title: A Highly Predictive MicroRNA Panel for Determining Delayed Cerebral Vasospasm Risk Following Aneurysmal Subarachnoid Hemorrhage

city: Lexington

first: Wang-Xia

state: Kentucky

address: 800 S Limestone

institute: University of Kentucky

summary: Approximately one-third of aneurysmal subarachnoid hemorrhage (aSAH) patients develop delayed cerebral vasospasm (DCV) 3-10 days after aneurysm rupture resulting in additional, permanent neurologic disability. Currently, no validated biomarker is available to determine the risk of DCV in aSAH patients. MicroRNAs (miRNAs) have been implicated in virtually all human diseases, including aSAH, and are found in extracellular biofluids including plasma and cerebrospinal fluid (CSF). We used a custom designed TaqMan Low Density Array miRNA panel to examine the levels of 47 selected brain and vasculature injury related miRNAs in CSF and plasma specimens collected from 31 patients with or without DCV at 3 days and 7 days after aSAH, as well as from 8 healthy controls. The analysis of the first 18-patient cohort revealed a striking differential expression pattern of the selected miRNAs in CSF and plasma of aSAH patients with DCV from those without DCV. Importantly, this differential expression was observed at the early time point (3 days after aSAH), before DCV event occurs. Seven miRNAs were identified as reliable DCV risk predictors along with a prediction model constructed based on an array of additional 19 miRNAs on the panel. These chosen miRNAs were then used to predict the risk of DCV in a separate, testing cohort of 15 patients. The accuracy of DCV risk prediction in the testing cohort reached 87%. The study demonstrates that our novel designed miRNA panel is an effective predictor of DCV risk and has strong applications in clinical management of aSAH patients.

overall_design: Cerebral spinal fluid (CSF) and plasma from a total of 31 aSAH patients and 8 controls were analyzed in 3 separated groups according to the availability of the specimens at the time of analysis. GroupA included 18 aSAH patients (10 DCV-, 8 DCV+) and 8 healthy controls (HCs). GroupB included 9 aSAH patients including 2 experimental duplicates from GroupA. GroupC included 6 aSAH patients.

first: Joe

last: Springer

first: Kevin

last: Xie

first: David

last: Fardo

last: Hatton


title: Deconvoluting ACS1 retrograde signaling networks that regulate leaf development

status: Public on Jun 02 2021

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

country: USA

institute: Donald Danforth Plant Science Center

type: Expression profiling by high throughput sequencing

summary: Signals originating within plastids modulate organelle differentiation by transcriptionally regulating nuclear-encoded genes. These retrograde signals are also integral regulators of plant development, including leaf morphology. The clb5 mutant displays severe leaf morphology defects due to Apocarotenoid Signal 1 (ACS1) accumulation in the developmentally arrested plastid. Transcriptomic analysis of clb5 validates ACS1 as a true retrograde signal impacting expression of hundreds of nuclear genes, including suppression of most genes encoding plastid ribosomal proteins.

overall_design: Examination of Arabidopsis mutant leaves and cotyledons; three replicates of six genotypes or stages were analyzed by RNA-seq.

first: Lina

last: Escobar-Tovar

first: Julio

last: Sierra

first: Arihel

last: Hernández-Muñoz

first: Sandra

middle: M

last: Mathioni

first: Elizabeth

last: Cordoba

first: Ryan

middle: P

last: McQuinn

middle: C

first: Barry

middle: J

last: Pogson

first: Patricia

last: León


title: Loss of DLX3 tumor suppressive function promotes progression of SCC through EGFR-ERBB2 pathway.

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: Emerging evidence suggests that homeoproteins can act as modulators of tumor initiation and progression. Our findings show that loss of DLX3 tumor suppressive function acts as a tumor promoter through regulation of ERBB2 and EGFR signaling and also support an important inhibitory role of DLX3 in skin cancer promotion and progression, that may potentially be used as a promising prognostic marker.

overall_design: This dataset includes RNA-seq data from five tumors and, skin tissues from three treated Wild Type and DLX3cKO mice. Molecular evaluation of the DLX3cKO tumor-permissive properties was done by performing RNAseq on tumors, DLX3cKO unaffected whole skin, and WT skin from the triple dose DMBA-only protocol. We compared differentially expressed genes (DEG) from DLX3cKO/WT treated skins against Tumor/DLX3cKO skin.

first: D

last: Bajpai

first: S

last: Mehdizadeh

first: A

last: Uchiyama

first: Y

last: Inoue

last: Sawaya

last: Overmiller

first: M

last: Kellett

first: E

last: Palazzo

last: Motegi

middle: H

last: Yuspa

first: C

last: Cataisson

middle: I

last: Morasso


title: Epigenome analysis of cirrhosis and dysplastic liver samples

city: New York

first: Gabriela

last: Hernandez-Meza

state: New York

address: 1 Gustave L. Levy Place

institute: Mount Sinai

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of cirrhosis and dysplastic liver samples. The Illumina Infinium 450k Human DNA methylation BeadChip was used to obtain DNA methylation profiles across approximately 485,577 CpGs sites. Samples included 130 cirrhosis and 8 exhibiting dysplasia. The manuscript includes an integrative analysis of these samples along with samples from normal liver and HCC already deposited under GSE63898.

overall_design: Bisulphite-converted DNA from the 138 samples were hybridised to the Illumina Infinium 450k Human Methylation BeadChip.

first: Augusto

last: Villanueva


title: Genome-wide mapping of histone modifications in two species of Leptosphaeria maculans showing contrasting genomic organization and host specialization

city: Thiverval-Grignon

first: Jessica

middle: Louise

last: SOYER

address: Avenue Lucien Brétignières

department: SPE

country: France

institute: INRAE

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism: Plenodomus lingam/Leptosphaeria maculans 'brassicae' group

sample_organism: Plenodomus lingam/Leptosphaeria maculans 'lepidii' group

overall_design: Refer to individual Series


title: The landscape of mouse epididymal cells defined by the single-cell RNA-Seq

city: Nantong

first: Gangcai

last: Xie

state: Jiangsu

address: Number 9, Se Yuan Road

department: Medical school

country: China

institute: Nantong University

summary: We reported the cell composition and segmental expression differences in three epididymis segments using single-cell RNA sequencing. A total of 13,949 cells were detected, which were further clustered into eight cell populations identified with all known constituent cells of mouse epididymis including principle cell, basal cell, clear/narrow cell and immune cells. Through the study of 35 known epididymal proteins linking to sperm function phenotypes (EPSFPs), we found they were mainly expressed in principle cells and also revealed their segmental specific expression patterns. Notably, a part of EPSFPs was associated with sperm protection and predominantly localized in caput principal cells, whereas some EPSFPs, highly expressed in corpus and cauda, were served as the regulating molecular for the sperm functions such as motility, capacitation or acrosome reactions.In addition, focused analyses uncovered 5 subtypes of the principal cell. Intriguingly, Prc5, the subpopulation of principle cells, was almost only existed in the caput epididymis.

overall_design: 56 days old of wild-type C57Bl/6J mice were sacrified, then the epididymis were dissected and divided into three regions (caput, corpus, and cauda)

first: Hao

last: Chen


title: Genome-wide maps of H3K9me3, H3K27me3 and H3K4me2 in two species of Leptosphaeria maculans during vegetative growth

summary: In plant-associated fungi, the role of the epigenome is increasingly recognized as an important regulator of genome structure and of the expression of genes involved in the interaction(s) with the host plant. Two closely-related phytopathogenic species, Leptosphaeria maculans ‘brassicae’ (Lmb) and L. maculans ‘lepidii’ (Lml) exhibit a large conservation of genome synteny but contrasted genome structure. Lmb has undergone massive invasion of its genome by transposable elements summing up one third of its genome and clustered in large TE-rich regions on chromosomal arms, while Lml genome has a low amount of repeats (3% of the genome). Previous information also showed that the TE-rich regions of Lmb host a few species-specific effector genes, expressed during plant infection, with main incidence on the adaptive potential of the fungus. The distinct genome organisation between Lmb and Lml thus provides us with a model of choice for the comparison of the epigenomic organization in two closely related phytopathogenic fungi, in order to investigate pathogenicity/effector gene landscape with respect to the chromatin landscape. To address this, we performed chromatin immunoprecipitation, targeting either histone modifications typical for heterochromatin or euchromatin, during axenic culture, combined with transcriptomic analysis to analyse the influence of the chromatin organisation on gene expression. Our data comfort in both species the postulate that facultative heterochromatin landscapes, associated with H3K27me3 domains, are enriched in genes with no annotation, including numerous candidate effector and species-specific genes. Notably orthologous genes located in the same H3K27me3 domains are enriched in genes encoding putative proteinaceous and metabolic effectors. These genes are mostly silenced in vegetative growth conditions and are likely to be involved in interaction with the host. Compared to other fungal species, including Lml, Lmb has the particularity to have large H3K9me3-domains within chromosomal arms, strongly associated to TEs, and hosting numerous species-specific effector-encoding genes. These two distinct heterochromatin landscapes hosting genes involved in interaction with the host now questions their involvement in regulation of pathogenicity, the dynamics of the domains during plant infection, and the selective advantage for the fungus to host effector genes in H3K9me3 or H3K27me3 domains.

platform_organism: Plenodomus lingam/Leptosphaeria maculans 'brassicae' group

platform_organism: Plenodomus lingam/Leptosphaeria maculans 'lepidii' group

overall_design: Analysis of the location of three distinct histone modifications during vegetative growth of two fungal species

middle: L

last: Soyer

first: Colin

last: Clairet

first: Elise

last: Gay

first: Nicolas

last: Lapalu

first: Thierry

last: Rouxel

first: Eva

last: Stukenbrock

first: Isabelle

last: Fudal


title: Role of Prdm16 in fibro-adipogenic progenitors

city: Rome

first: Chiara

last: Mozzetta

address: P.le Aldo Moro 5

department: IBPM

country: Italy

institute: CNR

summary: Here, we identified Prdm16 as a FAPs-enriched factor that mediates their developmental capacities by modulating H3K9me2-marked heterochromatin organization at the nuclear lamina. We show that deletion of Prdm16 prevents FAPs adipogenic differentiation and unlocks a myogenic capacity. We found that Prdm16 localizes at the nuclear lamina where it cooperates with the H3K9 methyltransferases (KMTs), G9a and GLP, to mediate H3K9me2 deposition.

overall_design: RNA-seq, H3K9me2 and LaminB1 ChIP-seq, in FAPs isolated from Prdm16Flox/Flox::PdgfrαCre-ERT/+ (Prdm16) and control Prdm16Flox/Flox::Pdgfrα+/+ (WT) mice.

first: Daniel

last: Fernande-Perez


title: Gene expression profile in MS medium for the phytopathogenic fungus Leptosphaeria maculans brassicae (Lmb) and lepidii (Lml)

summary: Full transcriptomes of Leptosphaeria maculans ‘brassicae’ v23.1.3 and Leptosphaeria maculans ‘lepidii’ IBCN84, grown in Fries medium, were studied.

overall_design: Leptosphaeria maculans ‘brassicae’ v23.1.3 and Leptosphaeria maculans ‘lepidii’ IBCN84 were grown in modified liquid Fries medium. 3 replicates were performed. The 6 total-RNA samples were used for RNA-SEQ sequencing.

first: Adeline

last: Simon

first: Muriel

last: Viaud

first: Enric

last: Zehraoui

first: Berengere

last: Dalmais

first: Nadia

last: Ponts


title: Expression data from Capsicum annuum inoculated with Fusarium oxysporum Fo47

city: A Coruña

first: Javier

last: Veloso

state: A Coruña

address: Campus da Zapateira s/n

country: Spain

institute: Universidad de A Coruña

summary:
The colonization of Capsicum annuum roots by Fusarium oxysporum Fo47 induces resistance responses on the plant. Fo47 is a non-pathogenic strain of Fusarium oxysporum. Fo47 colonizes only the most outer layers of the root surface but it does not colonize inner tissues. Pre-treatment of roots with Fo47 reduces the symptom development produced by later pathogen inoculation. The expression of genes in distal tissues was determined by microarray analysis of stems of Fo47-treated plants.
Capsicum annuum samples were analyzed using Affymetrix chips of the close-related species Solanum lycopersicum.

overall_design: Samples of Capsicum annuum stems were collected 48 h after inoculation with Fo47 and homogenized in mortar cooled with liquid nitrogen. Total RNA was extracted from the homogenized samples. Total RNA samples were prepared following the protocol of the Affymetrix GeneChip® 3’ IVT Express Kit and then hybridized following the steps of the protocol of the GeneChip® Hybridization, Wash, and Stain Kit. Control plants were inoculated with water (Co) and collected at the same time than Fo47-treated plants (47).

first: José

last: Díaz


title: Spatial RNA-seq data comparing lesional (papules) and non-lesional skin biopsies of acne patients

status: Public on Jun 01 2021

city: Los Angeles

first: Tran

middle: Hue

last: Do

state: CA

address: 615 Charles E Young Dr

institute: David Geffen School of Medicine

summary: We collected RNA from a 20µm thick frozen section of an acne lesion into 55µm wells containing spatially-barcoded capture oligonucleotides and performed transcriptome analysis. We detected 394 spatially defined spots with an average of 1,349 genes and 2,950 transcripts per spot.

overall_design: Examine the transcriptomics differences in acne lesional and non-lesional skin based on histological slide.

first: Chanyue

last: Hu

first: Olesya

last: Plazyo

first: Johann

middle: E

last: Gudjonsson

first: Matteo

last: Pellegrini

first: Robert

last: Modlin


title: A human mutation in STAT3 promotes type 1 diabetes through a defect in CD8+ T cell tolerance

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University


title: A human mutation in STAT3 promotes type 1 diabetes through a defect in CD8+ T cell tolerance [scATAC]

summary: scATAC-seq datasets of immune cells in K392R and WT mice

first: Jeremy

last: Warshauer

first: Quanming

last: Shi


title: Function and Mechanism of METTL5-mediated 18S rRNA m6A1832 modification in hepatocellular carcinoma

city: Guangzhou

first: Shuibin

last: Lin

state: China

address: Zhongshan 2nd road, Guangzhou

department: Clincial for Translational Medicine

institute: The First Affliliated Hospital, Sun Yat-sen University

summary: Tumor recurrence is main pattern of treatment failure for early-stage hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying disease recurrence remain poorly understood. Here, we showed that 18S rRNA N6-methyladenosine (m6A1832) modification and its methyltransferase complex METTL5/TRMT112 were upregulated in HCC and correlated with poor prognosis. Loss-of-function and gain-of-function assays demonstrated that METTL5/TRMT112 mediated 18S rRNA m6A1832 modification promotes HCC tumorigenesis in vitro and in vivo. Mechanistically, 18S rRNA m6A1832 modification selectively regulated the translation of mRNAs with long 5’UTR and short 3’UTR through affecting the assembly of 80S subunit at translation initiation and its dissociation at translation termination which was executed by weakening the interaction of ABCE1 with eRF1 and eRF3. Moreover, METTL5-mediated 18S rRNA m6A1832 modification regulated β-oxidation of long-chain fatty acid through ACSL4 to promote HCC progression. Our work uncovered a novel layer of mRNA translation regulation mechanism at ribosome 80S subunit assembly and dissociation step mediated by 18S rRNA m6A1832 modification and revealed a new crosslink between RNA epigenetic modification and fatty acid metabolism in HCC.

overall_design: Ribo-seq was used to study the differential translated genes in the METTL5 knockout and control cells.

first: Hao

last: Peng


title: Neuroinflammation creates an immune regulatory niche at the meningeal lymphatic vasculature near the cribriform plate

city: Madison

first: Zsuzsanna

last: Fabry

state: WI

address: 1111 Highland Ave.

department: Pathology and Laboratory Medicine

institute: University of Wisconsin Madison

summary: We report the use of single cell RNA sequencing of meningeal lymphatic endothelial cells near the cribriform plate in both naïve mice, and during experimental autoimmune encephalomyelitis (EAE), a mouse model of multiple sclerosis.  By sorting for meningeal lymphatics near the cribriform plate, we identified that these lymphatic endothelial cells acquire an altered phenotype during neuroinflammation, where they become enriched in genes involved in leukocyte crosstalk including adhesion molecules, antigen processing and presentation, and tolerance, thus becoming a unique site of immune regulation.

overall_design: Meningeal lymphatics near the cribriform plate were FACS sorted as Podoplanin+ CD31+ after excluding CD45+ leukocytes, doublets, and Ghost+ dead cells.  Cells were pooled from 5 healthy mice and compared to pooled cells from 5 EAE mice.

first: Hsu

last: Martin

first: Laaker

last: Collin

first: Madrid

last: Andy

first: Herbath

last: Melinda

first: Choi

last: Yun Hwa

first: Sandor

last: Matyas

first: Fabry

last: Zsuzsanna


title: Genome-wide analysis of SHOX targets in NHDF cells expressing SHOX WT vs SHOX HM mutant

city: Heidelberg

first: Sandra

last: Hoffmann

address: Im Neuneheimer Feld 366

department: Human Molecular Genetics

country: Germany

institute: University of Heidelberg

summary: To elucidate the underlying molecular mechanisms and to better understand the broad phenotypic spectrum of SHOX deficiency, we aimed to identify novel SHOX targets. We analyzed differentially expressed genes in SHOX-overexpressing human fibroblasts (NHDF)

overall_design: Total RNA obtained from SHOX WT and SHOX HM overexpressing NHDF cells after 6,12 and 24 hours of transfection

first: Ralph

last: Roeth


title: Next Generation Sequencing of wild-type HEK293 cells compared to STAT5b knock-out HEK293 cells using Crispr/Cas9

city: Paris

first: Aïssata

last: NIASSE

address: 4 rue de la Chine

institute: INSERM

summary: During kidney diseases, diverse tissue-specific pathways can regulate kidney injury and prognosis. In our study, we focused on STAT5, a member of the Janus Kinase/ Signal Transducer and Activator of Transcription (JAK/STAT) pathway, classically described in immune cells which has been recently described in intrinsic kidney cells. STAT5 activation is detected in both human podocytes and tubular cells in FSGS and ATI, respectively. Additionally, STAT5 deficiency in either glomerular or tubular epithelium aggravates the functional and structural alterations in a range of experimental models of glomerular or tubular disease. Using RNA sequencing, we show here that STAT5b inactivation in HEK-293 cells resulted in dysregulation of multiple metabolic pathways, including glycolysis and oxidative phosphorylation. In conclusion, activating renal epithelial STAT5 represents a new therapeutic avenue with the potential for a range of beneficial effects in kidney disease.

overall_design: 6 samples were used for this analysis : 3 HEK293 wildtype (WT) cells and 3 HEK293 knock-out (KO)

first: Yosu

last: Luque

last: Niasse


title: Core Circadian Clock Genes Per1 and Per2 regulate the Rhythm in Photoreceptor Outer Segment Phagocytosis [Photoreceptor]

city: Tampere

first: Nemanja

last: Milicevic

address: Arvo Ylpon katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: Retinal photoreceptors undergo daily renewal of their distal outer segments, a process indispensable for maintaining retinal health. Photoreceptor Outer Segment (POS) phagocytosis occurs as a daily peak, roughly about one hour after light onset. However, the underlying cellular and molecular mechanisms which initiate this process are still unknown. Here we show that, under constant darkness, mice deficient for core circadian clock genes (Per1 and Per2), lack a daily peak in POS phagocytosis. By qPCR analysis we found that core clock genes were rhythmic over 24h in both WT and Per1, Per2 double mutant whole retinas. More precise transcriptomics analysis of laser capture microdissected WT photoreceptors revealed no differentially expressed genes between time-points preceding and during the peak of POS phagocytosis. By contrast, we found that microdissected WT retinal pigment epithelium (RPE) had a number of genes that were differentially expressed at the peak phagocytic time-point compared to adjacent ones. We also found a number of differentially expressed genes in Per1, Per2 double mutant RPE compared to WT ones at the peak phagocytic time-point. Finally, based on STRING analysis we found a group of interacting genes which potentially drive POS phagocytosis in the RPE. This potential pathway consists of genes such as: Pacsin1, Syp, Camk2b and Camk2d among others. Our findings indicate that Per1 and Per2 are necessary clock components for driving POS phagocytosis and suggest that this process is transcriptionally driven by the RPE.

overall_design: Gene expression profiles of microdissected wild type (WT) and Per1-/-Per2Brdm1 (KO) mouse photoreceptors (PR) obtained at four time points (CT19, CT22, CT1 and CT10; CT: circadian time) over a 24h cycle

last: Milićević

first: Aldo

last: Jongejan

first: Perry

middle: D

last: Moerland


title: Core Circadian Clock Genes Per1 and Per2 regulate the Rhythm in Photoreceptor Outer Segment Phagocytosis


title: Heterogeneous immune cell types modulate the neonatal lung response to hyperoxia

city: Kensington

first: Fabio

last: Zanini

state: NSW

address: High and Botany St

country: Australia

institute: University of New South Wales

summary: During the first days of life, the lung surface area increases explosively to enable efficient oxygen exchange. Perturbations to the neonatal environment can profoundly affect the abundance, gene expression, organisation, and function of lung cells. Here, we build upon previous experiments and exposed newborn mice to 80% oxygen for the first seven days of life, followed by single cell transcriptomics of immune cells.

overall_design: scRNA-Seq on FACS sorted cells

first: Xibing

last: Che

first: Nina

last: Suresh

first: Carsten

last: Knutsen

first: Min

last: Liu

first: Racquel

last: Domingo-Gonzales

first: Robert

last: Jones

first: Paula

last: Klavina

first: Yike

last: Xie

first: Stephen

last: Quake

first: Cristina

last: Alvira

first: David

middle: N

last: Cornfield


title: Noncanonical mRNA decay by the endoplasmic-reticulum stress sensor IRE1-alpha promotes cancer cell survival [RNA-seq]

city: South San Francisco

first: Thomas

middle: D.

last: Wu

address: 1 DNA Way

institute: Genentech, Inc.

summary: Eukaryotic IRE1 mitigates endoplasmic-reticulum (ER) stress by orchestrating the unfolded-protein response (UPR). IRE1 spans the ER membrane, and signals through a cytosolic kinase-endoribonuclease module. The endoribonuclease generates the transcription factor XBP1s by intron excision between similar RNA stem-loop endomotifs, and depletes select cellular mRNAs through regulated IRE1-dependent decay (RIDD). Paradoxically, mammalian RIDD seemingly targets only mRNAs with XBP1-like endomotifs, while in flies RIDD exhibits little sequence restriction. By comparing nascent and total IRE1α-controlled mRNAs in human breast cancer cells, we discovered not only canonical endomotif-containing RIDD substrates, but also many targets lacking recognizable motifs—degraded by a process we coin RIDDLE, for RIDD lacking endomotif. IRE1α displayed two basic endoribonuclease modalities: endomotif-specific cleavage, minimally requiring dimers; and endomotif-independent promiscuous processing, requiring phospho-oligomers. An oligomer-deficient mutant that did not support RIDDLE failed to rescue cancer-cell viability. These results link IRE1α oligomers, RIDDLE, and cell survival, advancing mechanistic understanding of the UPR.

overall_design: RNAseq in MDAMB231 cells WT and IRE1 KO, during triggered ER stress (Thapsigargin for 8h). This dataset is used to identified genome wide IRE1 RIDD targets (n=3 per group).

first: Adrien

last: Le Thomas

first: Elena

last: Ferri

first: Scot

last: Marsters

first: Jonathan

last: Harnoss

first: Zora

last: Modrusan

first: Weihan

last: Li

first: Joachim

last: Rudolph

first: Weiru

last: Wang

first: Peter

last: Walter

first: Avi

last: Ashkenazi


title: RNA sequencing analysis of SczA-deficient Streptococcus agalactiae during Cu intoxication

city: Gold Coast

first: Glen

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

institute: Griffith University

summary: Total RNA was isolated from mid-log phase Streptococcus agalactiae cells deficient in SczA (∆sczA strain GU2791), grown in Todd-Hewitt broth (THB) medium supplemented with 0.5 mM Cu and sequenced using Illumina NextSeq500.

overall_design: Four biological replicate cultures of S. agalactiae deficient in SczA (∆sczA strain GU2791) were grown in THB + 0.5 mM Cu.


title: Noncanonical mRNA decay by the endoplasmic-reticulum stress sensor IRE1-alpha promotes cancer cell survival [GRO-seq]

overall_design: GROseq in MDAMB231 cells WT and IRE1 KO, during triggered ER stress (Thapsigargin for 8h). This dataset is used to identified genome wide IRE1 RIDD targets (n=3 per group).


title: RNA sequencing analysis of SczA-deficient Streptococcus agalactiae during Zn intoxication

summary: Total RNA was isolated from mid-log phase Streptococcus agalactiae cells deficient in SczA (∆sczA strain GU2791), grown in Todd-Hewitt broth (THB) medium supplemented with 0.25 mM Zn and sequenced using Illumina NextSeq500.

overall_design: Four biological replicate cultures of S. agalactiae deficient in SczA (∆sczA strain GU2791) were grown in THB + 0.25 mM Zn.


title: RNA sequencing analysis of CopY-deficient Streptococcus agalactiae during Cu stress

summary: Total RNA was isolated from mid-log phase Streptococcus agalactiae cells deficient in CopY (∆copY strain GU2857), grown in Todd-Hewitt broth (THB) medium supplemented with 0.5 mM Cu and sequenced using Illumina NextSeq500.

overall_design: Four biological replicate cultures of S. agalactiae deficient in CopY (∆copY strain GU2857) were grown in THB + 0.5 mM Cu.


title: Core Circadian Clock Genes Per1 and Per2 regulate the Rhythm in Photoreceptor Outer Segment Phagocytosis [RPE]

first: Nemanja

last: Milicevic

overall_design: Gene expression profiles of microdissected wild type (WT) and Per1-/-Per2Brdm1 (KO) mouse retinal pigment epithelium (RPE) obtained at four time points (CT19, CT22, CT1 and CT10; CT: circadian time) over a 24h cycle

last: Milićević

first: Aldo

last: Jongejan

first: Perry

last: Moerland


title: Transcriptomic approach reveal distinct responses between light and heavy rare earth elements in Saccharomyces cerevisiae

city: Vandoeuvre-les-Nancy

first: Damien

last: Blaudez

address: Faculté des Sciences et Technologies Bld des Aiguillettes, BP 70239

institute: LIEC UMR 7360 CNRS-Université de Lorraine

summary:
Purpose: The goals of this study is to compare the transcriptome (RNA-seq) modulations in Saccharomyces cerevisiae exposed to two rare earth elements. Lanthanum and ytterbium were used as representative of light and heavy rare earth elements, respectively.
Methods: mRNA were sequenced from Saccharomyces cerevisiae exposed to two different rare earth elements. Lanthanum and ytterbium were used as representative of light and heavy rare earth elements respectively. The transcriptome of S. cerevisiae was analysed after being exposed for one hour to the EC10 (Effective concentration 10 %) and the EC50 (Effective concentration 50 %) of lanthanum (50 and 160 µM) and ytterbium (6 and 8 µM). The sequence reads were trimmed using Trimmomativ v0.36.1 and FastQC v0.67 used for quality check. Reads passing the quality check were mapped on the reference genome (S288C R64-2-1 of 2015-01-31 from https://www.yeastgenome.org/) of S. cerevisiae using TopHat v2.1.1. Reads that were mapped on the reference genome were quantified using HTSeq-count v0.6.1p1. Finally, differential gene expression analysis between treatments was carried out using DESeq2 v1.14.1. Differentially expressed genes between conditions were obtained and expressed as log2-fold change with adjusted p-values calculated via a Benjamini-Hochberg test. A cut-off adjusted p-value of < 0.01 was applied.
Results: The transcription of genes related to several crucial pathways was modulated in response to both REEs, such as oxidative-reduction processes, DNA replication, and carbohydrate metabolism. REE-specific responses involving the cell wall and the pheromone signalling pathways were highlighted, while these were not reported for other metals. REE exposure also modified the expression and abundance of several ion transport systems, for which strong discrepancies were observed between the two contrasted REEs.
Conclusions: Our results demonstrate the discrepancies in yeast response to different rare earth elements (light vs heavy rare earth elements). This results are valuable to prioritize key genes and proteins involved in REE detoxification mechanisms that would deserve further characterisation to better understand the REE toxicity on the environment and human health.

overall_design: Retinal mRNA profiles of wild type Saccharomyces cerevisiae after being exposed for 1h to La and Yb at their respective EC10 (La_EC10 and Yb_EC10) and EC50 (La_EC50 and Yb_EC50) or non exposed (Ctrl)

first: Nicolas

last: Grosjean

first: Marie

last: Le Jean


title: RNA sequencing analysis of covR-deficient Streptococcus agalactiae during Cu intoxication

summary: Total RNA was isolated from mid-log phase Streptococcus agalactiae cells deficient in CovR (∆covR strain GU2400), grown in Todd-Hewitt broth (THB) medium, supplemented with 0.5 mM Cu and sequenced using Illumina NextSeq500

overall_design: Four biological replicate cultures of S. agalactiae deficient in CovR (∆covR strain GU2400) were grown in THB + 0.5 mM Cu.


title: Transcriptomic and epigenetic characterization of PVT neurons in bipolar disorder model mouse.

city: Wako

first: Emilie

middle: Kristine

last: Bagge

state: Saitama

address: 2-1 Hirosawa

department: Center for Brain Science

country: Japan

institute: RIKEN

summary: We have previosuly shown that our Polg(D181A) show spontaneous depressive episodes as a result of mtDNA mutations, but we do not know the cellular mechanisms that link mtDNA mutations to behavioural changes. We hypothesized that mtDNA mutation-induced mitochondrial dysfunction in PVT causes a dysregulation of epigenetics, causing a transcriptional response which ffects neuronal function and ultimately causes the depressive phenotype. We assessed this using a combination of RNA-seq, H3K27Ac ChIP-seq, and ATAC-seq and compared our H3K27Ac results to other brain regions.

overall_design: RNA-seq: 4 replicates per condition. ChIP- and ATAC seq: 2 replicates per condition.

middle: K

first: Tadafumi

last: Kato


title: RNA sequencing analysis of Streptococcus agalactiae 874391 (wild-type) during Cu intoxication

summary: Total RNA was isolated from mid-log phase Streptococcus agalactiae 874391 wild-type cells grown in Todd-Hewitt broth (THB) medium supplemented with 0.5 mM Cu and sequenced using Illumina NextSeq500

overall_design: Four biological replicate cultures of S. agalactiae 874391 (wild type) were grown in THB + 0.5 mM Cu.


title: RNA sequencing analysis of SczA-deficient Streptococcus agalactiae

summary: Total RNA was isolated from mid-log phase Streptococcus agalactiae cells deficient in SczA (∆sczA strain GU2791), grown in Todd-Hewitt broth (THB) medium and sequenced using Illumina NextSeq500.

overall_design: Four biological replicate cultures of S. agalactiae deficient in SczA (∆sczA strain GU2791) were grown in THB.


title: The molecular signature of Amerchol™ L-101-induced skin inflammation

city: Lyon

first: Simon

last: de Bernard

address: 30 rue Pré Gaudry

institute: AltraBio

summary: A transcriptomic comparative analysis was performed to gain further insight on the allergic or irritant molecular signature of skin reactions induced by amerchol L-101 patch tests.

overall_design: 10 patients with previously positive patch tests to Amerchol L-101 (AL-101) were retested in dose-response (10%-30%-50%-100%) and skin biopsies were collected from all tested sites as well as on control areas (petrolatum patch tests). Five subjects with previously negative patch tests to AL-101 were also retested with AL-101 100% and petrolatum and biopsied . All samples were analysed by gene microarray. Gene profiling results were compared with core molecular signatures of reference chemical allergen- and irritant-induced skin inflammation.

first: Marc

last: Vocanson

first: Cecilia

last: Svedman

first: Linda

last: Ljungberg Silic

first: Marine-Alexia

last: Lefevre


title: Noncanonical mRNA decay by the endoplasmic-reticulum stress sensor IRE1-alpha promotes cancer cell survival

first: Thomas

last: Wu

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

overall_design: Refer to individual Series


title: High-fat diet activated fatty acid oxidation mediates intestinal stemness and tumorigenicity

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Obesity is an established risk factor for cancer in many tissues such as the gastrointestinal tract. In the mammalian intestine, a pro-obesity high fat diet (HFD) promotes tumorigenesis in part by enhancing intestinal stem cell (ISC) numbers, proliferation and function. Although Ppar (Peroxisome proliferator-activated receptor) nuclear receptor activity has been proposed to mediate some of these effects in HFD ISCs, the exact role that different Ppar family members play in this process is unclear. Here, we find that in loss-of-function in vivo models, both Ppar family members alpha and delta contribute to the HFD response in ISCs. Mechanistically, both PPARs do so by robustly inducing a downstream fatty acid oxidation (FAO) metabolic program. Notably, pharmacologic and genetic disruption of CPT1a (the rate limiting enzyme of FAO) blunts the HFD phenotype in ISCs. Furthermore, just as HFD ISCs depend on CPT1a-mediated FAO, inhibition of CPT1a dampens the pro-tumorigenic consequences of a HFD on early tumor incidence and progression in the intestine. These findings demonstrate that inhibition of a HFD activated FAO program creates a therapeutic opportunity to counter the effects of a HFD on ISCs and intestinal tumorigenesis.

overall_design: Four replicates each of flow-isolated intestinal stem cell (GFP-HI) from Wildtype, Ppard, Ppara or Pparad double KO mice fed control or high fat diet.

first: Miyeko

last: Mana

first: Omer

last: Yilmaz


title: Traumatic brain injury results in unique microglial and astrocyte transcriptomes enriched for type I interferon response

city: Iowa City

first: Michael

middle: S

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary:
In this study, we performed bulk RNA sequencing of concurrently isolated microglia and astrocytes to evaluate their cell-specific transcriptional responses to TBI 7 days post-injury.
Our findings revealed sustained, cell-specific transcriptional changes in both microglia and astrocytes, with microglia showing a greater transcriptional response than astrocytes at this subacute timepoint. The microglia and astrocyte transcriptional response to TBI was unique from other neurodegenerative and neuroinflammatory diseases that have been described. In addition, microglia and astrocytes showed overlapping enrichment for genes related to type I interferon signaling and MHC class I antigen presentation.

overall_design: Astrocytes and microglia were FACs isolated from mouse forebrain 7 days following traumatic brain injury or sham control (n=5 FPI, n=5 sham). Gene expression changes were evaluated using RNA-seq.

first: Brittany

last: Todd

first: Zili

last: Luo

first: Polly

last: Ferguson

first: Alexander

middle: G

last: Bassuk

first: Elizabeth

middle: A

last: Newell


title: Identifying metabolic adaptations of rat cardiomyocytes in response to cardiotoxicity

city: Charlottesville

first: Jason

last: Papin

state: VA

address: 415 Lane Rd

department: Biomedical Engineering

institute: University of Virginia

summary: Improvements in the diagnosis and treatment of cancer has revealed the long-term side effects of chemotherapeutics, particularly cardiotoxicity. Current clinical measures to track cardiotoxicity are insufficient to diagnose damage before it has been done, necessitating new, early biomarkers of cardiotoxicity. Here, we collected paired transcriptomics and metabolomics data characterizing in vitro cardiotoxicity to three compounds: 5-fluorouracil, acetaminophen, and doxorubicin. Standard gene enrichment and metabolomics approaches identify some commonly affected pathways and metabolites but are not able to readily identify mechanisms of cardiotoxicity. Here, we integrate this paired data with a genome-scale metabolic network reconstruction (GENRE) of the heart to identify shifted metabolic functions, unique metabolic reactions, and changes in flux in metabolic reactions in response to these compounds. Using this approach, we are able to confirm known mechanisms of doxorubicin-induced cardiotoxicity and provide hypotheses for mechanisms of cardiotoxicity for 5-fluorouracil and acetaminophen.

overall_design: RNA was extracted from primary rat neonatal cardiomyocytes that were treated for 6 or 24 hours with 10mM 5-fluorouracil, 2.5 mM acetaminophen, or 1.25 uM doxorubicin with 6-7 replicates per condition and timepoint. Two controls were used: DMSO1 for the 5-fluorouracil condition and DMSO2 for the acetaminophen and doxorubicin condition.

first: Bonnie

middle: V

last: Dougherty

first: Kristopher

last: Rawls

first: Matthew

last: Jenior

first: Bryan

last: Chun

first: Sarbajeet

last: Nagdas

first: Jeffrey

middle: J

last: Saucerman

first: Glynis

last: Kolling

first: Anders

last: Wallqvist


title: Themis1-mediated repression of SHP-1 activity promotes regulatory T cell suppressive functions through a Vav1-RelA signaling axis

city: Toulouse Cedex 3

first: Mehdi

last: Benamar

address: CHU Purpan – BP 3028

institute: Inserm-CPTP

summary: Regulatory T cells (Tregs) expressing the transcription factor Foxp3 constitute a unique T cell lineage committed to suppressive functions and are crucial for suppressing aberrant immune responses in autoimmunity and allergy. Treg transcriptional landscape is tightly controlled by Foxp3-binding partners, including RelA. Although those DNA-binding complexes have been well characterized, the TCR signaling events that coordinate those dynamic molecular assembly are still poorly understood. Using a combination of genetic models, we show that the suppressive function of Tregs is controlled by a tri-molecular interplay between the signaling proteins Themis1, Vav1 and SHP-1. We identify the tyrosine phosphatase SHP-1 as a central component of an inhibitory circuit, which leads to the dephosphorylation of Vav1, which in turn is associated with a dramatic reduction of RelA activity and Treg suppressive function. Themis1 disconnects this circuit by blocking SHP-1 catalytic activity. Collectively, our results reveal a previously unappreciated pathway, whereby Themis1-mediated repression of SHP-1 activity promotes Tregs suppressive functions through a Vav1-RelA signaling axis.

overall_design: CD4+CD62L+CD25bright Tregs were sorted from Vav1R63W and Vav1R63WThemis1-T-/- mice. RNA was purified by using Rneasy Micro Kit (Qiagen). The RNA-sequencing was performed by Genoscreen company. The quality of the RNA-Seq data was assessed with FastQC. Then the reads were poly-A and adaptor-trimmed with Trim Galore. The reads were aligned to the transcriptome with STAR . MultiQC was used to assess the performance of the preprocessing steps . The genome assembly and annotation for the RNA-Seq data analysis was downloaded from ENSEMBL (version 90). The counts were normalized by the size factor method of DESeq2 . Next, the differential gene expression analysis was done with DESeq2 using SARTools R package with FDR<0.05. All analyses were performed within the R environment and most plots were produced with the ggplot2 package  and pheatmap package.

first: Benamar

last: Mehdi

first: Lebeurrier

last: Manuel

first: Saudi

last: Abdelhadi


title: Genome wide examination of alterations in mRNA translation in striatal D1 neurons in Fmr1 model mice

city: New York

first: Eric

last: Klann

state: NY

address: 4 Washington Pl

institute: New York University

summary: We immunoprecipitated GFP tagged ribosomes from Drd1 receptor-expressing cells in the striatum from adult WT and fragile X syndrome model mice and sequenced the co-purifying mRNA (IP). We also sequenced the RNA in the striatal lysate (total).

overall_design: Examination of ribosome bound mRNA in D1 neurons from FMRP mutant mice.

first: Sameer

last: Aryal

first: Francesco

last: Longo


title: Neuroinflammatory gene expression changes in the brain in a rat model of Gulf War Illness – effects of rosiglitazone

city: Baltimore

first: Stephen

last: Semick

address: 655 W Baltimore St S

institute: University of Maryland School of Medicine

summary: Gulf War Illness (GWI) is a diverse set of neurologic and systemic symptoms affecting many veterans deployed in the Persian Gulf War, but its etiology is unknown and treatment options are limited. Veterans with GWI were exposed to a variety of agents, including pyridostigmine bromide, used as prophylaxis against nerve agents, intranasal lipopolysaccharide (LPS) from desert sandstorms, and chronic unpredictable stress (CUS) from combat. Here, we investigated the gene expression effects of these three Gulf War-related exposures (GWE) in adult rat frontal cortex (FC) and lateral amygdala (LA) using Clariom S microarrays. We found 138 transcript clusters (TCs) in LA and 38 TCs in FC differentially expressed between the group with GWE (n=2) compared to naïve controls (n=3, FDR <10%). These TCs included genes involved in inflammation such as Fosb (pmin=1.02e-5) and Junb (pmin=1.13e-5). Gene ontology analysis found enrichment of differentially expressed genes in “T cell differentiation” (pmin=8.71e-5) and “response to organophosphorus” (pmin=1.74e-8), among other categories. Lastly, we found that prophylactic treatment with rosiglitazone, a PPAR- agonist, reduced gene expression changes associated with GWE (in LA: 115/138 [83.3%] TCs with reduced changes, χ2=61.33, p=4.82e-15). These results suggest our rat model of GWI is associated with gene expression changes related to neuroinflammation and that some of these molecular changes may be mitigated by rosiglitazone prophylaxis.

overall_design: Control (N=3), Gulf War exposure (N=2) and Gulf War exposure with rosiglitazine prophylaxis (N=3) samples from dissection of rat lateral amygdala (LA) and frontal cortex (FC). Please refer to the corresponding publication for additional details.

first: J

middle: M

last: Simard


title: RNA-seq of Kynurenine stimulated mouse splenocyte in vitro

city: Kunming

first: Jing

last: Sun

state: Yunnan

address: NO. 935,JIAO LIN ROAD

institute: Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: RNA-seq technology was conﬁrmed that mRNA and LncRNA expression have an important role in vaccine adjuvant in vivo and in vitro. Kynurenin, as an immunosuppressive adjuvant, but the exact mechanism of action with immune cells is still poorly understood. In the present study, mRNA and lncRNA sequencing was performed in mouse splenocytes stimulated by Kynurenin. These data provide an important basis for understanding the mechanisms underlying Kyn as an immunosuppressive adjuvant regulated the immune response.

overall_design: Four control samples and four Kynurenin(40μg/ml) treated samples

first: Sun

last: Jing


title: Activation of Kiss1 neurons in the preoptic hypothalamus stimulates testosterone synthesis in adult male mice

city: Houston

first: Jonathan

middle: Carter

last: Bean

state: TX

address: 1100 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

summary: Kisspeptin-expressing neurons in the rostral periventricular region of the third ventricle (RP3V) play an essential role in female reproduction. However, adult male mice were reported to have very few Kisspeptin-expressing neurons in the RP3V compared to females. This led to the hypothesis that Kiss1 RP3V neurons are responsible for the ability of females, but not males, to generate a surge of LH, triggering ovulation and steroid synthesis in the female. Using mouse genetics and cell type-specific gene expression analysis, we show that male mice harbor almost as many Kiss1 RP3V neurons as the female and that gene expression in these neurons is very similar. Specific activation of male Kiss1 RP3V neurons expressing viral-encoded hM3Dq caused a surge in serum testosterone levels. These results demonstrate that Kiss1 RP3V neurons are present in the adult male and fully capable of regulating the hypothalamic/pituitary/gonadal axis. We suggest that these neurons may continue to play a role in reproductive behavior in adult male mice.

overall_design: Examination  of Kiss1 neuron gene expression in 2 different hypothalamic nuclei, ARC and AVPV/RP3V, in both females and males.

first: Elisenda

last: Sanz

middle: C

first: Richard

last: Palmiter

first: Albert

last: Quintana

first: G

last: SMcKnight


title: ATP-Competitive Partial Antagonists—'PAIR's—Segregate IRE1α’s RNase-Mediated Biological Outputs

city: San Francisco

first: Vincent

last: Auyeung

department: Medicine

institute: University of California, San Francisco

summary: During mammalian cell growth and differentiation, the unfolded protein response (UPR) homeostatically adjusts endoplasmic reticulum (ER) protein-folding capacity to match changing cellular secretory demands. However, under high/chronic ER stress conditions the UPR triggers apoptosis. This dichotomy is promoted in part by differential activation levels of the ER transmembrane kinase/endoribonuclease (RNase) IRE1a.  IRE1a kinase auto-phosphorylation operates as a rheostat to control downstream RNase-induced outputs that either sustain adaptive ER protein-folding or cause apoptosis. We have previously shown that IRE1a’s RNase activity can be activated or fully inactivated by ATP-competitive kinase inhibitors. Here we developed a new class of ATP-competitive kinase inhibitors that partially antagonize the RNase of IRE1a at full occupancy. An atomic level resolution co-crystal structure shows that these small molecule partial antagonists—which we named ‘PAIR’s for (Partial Antagonists of IRE1a RNase)—occupy the ATP-binding site of IRE1a and partially displace a helix (helix aC) in the kinase domain that forms part of a dimeric interface. In insulin-producing beta cells, PAIRs permit adaptive XBP1 mRNA splicing, while quelling destructive/terminal outputs from extra-XBP1 mRNA endonucleolytic decay, thus preventing apoptosis. Preservation of XBP1 splicing by PAIRs permits B lymphocytes to differentiate into immunoglobulin-producing plasma cells. In summary, we propose that an intermediate RNase-inhibitory “sweet spot,” achieved by PAIR-bound IRE1a, may capture a structural conformation naturally available to IRE1a that could represent a desirable therapeutic state for drugging this master UPR sensor/effector.

overall_design: Rat INS1 cells with doxycycline-inducible mouse IRE1α expression were used in the study. IRE1α overexpression was induced with doxycycline and treated with small molecule modulators of IRE1α kinase activity (vehicle, PAIR1 or KIRA9). Control samples were treated only to drug vehicles (i.e., received neither doxycycline nor kinase modulators). Total RNA was collected at 4 hours or 24 hours after doxycyline induction. Experiments were performed in triplicate.

first: Rajarshi

last: Ghosh

first: Hannah

last: Feldman

first: Feroz

middle: R

last: Papa

first: Dustin

last: Maly


title: FMRP REGULATES GENOME STABILITY THROUGH DIRECT INTERACTIONS WITH R-LOOPS AND R-LOOP RESOLVASE

city: Syracuse

first: Wenyi

last: Feng

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

summary: We performed transcriptomic analyses on pateint derived FXS cells (GM03200) compared to those derived from an unaffected individual (GM06990).

overall_design: EBV transformed lymphocytes derived from a normal individual (GM06990) and a Fragile X individual (GM03200) were grown in RPMI1640, supplemented with GlutaMAX, 15% heat-inactivated FBS, 100 IU/ml penicillin and 100 ug/ml streptomycin.  Cells were either treated with DMSO, 0.3 micro molar aphidicolin or left untreated for 24 h before harvest.  3x106 cells were harvested for RNA-seq.  RNA was extracted using the Qiagen RNeasy Plus Mini Kit. The RNA was run on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano Chip to assess RNA quality and quantity.  1 µg of total RNA was used as input to the Illumina TruSeq Stranded Total RNA Library Prep Kit Ribo Zero Gold H/M/R.  Library size was assessed using the DNA 1000 chip on the Bioanalyzer, and the libraries were quantified using a Qubit fluorometer.  Pair-end sequencing was run on an Illumina NextSeq 500 instrument.  A total of four replicates were processed for treatment/conditions out of which three were biological replicates.

first: Arijita

last: Chakraborty


title: Bipartite histone H3 recognition by the PZP domain of PHF14 facilitates zygotic genome activation in zebrafish

city: Beijing

first: Shuangping

last: Zheng

state: Beijing

address: Qinghuayuan 1

department: School of medicine

institute: Tsinghua University

summary: Standard and Phf14 MOs were injected into 1-cell stage embryos and when developed into sphere stage (4.7 hpf), embryos were lysed for mRNA extraction for high-through put sequencing based on BGISEQ, in order to compare gene expression test at the whole genome level.

overall_design: mRNA profiles of standard (std_MO_4.7h) versus phf14 MO injected (phf_tMO_4.7h) zebrash embryos at 4.7 hpf.

first: Bo

last: Gong

first: Shunji

last: Jia

first: Haitai

last: Li


title: Organ-, sex-, and age-dependent patterns of endogenous LINE-1 mRNA expression at a single locus resolution

city: New Orleans

first: Victoria

last: Belancio

state: LA

address: 1430 Tulane Avenue

department: Structural and Cellular Biology

institute: Tulane University School of Medicine

summary: Expression of full-length LINE-1 mRNA, the first step in the L1 copy-and-paste amplification cycle, is a prerequisite for L1-associated genomic instability resulting from DNA damage and insertional mutagenesis. We used our stringent bioinformatics method to parse L1 mRNA transcripts and measure the level of full-length L1 mRNA expressed in mouse and rat organs at a locus-specific resolution. We find that expression of L1 loci in rodents exhibits striking organ specificity with less than 0.8% of loci shared between different organs of the same organism. This organ specificity in L1 mRNA expression is preserved in male and female mice and across different age groups. Unexpectedly, we discovered notable differences in L1 mRNA expression between sexes with only 5% of expressed L1 loci shared between male and female mice. Moreover, we report that the levels of total L1 mRNA expression and the number and spectrum of expressed L1 loci fluctuate with age as independent variables, demonstrating different patterns in different organs and sexes. Overall, our comparisons between organs and sexes and across ages ranging from 2 to 22 months establish previously unforeseen dynamic changes in L1 mRNA expression in vivo. These milestone findings establish a previously lacking atlas of endogenous L1 mRNA expression across a broad range of biological variables that will guide future studies addressing the understanding of mechanisms that govern expression of a limited number of L1 loci in any given organ and the impact of environmental and genetic perturbations on L1 mRNA expression and its involvement in disease initiation and progression.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design:
RNA Sequencing of multiple organs from 12 male mice, 9 female mice, and 3 rats. Mouse samples are from ages ranging 2-22 months. Testes, brains, and livers were collected from 6 mice: 3 at 7.6 months old (mo) and 3 at 12.8 mo. Lungs were collected from 5 mice: 2 at 7.6 mo and 3 at 12.8 mo. Only testes and livers were collected from 6 additional mice: 2 at 1.9 mo, 1 at 3.6 mo, and 3 at 22.3 mo. Brains, lungs, and ovaries were collected from 9 mice: 2 at 2.2 mo, 1 at 3.2 mo, 2 at 8 mo, 1 at 8.6 mo, 1 at 8.7 mo, and 2 at 16.5 mo. Uteri were collected from 6 mice: 1 at 2.2 mo, 1 at 8 mo, 1 at 8.6 mo, 1 at 8.7 mo, and 2 at 16.5- mo Testes, brains, livers, and lungs were collected from 3 rats, all 4.8 mo.
The .fastq files contain RNA-sequencing of the whole cytoplasm. The .txt files contain analysis of the LINE-1 retrotransposon which has ~3,000 full length copies scattered throughout the mouse genome.

first: Prescott

last: Deininger


title: Transcriptomic Characterization of Inhalation Phosphine Toxicity in Adult Male Sprague-Dawley Rats (16,500 ppm x min)

city: Aberdeen Proving Ground

first: Heidi

last: Hoard-Fruchey

state: MD

address: 2900 Ricketts Point Rd

institute: USAMRICD

summary:
Phosphine (PH3) is a highly toxic, corrosive, flammable, heavier-than-air gas that is a commonly used fumigant.  Although the mechanism of toxicity is unclear, PH3 is thought to be a metabolic poison.  PH3 exposure induces multi-organ toxicity and no effective antidotes or therapeutics have been identified.
To better characterize the mechanism(s) driving PH3-induced toxicity we have performed transcriptomic analysis on conscious adult male Sprague-Dawley rats following whole-body inhalation exposure to phosphine gas at three concentrations.  PH3 exposure induced concentration- and time-dependent changes in gene expression across multiple tissues.

overall_design: Following whole body exposure to phosphine, RNA was isolated from tissues and blood from adult male Sprague-Dawley rats at 1, 3, 6, or 24 hours post-exposure and processed for hybridization to affymetrix microarrays. The concentration x time products for phosphine exposure was 16,500 ppm x min corresponding to 0.71 x LCt50 (medium dose).

first: Benjamin

last: Wong


title: Transcriptomic Characterization of Inhalation Phosphine Toxicity in Adult Male Sprague-Dawley Rats (21,252 ppm x min)

overall_design: Following whole body exposure to phosphine, RNA was isolated from tissues and blood from adult male Sprague-Dawley rats at 1, 3, 6, or 24 hours post-exposure and processed for hybridization to affymetrix microarrays. The concentration x time product for phosphine exposure was 21,252 ppm x min corresponding to 0.91 x LCt50 (high dose).


title: Transcriptome-wide effects of cytosine and adenine deaminases on gene expression induced by base editors

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

summary: We used RNA-sequencing data to explore the  transcriptome-wide effects of cytosine and adenine deaminases on gene expression induced by base editors.

overall_design:
HEK293T cells that expressed only GFP, TadA–TadA* or BE3 and sequenced using Illumina.
HEK293T cells that expressed only GFP, TadA–TadA* or APOBEC1 in gradient concentration (1.5ug, 2.5ug, 3.5ug) were sequenced using Illumina.
HeLa cells expressed only GFP, TadA–TadA* or BE3 were sequenced using Illumina.

first: Yige

last: Ding

first: Jian

last: Fan

first: Xiaolong

last: Wang


title: Muscle regeneration controlled by a designated DNA dioxygenase

city: ShangHai

first: Hongye

address: Yue Yang Road,Shanghai 200031,China

institute: Shanghai Institute of Biochemistry and Cell Biology

type: Methylation profiling by high throughput sequencing


title: Muscle regeneration controlled by a designated DNA dioxygenase (RNA-Seq)

summary: DNA methylation plays critical roles in regulating muscle cell fate determination and myogenesis. Tet dioxygenases are responsible for active DNA demethylation. The functions of Tet proteins in muscle regeneration have not been well characterized. Here we find that Tet2 is required for complete regeneration after muscle injury. Loss of Tet2 in myoblasts leads to reduced fusion index and thinner myofibers. Tet2 activates transcription of key differentiation modulator Myogenin (MyoG) further promoting myoblast differentiation and fusion. Re-expressing of MyoG in Tet2 KO myoblasts rescues the differentiation and fusion defects. Further mechanistic analysis reveals that Tet2 facilitates the recruitment of H3K4me1 and H3K27ac, increases the chromatin accessibility, and MyoD binding on MyoG enhancer. These functions are specifically executed by Tet2, but not Tet1 and Tet3. We identified the Tet2 specific function during myogenesis and shed new lights on DNA methylation and pioneer transcription factor transcription activation.

overall_design: Examine RNA expression, DNA methylation and chromatin accessibility differences between Tet2 KO and WT mouse primary myoblasts.

first: Yile

last: Huang


title: 3' RNA sequencing of the mouse cortex at P6 following MMS and/or LPS

city: Edinburgh

first: Eamon

last: Fitzgerald

state: Midlothian

address: 47 Little France Cres

country: United Kingdom

institute: University of Edinburgh

summary: Mice were given PBS or LPS (1mg/kg) with or without subsequent MMS. 3' RNA sequencing was carried out on whole cortical tissue from P6.

overall_design: 4 groups (control, LPS, MMS and LPS+MMS).

first: Amanda

last: Drake


title: Virulence factor expression by Serratia marcescens during microbial keratitis is regulated by stress response protein GumB

city: Pittsburgh

first: Robert

middle: MQ

last: Shanks

state: PA

address: EEI 1020, 203 Lothrop st.

department: Ophthalmology

institute: University of Pittsburgh

summary: The goal of this project was to analyze virulence factor expression during microbial keratitis and to determine the impact of the Rcs system regulator GumB on the transcriptional profile

overall_design: Three eyes were injected with no bacteria controls were included, 5 with the wild-type keratitis isolate strain K904, and 4 with an isogenic gumB mutant

first: Eric

last: Romanowski

first: Nicholas

last: Stella


title: Muscle regeneration controlled by a designated DNA dioxygenase (ATAC-Seq)


title: Muscle regeneration controlled by a designated DNA dioxygenase (Methylation-Seq)


title: Investigating the role of Rgg1518 transcriptional regulator in Streptococcus pneumoniae biology

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

summary: Rggs are a group of transcriptional regulators found commonly in multiple homologous in a given species of streptococci, and they play diverse roles in metabolism and virulence. Here we studied Rgg1518’s (SPD_1518) role in sugar metabolism, and in vivo survival and virulence of Streptococcus pneumoniae. In vitro analysis showed that Rgg1518 is highly induced by galactose and mannose, and its isogenic mutant is attenuated in growth on these sugars compared to the wild type. The regulon information obtained by microarray analysis showed that Rgg1518 has by far the largest regulon on galactose compared to the other Rggs and controls the expression of functionally diverse set of genes involved in galactose uptake and catabolism, capsule biosynthesis, protein translation as well as those involved in other metabolic functions. We showed that Rgg1518 is the repressor of capsule biosynthesis, and identified Rgg1518 binding motif in the regulatory region of capsule locus. We demonstrated an interregulatory interactions among Rggs. Furthermore, the rgg1518 mutant was found to be attenuated in colonization and virulence in a mouse model of colonisation and pneumonia.

overall_design: One condition design comparision of two strains including a dye swap

first: Irfan

last: Manzoor

first: Bushra

last: Shlla

first: Hasan

last: Yesilkaya

first: Oscar

middle: P

last: Kuipers


title: AP-2α Regulates S-phase and is a Marker for Sensitivity to PI3K-inhibitor Buparlisib in Colon Cancer [RNA-seq]

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University

summary:
Abstract:AP-2α (encoded by TFAP2A) functions as a tumor suppressor and influences response to therapy in several cancer types. We aimed to characterize regulation of the transcriptome by AP-2α in colon cancer.
Results: Knockout of TFAP2A induced significant alterations in the transcriptome including repression of TGM2, identified as a primary gene target of AP-2α. Loss of AP-2α delayed progression through S-phase into G2/M and decreased phosphorylation of AKT, effects that were mediated through regulation of TGM2. Buparlisib (BKM120) repressed in vitro invasiveness of HCT116 and LS-180; however, loss of AP-2α induced resistance to Buparlisib. Similarly, Buparlisib repressed PHH3 and growth of tumor xenografts and increased overall survival of tumor-bearing mice, whereas, loss of AP-2α induced resistance to the effect of PI3K inhibition.
Conclusion: Loss of AP-2α in colon cancer leads to prolonged S-phase through altered activation of AKT leading to resistance to the PI3K inhibitor, Buparlisib. The findings demonstrate an important role for AP-2α in regulating progression through the cell cycle and indicates that AP-2α is a marker for response to PI3K inhibitors.

overall_design: Experimental Design: CRISPR-Cas9 and shRNA were used to eliminate TFAP2A expression in HCT116 and LS-180 colon cancer cell lines. AP-2a target genes were identified with RNA-seq and ChIP-seq. Effects on cell cycle were characterized in cells synchronized with aphidicolin and analyzed by FACS and Premo FUCCI. Effects on invasion and tumorigenesis were determined by invasion assay, growth of xenografts and phospho-histone H3 (PHH3).

first: Anna

last: Beck

first: Edward

last: Cho

first: Jeffrey

last: White

first: Lily

last: Paemka

first: Vivian

middle: W

last: Gu

first: Dakota

middle: T

last: Thompson

first: Kelsey

middle: E

last: Koch

first: Vincent

last: Wu

first: Shannon

last: Landers

first: Anthony

last: Pamatmat

first: Mikhail

last: Kulak

first: Ronald

last: Weigel


title: Serratia marcescens gene expression mediated by EepR, Rcs system, and GntR-family regulator

first: Robert

last: Shanks

summary: The goal of this project was to analyze the role of three different transcriptional regulator systems in regulation of gene expression

overall_design: Bacteria were synchronized, grown to culture density of OD600=1.0 in LB, and RNA was harvested, each sample represents at least two combined cultures.

first: Nicholas

last: Stella


title: Apoa1, a safe harbor locus for therapeutic genome editing in the liver

first: Charles

middle: Yang

last: Lin

address: 1 Baylor Plaza

department: Molecular and Human Genetics

summary: Clinical application of somatic genome editing requires therapeutics that are generalizable to a broad range of patients. Targeted insertion of promoterless transgenes can ensure that edits are permanent, broadly applicable, while minimizing risks of off-target integration. In the liver, the Albumin locus is currently the only well characterized site for promoterless transgene insertion. Using an unbiased ChIP-seq approach, we here identify Apolipoprotein a1 (Apoa1) as one of the most highly expressed and accessible loci in mouse and human liver. We target the Apoa1 locus with Adeno-Associated Viral (AAV) delivery of CRISPR/Cas9, and achieve rates of 6 to 16% with no evidence of toxicity. We further show that the endogenous Apoa1 promoter can drive robust and sustained expression of therapeutic proteins such as factor IX (FIX) or apolipoprotein E (APOE). Finally, we demonstrate that Apoa1-targeted fumarylacetoacetate hydrolase (FAH) can correct and rescue the severe metabolic liver disease hereditary tyrosinemia type I. In summary, we identify and validate Apoa1 as novel safe harbor site for genome editing therapeutics.

overall_design: ChIPmentation for H3K27ac and background control in primary mouse hepatocytes

middle: Y

first: Jonathan

middle: D

last: Brown

first: Marco

last: De Giorgi

first: William

last: Lagor


title: AP-2α Regulates S-phase and is a Marker for Sensitivity to PI3K-inhibitor Buparlisib in Colon Cancer [ChIP-seq]

first: Tiandao

last: Li

first: Anna

last: Beck

first: Edward

last: Cho


title: Genome-wide mRNA profiling of Edaravone (MCI-186) effects in human induced pluripotent stem cells-derived motor neurons

first: Mingyao

last: Ying

address: 733 N Broadway

department: Department of Neurology

institute: Johns Hopkins School of Medicine

summary: In this study, we used human motor neurons derived from induced pluripotent stem cell lines (N1) to identify universal transcriptomic signatures of MCI-186 cellular effects,  to highlight novel pathways responsible for its biological activity, and to unravel potential molecular actions in amyotrophic lateral sclerosis. Total RNA was extrated from cells after 24h exposure to 10μM MCI-186 or vehicle and subjected to RNA sequencing.

overall_design: Examination of  MCI-186 effects in human induced pluripotrnt stem cells-derived motor neurons


title: Genome-wide mRNA profiling of styrene oxide effects in human induced pluripotent stem cells-derived neurons

summary: In this study, we used human cortical neurons derived from induced pluripotent stem cell lines (N1) to identify universal transcriptomic signatures of styrene oxide neurotoxicity,  to highlight novel pathways responsible for its biological activity, and to unravel potential associations with autism spectrum disorders. Total RNA was extrated from cells after 24h exposure to 100μM styrene oxide or vehicle and subjected to RNA sequencing.

overall_design: Examination of  styrene oxide effects in human induced pluripotrnt stem cells-derived cortical neurons

first: Mingya

last: o Ying


title: EV-RNA sequencing with RNA TOP-PCR for healthy males

city: Taipei

first: Yu-Feng

last: Huang

address: 128 Academia Road, Section 2, Nankang

country: Taiwan

institute: Academia Sinica

summary: RNA sequencing via RNA TOP-PCR of EV from healthy males

overall_design: 3 healthy males

first: Kuo-Ping

last: Chiu

first: Hsin-Chieh

last: Shiau

first: Zee

middle: H

last: Goh

first: Pei-Chi

first: Yu-Shin

last: Nai


title: CDK4 overexpression is a predictive biomarker for resistance to conventional chemotherapy in osteosarcoma patients

city: Nitona, Chuo-ku

first: Yasutoshi

last: Tatsumi

state: Chiba

department: Research Institute

institute: Chiba Cancer Center

type: Genome variation profiling by genome tiling array

overall_design: Two-condition experiment, poor responder vs. good responder.

first: Shintaro

last: Iwata

first: Miki

last: Ohira


title: KDM5 inhibition is a novel therapeutic strategy for the treatment of KMT2D mutant lymphomas

city: London

first: James

last: Heward

state: England

address: Haemato Oncology, Barts Cancer Institute, Charterhouse Square

institute: Barts Cancer Institute

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

overall_design: Refer to individual Series


title: DEGs resulting from activating L-type calcium channel, CaV1.2, in mouse valvular interstitial cells (mVICs).

city: New York

first: Maiko

last: Matsui

address: 413 E69th Street

institute: Weill Cornell Medicine

summary: We report differentially expressed genes as a result of activation of L-type calcium channel CaV1.2 with GOF mutation in mVICs.

overall_design: Investigation of differentially expressed genes in response to activating floxed CaV1.2 with GOF mutation in mVICs with adenovirus expressing Cre recombinase.

first: Adrian

last: Tan


title: HFD activated FAO mediates intestinal stemness and tumorgenicity

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute


title: HFD activated FAO mediates intestinal stemness and tumorgenicity II

summary: Obesity is an established risk factor for cancer in many tissues such as the gastrointestinal tract. In the mammalian intestine, a pro-obesity high fat diet (HFD) promotes tumorigenesis in part by enhancing intestinal stem cell (ISC) numbers, proliferation and function. Although Ppar (Peroxisome proliferator-activated receptor) nuclear receptor activity has been proposed to mediate some of these effects in HFD ISCs, the exact role that different Ppar family members play in this process is unclear. Here, we find that in loss-of-function in vivo models, both Ppar family members alpha and delta contribute to the HFD response in ISCs. Mechanistically, both PPARs do so by robustly inducing a downstream fatty acid oxidation (FAO) metabolic program. Notably, pharmacologic and genetic disruption of CPT1a (the rate limiting enzyme of FAO) blunts the HFD phenotype in ISCs. Furthermore, just as HFD ISCs depend on CPT1a-mediated FAO, inhibition of CPT1a dampens the pro-tumorigenic consequences of a HFD on early tumor incidence and progression in the intestine. These findings demonstrate that inhibition of a HFD activated FAO program creates a therapeutic opportunity to counter the effects of a HFD on ISCs and intestinal tumorigenesis.

overall_design: At least 3 replicates each of intestinal stem cell organoids from Wildtype or Ppard, Ppara or Pparad double KO mice treated with either GW501516 or DMSO.

first: Miyeko

last: Mana

first: Omer

last: Yilmaz


title: Transcriptional impact of gumB mutation in Serratia marcescens

first: Robert

last: Shanks

summary: The GumB protein is an IgaA-family member that negatively regulates the Rcs stress response system in the bacterium Serratia marcescens. Mutation of the gumB gene results in increased RCs system activity of numerous genes including those involved in flagellar based motility and capsular polysaccharide formation.

overall_design: Three biological replicates were analyzed for each of 2 genotypes (each of the three biological replicates is a combination of three biological replicates).

first: Nicholas

middle: A

last: Stella


title: Gene expression profiling of glucocorticoid receptor signaling in a prostate cancer epithelial cell lines (LNCaPabl-Abi, LNCaPabl-Enza)

city: Innsbruck

first: Martin

last: Puhr

address: Anichstrasse 35

department: Department of Urology

country: Austria

institute: Medical University of Innsbruck

summary:
Glucocorticoid receptor (GR) has been recently identified as a candidate for acquired anti-androgen and chemotherapy resistance.
In order to identify GR targets and studying epithelial GR signaling gene expression profiling was performed in different prostate cancer cell lines treated with the glucocorticoide dexamethasone.

overall_design: Two prostate cancer cell lines (LNCaPabl-Abi, LNCaPabl-Enza) were treated with dexamethasones and compared to a control treatment (DMSO). Experiments were performed in triplicates.

first: Hubert

last: Hackl


title: Novel long non-coding RNAs involved in poly(I:C)-inducible immunoresponses in endometrial stromal cells

city: Chengdu

first: zhang

last: yan

state: Sichuan

address: Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

summary:
Background:Poly(I:C) is a synthetic double-stranded RNA that is often used as a substitute for dsRNA viral infection, and previous studies mainly focused the role of endometrial epithelium in immune response and mucosal barrier against dsRNA virus. Stromal cell is critically important for function of endometrial layer. However, whether endometrial stromal cells (ESCs) directly produce immune-response to the virus, and the biomolecules, long non-coding RNA in ESCs involve in immune-response still is unknown. In this study, we detected the immuno-response status in vitro cultured ESCs after Poly(I:C)-induction, and then analyzed mRNA and lncRNA expression profiles to explore the role of these RNAs in the immune response.
Results:291 lncRNAs and 1311 mRNAs were significantly differentially expressed (DE) between the control and Poly(I:C) groups (p<0.05). GO and KEGG analysis showed that DE genes and target genes of DE lncRNAs were enriched in many pathways related to immune and inflammatory responses, such as the toll-like receptor and the NF-κB and Jak-STAT signaling pathways. Co-expression analysis of lncRNAs and mRNAs revealed seven novel lncRNAs and their 78 targeted genes enriched in immune response pathways. In particular, the two novel lncRNA MSTRG.39626.1 and LncRNA MSTRG.137189.4-targeted genes widely involved in immune-related signaling pathways. The results suggested that the novel lncRNA MSTRG.39626.1 and MSTRG.137189.4 in the ESCs might be involved in extensive regulation of the immune response to Poly(I:C) through genes related to immune signaling pathways.
Conclusions:Our results provide both transcriptomic and epigenetic insights into the immune response of ESCs to dsRNA virus infection.

overall_design: Poly(I:C) stimulated or not stimulated rabbit endometrial stromal cells were analyzed by RNA-seq, in triplicate.

first: Yan

last: Zhang

first: Qiu

last: Wu

first: Ling

last: Xu

first: Yu

last: Zeng

first: Chuan

middle: Z

last: Lu

last: Ren

first: Zhi

last: Wang

first: Guang

middle: B

last: Zhou

first: Chang

last: Zuo

first: Tian

last: Song

first: Ming


title: Gene expression profiling of glucocorticoid receptor signaling in a prostate cancer associated fibroblast cell model (PF179TCAF-shGR-1)

summary:
Glucocorticoid receptor (GR) has been recently identified as a candidate for acquired anti-androgen and chemotherapy resistance.
In order to identify glucocorticoid receptor (GR) targets and studying stromal GR signaling gene expression profiling was performed in a prostate cancer associated fibroblast cell model (PF179TCAF-shGR-1) using different treatments.

overall_design: Cancer associated fibroblasts (PF179TCAF-shGR-1) were treated for 24h in 4 different treatment groups (1 DMSO=Control treatment, 2 Dexamthasone, 3 Doxycycline+Dexamethasone, 4 RU486+Dexamethasone). Experiments were performed in triplicates.


title: Identification of Genes Displaying Sex- and Tissue-biased Expression Patterns in the Monarch Butterfly (Danaus plexippus) with an Emphasis on Chemosensory Perception

city: Bethesda

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

summary: Monarch butterflies (Danaus plexippus) rely on milkweeds as larval host plants. Host plant seeking and verification by female butterflies may be mediated by gustatory (GRs) and olfactory receptors (ORs). Here we employed RNA-Seq, bioinformatics and RT-qPCR techniques to identify sex- and tissue-specific gene expression. We focused on chemosensation related genes and pathways, including putative ORs, GRs, ionotropic receptors (IRs), odorant-binding proteins, chemosensory proteins, and steroid hormone mediated signaling in specific chemosensory tissues (i.e., antennae, legs and proboscis). Twelve butterflies evenly split between males and females were caught and used for RNA extraction. Tissue-specific sequencing libraries were prepared and sequenced using Illumina NovaSeq 6000 or HiSeq 3000, generating 2 billion 150-bp, paired-end reads. Many more genes and gene sets were differentially expressed between tissue types than between sexes. A total of 148 chemosensation-related genes exhibited sex- and/or tissue-biased expression. RT-qPCR of a small set of genes confirmed their differential expression between tissue types or between males and females. These findings laid a solid foundation for further investigations into the biological roles of these identified genes underlying chemosensation-mediated behaviors such as foraging and reproduction.

overall_design: We first generated a large RNA-Seq dataset for antennae, leg and proboscis tissues of both male and female monarch butterflies, then applied various bioinformatic tools to infer differentially expressed chemosensory receptor (CR) genes and pathways relevant to chemosensation between either tissue types or sexes, and finally validated the differential expression of select CR genes

first: Ping

last: Gong

first: Aron

last: Katz

first: Dylan

middle: J

last: O'Hearn

first: Irene

last: MacAllister


title: Functional in vivo characterization of zebrafish sox10 enhancers in melanoma and neural crest

city: Saint Louis

first: Charles

middle: K

last: Kaufman

address: 660 S Euclid Ave

department: Oncology

institute: Washington University in St. Louis

summary: We analyzed the epigenetic landscape of five bulk (unsorted) melanoma tumors in a zebrafish melanoma model using ATAC-seq. We find that areas of open chromatin are consistent between tumor samples.

overall_design: ATAC-seq profiles of 5 bulk melanoma tumors isolated from Danio rerio BRAF(V600E)/p53(-/-) model

first: Eva

last: Kramer


title: CaptureSeq to study HIV-1 transcription after reversal of latency

first: Silvi

last: Rouskin

address: 455 Main Street

institute: Whitehead Institute

summary: The goal of this study was to utilize CaptureSeq to be able to measure HIV-1 transcription after reversal of latency in primary cells from antiretroviral-treated HIV-1 infected individuals.

overall_design: Non-naïve, resting CD4+ T cells were isolated from four HIV-1 infected individuals. The cells were treated with  one of 5 different latency reversal agents or left unstimulated for 24 hurs. The RNA was extracted and used for RNAseq and CaptureSeq library generation. CaptureSeq was performed using custom designed probes from Arbor Biosciences.

first: Athe

last: Tsibris

first: Phillip

last: Tomezsko


title: The changes of transcription profiles of tumor cells with the deletion of components of PRC1 complex, and of the infiltrated NK cells.

city: Winston-Salem

first: Swapan

last: Das

state: NC

address: Bowman Gray Center for Medical Education, 475 Vine St

department: Department of Internal Medicine, Section of Endocrinology and Metabolism

institute: Wake Forest School of Medicine

summary: We report the changes in the transcription profiles of the 4T1 breast cancer cells (control, RNF2 knockout (KO), and RSF1 KO), isolated and enriched from the tumor implanted in the 4th mammary pads by Fluorescence activated cell sorting, and the changes in the infiltrated NK cells. The transcription profiles were measured by RNA sequencing. We found that upon RNF2 KO or RSF1 KO, 4T1 tumor cells express multiple immune related genes, including chemokines, MHCII, and CD74 etc, which are otherwise repressed in cancer cells. We also found that the infiltrated NK cells in RNF2 KO tumors and RSF1 KO tumors express significantly higher levels of granzymes, compared to the NK cells infiltrated into control tumors, suggesting the activated status of these infiltrated NK cells.

overall_design: RNAseq examining the whole transcription profiles in control 4T1, RNF2 KO 4T1, and RSF1 KO 4T1 cells isolated and enriched from tumors implanted in the 4th mammary fat pads. RNAseq examining the whole transcription profiles in infiltrated NK cells in these tumors. ATACseq examining the chromatin accessibility in control, RNF2 KO, RSF1 KO and RNF2I53A/I53A mutant knockin 4T1 tumor cells enriched from corresponding tumors implanted into the 4th mammary pads of BALB/c. CHIPseq of Rnf2 determines the binding of Rnf2 to its target genes in the cultured murine breast cancer cells 4T1

first: Z

last: Zhang

first: J

last: Leavenworth

first: E

middle: S

last: Yang


title: Transcriptomic comparison of D39 WT and SPD_0588 deletion mutant in Streptococcus pneumoniae D39 with 1 µg/ml methionine

city: Beijing

first: Jing-Ren

address: Room 312, Renhuan Building, Tsinghua University

department: School of Medicine

institute: Tsinghua University

summary: metR (SPD_0588) mutant (TH9197) cannot grow in  chemically defined medium (CDM) without methionine and had significant growth defect in CDM with 1  µg/ml methionine. With the increasing concentration of mehtionine, the growth of TH9197 was restored and the growth of metR mutant is as same as D39 WT (TH4306) when the concentration of methionine reaches 50 µg/ml. SPD_0588 is a putative transcriptional regulator and is homologous to MetR in Streptococcus mutans (78.9 % amino acid identity), which regulates both methionine synthesis and transport. We compared the transcriptome of WT and metR mutant in CDM with 1 µg/ml methionine by RNA-seq to see if MetR regulates the metabolism of methionine in Streptococcus pneumoniae D39. We also want to identify the regulon of SPD_0588.

overall_design: Transcriptome comparison of D39 WT and metR mutant in CDM with 1 µg/ml methionine. It was done by deep sequencing, using Miseq instrument with 101 nt paired-end reads.

first: Chengwang


title: 14d OV scRNA-seq

city: Lexington

first: Kevin

last: Murach

state: KY

address: 900 South Limestone CTW 445

department: Physical Therapy

institute: University of Kentucky

summary: The goal of this project was to determine which mononuclear cell populations satellite cells communicate with throughout muscle during functional overload. Pooled mouse plantaris muscles from tamoxifen-treated Pax7-tdT mice were overloaded for 14 days, and a subset of mononuclear cells were submitted for sc-RNA-seq.

overall_design: One sample from pooled plantaris muscles (n=4 mice) was used for scRNA-seq. A single cell suspension was made, and a subset of cells were isolated via fluorescent activated cell sorting to probe for the transfer of reporter transcript from satellite cells.

first: Charlotte

last: Peterson


title: Inflammation drives alternative first exon usage of critical immune genes including Aim2

city: Santa Cruz

first: Sergio

last: Covarrubias

state: CA

address: Thimann Receiving/Department Carpenter Lab/Biomed 125, 1156 High St., Thimann Labs

department: MCD

institute: UCSC


title: Gene expression data from HEK293T cells stably expressing human TRAF7 wildtype or G536S mutant isoforms

city: Stanford

first: David

middle: A.

last: Solomon

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

summary:
The TRAF7 gene is recurrently mutated in meningiomas, adenomatoid tumors of the genital tract, well-differentiated papillary mesotheliomas, and intraneural perineuriomas.  However, the mechanisms by which these recurrent missense mutations contribute to tumorigenesis has not yet been described.
To elucidate the transcriptional differences between HEK293T cells overexpressing wildtype vs mutant TRAF7, we used Affymetrix microarrays to identify the gene transcripts that are upregulated and downregulated depedent on TRAF7 status.

overall_design: HEK239T cells were stably transduced with empty pCDF1, pCDF1-TRAF7 wildtype, or pCDF1-TRAF7 G536S mutant lentivirus using puromycin selection.  Total RNA was extracted using TRIzol (Invitrogen) according to the manufacturer’s instructions.

first: Meredith

last: Stevers


title: KDM1B is an important regulator of cytokine signaling in the tumor immune microenvironment and response to immune checkpoint therapy (ChIP-seq)

city: Boston

first: Yujiang

last: Shi

state: MA

address: 221 longwood Ave, EBRC (LMRC) 222A

department: Division of Endocrinology, Diabetes and Hypertension

institute: Brigham and Women's Hospital

summary: Tumor microenvironment (TME) plays an important role in immune evasion and resistance to immune checkpoint therapy. Here, by using genetic, epigenetic, tumor biology and immunology approaches, we unraveled a key function of KDM1B in TME. KDM1B is important for maintaining several pro-oncogenic cytokine/chemokine signaling pathways.  In vivo in resistant and inflammatory breast cancer models, ablation of KDM1B in tumor cells results in increased T cell activity and significantly improved response to anti-PD-1/anti-CTLA-4 therapy. Thus, this study identifies KDM1B as a key regulator of tumor immune microenvironment and offered the mechanistical basis for using KDM1B inhibitors in combinatory therapy to overcome resistance to immune checkpoint blockade.

overall_design: Use ChIP-seq to characterize the genome-wide KDM1B distritution in the genome.

first: Rui

last: Fang


title: Chromatin and transcriptome remodeling under EGFR chemical inhibition in lung cancer (RNA-seq)

first: Eric

middle: Edison

last: Gardner

state: New York

address: 413 East 69th Street, BRB-1352

department: Medicine

summary: We present paired ATAC and RNA-sequencing from EGFR-driven lung cancer cell lines genetically engineered to lose the tumor suppressors RB1 or RB1 with PTEN, and study the acute response of these cell lines to FDA-approved chemical inhibitors of EGFR

overall_design: Examination of chromatin accessibility and transcriptome following genetic and/or chemical perturbation of lung cancer cells

first: Harold

last: Varmus


title: Chromatin and transcriptome remodeling under EGFR chemical inhibition in lung cancer (ATAC-seq)

summary: We present paired ATAC and RNA-sequencing from EGFR-driven lung cancer cell lines genetically modified to lose  tumor suppressors RB1 and/or PTEN, and study the acute response of these cell lines to FDA-approved chemical inhibitors of EGFR


title: KDM1B is an important regulator of cytokine signaling in the tumor immune microenvironment and response to immune checkpoint therapy (RNA-seq)

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Use transcriptom analysis to examine the effect of KDM1B depletion to cancer cell in culture and tumors developed from s.q cancer cell injection.


title: HFD activated FAO mediates intestinal stemness and tumorgenicity I

first: Charles

last: Whittaker

overall_design: 4 replicates each of intestinal stem cells or intestinal stem cell progenitors from wild type or Cpt1a KO mice fed high fat diet or high fat control diet.

first: Miyeko

last: Mana

first: Omer

last: Yilmaz


title: Response of synovial fibroblasts to TNFα and IL6/sIL6R

city: Madrid

first: Manuel

last: Del Rey

address: Avda Córdoba s/n

department: Grupo de Enfermedades Inflamatorias y Autoinmunes

institute: Instituto de Investigación Hospital 12 de Octubre

summary:
Synovial fibroblasts (SF) are the main mesenchymal cell type constitutive in human synovial tissue. SF contribute to the homeostasis of normal joints by synthesizing extracellular matrix components and secreting the specific components of synovial fluid. SF are essential players in RA pathophysiology, they are  the primary source of IL6 in the RA synovium contributing to perpetuate the inflammation in the joint.
We used microarrays analysis to characterize the effector pro-inflammatory response of SF to TNFα and IL6/sIL6R signaling.

overall_design: Four SF lines from healthy donors stimulated for 24h with either TNFα (20ng/ml) or IL6 and sIL6R (20ng/ml each) was used to synthesize double-stranded cDNA (ds-cDNA) by using GeneChip 3’ IVT Pico Reagent Kit. The fragmented and labelled ds-cDNA was hybridized in Affymetrix GeneChip® PrimeView™ Human Gene Expression Array platform containing 49395 probesets.

first: Álvaro

last: Valín

first: José

middle: L

last: Pablos


title: Transcriptional profiling of murine germinal center (GC) B cells from GC-specific conditional Crebbp and Ep300 knock-out mice

first: Laura

last: Pasqualucci

state: NY

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

summary: Inactivating mutations of the CREBBP acetyltransferase and, at lower frequencies, its paralogue EP300 are among the most common genetic alterations in diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL), the two most frequent B cell malignancies. Here we uncover unexpected distinct functions for CREBBP and EP300 in the germinal center (GC), i.e. the target structure for most human B cell lymphomas. We show that these proteins modulate non-overlapping transcriptional programs that are preferentially enriched in biological functions associated with the separate anatomic compartments of the GC. Consistently, deletion of CREBBP or EP300 have opposing effects on GC formation in vivo. Nonetheless, these proteins partially compensate for each other to maintain a minimal threshold of acetyltransferase activity and guarantee homeostatic control of the GC, which is completely abrogated by their combined loss. This synthetic lethal interaction is retained in DLBCL cells, identifying an Achille’s heel in CREBBP-mutant lymphomas that could be pharmacologically targeted by using a novel, selective small molecule inhibitor of the CREBBP/EP300 bromodomain. These data shed light on the unique roles of CREBBP and EP300 in the physiology and pathology of GC B cells, and provide a proof-of-principle for the development and testing of EP300 inhibition as a therapeutic strategy in these diseases.

overall_design: Animals were immunized by intraperitoneal injection of sheep-red-blood-cells to induce T-cell dependent responses, and GC B cells (B220+CD95+PNA+) were sorted 12 days post immunization to extract total RNA for next generation sequencing analysis, as described in detail in the associated manuscript.

first: Antony

last: Holmes


title: RNA sequence of embryonic dorsal skin and AGM (Aorta-gonad-mesonephros) tissues

first: Yu-Jui

last: Ho

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary:
Purpose: The goals of this study are to identify the different gene expresion level in dorsal skin cells or AGM region at different embryonic stages
Methods: Dorsal skin cells were collected from different-staged embryo: E9.5, E10.5 E12.5 and E14.5. AGM were collected from different-staged embryo: E9.5, E10.5 and E11.5.  In duplicate. RNA were extrated and analyzed using RNA sequencing. For dorsal skine tissues, we screened the genes were highly expressed at early embryonic stage E9.5, but not later stages (E10.5, E12.5, and E14.5). For embryonic AGM tissues, we selected the genes were highly expressed at early embryonic stage E9.5, but not later stages (E10.5 and E11.5). The gene list were filtered based on secreted potein candidates. These gene candidates might function as novel embryonic anti-tumor factors
Results: Using an optimized data analysis workflow, we mapped the gene list for potential secretory anti-tumor factors.
Conclusions: One of the top gene from the gene lists is NEPN which we hypotherze it has unique anti-tumor function in the early embryonic microenvirnemt and might be used as a novel cancer therapeutic drug

overall_design: RNA seq analysis of embryonic doral skin cells , in duplicate

first: Tzu-Pei

last: Chang


title: Assembly of full-length macaque gene models

first: Shuxian

last: Li

address: No.5 Yiheyuan Road Haidian District

institute: Institute of Molecular Medicine，Peking University

summary: We reported an atlas of de novo-defined, full-length macaque gene models on the basis of single molecule long-read transcriptome sequencing (Iso-seq).

overall_design: We performed Isoform sequencing (Iso-seq) in 13 PacBio Sequel cells to profile the poly(A)-positive RNAs derived from macaque frontal cortex, heart and testis.

first: Chuan-Yun

first: Qing

last: Shen

first: Yumei

first: Qi

last: Peng

first: Jie

last: Zhang

first: Xiaoming

last: Zhong

first: Ni

last: An

first: Wei-Zhen

last: Zhou

first: Bertrand

middle: C

last: Tan


title: EWSR1 is critical for post-meiotic transcription and spermiogenesis

city: Bar Harbor

first: Hui

last: Tian

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

summary: Spermatogenesis is precisely controlled by complex gene expression programs. During mammalian male germ cell development, a crucial feature is the repression of transcription before spermatid elongation. Previously, we discovered that RNA-binding protein EWSR1 plays an important role in meiotic recombination and is highly expressed in late meiotic cells and post-meiotic cells. Here, we used a Ewsr1 pachytene stage-specific knockout mouse model to study its roles at late meiotic prophase I and in spermatozoa maturation. We show that loss of EWSR1 at this stage does not affect proper meiosis completion, but the developing germ cells exhibit defects in spermatid elongation and chromocenter formation. In the Ewsr1 conditional knockout testes, expression of many genes regulating spermatid differentiation is impaired, suggesting that EWSR1 may play important role in regulation of spermiogenesis related mRNA synthesis and spermatid differentiation.

overall_design: RNA-seq of spermatocytes and round spermatids isolated by FACS sorting from Ewsr1 control and conditional knockout mice

first: Petko

middle: M

last: Petkov


title: Liver gene expression profiling of obese C57BL/6J mice after chronic exposure to ethanol.

city: Rennes

first: Simon

last: Bucher

address: 2 Avenue du Pr. L. Bernard

institute: INSERM U1241

summary: The aim of this study was to determine the effects of a 3-month ethanol exposure in C57BL/6J mice fed a 60% high-fat diet (HFD).

overall_design: Adult male C57BL/6J mice were fed a 60% HFD during 4 months. At the end of the first month, half of the animals received ethanol provided in the drinking water (5 g/kg/d during 1 week and then 10 g/kg/d). Analyzed data correspond to the liver gene expression profiling of 10 mice (5 mice per group).

first: Cédric

last: Coulouarn

first: Bernard

last: Fromenty


title: Rare Copy Number Variation in Extremely Impulsively Violent Males

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

summary: The Illumina Human Omni2.5 array is a high resolution microarray platform for studying copy number variations in the human genome.  It is widely being used in both clinical and research settings for identifying causative variants as well as interrogating the genome for benign variants. We employed this platform to investigate the risk factor CNVs in 281 individuals diagnosed with Antisocial Personality Disorder.

overall_design: Three CNV calling algorithms were used to detect CNVs in cases and controls: i.e. iPattern, PennCNV, and QuantiSNP. We defined a stringent set of variants when each variant was called by at least by two algorithms. We defined the ancestry and relatedness of the samples using PLINK.

first: Stanislav

last: Kmoch

first: Jeffrey

middle: R

last: MacDonald


title: In-vivo inhibition of Fgfr2b signalling in FACS-isolated AECs from embryonic mouse lungs from E16.5 to E18.5

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

summary: Rosa26rtTA;tetOsFgfr2b (C75Bl6) induced from E16.5 until E18.5, lungs were harvest at E18.5, AECI and AECII were sorted using FACS. Mice were kept on water and food ad libitum.

overall_design: 4 groups, each with 2 biological replicates

first: Cho-Ming

last: Chao


title: Epigenomic Based Identification of the Global Gene Regulatory Map of the Murine Salivary Gland

city: Buffalo

first: Satrajit

last: Sinha

address: 701 Ellicott Street

department: Department of Biochemistry

institute: State University of New York at Buffalo

summary: The characterization of the epigenetic landscape of mouse salivary gland epithelial cells via histone modification ChIP-Seq  and whole tissue RNA-Seq Analysis

first: Christian

last: Gluck

first: Akinsola

last: Olyelakin

first: Christine

last: Song

first: Sangwon

last: Min

first: Rose-Anne

last: Romano


title: Single cell RNA sequencing of cultured endometrial mesenchymal stem cells

city: Hong Kong

first: William

last: Yeung

address: Pokfulam

department: Department of Obstetrics and Gynecology

institute: The University of Hong Kong

summary: Endometrial mesenchymal-like stem cells (eMSCs) are adult stem cells contributing to endometrial regeneration. One set of perivascular markers (CD140b+CD146+) have been widely used to enrich eMSCs. In this study, we applied 10X genomics single-cell RNA sequencing to eMSCs cultured in vitro after microbeading from 6 donors to investigate cellular heterogeneity in an unbiased manner.

overall_design: Endometrial tissue were obtained from 6 donors with regular menstrual cycle. eMSCs were isolated from the cultured primary stromal cells and investigated through singe cell RNA sequencing in 10X Genomics platform.

first: Dandan

last: Cao

first: William Shu Biu