title: ExoSTING, an extracellular vesicle loaded with STING agonists, promotes tumor immune surveillance

city: Cambridge

first: Kelvin

last: Zhang

state: Massachusetts

address: 35 CambridgePark Drive, Suite 500

institute: Codiak Biosciences

summary: Cyclic dinucleotide (CDN) agonists of the STimulator of InterferoN Genes (STING) pathway have shown immune activation and tumor clearance in pre-clinical models. However, CDNs administered intratumorally also promote STING activation leading to direct cytotoxicity of many cell types in the tumor microenvironment (TME), systemic inflammation due to rapid tumor extravasation of the CDN, and immune ablation in the TME. These result in a failure to establish immunological memory. ExoSTING, an engineered extracellular vesicle (EV) exogenously loaded with CDN, enhances the potency of CDN and preferentially activates antigen presenting cells in the TME. Following intratumoral injection, exoSTING was retained within the tumor, enhanced local Th1 responses and recruitment of CD8+ T cells, and generated systemic anti-tumor immunity to the tumor. ExoSTING at therapeutically active doses did not induce systemic inflammatory cytokines, resulting in an enhanced therapeutic window. ExoSTING is a novel, differentiated therapeutic candidate that leverages the natural biology of EVs to enhance the activity of CDNs.

overall_design: Examination of mRNA profile in B16F10 tumors after exoSTING treatment

first: Su

last: Jang


title: Classical and variant Merkel cell carcinoma cell lines display different degrees of epithelial-mesenchymal transition

status: Public on Mar 11 2021

city: Essen

first: Jan

last: Gravemeyer

address: Universitätstraße 1

country: Germany

institute: DKZF

type:
Expression profiling by array
Non-coding RNA profiling by array
Methylation profiling by array

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

overall_design: Refer to individual Series


title: The translational landscape of phenylephrine-treated neonatal rat cardiomyocytes [ssRNA-seq]

city: Guangzhou

first: Youchen

last: Yan

state: Guangdong

address: No.58 Zhongshan Road II

country: China

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

type: Expression profiling by high throughput sequencing

summary: In this study, we generated nucleotide-resolution translatome as well as transcriptome data of isolated primary cardiomyocytes undergoing hypertrophy. More than 10,000 open reading frames (ORF) were detected from the deep sequencing of ribosome protected fragments orchestrating the shift of translatome in hypertrophied cardiomyocytes.We further identified more than 100 potential micropeptides encoded by uncharacterized small open reading frames (sORFs) in the long noncoding RNA genes. Over two-thirds of these micropeptide candidates were experimentally validated in a random test with three micropeptides showing regulatory function in cardiomyocyte hypertrophy via modulating the activities of Oxidative phosphorylation, Calcium signaling pathway, and MAPK signaling pathway.Our study provided a genome-wide overview of the translational controls of cardiomyocyte hypertrophy and demonstrated an unrecognized role of micropeptides in cardiomyocyte biology.

overall_design:
Ribo-seq and RNA-seq of neonatal rat cardiomyocytes treated with or without PE; RNA-seq of neonatal rat cardiomyocytes infected with ad-sORF or control virus
ssRNA-seq data presented here.

first: Rong

last: Tang

first: Bin

last: Li

first: Liangping

last: Cheng

first: Jian-Hua

last: Yang

first: Zhan-Peng

last: Huang


title: Methylated RNA immunoprecipitation sequencing in the Kasumi-1 cell line treated with CoCl2

status: Public on Mar 12 2021

city: Beijing

first: Xiao-ning

last: Gao

state: Beijing

address: 28 Fuxing Road

department: Department of Hematology

institute: Chinese PLA General Hospital

summary: To evaluate the role of HIF1α in modulating the m6A abundance, we conducted m6A sequencing in the Kasumi-1 cell line treated with CoCl2, which could mediate the stabilization of HIF1α protein.

overall_design: Kasumi-1 cells were treated with 100 uM CoCl2 for 24 hours. The untreated cells served as the control. A total of 3 biological replicates were performed for each condition.


title: Transcriptome Analysis of Human Hemorrhoids Tissue

city: Kiel

first: Simonas

last: Juzenas

address: Am Botanischen Garten 11

department: Institute of Clinical Molecular Biology

institute: Christian-Albrechts-University of Kiel

summary: RNA-Seq libraries of hemorrhoids tissue containing combined small RNAs and poly(A) RNA species.

overall_design: A group of 38 patients undergoing surgery for hemorrhoids (n=20; cases) and anal fissures (n=18; controls) were enrolled to the study. Next-generation RNA sequencing (Combo-Seq) of both mRNA and miRNA transcripts was performed on total RNA of hemorrhoidal tissue from 20 patients and 18 healthy controls.

first: Andre

last: Franke


title: Mapping the regulatory landscape of auditory hair cells from single cell multi-omics data

city: Ann Arbor

first: Joerg

last: Waldhaus

state: MI

address: Medical Sciences I Building, Rm. 5315A, 1150 West Medical Center Drive

department: Department of Otolaryngology–Head and Neck Surgery, Kresge Hearing Research Institute

country: USA

institute: University of Michigan

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Auditory hair cells transduce sound to the brain and in mammals these cells reside together with supporting cells in the sensory epithelium of the cochlea, called the organ of Corti. To establish the organ’s delicate function during development and differentiation, spatiotemporal gene expression is strictly controlled by chromatin accessibility and cell type specific transcription factors, jointly representing the regulatory landscape. Bulk-sequencing technology and cellular heterogeneity obscured investigations on the interplay between transcription factors and chromatin accessibility in inner ear development. To study the formation of the regulatory landscape in hair cells, we collected single-cell chromatin accessibility profiles accompanied by single-cell RNA data from genetically labeled murine hair cells and supporting cells after birth.

overall_design: Examination of transcriptional and chromatin accessibility profiles in the organ of Corti with apical and basal compartment separately at P2

first: Shuze

last: Wang

first: Mary

last: Lee

first: Scott

last: Jones


title: Comparison of global gene expression in the Gluconobacter oxydans DgoxR mutant and the parental strain by RNA-Seq

city: Jülich

first: Angela

last: Kranz

state: NRW

address: Wilhelm-Johnen-Strasse

department: IBG-1: Biotechnology

institute: Forschungszentrum Jülich GmbH

summary: Gene expression in the obligatory aerobic acetic acid bacterium Gluconobacter oxydans was shown to respond to oxygen limitation, but the regulators involved are unknown. In this study, we analyzed the function of a transcriptional regulator named GoxR, which belongs to the FNR family. Here, we aplied RNAseq to identify target genes of GoxR by comparing genes expression of a delta-goxR and its parental strain after 20 min of oxygen limitation.

overall_design: A transcriptome comparison of the delta-goxR mutant and the parental strain was performed by RNAseq to identify genes with altered expression in the absence of GoxR. For this purpose, the two strains were cultivated in a bioreactor at 15% DO and pH 6 using mannitol medium. As GoxR was assumed to be active under oxygen-restricted conditions, the oxygen supply was switched from 15% DO to 0% DO by gassing with a mixture of 2% O2/98% N2 when the strains had reached an OD600 of 2.5. The cells were harvested 20 min after the switch and used for RNA isolation and RNAseq analysis.

first: Michael

last: Bott


title: Diurnal transcriptomics analysis reveals the regulatory role of the circadian rhythm in super-hybrid rice LY2186

first: Zhen

last: Zhu

address: No.1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology

summary: Heterosis, an important biological phenomenon wherein F1 hybrids exhibit better performance than any of their parents, has been widely applied; however, its underlying mechanism remains largely unknown. Here, we studied and compared the dynamic transcriptional profiles of super-hybrid rice LY2186 and its parents at 17 time points during 2 day/night cycles and identified 1,552 rhythmic differentially expressed genes (RDGs). Cluster and functional enrichment analyses revealed that the day- and night-phased RDGs were mainly enriched in the photosynthesis and stress response categories, respectively. Regulatory network analysis indicated that circadian-related RDGs are core components in both the day and night phases and extensively regulate downstream genes involved in photosynthesis, starch synthesis, plant hormone signal transduction, and other pathways. Furthermore, among the 282 RDGs mapped onto the quantitative tract loci of small intervals (≤100 genes), 72.3% were significantly enriched in the yield, vigor, and anatomy categories. These findings provide valuable information for exploring heterosis mechanisms further and guiding breeding practices.

overall_design: We constructed 51 ssRNA sequencing libraries of flag leaves of the super-hybrid rice Liangyou2186 (LY2186)and its parental lines including the male-sterile line SE21s and the restorer line  Minghui86 (MH86) at the grain-filling stage during 17 serial time points (circadian clock ZT0~ZT48, 3h interval).

first: Yue

first: Yufei

last: Lu

first: Yun

last: Zhou

first: Xiaoli

last: Wei

first: Yonggang

last: Peng

first: Yan

last: Dai

first: Lei

last: Zhang


title: The translational landscape of phenylephrine-treated neonatal rat cardiomyocytes

first: Youchen

last: Yan


title: The translational landscape of phenylephrine-treated neonatal rat cardiomyocytes [nsRNA-seq]

overall_design:
Ribo-seq and RNA-seq of neonatal rat cardiomyocytes treated with or without PE; RNA-seq of neonatal rat cardiomyocytes infected with ad-sORF or control virus
nsRNA-seq data presented here.

first: Rong

last: Tang

first: Bin

last: Li

first: Liangping

last: Cheng

first: Jian-Hua

last: Yang

first: Zhan-Peng

last: Huang


title: Histone acetylation dynamics modulate chromatin conformation and allele-specific interactions at oncogenic loci (ChIPSeq)

status: Public on Mar 09 2021

city: Lausanne

first: Yuanlong

last: Liu

address: Quartier UNIL-Sorge

department: Department of Computational Biology

country: Switzerland

institute: University of Lausanne

summary: In cancer cells, enhancer hijacking mediated by chromosomal alterations and/or increase of histone H3 lysine 27 acetylation (H3K27ac) can support oncogene expression. However, how the chromatin conformation of enhancer-promoter interactions is affected by these events is unclear. Here, by comparing chromatin structure and H3K27ac levels in normal and lymphoma B-cells, we show that enhancer-promoter interacting regions assume different conformations according to the local abundance of H3K27ac. Genetic or pharmacologic depletion of H3K27ac decreases the frequency and the spreading of these interactions, altering oncogene expression. Moreover, enhancer hijacking mediated by chromosomal translocations influences the epigenetic status of the regions flanking the breakpoint, prompting the formation of distinct intra-chromosomal interactions in the two homologous chromosomes. These interactions are accompanied by allele-specific gene expression changes. Overall, our work indicates that H3K27ac dynamics modulate interaction frequency between regulatory regions and can lead to allele-specific chromatin configurations to sustain oncogene expression.

overall_design: duplicates or triplicates for each samples except for patient sample due to limited material

first: Stephanie

last: Sungalee

last: LIU

first: Ruxandra

middle: A

last: Lambuta

first: Natalya

last: Katanayeva

first: Maria

middle: D

last: Collier

first: Daniele

last: Tavernari

first: Sandrine

last: Roulland

first: Giovanni

last: Ciriello

first: Elisa

last: Oricchio


title: Targeted single cell RNA-sequencing of transcription factors facilitates biological insights from human cell experimental models [intestinal stromal cells pre-capture]

status: Public on Mar 10 2021

city: Oxford

first: Alexandra

last: Pokhilko

address: John Radcliffe Hospital, Headington

department: Nuffield Department of Clinical Neurosciences

country: United Kingdom

institute: University of Oxford

summary: Single cell RNA sequencing (scRNA-seq) is a widely used method for identifying cell types and trajectories in biologically heterogeneous samples, but is limited in its detection and quantification of lowly expressed genes. This results in missing important biological signals, such as the expression of key transcription factors (TFs) driving cellular differentiation. We show that targeted sequencing of ~1000 TFs (scCapture-seq) in iPSC-derived neuronal cultures greatly improves the biological information garnered from scRNA-seq. Increased TF resolution enhanced cell-type identification, developmental trajectories and gene regulatory networks. This allowed us to resolve differences amongst neuronal populations, which were generated in two different labs using the same differentiation protocol. ScCapture-seq improved TF gene-regulatory network inference and thus identified divergent patterns of neurogenesis into either excitatory cortical neurons or inhibitory interneurons. Furthermore, scCapture-seq revealed a role for of retinoic acid signalling in the developmental divergence between these different neuronal populations. Our results demonstrate that TF targeting improves the characterization of human cellular models and allows identification of the essential differences between cellular populations, which would otherwise be missed in traditional scRNA-seq. scCapture-seq TF targeting represents a cost-effective enhancement of scRNA-seq, which could be broadly applied to any cellular models to improve scRNA-seq resolution

overall_design: RNAseq profiles of 188 intestinal stromal cells from UC patients made using the 10x droplet-based protocol (Kinchen et.al., Cell, 2018; PMID: 30270042). Post-capture libraries were sequenced on 1 lane of a HiSeq 4000 at 75 bp paired end. RNA from each cell was sequenced twice: the PRE-capture libraries have all human genome sequenced, while only chosen set of transcription factors was sequenced in POST-capture libraries

first: A

middle: E

last: Handel

first: F

last: Curion

first: V

last: Volpato

first: E

middle: S

last: Whiteley

first: S

last: BÃ¸strand

last: Newey

first: C

middle: J

last: Akerman

last: Webber

first: M

middle: B

last: Clark

first: R

last: Bowden

first: Z

last: Cader


title: The translational landscape of phenylephrine-treated neonatal rat cardiomyocytes [Ribo-seq]

first: Youchen

last: Yan

overall_design:
Ribo-seq and RNA-seq of neonatal rat cardiomyocytes treated with or without PE; RNA-seq of neonatal rat cardiomyocytes infected with ad-sORF or control virus
Ribo-seq data presented here.

first: Rong

last: Tang

first: Bin

last: Li

first: Liangping

last: Cheng

first: Jian-Hua

last: Yang

first: Zhan-Peng

last: Huang


title: Next-generation sequencing of the transcriptomes of prostate cancer cells with or without ectopic expression of LINC00888

city: Orlando

first: Ratna

last: Chakrabarti

address: 12722 Research Parkway

institute: University of Central Florida

summary: Transcriptome analysis was performed to determine the effect of overexpression of LINC00888 on global gene expression in prostate cancer cells.

overall_design: Prostate cancer cells C4-2B transfected with expression vector containing LINC00888 or the empty vector were used for RNA-seq analysis.

last: Cakrabarti


title: Cooperative Binding between distant Transcription Factors is a Hallmark of Active Enhancers

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary: Enhancers harbor binding motifs that recruit transcription factors (TFs) for gene activation. While cooperative binding of TFs at enhancers is known to be critical for transcriptional activation of a handful of developmental enhancers, the extent TF cooperativity genome-wide is unknown. Here, we couple high-resolution nuclease footprinting with single-molecule methylation profiling to characterize TF cooperativity at active enhancers in the Drosophila genome. Enrichment of short MNase-protected DNA segments indicates that the majority of enhancers harbor two or more TF binding sites, and we uncover protected fragments that correspond to co-bound sites in thousands of enhancers. We integrate MNase-seq, methylation accessibility profiling, and CUT&RUN chromatin profiling as a comprehensive strategy to characterize co-binding of the Trithorax-like (TRL) DNA binding protein and multiple other TFs. We identify states where an enhancer is bound by no TF, by either single factor, by multiple factors, or where binding sites are occluded by nucleosomes. From the analysis of co-binding, we find that cooperativity dominates TF binding in vivo at a majority of active enhancers. Factor cooperativity occurs predominantly between sites spaced 50 bp apart in active enhancers, indicating that most TF cooperativity in cells occurs without apparent protein-protein interactions. Our findings suggest a mechanism for nucleosomes to promote cooperativity by requiring co-binding to effectively clear nucleosomes and promote enhancer function.

overall_design: CUT&RUN Profiling of TRL

first: Kami

last: Ahmad


title: Expression data from baicalein treated C. elegans

city: Murcia

first: Fernando

last: Gandía-Herrero

state: Murcia

address: Universidad de Murcia, Campus Espinardo - Edificio Veterinaria

department: Biochemistry and Moleular Biology

country: Spain

institute: University of Murcia

summary:
Effects of baicalein in C. elegans gene expression is studied, as our results indicate a lifespan extension effect produced by this molecule.
Microarrays were used to detail the global programme of gene expression underlying the lifespan extension and identified distinct classes of up/down-regulated genes in animals treated with baicalein.

overall_design: C. elegans young adults treated with baicalein from L1 stage were selected  for RNA extraction and hybridization on Affymetrix microarray chips.

last: Guerrero-Rubio

last: Lopez-Andreo

last: Hernandez-Garcia

first: F

last: Garcia-Carmona

last: Gandia-Herrero


title: Flg22 treatment of Brassicaceae and Arabidopsis thaliana accessions

city: Wuhan

first: Kenichi

last: Tsuda

address: No.1 Shizishan Road

institute: Huazhong Agricultural University

summary: We used RNA-seq to profile gene expression changes during flg22 activated pattern-triggered immunity in multiple Brassicaceae including Capsella rubella, Cardamine hirsuta and Eutrema salsugineum as well as in multiple Arabidopsis thaliana accessions. This allows comparative transcriptomics within and across species to investigate the evolution of stress-responsive transcrption changes in these species.

sample_organism:
Arabidopsis thaliana
Cardamine hirsuta
Eutrema salsugineum
Capsella rubella

overall_design: Gene expression profiling via mRNA sequencing of 12-day-old seedlings treated with mock or 1µM flg22 for 1 h, 9 h or 24 h. We used the A. thaliana accessions Can-0, Col-0, Gy-0, Kn-0, Kon and No-0 and the Brassicaceae species Capsella rubella, Cardamine hirsuta and Eutrema salsugineum

first: Thomas

last: Winkelmüller


title: Targeted single cell RNA-sequencing of transcription factors facilitates biological insights from human cell experimental models [iPSC neuron pre-capture]

first: Alexandra

last: Pokhilko

overall_design: NG (neuroGWAS) gene capture in iPSC-derived neurons. RNAseq profiles of 376 single cells from 2 laboratories harvested at day 55 after plating. Single cells were isolated by FACS onto 96-well plates and sequenced on 1 lane of HiSeq4000 at 75bp paired end. RNA from each cell was sequenced twice: the PRE-capture libraries have all human genome sequenced, while only chosen set of neuro-GWAS genes was sequenced in POST-capture libraries

first: A

last: Handel

last: Curion

first: V

last: Volpato

first: E

last: Whiteley

first: S

last: BÃ¸strand

last: Newey

first: C

last: Akerman

last: Webber

last: Clark

last: Bowden

last: Cader


title: Staphylococcus aureus responds to physiologically relevant temperature changes by altering its global transcript and protein profile

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

summary: Staphylococcus aureus is an opportunistic pathogen that colonizes the anterior nares of about 30-50% of the population. Colonization is most often asymptomatic, however, self-inoculation through inhalation, ingestion, or an open wound, can give rise to potentially fatal infections of the deeper tissues and blood. Like all bacteria, S. aureus is able to sense and respond to environmental cues and modify gene expression to adapt to specific environmental conditions. The transition of S. aureus from the nares to the deeper tissues and blood is accompanied by a number of changes in environmental conditions, such as nutrient availability, pH, and temperature. On average, the human anterior nares are 34 ˚C while a healthy individual maintains a core body temperature of 37 ˚C. In this study we investigate the response of S. aureus to changing temperature.  Transcriptomics and proteomics were performed on S. aureus cultures growing at three physiologically relevant temperatures, 34˚C (nares), 37˚C (body), and 40˚C (pyrexia), to determine if small scale, biologically meaningful alterations in temperature have an impact on S. aureus gene expression. Results show that small but definite temperature changes elicit a large-scale restructuring of the S. aureus transcriptome and proteome. We demonstrate that these changes have physiological relevance through phenotypic analyses. Finally, using a human epithelial cell line infection assay, we investigate the impact that temperature dependent alterations in gene expression have on S. aureus pathogenesis and demonstrate decreased intracellular invasion of S. aureus cells grown at 34˚C. Collectively, our results demonstrate that small but biologically meaningful alterations in temperature can influence on S. aureus gene expression and may be a major contributor to the transition from a commensal to pathogen.

overall_design: Nine data sets in total. Three biological replicates of S. aureus grown at each of the three temperatures used in the study, i.e. 34 C, 37 C, and 40 C

first: Raeven

last: Bastock

first: Richard

last: Wiemels

first: Donald

middle: L

last: Holzschu

first: Rebecca

last: Keogh

first: Emily

middle: C

last: Marino

first: Rachel

last: Zapf

first: Erin

middle: R

last: Murphy

middle: K


title: Histone acetylation dynamics modulate chromatin conformation and allele-specific interactions at oncogenic loci.

first: Yuanlong

last: Liu

overall_design: Refer to individual Series


title: Human gastrointestinal epithelia of the esophagus, stomach and duodenum resolved at single-cell resolution

city: Vienna

first: Georg

last: Busslinger

address: Lazarettgasse 14

country: Austria

institute: Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: The upper gastrointestinal tract consisting of the esophagus, stomach and duodenum controls food transport, digestion, nutrient uptake and hormone production. By single-cell analysis of healthy epithelia of these human organs, we molecularly defined their distinct cell types. We identified a quiescent COL17A1high stem/progenitor cell population within the basal cell layer of the esophagus and detected substantial gene expression differences between identical cell types of the human and mouse stomach. Selective and high expression of BEST4, CFTR, guanylin and uroguanylin identified the rare duodenal BCHE cells, which likely mediate high-volume fluid secretion due to continual activation of the CFTR channel by guanylin/uroguanylin-mediated autocrine signaling. Unexpectedly, the previously uncharacterized serotonin-producing enterochromaffin cells in the antral stomach significantly differ in gene expression from the duodenal enterochromaffin cells. We furthermore discovered that the histamine-producing enterochromaffin-like cells in the oxyntic stomach express luteinizing hormone, not previously seen in enteroendocrine cells.

overall_design: single cell sequencing (SORT-seq) on gastric epithelium of C57BL/6 mice

first: Bas

last: Weusten

first: Auke

last: Bogte

first: Harry

last: Begthel

first: Lodewijk

last: Brosens

first: Hans

last: Clevers


title: Histone acetylation dynamics modulate chromatin conformation and allele-specific interactions at oncogenic loci (RNASeq)

overall_design: 3 samples, paired treated and untreated , duplicates or triplicates were considered for each sample

first: Stephanie

last: Sungalee

last: LIU

first: Ruxandra

last: Lambuta

first: Natalya

last: Katanayeva

first: Maria

last: Collier

first: Daniele

last: Tavernari

first: Sandrine

last: Roulland

first: Giovanni

last: Ciriello

first: Elisa

last: Oricchio


title: Examination of NK, ILC, macrophage and dendritic cells from human adipose tissue in lean and obese donors.

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: We sorted  NK, ILC, macrophage and dendritic cells from human adipose tissue and did single cell RNA sequencing on these cells. We observed cell type compositon changes and expression changes in the lean and obese donors.

first: Andrew

last: Hildreth

first: Timothy

last: O'sullivan

first: Matteo

last: Pellegrini


title: Interferon Regulatory Factor 7 (IRF7) in aging of adipose-derived mesenchymal stromal cells

city: Verona

first: Mirco

last: Galiè

address: via Le Grazie, 8

department: Neuroscience, Biomedicine and Movement Sciences

country: Italy

institute: University of Verona

summary:
We found that Interferon Regulatory Factor 7 (IRF7) is upregulated  in adipose-derived stromal cells (MSC) of 12 months-old (middle-age) mice compared with 1 month-old mice. To go in depth into the role of IRF7 in aging of MSC we knocked-down it in 12 months MSC and assessed the transcriptional changes though whole-genome microarray analysis.
We  investigated the transcriptional changes induced by the Interferon Regulatory Factor 7 (IRF7) knock-down in mesenchymal stromal cells established from the inguinal fat pad  of 12-months-old mice.

overall_design: MSCs from the inguinal fat pad of 12months-old male FVB mice were infected with pLKO.1 lentiviral vector either empty (n=2), scramble (n=2)  or encoding for the a shRNA specific for IRF7 (n=4). Afterwards, total RNA was extraced and used to profile the transcriptional gene expression pattern by microarray analysis.

first: Alice

last: Nodari


title: Targeted single-cell RNA sequencing of transcription factors facilitates biological insights from human cell experimental models

first: Alexandra

last: Pokhilko

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


title: Examination of human adipose celltypes in lean and obese donors

summary: We did single cell RNA sequencing on three lean and three obese donors. For each donor, we sorted CD45 positive and CD45 negative cells and prepared 10X scRNA-seq libaries. We observed cell type compositon changes and expression  changes in the lean and obese donors.


title: High-content, targeted RNA-seq screening in organoids for drug discovery in colorectal cancer

first: Maxim

last: Norkin

address: SV 2521 (Bâtiment SV)  Station 19

department: SV

institute: EPFL

summary: We present TORNADO-seq —a high-throughput, a high-content drug discovery platform that for the first time uses next-generation sequencing (NGS) based, targeted RNA-seq in organoids monitoring the expression of 206 genes for the evaluation of complex mixtures of cellular phenotypes. TORNADO-seq is a fast, highly-reproducible, time- and cost-effective (5$ per sample including sequencing cost) method that we used to find drugs that enrich for differentiated cell phenotypes in intestinal organoids. These drugs are highly efficacious against cancer compared to wild type organoids and may therefore become promising candidates in CRC treatment. Further, TORNADO-seq facilitated in-depth insight on the mode of action of these drugs.

overall_design: We have screened 320 compounds from a library of FDA-approved drugs on WT and AKP (APC, KRAS, p53) mutant intestinal organoids in 96-well plate format. 2-4 biological replicates were used, and 1 or 2 days treatment duration.

first: Paloma

last: Ordonez-Moran

first: Joerg

last: Huelsken


title: Tumor endothelial cell single-cell sequencing from wild-type mice

city: Palo Alto

first: Christoph

last: Thaiss

address: 3181 Porter Dr.

department: Immunology and Pathology

institute: Arc Institute

summary: Edothelial cells were FACS sorted as CD31+CD45- population from LLC transplant tumor bearing WT mice on Day 14 post tumor transplantation

overall_design: Single-cell RNA-seq libraries were prepared using version 1 Chromium Single-cell 3′ Library, Gel Bead & Mutiplex Kit (10X Genomics). Sequencing was performed on Illumina NextSeq2500

first: Kyunghee

last: Choi

first: Ashraf

middle: l

last: Kabir

first: Madhav

last: Subramanian


title: SARS-CoV-2 infects human pluripotent stem cell-derived cardiomyocytes, impairing electrical and mechanical function

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

summary: RNA-sequencing used to investigate the transcriptome response to Sars-cov-2 in ESC differentiated female cardiomyocytes and iPSC differentated male cardiomyctes

overall_design: ESC differentiated female cardiomyocytes, subtype H7 infected with Sars-cov-2 at MOI of 0.1 (collected at 48hrs and 72hrs) and 5 (collected at 24hrs and 48 hrs) compared to mock (each done in triplicate) and iPSC differentiated male cardiomyocytes, subtype WTC infected with Sars-cov-2 at MOI of 0.1 (collected at 48hrs and 72hrs) and 5 (collected at 24hrs and 48 hrs) compared to mock (each done in triplicate)

first: Tien-Ying

last: Hsiang

first: Leanne

last: Whitmore

first: Akinobu

last: Ota

first: Lynn

last: Law

first: Elise

last: Smith

first: Daniel

last: Newhouse

first: Jean

last: Chang

first: Silvia

last: Marchiano

first: Charles

last: Murray

last: Gale Jr


title: Nuclear organization and replication timing are coupled through RIF1-PP1 interaction

city: Basel

first: Ilya

middle: M.

last: Flyamer

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

summary: Three-dimensional genome organisation and replication timing are known to be correlated, however, it remains unknown whether nuclear architecture overall plays an instructive role in the replication-timing program and, if so, how. Here we demonstrate that RIF1 is a molecular hub that co-regulates both processes. Both nuclear organisation and replication timing depend upon the interaction between RIF1 and PP1. However, whereas nuclear architecture requires the full complement of RIF1 and its interaction with PP1, replication timing is not sensitive to RIF1 dosage. RIF1’s role in replication timing also extends beyond its interaction with PP1. Availing of this separation-of-function approach, we have therefore identified in RIF1 dual function the molecular bases of the co-dependency of the replication-timing program and nuclear architecture.

overall_design: Hi-C experiments were performed on RIf1 WT, targeted WT (tgWT), heterozygous (het), non-PP1-interacting (DP) and knock-out (KO) mouse ES cells. For all conditions three replicates were analyzed (except het, with one replicate).

first: Stefano

last: Gnan

middle: M

first: Kyle

middle: N

last: Klein

first: Eleonora

last: Castelli

first: Alexander

last: Rapp

first: Andreas

last: Maiser

first: Naiming

last: Chen

first: Patrick

last: Weber

first: Elin

last: Enervald

first: M

last: Cardoso

first: Wendy

last: Bickmore

first: David

last: Gilbert

first: Sara

last: Buonomo


title: Adaptive laboratory evolution of E. coli pdhR gene deletion strain

status: Public on Mar 08 2021

city: San Diego

first: Amitesh

last: Anand

state: California

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

summary: We have performed adaptive laboratory evolution of E. coli pdhR gene deletion strain to examine the adaptive strategies of E. coli.

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

overall_design: Growth of E. coli on M9 minimal media supplemented with 4g/l Glucose at 37C was performed with biological duplicates. Total RNA was extracted from mid-log phase culture for RNA-Seq library preparation.


title: Histone acetylation dynamics modulate chromatin conformation and allele-specific interactions at oncogenic loci (Hi-C)

first: Yuanlong

last: Liu

summary: In cancer cells, enhancer hijacking mediated by chromosomal alterations and/or increase of histone H3 lysine 27 acetylation (H3K27ac) can support oncogene expression. However, how the chromatin conformation of enhancer-promoter interactions is affected by these events is unclear. Here, by comparing chromatin structure and H3K27ac levels in normal and lymphoma B-cells, we show that enhancer-promoter interacting regions assume different conformations according to the local abundance of H3K27ac. Genetic or pharmacologic depletion of H3K27ac decreases the frequency and the spreading of these interactions, altering oncogene expression. Moreover, enhancer hijacking mediated by chromosomal translocations influences the epigenetic status of the regions flanking the breakpoint, prompting the formation of distinct intra-chromosomal interactions in the two homologous chromosomes. These interactions are accompanied by allele-specific gene expression changes. Overall, our work indicates that H3K27ac dynamics modulate interaction frequency between regulatory regions and can lead to allele-specific chromatin configurations to sustain oncogene expression.

overall_design: 6 different samples and for each sample the number of replicates were based in sample availability and sequencig depth

first: Stephanie

last: Sungalee

last: LIU

first: Ruxandra

last: Lambuta

first: Natalya

last: Katanayeva

first: Maria

last: Collier

first: Daniele

last: Tavernari

first: Sandrine

last: Roulland

first: Giovanni

last: Ciriello

first: Elisa

last: Oricchio


title: Cornelia-de-Lange syndrome associated mutations cause a DNA damage signalling and repair defect

first: Ilya

last: Flyamer

summary: Cornelia de Lange Syndrome is a multisystem developmental disorder typically caused by mutations in the gene encoding the cohesin loader NIPBL. The associated phenotype is generally assumed to be the consequence of aberrant transcriptional regulation. Recently, we identified a residue substitution in BRD4 associated with a Cornelia de Lange-like Syndrome, that reduces BRD4 binding to acetylated histones. Here we show that, although this mutation reduces BRD4-enhancer interaction in mouse embryonic stem cells, it does not affect transcription. Rather it delays the cell cycle, increased DNA damage signalling, and perturbs regulation of DNA repair in mutant cells. This uncovers a new role for BRD4 in DNA repair pathway choice. Furthermore, we find evidence of a similar increase in DNA damage signalling in cells derived from NIPBL-deficient individuals, suggesting that defective DNA damage signalling and repair is also a feature of typical Cornelia de Lange Syndrome.

overall_design: Examination of Y430C BRD4 mutation in mESCs. Two cell lines were used, a wild type one (WT) and CRISPR-Cas9 generated Y430C mutant one (MUT)

first: Gabrielle

last: Olley

first: Pradeepa

last: Madapura

last: FitzPatrick

first: Charlene

last: Boumendil


title: Coordination of two enhancers drives expression of olfactory trace amine-associated receptors VIII

city: Shanghai

first: Qian

last: Li

address: 280 South Chongqing Road, Building No.5, Room 408

department: Department of Anatomy and Physiology

institute: Shanghai Jiao Tong University School of Medicine

summary: Olfactory sensory neurons (OSNs) are functionally defined by their expression of a unique odorant receptor (OR). Mechanisms underlying singular OR expression are well studied, and involve a massive cross-chromosomal enhancer interaction network. Trace amine-associated receptors (TAARs) form a distinct family of olfactory receptors, and here we find that mechanisms regulating Taar gene choice display many unique features. The epigenetic signature of Taar genes in TAAR OSNs is different from that in OR OSNs. We further identify that two TAAR enhancers conserved across placental mammals are absolutely required for expression of the entire Taar gene repertoire. Deletion of either enhancer dramatically decreases the expression probabilities of different Taar genes, while deletion of both enhancers completely eliminates the TAAR OSN populations. In addition, both of the enhancers are sufficient to drive transgene expression in the partially overlapped TAAR OSNs. We also show that the TAAR enhancers operate in cis to regulate Taar gene expression. Our findings reveal a coordinated control of Taar gene choice in OSNs by two remote enhancers, and provide an excellent model to study molecular mechanisms underlying formation of an olfactory subsystem.

overall_design: We constructed PiggyBac transgenic plasmids with one of the two TAAR enhancers placed upstream of the minimal promoter sequence from mouse Hsp68 (heat shock protein 68 kDa) and followed by the GFP or tdTomato reporter gene. We then generated transgenic mice by injecting PiggyBac plasmids into the pronucleus of fertilized eggs. We obtained TAAR enhancer 1-GFP and TAAR enhancer 2-tdTomato transgenic mice. Then we FCA sorted GFP-positive and GFP-negative cells from TAAR enhancer 1-GFP mice, and tdTomato-positive and tdTomato-positive cells from TAAR enhancer 2-tdTomato mice for RNA-seq analyses.


title: DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus

city: Ithaca

first: Lori

last: Huberman

state: NY

address: 236 Tower Rd.

department: Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science

institute: Cornell University

summary: Sensing available nutrients and efficiently utilizing them is a challenge common to all organisms. The model filamentous fungus Neurospora crassa is capable of utilizing a variety of inorganic and organic nitrogen sources. Nitrogen utilization in N. crassa is regulated by a network of pathway-specific transcription factors in combination with nitrogen catabolite repression regulatory proteins. We identified an uncharacterized pathway-specific transcription factor, amn-1, that is required for utilization of proline, branched chain amino acids, and aromatic amino acids. AMN-1 also plays a role in regulating genes involved in responding to the simple sugar mannose, suggesting an integration of nitrogen and carbon metabolism. The utilization of nonpreferred nitrogen sources is also regulated by the nitrogen catabolite regulator NIT-2. Using RNA sequencing combined with DNA affinity purification sequencing, we performed a survey of the role of NIT-2 and pathway-specific transcription factors in directly regulating genes involved in nitrogen utilization. Our data shows that pathway-specific transcription factors regulate genes involved in the catabolism of specific nitrogen sources, while NIT-2 regulates genes involved in utilization of all nonpreferred nitrogen sources, such as nitrogen transporters. Together, these transcription factors form a nutrient sensing network that allows N. crassa cells to regulate nitrogen utilization.

overall_design: mRNA profiles of wild type and mutant N. crassa cells exposed to carbon starvation, mannose, nitrogen starvation, alanine, arginine, glutamine, glutamate, glycine, isoleucine, proline, tryptophan, ammonium, and nitrate. There are 27 different strains and conditions each done in at least biological triplicate, which includes wild type controls for a total of 86 samples.

first: Vincent

middle: W

last: Wu

first: David

last: Kowbel

first: Igor

middle: V

last: Grigoriev

first: Ronan

last: O'Malley

first: N

last: Glass


title: Multiomics analysis reveals molecular abnormalities in granulosa cells of women with polycystic ovary syndrome

city: Jinan

first: Rusong

last: Zhao

state: Shandong

address: 44 Wenhua xi Road

department: Center for Reproductive Medicine

institute: Shandong University

type: Methylation profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

summary: Polycystic ovary syndrome (PCOS) is the most common complex endocrine and metabolic disease in women of reproductive age. It is characterized by anovulatory infertility, hormone disorders, and polycystic ovarian morphology. Regarding the importance of granulosa cells (GCs) in the pathogenesis of PCOS, few studies have investigated the etiology at a single “omics” level, such as with an mRNA expression array or methylation profiling assay, but this can provide only limited insights into the biological mechanisms. Here, genome-wide DNA methylation together with lncRNA-miRNA-mRNA profiles were simultaneously detected in GCs of PCOS cases and controls. A total of 3579 lncRNAs, 49 miRNAs, 669 mRNAs, and 890 differentially methylated regions (DMR)-associated genes were differentially expressed between PCOS cases and controls. Pathway analysis indicated that these differentially expressed genes were commonly associated with steroid biosynthesis and metabolism-related signaling, such as glycolysis/gluconeogenesis. In addition, we constructed ceRNA networks and identified some known ceRNA axes, such as lncRNAs-miR-628-5p-CYP11A1/HSD17B7. We also identified many new ceRNA axes, such as lncRNAs-miR-483-5p-GOT2. Interestingly, most ceRNA axes were also closely related to steroid biosynthesis and metabolic pathways. These findings suggest that it is important to systematically consider the role of reproductive and metabolic genes in the pathogenesis of PCOS.

overall_design: Granulosa cells of five women with PCOS and five age/body mass index (BMI)-matched control subjects

first: Yonghui

last: Jiang

first: Shigang

first: Han


title: Coordination of two enhancers drives expression of olfactory trace amine-associated receptors V

overall_design: ATAC-seq of TAAR OSNs sorted from Taar5-ires-Cre; lox-L10-GFP, Taar5-ires-Cre; lox-ZsGreen or Taar6-ires-Cre; lox-ZsGreen mice. As a control, all mature OSNs that are mainly composed of OR OSNs were sorted from Omp-ires-GFP mice.


title: A histone H3K4me1 specific binding protein is involved in RdDM

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

summary: In plants, RNA-directed DNA methylation (RdDM) pathway is a well-known de novo DNA methylation pathway that is involved in many important biological processes, such as pathogen defense, stress response and plant development. RdDM involves two plant-specific RNA polymerases, Pol IV and Pol V. In previous studies, several genetic screen systems, including a release of silencing 1 (ros1) suppressor screen, have been designed and used to discover new RdDM components. Through the ros1 suppressor screen, several new RdDM components, such as RDM1 and KTF1, have been reported. In this study, we isolated a new ros1 suppressor mutant, rdm15. Through DNA methylome and whole-genome siRNA analyses, we showed that RDM15 was required for RdDM-dependent DNA methylation and siRNA accumulation at a subset of RdDM target loci. Our further investigation revealed that RDM15 mainly contributes to Pol V-dependent downstream siRNA accumulation, and can interact with NRPE3B, a subunit specific to Pol V. DNA methylation and histone modifications are known to interact with each other to determine DNA methylation and chromatin states. Here, we showed that RDM15 can specifically recognize the histone 3 lysine 4 monomethylation (H3K4me1) mark by its C-terminal tudor domain. The structure of RDM15 tudor domain in complex with an H3K4me1 peptide highlights the specific recognition of H3K4me1 by an aromatic cage and specific hydorgen bonding interactions, which is different from all previously reported lower methyllysine recognition mechanisms. In addition, at the genome wide level, RDM15 and H3K4me1 showed similar distribution patterns at RDM15-dependent RdDM loci, suggesting that RDM15 recognition of H3K4me1 is associated with RDM15 function in RdDM. In summary, we identified and characterized a histone H3K4me1 specific binding protein as a new RdDM component, and the structural analysis of RDM15 revealed a new type of chemical feature-based lower methyllysine recognition mechanism.

overall_design: Study the function of gene RDM15 using Bisulfite-Seq, Small RNA Sequencing, and ChIP-Seq.

first: Qingfeng

last: Niu

first: Zhe

last: Song

first: Kai

last: Tang

first: Rui

last: Liu

first: Ting

last: Ban

first: Zhongxin

last: Guo

first: Heng

last: Zhang

first: Cheng-Guo

last: Duan

first: Huiming

first: Jiamu

last: Du

first: Zhaobo

last: Lang


title: Effect of ecdysterone on the hepatic transcriptome and lipid metabolism in lean and obese Zucker rats

status: Public on Mar 07 2021

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

institute: JLU Gießen

summary: Ecdysteroids are a class of steroid hormones occurring in insects, where they are referred as zooecdysteroids, and in plants, where they are termed phytoecdysteroids. While zooecdysteroids in insects regulate important developmental processes, such as embryogenesis, molting (ecdysis), metamorphosis, reproduction, and diapause, phytoecdysteroids provide protection against invertebrate predators by acting as feeding deterrents and by disrupting critical developmental processes of such invertebrates. The ecdysteroids in insects and plants comprise a great number of different analogues, with 20‐hydroxyecdysone, also called ecdysterone, being the quantitatively dominating biologically active analogue in both, insects and plants. Although phytoecdysteroids are effective toxins or antifeedants towards non-adapted herbivorous invertebrate predators, ecdysteroids are apparently non-toxic to mammals and even have been shown to exert a variety of interesting metabolic actions, such as antiobesity, hypoglycemic and protein-anabolic effects. In the present study aimed to test the hypothesis that ecdysterone causes lipid-lowering effects in obese Zucker rats. To test this hypothesis, two groups of obese Zucker rats were fed a nutrient-adequate diet supplemented without or with 0.05% ecdysterone. This ecdysterone concentration was appropriate to achieve a similar dose of ecdysterone per kg body weight BW as applied in other rodent studies, in which ecdysterone caused either hepatic and plasma lipid-lowering effects or antiobesity effects in different rodent models. In order to decipher the potential lipid-lowering actions of ecdysteroids in Zucker rats, measurements of liver and plasma lipid concentrations and hepatic transcriptome analysis was carried out. To further study if ecdysterone is capable of alleviating the strong lipid-synthetic activity in the liver of obese Zucker rats, the study included also two groups of lean Zucker rats which also received either the ecdysterone-supplemented or the non-supplemented diet.

overall_design: The experiment included 16 male, 25-week-old, homozygous (fa/fa) obese Zucker rats (Crl:ZUC-Leprfa) and 16 male, 25-week-old, heterozygous (fa/+) lean Zucker rats, which were purchased from Charles River (Sulzfeld, Germany). The animals were kept in groups of two animals each under controlled conditions (12-h light:12-h dark, 22 ± 1°C ambient temperature, 50-60 % relative humidity). The lean rats were randomly assigned to two groups [lean control (LC), lean ecdysterone (LE)] of 8 rats each. Also, the obese rats were randomly assigned to two groups [obese control (OC), obese ecdysterone (OE)] of 8 rats each. All groups received the same basal diet, which was sufficient to meet requirements of the rat for maintenance according to National Research Council (NRC) and supplemented (groups LE and OE) or not (groups LC and OC) with 0.5 g ecdysterone (provided from Alibaba, China) per kg diet. For microarray analysis, six liver total RNA samples per group were randomly selected for array hybridization.

first: Denise

last: Gessner

first: Magdalena

last: Marschall

first: Klaus

last: Eder


title: CTLA-4 blockade drives loss of Treg stability in glycolysis-low tumors

city: New York

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Here, we report the immune-mediated mechanisms underlying the improved activity of immune checkpoint blockade in glycolysis-defective tumor models.

overall_design: Evaluate gene expression in control and LDHA-deficient tumors from syngeneic mice treated with anti-CTLA-4 or IgG control

first: Roberta

last: Zappasodi

first: Inna

last: Serganova

first: Ivan

last: Cohen

first: Masatomo

last: Maeda

first: Masahiro

last: Shindo

first: Yasin

last: Senbabaoglu

first: McLane

last: Watson

first: Avigdor

last: Leftin

first: Rachana

last: Maniyar

first: Svena

last: Verma

first: Matthew

last: Lubin

first: Myat

last: Ko

first: Mayuresh

last: Mane

first: Hong

last: Zhong

first: Aranb

last: Ghosh

first: Mohsen

last: Abu-Akeel

first: Ellen

last: Ackerstaff

first: Jason

middle: A

last: Koutcher

first: Ping-Chih

last: Ho

first: Greg

last: Delgoffe

first: Ronald

last: Blasberg

first: Jedd

last: Wolchok

first: Taha

last: Merghoub


title: Epigenetic targeted therapy of leukemia through a hyper-activated BAP1-ASXL1-mutant axis

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: The ASXL1 gene is the human homolog of the Drosophila Asx gene, a core subunit in the BAP1 histone H2A deubiquitinase complex. Mutations of ASXL1 occur in multiple myeloid neoplasms and are uniformly associated with poor prognosis. However, the molecular mechanism through which ASXL1 mutations alter BAP1 activity to drive leukemogenesis remains unclear. Here we demonstrate that cancer-associated frame-shift ASXL1 mutations, which were originally proposed to act as destabilizing loss-of-function mutations, in fact encode truncated stable gain-of-function proteins. Truncated ASXL1 protein stabilizes BAP1, enhances BAP1 complex recruitment to chromatin and promotes the expression of numerous leukemia associated genes. Chemical inhibition of BAP1 rescues these changes in gene expression in leukemic cells and inhibits tumor progression. This study represents a breakthrough advance in our understanding of the molecular mechanisms of ASXL1 mutations in leukemic pathogenesis and identifies small molecular inhibitors of BAP1 function as a potential targeted therapy for leukemia.

overall_design: We will evaluate the function of mutant ASXL1 in human leukemia, and target the hyper-activated BAP1-ASXL1-mutant axis by small molecule inhibitors

first: Lu

last: Wang

first: Zibo

last: Zhao


title: Expression profile of primary mouse microglial cultures exposed to hypoxia

city: Seville

first: Clara

last: Ortega-de San Luis

address: Av. Manuel Siurot S/N

institute: Instituto de Biomedicina de Sevilla (IBiS); Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla

summary: Primary microglial cultures from neonatal mice were exposed to hypoxia (1% O2, 6 h) and their global gene expression profile was analyzed. This data were used to described the Hypoxic Microglia Signature, genes that were up- or down-regulated by hypoxia in microglial cells in culture.

overall_design: 6 Total samples were analyzed (3 samples per group). We compared Hypoxic treatment with Normoxic controls.

first: Manuel

last: Sanchez-Garcia

first: Rosana

last: March-Diaz

first: Antonio

last: Heras-Garvin

first: Nieves

last: Lara-Ureña

first: Alberto

last: Pascual


title: FaDu STING Isogenic RNA-Seq

city: New Haven

first: Thomas

last: Hayman

state: CT

address: 15 York Street

department: Department of Therapeutic Radiology

institute: Yale University

summary: RNA-Seq of FaDu Cas9 isogenic cells treated with fractionated RT.

overall_design: Effects of STING KO on baseline and radiation-induced gene expression.

first: Sameet

last: Mehta

first: James

last: Knight

first: Joesph

last: Contessa


title: Coordination of two enhancers drives expression of olfactory trace amine-associated receptors VII

first: Qian

last: Li

overall_design: In order to gain genetic access to TAAR-expressing OSNs, we generated Taar5-ires-Cre and Taar6-ires-Cre knockin mouse lines, in which Cre recombinase is co-transcribed with Taar5 and Taar6 gene, respectively. Each Cre line was crossed with Cre-dependent reporter lines, including lox-L10-GFP and lox-ZsGreen, to fluorescently label the specific population of TAAR OSNs. The GFP- or ZsGreen-negative cells were also sorted to serve as control cells, approximately 70-80% of which are composed of OR-expressing OSNs.


title: Coordination of two enhancers drives expression of olfactory trace amine-associated receptors VI

overall_design: H3K9me3 native ChIP-seq analysis on purified TAAR OSNs from Taar5-ires-Cre; lox-L10-GFP mice and sorted GFP-negative cells that are mainly OR OSNs


title: CTLA-4 blockade drives loss of Treg stability in glycolysis-low tumors.

first: Bic

last: MSKCC

overall_design: Correlate glycolysis-related genes with immune infiltration in human melanoma tumors before and after ipilimumab treatment.

first: Roberta

last: Zappasodi

first: Inna

last: Serganova

first: Ivan

last: Cohen

first: Masatomo

last: Maeda

first: Masahiro

last: Shindo

first: Yasin

last: Senbabaoglu

first: McLane

last: Watson

first: Avigdor

last: Leftin

first: Rachana

last: Maniyar

first: Svena

last: Verma

first: Matthew

last: Lubin

first: Myat

last: Ko

first: Mayuresh

last: Mane

first: Hong

last: Zhong

first: Cailian

last: Liu

first: Aranb

last: Ghosh

first: Mohsen

last: Abu-Akeel

first: Ellen

last: Ackerstaff

first: Jason

last: Koutcher

first: Ping-Chih

last: Ho

first: Greg

last: Delgoffe

first: Ronald

last: Blasberg

middle: D


title: Coordination of two enhancers drives expression of olfactory trace amine-associated receptors

first: Qian

last: Li

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

overall_design: Refer to individual Series


title: Single-cell RNAseq of mouse pancreatic cells treated with proliferative compounds

city: Stockholm

first: Olov

last: Andersson

state: Solna

address: Tomtebodavägen 16

department: CMB

country: Sweden

institute: Karolinska Institute

summary: It is known that β-cell proliferation expands the β-cell mass during development and under certain hyperglycemic conditions in the adult, a process that may be used for β-cell regeneration in diabetes. Here we used a novel high-throughput technique in zebrafish and screened 3119 chemicals to determine whether they promoted β-cell proliferation. We identified HG-9-91-01, which was further confirmed to drive the proliferation of zebrafish, mouse, and human β-cells. HG-9-91-01 is an inhibitor of salt-inducible kinases (SIK), and β-cell specific overexpression of Sik1 blocked its effect on β-cell proliferation. Single-cell transcriptomic analyses of mouse β-cells demonstrated that HG-9-91-01 induced an early wave of ATF6-dependent unfolded protein response (UPR), which was not related to increased insulin expression. Additional mechanistic studies indicated that HG-9-91-01 induced multiple signaling effectors downstream of SIK inhibition, including CRTC, ATF6/IRE1, and mTOR, which integrated to collectively drive β-cell proliferation.

overall_design: Examination of six 384-well plates corresponding to pancreatic mouse enocrine cells treated for 6, 48 or 96 h with different compounds. Plate layout was as follows: single-cells treated with negative control DMSO (96 wells),  positive control Harmine (96 wells)  and with one of the other compounds (96 wells per compound) at a specific time point.

first: Jeremie

last: Charbord

first: Anna

last: Johansson


title: Mesenchymal glioblastoma constitutes a major ceRNA signature in the TGF-Beta pathway

city: Harbin

first: Jinquan

last: Cai

address: Xuefu Road

institute: Harbin Medical University


title: Coordination of two enhancers drives expression of olfactory trace amine-associated receptors IV

overall_design: Main olfactory epithelium (MOE) mRNA profiles of wild type (WT), TAAR enhancer 2 +/- (het) and TAAR enhancer 2 -/- (homo) mice


title: Coordination of two enhancers drives expression of olfactory trace amine-associated receptors II

overall_design: Main olfactory epithelium (MOE) mRNA profiles of wild type (WT), TAAR enhancer 1and2 double knockout +/- (het) and TAAR enhancer 1and2 double knockout -/- (homo) mice


title: Translational activation by an alternative sigma factor in Bacillus subtilis

status: Public on Mar 06 2021

city: Cambridge

first: Gene-Wei

state: MA

address: 31 Ames Street, 68-223A

department: Biology

institute: Massachusetts Institute of Technology

summary: Sigma factors are an important class of bacterial transcription factors that lend specificity to RNA polymerases by binding to distinct promoter elements for genes in their regulons. Here we show that activation of the general stress sigma factor, B, in Bacillus subtilis paradoxically leads to dramatic induction of translation for a subset of its regulon genes. These genes are translationally repressed when transcribed by the housekeeping sigma factor, A, owing to extended RNA secondary structures as determined in vivo using DMS-MaPseq. Transcription fromB-dependent promoters liberates the secondary structures and activates translation, leading to dual induction. Translation efficiencies between B- and A-dependent RNA isoforms can vary by up to 100-fold, which in multiple cases exceeds the magnitude of transcriptional induction. These results highlight the role of long-range RNA folding in modulating translation and demonstrate that a transcription factor can regulate protein synthesis beyond its effects on transcript levels.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: RNA was isolated from BS168 cells treated with DMS in vivo and from untreated cells. Regions of the σA-dependent isoforms of ctc and yvrE were specifically reverse-transcribed from each sample using TGIRT-III, which encoded DMS-induced RNA modifications as mutations in the resulting DNA amplicons. Libraries were prepared for sequencing following the established DMS-MaPseq protocol from Tomezsko et al., Nature, 2020 and Zubradt et al., Nature Methods, 2016. DMS signals were quantified using the DREEM algorithm from Tomezsko et al., Nature, 2020 and used as folding constraints to determine the RNA structure for each isoform.

first: Dylan

last: McCormick

first: Jean-Benoît

last: Lalanne

first: Tammy

last: Lan

first: Silvi

last: Rouskin


title: Coordination of two enhancers drives expression of olfactory trace amine-associated receptors III

overall_design: Main olfactory epithelium (MOE) mRNA profiles of wild type (WT), TAAR enhancer 1 +/- (het) and TAAR enhancer 1 -/- (homo) mice


title: Coordination of two enhancers drives expression of olfactory trace amine-associated receptors I

overall_design: Main olfactory epithelium (MOE) mRNA profiles of wild type (WT), TAAR cluster +/- (het) and TAAR cluster -/- (homo) mice


title: FaDu RT CRISPR Screen

first: Thomas

last: Hayman

summary: CRISPR-Cas9 screen of FaDu Cas9 cells treated with fractionated RT.

overall_design: Irradiated cell gRNA representation vs control cell gRNA representation.

first: Sameet

last: Mehta

first: James

last: Knight

first: Wei

last: Cui

first: Joesph

last: Contessa


title: Targeted single-cell RNA sequencing of transcription factors facilitates biological insights from human cell experimental models [iPSC-derived neurons]

city: Oxford

first: Alexandra

last: Pokhilko

address: John Radcliffe Hospital, Headington

department: Nuffield Department of Clinical Neurosciences

institute: University of Oxford

summary: Single cell RNA sequencing (scRNA-seq) is a widely used method for identifying cell types and trajectories in biologically heterogeneous samples, but is limited in its detection and quantification of lowly expressed genes. This results in missing important biological signals, such as the expression of key transcription factors (TFs) driving cellular differentiation. We show that targeted sequencing of ~1000 TFs (scCapture-seq) in iPSC-derived neuronal cultures greatly improves the biological information garnered from scRNA-seq. Increased TF resolution enhanced cell-type identification, developmental trajectories and gene regulatory networks. This allowed us to resolve differences amongst neuronal populations, which were generated in two different labs using the same differentiation protocol. ScCapture-seq improved TF gene-regulatory network inference and thus identified divergent patterns of neurogenesis into either excitatory cortical neurons or inhibitory interneurons. Furthermore, scCapture-seq revealed a role for of retinoic acid signalling in the developmental divergence between these different neuronal populations. Our results demonstrate that TF targeting improves the characterization of human cellular models and allows identification of the essential differences between cellular populations, which would otherwise be missed in traditional scRNA-seq. scCapture-seq TF targeting represents a cost-effective enhancement of scRNA-seq, which could be broadly applied to any cellular models to improve scRNA-seq resolution.

overall_design: RNAseq profiles of 376 single cells (iPSC-derived neurons) from 2 laboratories harvested at day 55 after plating. Single cells were isolated by FACS onto 96-well plates and sequenced on 1 lane of HiSeq4000 at 75bp paired end. RNA from each cell was sequenced twice: the PRE-capture libraries have all human genome sequenced, while only chosen set of transcription factors was sequenced in POST-capture libraries.

first: A

middle: E

last: Handel

first: F

last: Curion

first: V

last: Volpato

first: E

last: Whiteley

first: S

last: Bøstrand

last: Newey

first: C

last: Akerman

last: Webber

first: M

last: Clark

first: R

last: Bowden

first: Z

last: Cader


title: RNA-seq of glioma patient-derived xenografts treated by DMSO or LY2109761

first: Jinquan

last: Cai

summary: We employed the patient-derived xenografts (PDX) model to test the efficiency of LY2109761 in vivo. The drug was intraperitoneally administered, and the mice were sacrificed on the 31st day. The tumors were excised and subjected to RNA-seq. All groups had similar expression density distributions. Hierarchical clustering showed that the same processing groups had the closest distances.

overall_design: Examination of differential expressive genes in glioma tissues from PDX treated by DMSO or LY2109761.

first: Qixue

last: Wang

first: Jing

last: Zhang

first: Chunsheng

last: Kang


title: Comparison of HCMV nascent and steady state transcriptomes expresssed in the Kasumi-3 latency model at early times post-infection

status: Public on Mar 05 2021

first: Mary

last: Hummel

address: 303 E. Chicago Ave

institute: Northwestern University

summary: Purpose: to compare newly transcribed and steady-state HCMV RNAs expressed in Kasumi-3 cells at 24 hr post-infection

sample_organism:
Homo sapiens
Human betaherpesvirus 5

platform_organism:
Homo sapiens
Human betaherpesvirus 5

overall_design: Kasumi-3 cells were infected with the TB40/E wtGFP strain of HCMV.  At 24 hr post-infection, cells were sorted for GFP expression, and newly synthesized RNA was labeled for 4 hr with 5-ethynyl uridine. Mock-infected cells were sorted for live cells and labeled in parallel.  A portion of the RNA was save for analysis of steady state RNA, and the nascent RNA was purified by biotinylation of EU-labeled RNA and selection on Streptavidin beads.  cDNA was prepared from each of the four RNA populations and the cDNA was purified with a Qiagen minElute PCR purification kit.  Nextera libraries were prepared and sequenced with Illumina NextSeq paired end technology.

first: Eleonora

last: Forte

first: Matthew

last: Schipma


title: RNA-seq of glioma patient tissues treated by DMSO or LY2109761

summary: Glioma tissues from patients were cultured in complete DMEM and treated with either DMSO or LY2109761, an inhibitor of TGFBR2. Tissue blocks of TBD0207 and TBD0220 were subjected to RNA-seq.

overall_design: Examination of differential expressive genes in glioma tissues treated by DMSO or LY2109761 from patients.


title: Pol2 occupancy of the viral and host genomes in HCMV infected Kasumi-3 cells at 24 hpi

summary: Purpose: to compare Pol2 occupancy of the host genome in HCMV infected  and mock infected Kasumi-3 cells at 24 hours post infection and analyze Pol2 occupancy of the viral genome in GFP+ infected cells

overall_design: Kasumi-3 cells were infected with the TB40/E wtGFP strain of HCMV.  At 4 hr post-infection, virus was inactivated and cells left in culture for additional 20 hours. Infected cells were sorted for GFP expression and live cells. Mock infected cells were sorted for live cells. After fixation, cells were lysed and sonication with Covaris Focused-ultrasonicator at 10% Duty Cycle, 140 peak, 200 cycles per burst, 360 seconds. ChIP was performed by incubating the sonicated sample with  Rpb1 NTD (D8L4Y) Rabbit mAb #14958 (Cell Signaling Technologies) and the  protein A/G agarose beads. Beads were washed and eluted in 200μl of elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1.0% SDS). The eluates were de-cross-linked and the DNA purified using the Qiagen PCR purification kit. Libraries were prepared with the KAPA HTP Library Preparation Kit multiplexed with NEXTflex DNA Barcodes (Bioo Scientific) and size selected with AMPure XB beads (Beckman Coulter) to have fragments 250-450 bp in length. Library quality control was assessed using Bioanalyzer High Sensitivity DNA Analysis kit (Agilent) and sequencing was performed with Illumina NextSeq technology (50bp single- end reads).


title: Pol2 and H3K27Ac and H3K27me3 occupancy of the viral genome in HCMV infected Kasumi-3 cells at early times post infection

summary: Purpose: to compare Pol2 and H3K27Ac and H3K27me3 in HCMV infected Kasumi-3 cells at 4 and 24 hours post infection

overall_design: Kasumi-3 cells were infected with the TB40/E wtGFP strain of HCMV.  At 4 hr post-infection, virus was inactivated and cells were either fixed immediately (4hpi) or left in culture for additional 24 hours. After fixation, cells were lysed and sonication with Covaris Focused-ultrasonicator at 10% Duty Cycle, 140 peak, 200 cycles per burst, 360 seconds. ChIP was performed by incubating the sonicated sample with either Rpb1 NTD (D8L4Y) Rabbit mAb #14958, Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb #8173, or Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9733 (Cell Signaling Technologies) and the  protein A/G agarose beads. Beads were washed and eluted in 200μl of elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1.0% SDS). The eluates were de-cross-linked and the DNA purified using the Qiagen PCR purification kit. Libraries were prepared with the KAPA HTP Library Preparation Kit multiplexed with NEXTflex DNA Barcodes (Bioo Scientific) and size selected with AMPure XB beads (Beckman Coulter) to have fragments 250-450 bp in length. Library quality control was assessed using Bioanalyzer High Sensitivity DNA Analysis kit (Agilent) and sequencing was performed with Illumina NextSeq technology (50bp single- end reads).


title: miRNA-seq of glioma patient tissues treated by DMSO or LY2109761

summary: Glioma tissues from patients were cultured in complete DMEM and treated with either DMSO or LY2109761, an inhibitor of TGFBR2. Tissue blocks of TBD0207 and TBD0220 were subjected to miRNA-seq.


title: Healing human gingiva transcriptome

city: Columbus

first: Dimitris

last: Tatakis

state: OH

address: 305 W. 12th ave

department: Periodontology

institute: The Ohio State University

summary: This study is the first to report on the transcriptome of healing gingiva and to provide an integrative analysis of mRNA/miRNA expression during human oral wound healing; the results offer novel insights into the participating molecular mechanisms and suggest that miR-124-3p and PXDN could be potential wound healing therapeutic targets.

overall_design: Tissue samples in huamn FGG form were harvested from each volunteer; one represented normal gingiva and the contralateral represented healing gingiva (wounded 5 days prior). Tissue samples were used for next generation mRNA and miRNA sequencing analysis,

first: Yun


title: Healing human gingiva miRNome

summary: This study is the first to report on the miRNome of healing gingiva and to provide an integrative analysis of mRNA/miRNA expression during human oral wound healing; the results offer novel insights into the participating molecular mechanisms and suggest that miR-124-3p and PXDN could be potential wound healing therapeutic targets.


title: Pathochip data of tonsil and lymph node samples

city: Durham

first: Gao

state: NC

address: 203 Research Dr | MSRB1, Rm 179

department: The Preston Robert Tisch Brain Tumor Center

institute: Duke University School of Medicine

summary: The Microbiome of HPV-Positive Tonsil Squamous Cell Carcinoma and Neck Metastasis

sample_organism:
Homo sapiens
human metagenome

overall_design: Analysis of the different microbial species detected in the primary tumor specimens and lymph nodes

first: Karthik

last: Rajasekaran

first: Ryan

last: Carey

first: Xiang

last: Lin

first: Tyler

last: Seckar

first: Zhi

last: Wei

first: Erle

last: Robertson


title: Mutant PRPF8 causes widespread splicing changes in spliceosome components in retinitis pigmentosa patient RPE cells

city: Madrid

first: Alberto

last: Benguria

address: Melchor Fernadez Almagro

institute: Centro Nacional Investigaciones Cardiovasculares

summary: Retinitis pigmentosa is a rare, progressive disease which affects photoreceptors and retinal pigment epithelial (RPE) cells with blindness as a final outcome. Despite high medical and social impact, there is currently no therapeutic options to slow down the progression or cure the disease. The development of effective therapies was largely hindered by high genetic heterogeneity, inaccessible disease tissue and unfaithful model organisms. The fact that components of ubiquitously expressed splicing factors lead to the retina-specific disease is an additional intriguing question. Herein, we sought to correlate the retinal cell type-specific disease phenotype with the splicing profile shown by a patient with autosomal recessive RP, caused by a mutation in pre–mRNA splicing factor 8 (PRPF8). In order to get insight into the role of PRPF8 in homeostasis and disease, we capitalize on the ability to generate patient-specific RPE cells and reveal differentially expressed genes unique to RPE cells. We found that spliceosomal complex and ribosomal functions are crucial in determining cell type specificity through differential expression and alternative splicing (AS), and that PRPF8 mutation causes global changes in splice site selection and exon inclusion that particularly affect genes involved in these cellular functions. This finding corroborates the hypothesis that retinal tissue identity is conferred by specific splicing program, and identifies retinal AS events as a framework towards the design of novel therapeutic opportunities.

overall_design: Comparison between a patient diagnosed with autosomal dominant retinitis pigmentosa (adRP) bearing a mutation in PRPF8 (NM_006445:c.6974-6994del, p.Val2325_Glu2331del),  and a healthy individual used as control. For both individuals, retinal pigment epithelium (RPE) cells were generated from reprogrammed dermal skin fibroblasts. Two samples per individual (patient and control) were therefore analyzed, namely iPSC-RPE cells and  fibroblasts. Three independent experimental replicates per sample were generated.

first: Ángeles

last: Arzalluz-Luque

first: Heli

last: Skottman

first: Inma

last: Hernan

first: Miguel

last: Carballo

first: Beatriz

last: Pascual

first: Ana

last: Dopazo

first: José

last: Cabrera

first: Arantxa

last: Bolinches-Amorós

first: Benguria

last: Alberto

first: Nicolás

last: Cuenca

first: Vincenzo

last: Lupo

first: Bárbara

last: Delás

first: Sonia

last: Tarazona

first: Erceg

last: Slaven

first: Lukovic

last: Dunja


title: Eukaryotic enteric virus infections modulate the host tissue transcriptome

first: Simone

last: Dallari

address: 550 1st Ave

institute: New York University Grossman School of Medicine

summary: Contributions of the viral component of the microbiome, the virome, to the development of innate and adaptive immunity are largely unknown. In this study, we systematically defined the tissue host response to a panel of eukaryotic enteric viruses inducing asymptomatic infection in mice. Small intestinal and colon transcriptomes from GF mice were compared to the ones from germ-free mice mono-infected with each of the viruses in the panel. This transcriptional profiling unveiled general adaptations by the host as well as numerous viral strain-specific responses that persist.

overall_design: Bulk transcriptome of colonic and small intestinal tissues nodes from uninfected and virus-infected germ free mice

first: Ken

last: Cadwell


title: Chromatin accessibilty analysis of HCMV infected and mock-infected Kasumi-3 cells at 24 hours  post infection

first: Mary

last: Hummel

summary: Purpose: to compare host gene expression in HCMV infected and mock infected Kasumi-3 cells at 24 hours post infection and analyze viral chromatin accessibility

overall_design: Kasumi-3 cells were infected with the TB40/E wtGFP strain of HCMV.  At 4 hr post-infection, virus was inactivated and cells were kept in culture for additional 20 hours. Infected cells were sorted for GFP expression and live cells while mock infected cells for live cells. Sorted cells were  collected and lysed in transposase reaction buffer as described below.

first: Eleonora

last: Forte

first: Matthew

last: Schipma


title: Single cell transcriptomics reveals involution mimicry during the specification of the basal breast cancer subtype

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

summary: Here, we use spatially and time controlled induction of Elf5 within the mammary epithelium in the context of the luminal MMTV-PyMT mouse mammary cancer to study tumour progression mechanisms associated to the specification of the basal breast cancer subtype at single-cell resolution.

overall_design: In this study we used two mouse models, the well-established MMTV-PYMT mouse mammary tumour model (PyMT/WT) and a mammary restricted (MMTV) doxycycline-inducible (rtTA) Elf5 expression model crossed with the PyMT/WT model (PyMT/Elf5) . Consistent with previous reports, the specific induction of Elf5 in the mammary gland epithelium results in a significant increase of lung metastases and a dramatic leaky vasculature phenotype in the PyMT model. A total of fifteen mouse mammary tumours at metastatic stage (14 weeks old FBVn background) from the MMTV-PyMT/WT and /ELF5 model were harvested and analysed using Drop-seq[24].

first: Fatima

last: Valdes-Mora

first: David

last: Gallego-Ortega


title: Patient-derived organoids as a platform to study cervical cancer and viral infection

city: Utrecht

first: Kadi

last: Lõhmussaar

state: -- Select State/Province --

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary:
Cervical cancer is a common gynecological malignancy, often caused by high-risk human papillomavirus. There is a paucity of human-derived culture systems to study cervical epithelium and the cancers derived thereof. Here, we describe a long-term culturing protocol for ecto- and endocervical epithelia, which generates 3D organoids that stably recapitulate the two tissues of origin. In the example of successful HSV-1 infection, we show that the organoid-based cervical models serve as promising platforms for studying sexually transmitted pathogens. Starting from Pap-brush material, a small biobank of patient-derived tumoroids was established that retained the causative HPV genomes. One of these uniquely carried the poorly characterized HPV30 subtype, implying a potential role in carcinogenesis. The tumoroids displayed differential responses to common chemotherapeutics and grew as xenografts in mice. This study describes an experimental platform for cervical (cancer) research and for future personalized medicine approaches.
Purpose: Transcriptome analysis was performed on organoids/tissues derived from human ecto- and endocervix as well as associated malignancies to characterize the new organoid-based platform.
Methods: Ectocervical organoids and tumoroid lines were cultured in M7 media, whereas endocervical organoids in M7+4 media prior harvesting for RNA extraction (see paper for details). Additionally, RNA was extracted from healthy ecto-and endocervical tissue biopsies as well as from primary cells collected via Pap brush method from cervical cancer patients. The libraries were prepared by the Utrecht Sequencing Facility (USEQ) based on polyA enrichment. Sequencing was performed on an Illumina NextSeq500 by using 75-bp single-end or paired-end sequencing. Reads were aligned to the human reference genome (GRCh37) using Burrows-Wheeler Aligner (BWA) (v0.5.9). Viral sequences of different HPV subtypes were detected in the RNA-seq data of the different tumoroid lines and tissues by using VirusSeq-CLI, a wrapper around the VirusSeq pipeline.
Results: Ectocervical and endocervical organoids display distinct transcriptomic profiles that can be maintained in cultures for long term. Similarily, the the gene expression profile of tumor organoids clusters apart from healthy counterparts and shows evident tumor-like characteristics. Tumor organoids show expression of causative HPV oncogenes.

overall_design: mRNA profiles of primary tissues and organoids were generated by Deep Sequencing (Illumina NextSeq500 by using 75-bp single- or paired-end sequencing). Transcriptome profiles were generated from 3 biologically independent organoid lines derived from healthy ectocervix and endocervix of patients undergoing hysterectomy due to other than cervix related conditions (organoids in both early and late passages were sequenced). In total of 9/12 established tumoroid lines were sequenced (3 of the lines in both early and late passages). Additionally, 3 tissue samples were sequenced from normal ecto- and endocervix as well as from 3 independent cervical squamous cell carcinomas.

first: Hans

last: Clevers


title: The BAF chromatin remodeling complex regulates gene expression programs essential for mammalian neural crest development

city: Singapore

first: Manvendra

middle: K.

last: Singh

address: 8 College Road

department: Programme in Cardiovascular & Metabolic Disorders

country: Singapore

institute: Duke-NUS MEDICAL SCHOOL

summary: Neural crest cells (NCCs) are a multipotent cell population that contributes to the development  of many tissues including craniofacial, pharyngeal arch arteries, and cardiac outflow tract  (OFT). The BAF complex plays an important role in the development of a wide range of tissues  by modulating gene expression programs at the chromatin level. However, its role in neural  crest development has remained unclear. To determine the role BAF complex, we deleted  BAF155 and BAF170, the core subunits required for the assembly, stability, and functions of  the BAF complex in NCCs. Mouse embryos lacking BAF155/170 in NCCs displayed early  lethality due to a wide range of developmental defects including craniofacial defects,  pharyngeal arch artery defects, and OFT defects. We observed reduced proliferation,  increased cell death, and impaired migration of cardiac NCCs to the OFT in BAF155/170  mutants. RNAseq analysis on sorted NCCs revealed that the BAF complex regulates the  expression of numerous genes essential for neural crest development. We observed  downregulation of Hippo and Notch signaling pathways, both essential for the migration,  proliferation, and differentiation of the NCCs. The BAF complex interacts with transcription  factors to modulate the transcriptional program. Therefore, we performed transcription factor  enrichment analysis on the RNAseq data set and identified several transcription factors  including Hey1, Hey2, and Hes5 that may directly or indirectly interact with the BAF complex  in NCCs. We also found that Brg1 interact with Tead transcription factors and the interaction  was impaired in BAF155/170 knockdown cells. Together, our results demonstrate an  important role of the BAF complex in modulating the gene regulatory network essential for  neural crest development.

overall_design: 6 samples are analyzed comprises of control (n = 3) and mutant (n = 3)

first: Kathleen

last: Wung Bi-Lin

first: Pratap

last: Veerabrahma Seshachalam

first: Tran

last: Tuoc

first: Anastassia

last: Stoykova

first: Sujoy

last: Ghosh

first: Manvedra


title: Direct and indirect podocyte injury manifested in a partial podocytectomy mouse model

city: Isehara

first: Masahiro

last: Okabe

address: 143 Shimokasuya

country: Japan

institute: Tokai University School of Medicine

summary: Injured podocytes indirectly influence neighboring podocytes. To study the indirect effect, we generated mosaic mice, Pod-hCD25T/G, in which podocytes express either hCD25 + tdTomato or EGFP alone. A hCD25-targetting immunotoxin LMB2 was injected into the mosaic mice to induce injury selectively in tdTomato(+) podocytes. We analyzed RNA expressing profile in tdTomato(+) (hCD25 expressing) and EGFP(+) (hCD25 not expressing) podocytes before and after LMB2 injection.

overall_design: Glomeruli were harvested from Pod-hCD25T/G mouse before and 1, 4, and 7 days after LBM2 treatment. tdTomato(+) and EGFP(+) podocytes were collected by cell sorter and RNA expressing profile was analyzed.

first: Kazuyoshi

last: Yamamoto

first: Yoichi

last: Miyazaki

first: Masaru

last: Motojima

first: Masato

last: Ohtsuka

first: Ira

last: Pastan

first: Takashi

last: Yokoo

first: Taiji

last: Matsusaka


title: Myeloid-stromal subtypes reveal NOD2-mediated Crohn's and rescue pathways

city: new york

first: Mamta

last: Giri

state: new york

address: 1470 madison ave

department: Institute of Personalized medicine

institute: Mount Sinai hospital

summary: Crohn’s disease (CD) is a chronic inflammatory intestinal disease, often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2-pathogenicity and salvage pathways in anti-TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature, and propose new precision therapeutic approaches involving gp130 blockade for select CD patients, to potentially supplement anti-TNF therapy

overall_design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS-treated fish

first: Judy

last: Cho


title: Viral transcriptome analysis of HCMV infected Kasumi-3 cells at early time post infection

first: Mary

last: Hummel

summary: Purpose: to compare viral gene expression in HCMV infected Kasumi-3 cells at 4 and 24 hours post infection

overall_design: Kasumi-3 cells were infected with the TB40/E wtGFP strain of HCMV.  At 4 hr post-infection, virus was inactivated and cells were either collected immediately (4hpi) or left in culture for additional 24 hours. Cells were collected and lysed in trizol. Total RNA was prepared using the Direct-zol RNA miniprep kit (Zymo Research) with an on-column DNase digestion.  RNA was rRNA depleted with Ribo-zero (Illumina) and RNA-seq libraries were prepared with TrueSeq Stranded mRNA (Illumina). RNA-seq libraries were sequenced on the Illumina NextSeq 500 Sequencing System (50 bp single-end reads, 50 million reads/sample).

first: Eleonora

last: Forte

first: Matthew

last: Schipma


title: Transcriptome analysis of HCMV infected and mock-infected Kasumi-3 cells at 24 hours post infection

summary: Purpose: to compare host gene expression in HCMV infected and mock infected Kasumi-3 cells at 24 hours post infection

overall_design: Kasumi-3 cells were infected with the TB40/E wtGFP strain of HCMV.  At 4 hr post-infection, virus was inactivated and cells were kept in culture for additional 20 hours. Infected cells were sorted for GFP expression and live cells while mock infected cells for live cells. Sorted cells were  collected and lysed in trizol. Total RNA was prepared using the Direct-zol RNA miniprep kit (Zymo Research) with an on-column DNase digestion.  RNA was rRNA depleted with Ribo-zero (Illumina) and RNA-seq libraries were prepared with TrueSeq Stranded mRNA (Illumina). RNA-seq libraries were sequenced on the Illumina NextSeq 500 Sequencing System (50 bp single-end reads).


title: The TAZ-CAMTA1 and YAP-TFE3 fusion proteins modulate the basal TAZ/YAP transcriptional program by recruiting the Ada2a-containing histone acetyltransferase complex [ChIP-seq]

status: Public on Mar 04 2021

city: Iowa City

first: Michael

last: Chimenti

state: IA

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary:
The WWTR1(TAZ)-CAMTA1 and YAP1-TFE3 gene fusions are disease defining gene alterations for epithelioid hemangioendothelioma, a vascular cancer. The resultant fusion proteins fuse the C terminus of CAMTA1 and TFE3 in frame to the N terminus of TAZ and YAP, respectively. An unbiased BioID-mass spectrometry/RNAi screen identified YEATS2 and ZZZ3 as components of the Ada2a-containing histone acetyltransferase complex and key interactors of both TAZ-CAMTA1 and YAP-TFE3.
An integrative NGS approach validating the chromatin occupancy of TAZ-CAMTA1 and YAP-TFE3 with distal regulatory elements, such as enhancer regions marked by the presence of H3K27ac marks.
The altered transcriptional program of the fusion proteins owing to altered DNA binding as well as shifts in the chromatin landscape.

overall_design: H3K27ac ChIP-seq  profiles of SW872 liposarcoma cells transduced with fusion gene constructs and full length controls  were generated by deep sequencing, in biological duplicate.

first: Munir

last: Tanas


title: Transcriptome of Chat positive and negative ILC2s

city: New York

first: Gregory

last: Putzel

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

summary: Group 2 innate lymphoid cells (ILC2s) reside in multiple tissues including lymphoid organs and barrier surfaces, and secrete type 2 cytokines including interleukin (IL)-5, IL-9 and IL-13. These cells participate in multiple physiological processes including allergic inflammation, tissue repair, metabolic homeostasis and host defense against helminth infections. Recent studies indicate that neuropeptides can play an important role in regulating ILC2 responses, however, the mechanisms that underlie these processes in vivo remain incompletely defined. Here, we identify that activated ILC2s upregulate choline acetyltransferase (ChAT)—the enzyme responsible for the biosynthesis of acetylcholine (ACh)—following infection with the helminth parasite Nippostrongylus brasiliensis or treatment with alarmins or cytokines including IL-25, IL-33 and thymic stromal lymphopoietin (TSLP). ILC2s also express acetylcholine receptors (AChRs), and ACh administration promotes ILC2 cytokine production and elicits expulsion of helminth infection. In accordance with this, ChAT deficiency in ILC2s leads to defective ILC2 responses and impaired immunity against helminth infection. Together, these results reveal a previously unrecognized role of the ChAT-ACh pathway in promoting type 2 innate immunity to helminth infection.

overall_design: Six samples.

first: Coco

last: Chu

first: David

last: Artis


title: Hypothalamus transcriptome signatures underlying metabolic malprogramming in offspring mice exposed to a maternal obesogenic environment

city: Shenzhen

first: Yizhe

last: Tang

state: Guangdong Province

address: 3002 Sun Gang West Road, Futian District

institute: Shenzhen Second People's Hospital Department of Geriatrics

summary:
Purpose: Identify the potential effector that might responding to the irritated hypothalamic ER stress as early as postnatal resulting from maternal obesity exposure.
Methods: Three-week-old male offspring were selected for extracting RNA sample from the three groups (triplicate in sample): LP (Lg42_P1, Lg63_P2, Lg63_P3), HP (Hg43_P1, Hg43_P2, Hg13_P3) and HA (Hg43_A1, Hg43_A2, Hg13_A3). After standard RNA quantification and qualification, library preparation, clustering, sequencing and quality control, reads were mapped to the reference genome, and quantified of gene expression level with FPKM. The data were further processed for differential expression and other functional analysis.
Results: We identified 789 differentially expressed genes (DEGs) (DESeq2, pvalue<0.05, |log2FoldChange|>0.0) in the mice from HP compared with those from LP, of which 408 (52%) were upregulated, while 381 (48%) downregulated. Whereas, for those of HA versus HP, 726 DEGs were detected, with 401 (55%) upregulated and 325 (45%) downregulated. There was a total of 158 overlapped DEGs between the two compared groups. In the following Gene Ontology enrichment analysis, we found that the upregulated DEGs in the HP group were significantly enriched in the categories related to molecular chaperon mediated protein processing. While for those downregulated DEGs in HA, similar theme was enriched with most of the genes from family members of the heat shock protein (Hsp), especially Hsp70. We validated the alteration of two members of Hsp70 in the hypothalamus of the weaning offspring given their crucial role in the stress response.
Conclusions: Hspa1b might be the potential effector for the irritated early hypothalamic ER stress and the root of unbalanced stress balance in the hypothalamus undergoing feeding-related circuit axon projection in male offspring from obese dams.

overall_design: Animal model building and RNA sample extraction: Five-week-old ICR female mice were given low-fat diet (LFD) or high-fat high-sucrose diet (HFHS) for five weeks before breeding. The dams were keeping with the same diets of the pregestational one during the gestation and lactation. Ten pups per litter were adapted on the day of production. During the postnatal 4 to 16, pups from dams feeding with LFD or HFHS were peripherally injected with PBS (vehicle) or 4-PBA daily. Thus there were offspring from LFD fed dams receiving vehicle (referred to as LP) or from HFHS fed dams receiving vehicle (referred to as HP) or 4-PBA (referred to as HA). At weaning, male offspring were selected for extracting RNA sample from the three groups (triplicate in sample): LP (Lg42_P1, Lg63_P2, Lg63_P3), HP (Hg43_P1, Hg43_P2, Hg13_P3) and HA (Hg43_A1, Hg43_A2, Hg13_A3).

last: Chen

first: Xiaoqiu

last: Xiao


title: Transcriptome differences between primary brown and white preadipocytes treated with Fgf8b or control

city: Freising

first: Tobias

last: Fromme

address: Gregor-Mendel-Str. 2

department: Molecular Nutritional Medicine

institute: Technical University of Munich

summary: We analyzed coding transcript abundance in primary brown and white preadipocytes from murine, interscapular brown adipose tissue or inguinal white adipose tissue, respectively.

overall_design: We prepared primary preadipocytes from the stromal-vascular fraction of murine interscapular brown fat or inguinal white fat. Three independent cultures each were generated from C57BL/6N UCP1-reporter mice (described in PMID: 30580967). We sequenced total RNA and determined transcript abundance.

first: Thomas

last: Gantert

first: Martin

last: Klingenspor

first: Christine

last: Wurmser


title: Microparticles enhance the formation of seven major classes of natural products in native and metabolically engineered actinobacteria through accelerated morphological development.

city: Bielefeld

first: Christian

last: Ruckert-Reed

address: Sequenz 1

department: Medical School OWL

institute: Bielefeld University

summary: Actinobacteria provide a rich spectrum of bioactive natural products and therefore display an invaluable source towards commercially valuable pharmaceuticals and agrochemicals.  Here, we studied the use of inorganic talc microparticles (hydrous magnesium silicate, 3MgO·4SiO2·H2O, 10 µm) as a general supplement to enhance natural product formation in this important class of bacteria. Added to cultures of recombinant Streptomyces lividans, talc (10 g L-1) enhanced production of the macrocyclic peptide antibiotic bottromycin A2 and its methylated derivative Met-bottromycin A2 up to 43%. Hereby, the microparticles fundamentally affected metabolism. With talc, S. lividans grew to 40% smaller pellets and, using RNA sequencing, revealed accelerated morphogenesis and aging, indicated by early upregulation of developmental regulator genes such as ssgA, ssgB, wblA, sigN and bldN. Furthermore, the microparticles re-balanced the expression of individual bottromycin cluster genes, resulting in a higher macrocyclization efficiency at the level of BotAH and correspondingly lower levels of non-cyclized shunt by-products, driving the production of mature bottromycin. Testing a variety of Streptomyces species, talc addition resulted in up to 13-fold higher titers for the RiPPs bottromycin and cinnamycin, the alkaloid undecylprodigiosin, the polyketide pamamycin, the tetracycline-type oxytetracycline, and the anthramycin-analogues usabamycins. Moreover, talc addition boosted production in other actinobacteria, outside of the genus of Streptomyces: vancomycin (Amycolatopsis japonicum DSM 44213), teicoplanin (Actinoplanes teichomyceticus ATCC 31121), and the angucyclinone-type antibiotic simocyclinone (Kitasatospora sp. DSM 102431). For teicoplanin, the microparticles were even crucial to activate production. Taken together, the use of talc was beneficial in 75% of all tested cases and optimized natural and heterologous hosts forming the substance of interest with clusters under native and synthetic control. Given its simplicity and broad benefits, microparticle-supplementation appears as an enabling technology in natural product research of these most important microbes.

overall_design: Whole transcriptomes of a bottromycin production strain derived from three time points and two treatments (+/- talc microparticles) using 3 biological replicates each.

last: Kuhl

last: Rueckert

first: Lars

last: Glaeser

first: Selma

last: Beganovic

first: Andriy

last: Luzhetskyy

first: Jörn

last: Kalinowski

first: Christoph

last: Wittmann


title: EBF1 and PAX5 control pro-B cell expansion via oppose regulation of the Myc gene

city: Lund

first: Mikael

last: Sigvardsson

address: Sölvegatan 19

institute: Lund University

summary: Lineage restricted transcription factors are frequently found mutated in B-lymphoid leukemia, suggesting a close link between normal and malignant B-cell development. One of these transcription factors is EBF1, a protein of critical importance for specification but also survival of B-lymphoid progenitors. We here report that impaired EBF1 function in mouse B-cell progenitors results in reduced expression of Myc. Ectopic expression of MYC rescued B-cell expansion in the absence of EBF1 both in vivo and in vitro. Using chromosome conformation analysis in combination with ATAC, ChIP-seq and reporter gene assays, identified six EBF responsive enhancer elements that could be annotated to the Myc gene. Crispr-Cas9 mediated targeting of EBF1 binding sites identified one element of importance for Myc expression and pro-B cell expansion providing evidence for that Myc is a direct target for EBF1. Furthermore, ChIP-seq analysis suggested that several regulatory elements in the Myc gene were targeted by PAX5. However, ectopic expression of PAX5 in EBF1 deficient cells was found to induce a cell cycle block and reduce Myc expression suggesting that EBF1 and PAX5 act in an opposing manner at this shared target gene. This hypothesis was further substantiated by the finding that Pax5 inactivation reduced the need for EBF1 in pro-B cell expansion. The binding of EBF1 and PAX5 to regulatory elements in the human MYC gene in a B-ALL cell line indicate that this regulatory loop may be of relevance for our understanding of both normal and malignant B-cell development.

overall_design: Murine B-cell progenitor cell lines or cultured primary cells of Wt, Ebf1-KO or Pax5-KO genotype were subject to Ebf1-ChIP seq analysis, H3K4me3 PLAC seq or RNA-seq after  transduction vectors expressing Ebf1 or Pax5.

first: Kazuki

last: Okuyama

last: Strid

first: Jonas

last: Ungerbäck

first: Rajesh

last: Somasundaram

first: Mahadesh

last: Prasad