compared to the vehicle-treated ovary.

overall_design: Fragments of the cortical region were isolated from bovine ovaries. Follwing removal of antral follicles, cortical fragments were randomly assigned to not be cultured (day 0 control) or be cultured with recombinant human FSH (100 ng/ml) or a vehicle control (FSH diluent, i.e., water in culture medium) for 2 or 4 days. Three replicates were performed. Samples were submitted to 3'Tag RNA sequencing using Illumina HiSeq.

first: Juliana

middle: I

last: Candelaria

middle: B

first: Anna

last: Denicol


title: The Hepatocyte Clock and Feeding Interdependently Control Chrono-Homeostasis of Multiple Liver Cell Types (RNA-seq)

first: Dongyin

last: Guan

first: Ying

last: Xiong

first: Trang

last: Trin

first: Yang

last: Xiao

first: Wenxiang

last: Hu

first: Chunjie

last: Jiang

first: Pieterjan

last: Dierickx

first: Cholsoon

last: Jang

first: Joshua

last: Rabinowit

first: Mitchell

last: Lazar


title: ERBB2 drives YAP activation and EMT-like processes during cardiac regeneration

city: Rehovot

first: Eldad

last: Tzahor

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

summary: RNA-seq comparing WT and caERBB2 over expresising hearts with/out injury

overall_design: For this experiment, 4 animals for each experimental group were used (WT Sham, ERBB2 - OE Sham, WT MI, ERBB2 - OE MI). Truseq libraries were made and barcoded, and subsequently subjected to 60bp single read solexa illumine sequencing, using the Solexa HiSeq. For RNA analysis, Adapters were trimmed using the cutadapt tool. Following adapter removal, reads that were shorter than 40 nucleotides were discarded (cutadapt option –m 40). Reads were sub-sampled randomly to have 23M Reads. TopHat (v2.0.10) was used to align the reads to the mouse genome (mm10). Counting reads on mm10 RefSeq genes (downloaded from igenomes) was done with HTSeq-count (version 0.6.1p1) . Differential expression analysis was performed using DESeq2 (1.6.3). Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.

first: Kfir-Baruch

last: Umansky

first: Alla

last: Aharonov

first: David

last: Kain


title: Mouse embryonic stem cells (mESCs) differentiation towards ventral hindbrain neuronal cell types [d4.5, d5.5 and d6.5]

city: Stockholm

first: Johan

last: Ericson

address: Solnavägen 9

department: Cell and Molecular Biology

institute: Karolinska Instituet

summary: mESCs treated with retinoic acid (RA) and a Shh agonist (SAG) recapitulated ventral hindbrain development and produced a population of neural progenitors with a minor presence of other cell types.

overall_design: The differentiation in mESCs was induced by RA and SAG in monolayer condition. The sorted cells were collected at different timepoints (i.e., d4.5, d5.5, d6.5) and processed for RNA isolation and RNA-seq.

first: Zhanna

last: Alekseenko


title: Transcriptomic Atlas of Embryonic Human Heart Development

city: Farmington

first: Tara

middle: N

last: Yankee

state: CT

address: 400 Farmington Avenue

department: Genetics and Developmental Biology

institute: University of Connecticut Health Center

summary: Human heart tissue transcriptome was analyzed over a developmental period of 4-8 weeks post-conception. The analysis identifies several modules of co-expressed genes. These modules were tested for significance and disease relevance using other publically available data. This gene expression data was also integrated with the epigenetic data generated in this study to elucidate complex regulatory networks.

overall_design:
mRNA was extracted from extracted from human heart tissue from three replicates of 8 time points and coverted to cDNA for sequencing.
---------------------------------------
Author state "All Raw FASTQ files are being deposited in dbGAP".

first: Jennifer

last: VanOudenhove

first: Justin

last: Cotney


title: Robust intrathymic development of regulatory T cells in young NOD mice is rapidly restrained by recirculating cells

city: Toulouse

first: Joost

last: van Meerwijk

state: HG

address: CHU Purpan – BP 3028

country: France

institute: INSERM

summary: Regulatory T lymphocytes (Treg) play a vital role in the protection of the organism against autoimmune pathology. It is therefore paradoxical that comparatively large numbers of Treg were found in the thymus of type I diabetes‐prone NOD mice. The Treg population in the thymus is composed of newly developing cells and cells that had recirculated from the periphery back to the thymus. We here demonstrate that exceptionally large numbers of Treg develop in the thymus of young, but not adult, NOD mice. Once emigrated from the thymus, an unusually large proportion of these Treg is activated in the periphery, which causes a particularly abundant accumulation of recirculating Treg in the thymus. These cells then rapidly inhibit de novo development of Treg. The proportions of developing Treg thus reach levels similar to or lower than those found in most other, type 1 diabetes‐resistant, inbred mouse strains. Thus, in adult NOD mice the particularly large Treg‐niche is actually composed of mostly recirculating cells and only few newly developing Treg.

overall_design: Here we show the gene expression by RNAseq from regulatory T cells recirculating to the thymus, in NOD and B6, 3 weeks old mouse strains.

first: Julie

last: Darrigues

first: Jeremy

middle: C

last: Santamaria

first: Ariel

middle: O

last: Galindo-Albarrán

first: Ellen

last: Robey

first: Olivier

middle: P

last: Joffre

first: Paola

last: Romagnoli


title: FGFR4 is a key regulator of tumor subtype differentiation in luminal breast cancer and metastatic disease [set 1]

first: Charles

last: Perou

summary: Mechanisms driving tumor progression from less aggressive subtypes to more aggressive states represent key targets for breast cancer therapy. We observed that a subset of Luminal A primary breast tumors give rise to HER2-enriched (HER2E) subtype metastases, but remain clinically HER2 negative (cHER2-). By testing the unique genetic and transcriptomic features of these cases, we developed the hypothesis that FGFR4 drives this subtype switching. To evaluate this, we developed two FGFR4 signatures using a PDX model treated with a FGFR4 inhibitor (BLU9931), which inhibited PDX growth in vivo. Examining patient outcomes in the METABRIC breast cancer cohort showed that the FGFR4-induced and FGFR4-repressed signatures each predicted overall survival (OS) (HR=6.30, P<0.0001; HR=0.33; P<0.0001, respectively). Multivariate analysis showed that the FGFR4-induced signature was also an independent prognostic factor beyond subtype and stage for OS (HR=2.34, P=0.014). Supervised analysis of 77 primary tumors with paired metastasis revealed that the FGFR4-induced signature was significantly higher in luminal/ER+ tumor metastases compared with their primaries. Finally, multivariate analysis demonstrated that the FGFR4-induced signature also predicted site-specific metastasis for lung, liver and brain, but not for bone or lymph nodes. These data identify a link between FGFR4-regulated genes and metastasis, suggesting a treatment options for FGFR4-positive patients, whose high expression is non-genetically determined.

overall_design: There are 41 samples in this set. We analyzed 4 replicates of MCF7 and 4 replicates of T47D (both cell lines used as FGFR4 control group: low FGFR4 gene expression) plus 9 replicates of MCF7_FGFR4 and 4 replicates of T47D_FGFR4 (both cell lines used as FGFR4 Active group: high FGFR4 gene expression). As a second approach, we used 6 replicates of CAMA-1 and 4 replicates of MDA-MB-453 (both cell lines used as a FGFR4 Active group: high FGFR4 gene expression) and finally 6 replicates of CAMA-1 and 5 replicates of MDA-M-453 cell lines both treated with BLU9931 (both cell lines were used as control group: low FGFR4 gene expression).

first: Susana

last: Garcia-Recio

first: Joel

middle: S

last: Parker

first: Cheng

last: Fan

first: Kevin

last: Mott

first: Xiaping

last: He

first: Daniel

last: Hollern

first: Juan

last: Cejalvo

first: Fara

last: Brasó-Maristany

first: Patricia

last: Galván

first: Octavio

last: Burgués

first: Joan

last: Albanell

first: Federico

last: Rojo

first: Ana

last: Lluch

first: Eduardo

last: de Dueñas

first: Lisa

last: Carey

first: Aleix

last: Prat


title: FGFR4 is a key regulator of tumor subtype differentiation in luminal breast cancer and metastatic disease [set 2]

first: Charles

last: Perou

overall_design: There are 13 samples in this set. We analyzed 5 replicates of the untreated tumors (control) plus 4 replicates of the BLU9931 treated and Lapatinib treated PDX tumors. [set1]

last: Brasó-Maristan

last: Martinez de Dueñas

middle: M


title: FGFR4 is a key regulator of tumor subtype differentiation in luminal breast cancer and metastatic disease

overall_design: Refer to individual Series


title: AKT dependent NOTCH3 activation drives tumor progression in a model of mesenchymal colorectal cancer subtype

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen


title: AKT dependent NOTCH3 activation drives tumor progression in a model of mesenchymal colorectal cancer subtype [2015]

summary: Recently a consensus molecular subtype (CMS) classification of colorectal cancer (CRC) has been established that is based on the transcriptional rather than the genetic profile of an individual tumor and which may ultimately help to individualize CRC therapy. So far, however, the lack of appropriate animal models that faithfully recapitulate the different molecular subtypes impedes adequate preclinical testing of stratified therapeutic concepts. Here we demonstrate that constitutive AKT activation in intestinal epithelial cells markedly enhances colonic tumor invasion and metastasis in Trp53DIEC mice (Trp53ΔIECAktE17K) upon challenge with the carcinogen azoxymethane (AOM). Gene-expression profiling indicates that Trp53ΔIECAktE17K tumors closely resemble the human mesenchymal colorectal cancer subtype (CMS4), which is characterized by the poorest survival rate among the four consensus molecular subtypes of CRC. Trp53ΔIECAktE17K tumors are further characterized by a NOTCH pathway gene signature and a distinct cell autonomous upregulation of Notch3 in tumor epithelia while treatment of Trp53ΔIECAktE17K mice with a NOTCH3-inhibiting antibody reduces invasion and metastasis. Conversely, selective activation of NOTCH3 by overexpression of NOTCH3-IC in Akt wt tumor organoids strongly promotes development of metastasis in an orthotopic transplantation model. In CRC patients NOTCH3 expression correlates positively with tumor grading and the presence of lymph node as well as distant metastases and is specifically upregulated in CMS4 tumors. Therefore, we suggest NOTCH3 as a putative target for advanced CMS4 CRC patients.

overall_design: RNA was isolated from 1 whole colon tumor of 4 Trp53ΔIEC and 4 Trp53ΔIECAktE17K mice

first: Florian

last: Greten

first: Julia

last: Varga


title: AKT dependent NOTCH3 activation drives tumor progression in a model of mesenchymal colorectal cancer subtype [2016]

overall_design: Trp53ΔIECAktE17K mouse colon tumor organoids were transduced with a doxycycline-inducible conrtol hairpin (shRen) or 2 different hairpins against Notch3. Samples were analyzed 10 days after doxycycline induction in duplicates.


title: Single-cell transcriptomics of chimeric antigen receptor T-cell infusion products

status: Public on Jul 28 2020

first: Michael

last: Green

address: 1515 Holcombe Blvd, Unit 903

department: Lymphoma/Myeloma

institute: MD Anderson Cancer Center

summary: Single-cell RNA sequencing of residual cells from 24 CAR T-cell infusion products.

overall_design:
Single cell gene expression profiles for 24 samples from patients treated with CAR T-cell product.
Raw data are available through the European Genome-Phenome Archive: EGAR00002301477


title: CapID sequencing of 40 chimeric antigen receptor T-cell infusion products were reported

summary: Hybrid capture single-cell RNA sequencing of residual cells from 24 CAR T-cell infusion products.


title: Identification of an Anti-diabetic, Orally Available Small Molecule that Regulates TXNIP Expression and Glucagon Action

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

summary: Diabetes is characterized by hyperglycemia, loss of functional islet beta cell mass, deficiency of glucose-lowering insulin, and persistent alpha cell secretion of gluconeogenic glucagon. Still, no therapies that target these underlying processes are available. We therefore performed high-throughput screening of 300,000 compounds and extensive medicinal chemistry optimization and here report the discovery of SRI-37330, an orally bioavailable, non-toxic small molecule, which effectively rescued mice from streptozotocin- and obesity-induced (db/db) diabetes. Interestingly, in rat cells and in mouse and human islets, SRI-37330 inhibited expression and signaling of thioredoxin-interacting protein, which we have previously found to be elevated in diabetes and to have detrimental effects on islet function. In addition, SRI-37330 treatment inhibited glucagon secretion and function, reduced hepatic glucose production, and reversed hepatic steatosis. Thus, these studies describe a newly designed chemical compound that, compared to currently available therapies, may provide a distinct and effective approach to treating diabetes.

overall_design: High-throughput screening of 300,000 compounds and extensive medicinal chemistry optimization.

first: Anath

last: Shalev

first: Matt

last: Kanke


title: RNA-seq analysis of mRNA profiles in β-Gal-overexpressing, NIK-overexpressing, and NIK(KA)-overexpressing INS-1 832/13 cells

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

country: China

institute: Harbin Institute of Technology

summary:
Purpose: The goal of this study is to investigate how NIK regulates islet β-cell function.
Methods: mRNA profiles of β-Gal-overexpressing, NIK-overexpressing, and NIK(KA)-overexpressing INS-1 832/13 cells were generated by deep sequencing using an Illumina Hiseq platform. Paired-end clean reads were aligned to the rat reference genome (ftp://ftp.ensembl.org/pub/release-90/fasta/rattus_norvegicus/dna/) with TopHat (version 2.0.12), and the aligned reads were used to quantify mRNA expression by using HTSeq-count (version 0.6.1).
Conclusion: Our study represents the first detailed analysis of mRNA profiles in NIK-overexpressing and NIK(KA)-overexpressing INS-1 832/13 cells, generated by RNA-seq technology. Our results show that 471 genes were upregulated and 249 genes were downregulated following NIK overexpression. GO analysis indicated that the upregulated genes were primarily related to the immune response. KEGG pathway enrichment analysis showed that immune signaling pathways, including the TNF, NF-κB, antigen processing and presentation signaling pathways, were significantly activated by NIK overexpression in INS-1 832/13 cells, whereas genes related to insulin secretion and regulation of secretion were significantly decreased. NIK(KA), the dominant-negative mutant of NIK, does not induce the expression of genes related to immune response in INS-1 832/13 cells.

overall_design: mRNA profiles in β-Gal-overexpressing, NIK-overexpressing, and NIK(KA)-overexpressing INS-1 832/13 cells were generated by deep sequencing, in a single test, using Illumina

first: Xinzhi

last: Li


title: RNA-seq for DIMT1 wild-type and E85A mutant overexpression in DIMT1 heterozygous knockout HEK cells

city: philadelphia

first: Fange

last: Liu

state: PA

address: 415 curie blvd, Clinical Research Building Rm 350

country: USA

institute: UPENN

summary: Dimethyladenosine transferase 1 (DIMT1), an 18S rRNA N6,6-dimethyladenosine (m26,6A) methyltransferase, participates in ribosome assembly. However, whether the catalytic activity is of importance in ribosome assembly and other cellular processes are not fully understood. To better understand the role of DIMT1 catalysis in gene regulation and cellular function, we performed RNA-seq with purified poly(A)-RNA from DIMT1+/- + wild type cells and +E85A variant cells.

overall_design: RNA-seq in DIMT1 wild-type and E85A variant overexpression cells

first: Kathy

middle: F

first: Hui

last: Shen


title: Quantitative mapping of transcriptome dynamics during polarization of human iPSC-derived neurons

first: Robbelien

last: Kooistra

state: Utrecht

address: Padualaan 8

department: Cell Biology

summary: Early neuronal development is a well-coordinated process in which neuronal stem cells differentiate into polarized neurons. This process has been well studied in classical non-human model systems, but to what extent this is recapitulated in human neurons remains unclear. To study neuronal polarization in human neurons, we cultured human iPSC-derived neurons, characterized early developmental stages, measured electrophysiological responses, and systematically profiled transcriptomic and proteomic dynamics during these steps. We found extensive remodeling of the neuron transcriptome and proteome, with altered mRNA expression of ~1,100 genes and different expression profiles of ~1,500 proteins during neuronal differentiation and polarization. We also identified a distinct stage in axon development marked by an increase in microtubule remodeling and apparent relocation of the axon initial segment from the distal to proximal axon. Our comprehensive characterization and quantitative map of transcriptome and proteome dynamics provides a solid framework for studying polarization in human neurons.

overall_design: ~100,000 hiPSC-derived NPCs were plated per well for bulk RNA sequencing samples. Prior to sample preparation, all equipment and surfaces were cleaned with RNaseZap (Sigma-Aldrich). Replicates of hiPSC-derived neurons were harvested at three different timepoints of differentiation (days 1, 3, and 7) with 200 µl Trizol (Invitrogen) per sample and stored at -80 °C until sequencing. RNA extraction, cDNA library preparation (CEL-Seq2 protocol), quality control for aRNA and cDNA, and sequencing on a NextSeq500 High output 1x75 bp paired end run with 2% sequencing depth were performed by Single Cell Discoveries (Utrecht, The Netherlands).

first: Feline

last: Lindhout

first: Sybren

last: Portegies

first: Lotte

middle: J

last: Herstel

first: Riccardo

last: Stucchi

first: Basten

middle: L

last: Snoek

first: Maarten

last: Altelaar

first: Harold

last: MacGillavry

first: Corette

last: Wierenga

first: Casper

last: Hoogenraad


title: Presynaptic dysfunction in CASK-related neurodevelopmental disorders

status: Public on Jul 27 2020

city: Solna

first: Martin

last: Becker

address: Akademiska stråket 1

department: Department of Women's and Children's Health

country: Sweden

institute: Karolinska Institutet

summary: CASK-related disorders are a growing group of genetic neurodevelopmental syndromes. There is limited information about the effects of CASK mutations in human neurons. Therefore, we sought to delineate CASK mutation consequences and neuronal level effects using induced pluripotent stem cell-derived neurons from two mutation carriers; one male diagnosed with ASD and a female with MICPCH. We show a reduction of the CASK protein in maturing neurons from the mutation carriers, which leads to significant downregulation of gene sets involved in presynaptic development and CASK protein interactors. Furthermore, CASK-deficient neurons showed decreased inhibitory presynapse size as indicated by VGAT stainings, which may alter E/I balance in developing neural circuitries. Using in vivo magnetic resonance spectroscopy quantification of GABA in the male mutation carrier, we further highlight the possibility to validate in vitro cellular data in brain. Our data shows that future pharmacological and clinical studies on targeting presynapses and E/I imbalance could lead to specific treatments for CASK-related disorders.

overall_design:
Transcriptomes of two case and two control iPSC derived neuronal cultures were sequenced in quintuplicate
***The submitters are not legally permitted to submit the raw data to GEO or a restricted-access database such as dbGaP or EGA. Therefore, raw data is not provided.

first: Francesca

last: Mastropasqua

first: Jan

last: Reising

first: Simon

last: Maier

first: Mai-Lan

last: Ho

first: Ielyzaveta

last: Rabkina

first: Danyang

first: Janina

last: Neufeld

first: Lea

last: Ballenberger

first: Lynnea

last: Myers

first: Viveka

last: Moritz

first: Malin

last: Kele

first: Josephine

last: Wincent

first: Charlotte

last: Willfors

first: Rouslan

last: Sitnikov

first: Eric

last: Herlenius

first: Britt-Marie

last: Anderlid

first: Anna

last: Falk

first: Sven

last: Bölte

first: Kristiina

last: Tammimies


title: The effect of active YAP in neonatal heart of Xinβ knockout mice

city: Los Angeles

first: Yao Wei

last: Lu

state: CA

address: 2011 Zonal Ave

department: Department of Medicine

institute: University of Southern California

summary:
Purpose: The goals of this study are 1) to define the transcriptome changes in the heart in the absence of intercalated-disc protein Xinβ, and 2) to define the effect of active Yap overexpression on the cardiac transcriptome in the absence of Xinβ.
Methods: Total RNA from heart apex of postnatal day (P) 7.5 Xinβ KO or WT mice were profiled by bulk-RNA sequencing (50bp SE). Total RNA from heart apex of P7.5 Xinβ KO or WT mice injected with AAV9 carrying cardiac troponin T promoter driven active Yap (S127A) or GFP (control) at P1 were profiled by bulk-RNA sequencing (150bp PE). FASTQ files were extracted, and the TruSeq sequencing adapters and low-quality reads were removed from FASTQ files with Cutadapt v.2.3. The cleaned FASTQ files were quality checked using FastQC (Babraham Bioinformatics), then aligned to the mouse genome (Esembl GRCm38 genome obtained from GENCODE) using HISAT2 (v.2.1.0). Subsequently, transcript assembly was performed using StringTie (v.1.3.4) with the annotated transcriptome as a reference. The assembled transcriptomes were quantified using prepDE.py script provided by the StringTie developer to generate gene matrix files. EdgeR (v.3.26.1) was used to compute Counts Per Million (CPM) as a normalized measurement for gene expression. Differentially expressed genes were tested using the Fisher’s exact test, and multiplicity correction is performed with the Benjamini-Hochberg method on the p-values, to control the false discovery rate (FDR).
Results: We find that Xinβ knockout heart have changes on the transcriptome with hallmark of decrease proliferation etc. and subsets of the transcriptome alteration induced by the absence of Xinβ could be rescued by overexpressing active Yap in the neonatal mice.

overall_design: Total RNA from heart apex of postnatal day (P) 7.5 Xinβ KO or WT mice (n=4 for each group) were profiled by bulk-RNA sequencing (50bp SE). Total RNA from heart apex of P7.5 Xinβ KO or WT mice injected with AAV9 carrying cardiac troponin T promoter driven active Yap (S127A) or GFP (control) at P1 (n=4 for each group) were profiled by bulk-RNA sequencing (150bp PE).

first: Haipeng

last: Guo

first: Da-Zhi

last: Wang


title: Wild-type and TP53 genetic knockout BOBSC hiPS cells were maintained in the undifferentiated state or differentiated to definitive endoderm over 72 hours, with or without 5 ppm MMS treatment at 24 hours.

city: Cambridge

first: Alastair

last: Crisp

address: Francis Crick Avenue

institute: MRC Laboratory of Molecular Biology

summary: The ability of human induced pluripotent stem cells (hiPSCs) to differentiate in vitro to each of the three germ layer lineages has made them an important developmental model and tool for tissue engineering. Here we explore the impact of inducing DNA damage at different points during differentiation. We show that, during a critical window in this program, DNA damage diverts cells from an endodermal to mesodermal fate without significant upregulation of an apoptotic program. This change in transcriptional program is driven by p53: cells lacking p53 continue to differentiate towards endoderm with high efficiency despite significant genomic damage and G2/M cell cycle arrest. Thus, DNA damage-induced upregulation of p53 decreases the efficiency of hiPSC differentiation to definitive endoderm by diverting cells towards a mesodermal fate.

overall_design: On day -1 wild type and TP53-/- cells were passaged and on day 0 the sequencing experiment was started. Undifferentiated (UD) cells were cultured, in parallel to the differentiating (ENDO) cells, in Essential 8 Flex medium. RNA was extracted from both cell lines in the undifferentiated state and during differentiation every 24 hours. In parallel, both undifferentiated and differentiated cells were treated with 5 ppm MMS at 24 hours and the RNA was extracted at day 2 (48 hours) and day 3 (72 hours). This gives 20 conditions and there were three biological replicates of each condition.

first: Cara

last: Eldridge

first: Julian

last: Sale


title: The effect of African Swine Fever Virus infection on porcine host microRNAs

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

type: Non-coding RNA profiling by high throughput sequencing

summary: Large DNA viruses are known to manipulate and modify host miRNAs during infection. Therefore the aim of this study was to investigate the impact of infection with the large DNA virus; African swine fever virus (ASFV) on host miRNAs. Small RNA sequencing libraries were prepared from RNA extracted from ASFV (Benin 97/1) infected primary porcine macrophages at 0, 6 and 16 hours post infection. Libraries were pooled and sequenced on 1 lane of an Illumina HiSeq, yielding sequences aligning to a total of 247 different mature Sus scrofa miRNAs. On average, 3779095 (± 1911525) miRNA reads were obtained per sample. The results revealed no widespread modification to host miRNAs, though a number of specific miRNAs were differentially expressed during ASFV infection. Notably, a small number of miRNAs (Ssc-miR-10b, Ssc-miR-144 and Ssc-miR-486) were rapidly upregulated 2-6 fold within the first hour of infection.

first: Laura

last: Dunn

first: Pip

last: Beard


title: KAT7 maintains myeloid leukemogenesis recruits BRD4 to the promoters of target loci to maintain then MLL-AF9 transcriptional programme

first: Muxin

last: Gu

email: muxingu@gmail.com, mg445@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

institute: University of Cambridge

summary: Here we investigate the essentiality of lysine acetyltransferase KAT7 in AMLs driven by the MLL-X fusions. We find that KAT7 activity is required for the recruitment of the MLL-fusion associated adaptor proteins such as BRD4 to gene promoters, which are critical for the maintenance of the MLL-AF9 transcriptional programme. Our findings propose that KAT7 is a plausible therapeutic target for this poor prognosis subtype of AML.

overall_design: Study KAT7 binding and the effects of its knockout on the transcriptome in MOLM13 and OCIAML3 cell lines

first: Yanzi

last: Au

first: Etienne

last: DeBraekeleer

first: Malgorzata

last: Gozdecka

first: Demetrios

last: Aspris

first: Yusuke

last: Tarumoto

first: Jonathan

last: Cooper

first: Jason

last: Yu

first: Sweehoe

last: Ong

first: Xi

last: Chen

first: Konstantinos

last: Tzelepis

first: Brian

last: Huntly

first: George

last: Vassiliou

first: Kosuke

last: Yusa


title: GATA6-AS1 Regulates GATA6 Expression to Modulate Human Endoderm Differentiation

status: Public on Jul 26 2020

city: WuHan

first: Jie

last: Yang

state: Hubei Province

address: Donghu Road, No. 115

department: Medical Research Insitiute

institute: WuHan university

summary: Transcriptome analysis has uncovered a series of long noncoding RNAs (lncRNAs) transcribed during cell differentiation. Here, we uncovered lncRNA GATA6-AS1 is a functional lncRNA in definitive endoderm (DE) differentiation. We found GATA6-AS1 positively regulated the expression of endoderm key factor GATA6, which was different from previous reports in other biological contexts. Further investigation showed GATA6-AS1 interacted with SMAD2/3 and recruited SMAD2/3 to the promoter region of the GATA6 gene locus. In addition, overexpression of GATA6 was able to rescue the defect of DE differentiation due to the absence of GATA6-AS1, suggesting GATA6 was the functional target of GATA6-AS1 during endoderm differentiation. Ultimately, our study uncovers GATA6-AS1 is necessary for DE and pancreas differentiation, and reveals the detailed regulation mechanism between GATA6-AS1 and DE differentiation.

overall_design: We performed RNA-seq using ES-derived definitive endoderm cells and GATA6-AS1 knockdown definitive endoderm cells (three replicates for each).

first: Wei

last: Jiang


title: ATF4 regulates MYB to increase g-globin in response to loss of β-globin [ChIP-seq]

city: ZURICH

first: Jacob

middle: Corn

last: Lab

state: zURICH

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

summary: Boontanrart et al model the cellular stress that occurs upon reduction in β-globin in human erythroid cells. Decrease in β-globin attenuates the eIF2aP-ATF4 pathway and results in upregulating fetal -globin. Down-regulation of ATF4 leads to decreased levels of the -globin repressor MYB through direct binding at the HBS1L-MYB intergenic region.

overall_design: ATF4 ChIP-seq in HUDEP-2 and primary erythroid progenitors

first: Mandy

last: Boontanrart


title: ATF4 regulates MYB to increase g-globin in response to loss of β-globin [RNA-seq]

summary: Boontanrart et al model the cellular stress that occurs upon reduction in β-globin in human erythroid cells. Decrease in β-globin attenuates the eIF2aP-ATF4 pathway and results in upregulating fetal g-globin. Down-regulation of ATF4 leads to decreased levels of the g-globin repressor MYB through direct binding at the HBS1L-MYB intergenic region.

overall_design: RNA-seq of WT and HBBko HUDEP-2 cells


title: Loss of TMEM106B potentiates lysosomal and FTLD-like pathology in progranulin deficient mice [neuroinflammation panel]

status: Public on Jul 25 2020

city: Munich

first: Anja

last: Capell

state: Bavaria

address: Feodor-Lynen Str 17

department: Biomedical Center (BMC)

institute: Ludwig-Maximilians-University

summary: Polygenic risk factors influence onset and progression of neurodegenerative diseases, but are difficult to be functionally explored in isolation. Single nucleotide polymorphisms (SNPs) in TMEM106B increase the risk for frontotemporal lobar degeneration (FTLD) of GRN mutation carriers. Currently, it is not clear if progranulin (PGRN) and TMEM106B are synergistically linked and if a gain or a loss-of-function of TMEM106B is responsible for the increased disease risk of patients with PGRN haploinsufficiency. We therefore compared behavioral abnormalities, gene expression patterns, lysosomal activity and TDP-43 pathology in single and double knockout animals. Grn–/–/Tmem106b–/– mice showed a strongly reduced life span and massive motor deficits. Gene expression analysis revealed an upregulation of molecular signatures characteristic for disease associated microglia and autophagy. Dysregulation of maturation of lysosomal proteins as well as a pronounced accumulation of ubiquitinated proteins and wide spread p62 deposition suggest that proteostasis is impaired. Moreover, while single Grn–/– knockouts only occasionally showed TDP-43 pathology, the double knockout mice exhibit robust deposition of phosphorylated TDP-43. Thus, a loss-of-function of TMEM106B may enhance the risk for GRN-associated FTD by reduced protein turnover in the lysosomal/autophagic system.

overall_design: In this study we analyzed gene expression in total RNA isolated from whole brain of adult mice. We compared the expression profile of Tmem106b knockout mice , Grn knockout mice, and Grn/Tmem106b double knockout mice (for each genotype n=3, 4.5 months) to wild type mice (n=5, 4.5 months).

first: Georg

last: Werner


title: Loss of TMEM106B potentiates lysosomal and FTLD-like pathology in progranulin deficient mice [neuropathology panel]


title: Transcriptomic profiling of effects of emamectin benzoate on the pine wood nematode Bursaphelenchus xylophilus

city: Hangzhou

first: Xiang

last: Zhou

state: Zhejiang

address: No. 666 Wusu

institute: Zhejiang Agricultural and Forestry University

summary: to profile the adverse effects of an emamectin benzoate trunk-injection agent on pine wood nematode Bursaphelenchus xylophilus by analysing differential transcripts from the nematode whole genome through next-generation high-throughput sequencing.

overall_design: mRNA profiles of adult nematodes treated with either emamectin benzoate or ajuvaent for 12 h and 24 h were generated by deep sequencing , in triplicate, using Illumina HiSeq X Ten

first: Linlin

last: Pan


title: Brassica oleracea-Alternaria brassicicola interaction during the early stages of leaf infection

city: Poznan

first: Agnieszka

last: Zmienko

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

summary: Gene expression changes during the initial stages of black spot disease caused by Alternaria brassicicola on Brassica oleracea (Brassica oleracea var. capitata f. alba, white cabbage) leaves were investigated with Arabidopsis thaliana oligonucleotide microarrays. Transcriptional profiling of infected B. oleracea leaves revealed that photosynthesis was the most negatively regulated biological process. The negative regulation of 6 photosynthesis-related genes, mainly the genes involved in the photosynthesis light reaction and Calvin cycle, was observed as early as 12 hours post infection (hpi). It progressed through 48-hpi stage, when 44 down-regulated photosynthesis-related genes were detected. The analyses of infected leaves at microscopic, ultrastructural and physiological levels supported the microarray-based observations and indicated that the photosynthetic processes  are suppressed in B. oleracea as a result of the fungal infection.

overall_design: Time-course experiment, two-color, common reference design, involving two biological replicates for each time point. Samples represent plant leaves harvested before infection (0hpi) and at different time points post infection with fungus (12h, 24h and 48h). Each biological replicate sample was prepared from leaves harvested from three plants. Cy-5 labeled samples for each time point and each replicate were individually hybridized to Cy3-labeled  common reference (representing pooled RNA samples from mock-treated plants, harvested at the same time points as infected plants), on a total of 8 microarrays.

first: Violetta

last: Macioszek


title: Meningeal lymphatic dysfunction exacerbates traumatic brain injury pathogenesis

city: Charlottesville

first: Ashley

middle: Catherine

last: Bolte

state: Virginia

address: 409 Lane Road MR4

department: Neuroscience

institute: University of Virginia

summary: The goal of this study is to use bulk RNA-sequencing of the right brain hemisphere to observe the effects of TBI in the context of pre-existing meningeal lymphatic dysfunction in mice. We find that pre-existing meningeal lymphatic dysfunction potentiates the inflammatory response to TBI, suggesting an important role for the meningeal lymphatics in injury site drainage and proper recovery.

overall_design: Mice were subjected to an injection of Visudyne or vehicle i.c.m., and 15 minutes later a red laser was directed at 5 spots along the sinuses through the skull. After a week of rest, mice received TBI or a sham procedure. 24 hours after injury, RNA was isolated from homogenized brains. Bulk RNA sequencing was performed on 4 experimental groups with 4 samples per group (Not Ablated + Sham, Ablated + Sham, Not Ablated + TBI, Ablated + TBI).

first: Arun

last: Dutta

first: Mariah

middle: E

last: Hurt

first: Igor

last: Smirnov

first: Michael

middle: A

last: Kovacs

first: Celia

last: McKee

first: Hannah

last: Ennerfelt

first: Daniel

last: Shapiro

first: Bao

middle: H

last: Nguyen

first: Elizabeth

last: Frost

first: Catherine

last: Lammert

first: Jonathan

last: Kipnis

first: John

last: Lukens