title: Gene expression profiles of young and aged endothelial cells isolated from the murine liver

status: Public on Aug 13 2023

city: Suita

first: Shota

last: Shimizu

state: Osaka

address: 3-1 Yamadaoka

department: Department of Signal Transduction

institute: Research Institute for Microbial Diseases, Osaka University

summary: To investigate the effect of aging on liver endothelial cells, we performed RNA sequencing of liver endothelial cells isolated from young (10-week-old) and aged (127-136 week-old) C57BL/6J mice.

overall_design: CD31+CD45- cells were isolated from the murine liver with fluorescence-activated cell sorting (FACS) and underwent RNA sequencing analysis

first: Hisamichi

last: Naito

first: Nobuyuki

last: Takakura


title: Metformin Targets Intestinal Immune System Signaling Pathways in High-Fat Diet-Induced Type 2 Diabetes Mouse Model

status: Public on Aug 12 2023

city: Riga

first: Monta

last: Brīvība

address: Ratsupites 1

country: Latvia

institute: Latvian Biomedical Research and Study Centre

type: Expression profiling by high throughput sequencing

summary: Research findings of the past decade have highlighted the gut as the main site of action of the oral antihyperglycemic agent metformin despite its pharmacological role in the liver. Extensive evidence supports metformin’s modulatory effect on the composition and function of gut microbiota, nevertheless, the underlying mechanisms of the host responses remain elusive. Our study aimed to evaluate metformin-induced alterations in the intestinal transcriptome profiles at different metabolic states. The high-fat diet-induced type 2 diabetes mouse model of both sexes was developed in a randomized block experiment and bulk RNA-Seq of the ileum tissue was the method of choice for comparative transcriptional profiling after metformin intervention for ten weeks. We found a prominent transcriptional effect of the diet itself with comparatively fewer genes responding to metformin intervention. The overrepresentation of immune-related genes was observed, including pronounced metformin-induced upregulation of immunoglobulin heavy-chain variable regioncoding Ighv1-7 gene in both high-fat diet and control diet-fed animals, supporting the contribution of intestinal immunoglobulin responses. Finally, we provide evidence of the downregulation NF-kappa B signaling pathway in the small intestine of both hyperglycemic and normoglycemic animals after metformin treatment. Moreover, our data pinpoint the gut microbiota as a crucial component in the metformin-mediated downregulation of NF-kappaB signaling evidenced by a positive correlation between the Rel and Rela gene expression levels and abundances of Parabacteroides distasonis, Bacteroides spp., and Lactobacillus spp. in the gut microbiota of the same animals.

overall_design: We provide bulk RNA-Seq data of the distal part of the small intestine of high-fat diet-fed and metformin-treated C57BL/6N mice of both sexes with appropriate control arms. Experimental units/cages were organized in three blocks (one unit per each block), and animals were randomly divided into eight groups according to three different factors (sex, diet, and therapeutic intervention): (1) high-fat diet-fed (HFD-fed) male mice receiving metformin; (2) HFD-fed male mice with no metformin intervention; (3) HFD-fed female mice receiving metformin; (4) HFD-fed female mice with no metformin intervention; (5) control diet-fed (CD-fed) male mice receiving metformin; (6) CD-fed male mice with no metformin intervention; (7) CD-fed female mice receiving metformin; (8) CD-fed female mice with no metformin intervention. a type 2 diabetes mellitus (T2DM)-like phenotype was induced by HFD for 20 weeks. After week 20 metformin therapy was provided for randomly selected animals (half of both HFD-fed and CD-fed mice) with drinking water for 10 weeks in a concentration of 50 mg/kg body mass/day.

first: Laila

last: Silamiķele

first: Ineta

last: Kalniņa

first: Ivars

last: Silamiķelis

first: Līga

last: Birzniece

first: Laura

last: Ansone

first: Lauma

last: Jagare

first: Ilze

last: Elbere

first: Jānis

last: Kloviņš


title: Endocrine disruption of early uterine differentiation causes adenocarcinoma mediated by Wnt/β-catenin- and PI3K/AKT signaling

status: Public on Aug 11 2023

city: RTP

first: Wendy

last: Jefferson

state: NC

address: 111 Alexander Drive

country: USA

institute: NIH

summary: Developmental exposure to non-mutagenic environmental factors can contribute to cancer risk, but the underlying mechanisms are not understood. We used a mouse model of endometrial adenocarcinoma that results from brief developmental exposure to an estrogenic chemical, diethylstilbestrol (DES), to determine causative factors. Single cell RNA sequencing and spatial transcriptomics of adult uteri revealed new markers of uterine epithelial stem cells, identified luminal and glandular progenitor cells, and defined a glandular epithelial differentiation trajectory. Neonatal DES exposure disrupted uterine epithelial differentiation, resulting in widespread activation of Wnt signaling and a failure to generate epithelial stem cells or distinguishable glandular and luminal epithelial cells. The endometrial stromal cells activated inflammatory signals and oxidative stress. Together, these changes activated PI3K/AKT signaling to drive malignant transformation. These findings explain how human cancers, which are often associated with abnormal activation of PI3K/AKT signaling, could result from exposure to environmental insults during development.

overall_design: Briefly, female pups delivered from timed pregnant CD-1 dams were randomly distributed to 10 female pups per litter and then randomly assigned treatment groups of either corn oil (CO) or DES (1 mg/kg/day). Pups were exposed on neonatal days 1-5 by subcutaneous injection using a volume of 0.02 mL; mice were weaned and housed 5/cage. Utreri were collected at 12 months of age for single cell RNA-seq analysis and spatial transcriptomics.

first: Elizabeth

last: Padilla-Banks

middle: N

first: Brian

last: Papas

first: Alisa

middle: A

last: Suen

first: Xin

last: Xu

first: Diana

middle: V

last: Carreon

first: Cynthia

middle: J

last: Wilson

first: Erin

middle: M

last: Quist

first: Carmen

last: Williams


title: Profiling tRNA modifications in Mycobacterium tuberculosis

city: Boston

first: Satoshi

last: Kimura

state: Massachusetts

address: 181 Longwood Avenue

institute: Brigham and Women's Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Diverse chemical modifications fine-tune the function and metabolism of tRNA. Although tRNA modification is universal in all kingdoms of life, profiles of modifications, their functions, and physiological roles have not been elucidated in most organisms including the human pathogen, Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis. To identify physiologically important modifications, we surveyed the tRNA of Mtb, using tRNA sequencing (tRNA-seq). Reverse transcription-derived error signatures in tRNA-seq predicted the sites and presence of 9 modifications. Several chemical treatments prior to tRNA-seq expanded the number of predictable modifications. Deletion of Mtb genes encoding two modifying enzymes, TruB and MnmA, eliminated their respective tRNA modifications, validating the presence of modified sites in tRNA species.

sample_organism:
Escherichia coli
Mycobacterium tuberculosis

overall_design: High-throughput sequencing of tRNA fractions from Escherichia coli and Mycobacterium tuberculosis was performed using Illumina miSeq. To detect specific tRNA modifications, two chemical treatments (IAA and CMC treatments) were conducted prior to sequencing.

first: Francesca

middle: G

last: Tomasi

first: Eric

last: Rubin

first: Matthew

middle: K

last: Waldor


title: Conformational dynamics of cohesin/Scc2 loading complex are regulated by Smc3 acetylation and ATP association

status: Public on Aug 16 2023

city: Oxford

first: Kim

last: Nasmyth

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The ring-shaped cohesin complex is the key player in sister chromatid cohesion, DNA repair, and gene transcription. The loading of cohesin to chromosomes requires the loader Scc2 and is regulated by ATP. This process is also hindered by Smc3 acetylation. However, the molecular mechanism behind this inhibition remains mysterious. Here we identify a novel configuration of Scc2 with pre-engaged cohesin and reveal dynamic conformations of the cohesin/Scc2 complex in the loading reaction. We demonstrate that Smc3 acetylation blocks the association of Scc2 with pre-engaged cohesin by impairing the interaction of Scc2 with Smc3’s head. Lastly, we show that ATP binding induces the cohesin/Scc2 complex to clamp DNA by promoting the interaction between Scc2 and Smc3 coiled-coil. Our results illuminate a dynamic reconfiguration of the cohesin/Scc2 complex during loading and indicate how Smc3 acetylation and ATP regulate this process.

overall_design: Characterization of the effect of WT and mutant cohesin complexes on loading onto chromosomes in S. cerevisiae, assessed by calibrated ChIP-seq on an Ion Torrent Proton (Life Technologies)

first: Naomi

last: Petela

first: Bin

last: Hu


title: Selection of cross-reactive T cells by commensal and food-derived yeasts drives pathogenic cytotoxic Th1 responses in Crohn´s disease

status: Public on Aug 15 2023

city: Kiel

first: Ekaterina

last: Tikhonova

address: Arnold-Heller-Straße 3

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

summary: Aberrant CD4+ T cell reactivity against intestinal microbes is considered to drive mucosal inflammation in inflammatory bowel diseases. The disease-relevant microbial species and the corresponding microbe-specific pathogenic T cell phenotypes remain unknown. Here, we identify common gut commensal and food-derived yeasts, as direct activators of aberrant CD4+ T cell reactions in patients with Crohn´s disease (CD). Yeast-responsive CD4+ T cells in CD display a cytotoxic Th1 phenotype and selective clonal expansion of cells highly cross-reactive to several commensal, as well as food-derived, fungal species. This indicates cross-reactive T cell selection by repeated encounter with conserved fungal antigens in the context of chronic intestinal disease. Our results highlight a role of fungi in driving immunopathology in patients with CD and suggest that both, gut-resident fungal commensals, and daily dietary intake of yeasts, may contribute to chronic activation of pathogenic CD4+ T cell responses involved in disease pathophysiology.

overall_design: Yeast-reactive CD4+ T cells from PBMCs of 3 healthy donors and 3 Crohn's disease patients were isolated and analyzed using scRNASeq of total mRNA and TCR libraries

first: Gabriela

last: Rios Martini

first: Elisa

last: Rosati


title: Genome-wide maps of chromatin state in CTRLcas9 and SCARB2cas9 HepG2 cells.

city: Beijing

first: Yang

last: Gao

address: Dongcheng District, Tiantan Xili

country: China

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of c-Myc with core promoters of its target genes in mammalian cells. We performed ChIP sequencing with antibody to total c-Myc with core promoters of its target genes in CTRLcas9 and SCARB2cas9 group. Inspection of multiple individual traces and global analyses showed that SCARB2cas9 globally reduced association of c-Myc with core promoters of its target genes.

overall_design: we precipitated chromatin with tag antibody to CTRLcas9 and SCARB2cas9 HepG2 cells, and sequenced the precipitated material. SCARB2cas9 reduced association of c-Myc with core promoters of its target genes

first: Ke

last: Li

first: Jiandong

last: Jiang

first: Feng

last: Wang

first: Situ

last: Xue


title: Next Generation Sequencing Facilitates Quantitative Analysis of CreAlbMYC and CreAlbScarb2F/FMYC mice liver tissue Transcriptomes

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in   liver tissue of CreAlbMYC and CreAlbScarb2F/FMYC mice by using RNA-seq.
Methods:  CreAlbMYC and CreAlbScarb2F/FMYC liver tissue mRNA profiles were generated by deep sequencing, using Illumina Novaseq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with  following methods: Alignment by using HISAT2 , IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq  was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including  GO enrichment analysis and KEGG .
Conclusions:Our study represents the first detailed analysis of CreAlbMYC and CreAlbScarb2F/FMYC liver tissue transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: CreAlbMYC and CreAlbScarb2F/FMYC liver tissue mRNA profiles were generated by deep sequencing using Illumina Novaseq 6000..


title: Dominant-negative HNF1α mutant promotes liver steatosis and inflammation by regulating hepatic complement factor D

status: Public on Aug 09 2023

city: Jinan

first: Moke

last: Liu

address: Jingsi road No.544

institute: Shandong Provincial Hospital

summary: Heterozygous mutations of HNF1A gene are the pathogenic cause of MODY3. A few studies reported that MODY3 patients may have dyslipidemia and early onset of liver steatosis in some cases. However, there is a lack of sufficient and reliable experimental evidence on how HNF1α regulates NAFLD progression under the genetic background of MODY3. We established a novel mouse model carrying the dominant-negative human HNF1α P291fsinsC mutation (termed as hHNF1Amut/- mice). The hepatic morphological phenotypes and the changes of lipid metabolism were investigated. To reveal the molecular changes, we performed the transcriptome and proteome analysis.

overall_design:
As the transcriptome and proteome analysis suggested, the expression of complement factor D (CFD), which was reported to promote HFD-induced hepatic steatosis and inflammation, was significantly upregulated.
Comparative gene expression profiling analysis of RNA-seq data for hHNF1A-/- and hHNF1Amut/- mice liver (3 Control vs 4 KI).

first: Peng

last: Lu


title: Gene expression in macrophages polarized with conditioned medium from wild-type or Snail1-depleted cancer-activated fibroblasts

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

summary: Snail1 is a transcriptional factor required for activation of cancer-associated fibroblasts (CAF). In a murine model of mammary gland cancer, mice with Snai1 gene deletion presented a greater survival and differences in macrophage differentiation with fewer M2 macrophages. Snail1 was not expressed in macrophages and in vitro polarization of monocytes towards M1 or M2 phenotypes was not altered by Snai1 gene depletion. In contrast, when macrophages were incubated with Snail1-expressing CAF or with conditioned medium derived from these cells, they exhibited a lower cytotoxic capability than when incubated with Snail1 KO (inactive) CAFs. We compared gene expression of macrophages polarized by CAF WT versus CAF KO-conditioned medium with that promoter by IFN gamma and IL4, classical M1 and M2 inducers, respectively. We observed that, compared to inactive fibroblasts, active CAF specifically upregulated the expression of some M2 genes as Arg1 and also of genes normally reduced in M1 polarization, such as Arg2, although the gene pattern differed from that stimulated by IL4. A complete list of these genes is presented here.

overall_design: 10 samples were analysed

first: Antonio

last: Garcia de Herreros


title: Effects of deletion of SAT1, a polyamine-metabolic enzyme, on mouse HeLa xenograft tumor

status: Public on Aug 14 2023

city: Tokyo

first: Ryuichi

last: Nakahara

address: 4-6-1 Komaba, Meguro

department: the Research Center of Advanced Science and Technology

country: Japan

institute: the University of Tokyo

summary: An acidic tumor microenvironment plays a critical role in tumor progression. However, understanding of metabolic reprogramming of tumors in response to acidic extracellular pH has remained elusive. Using comprehensive metabolomic analyses, we demonstrated that acidic extracellular pH (pH 6.8) leads to the accumulation of N1-acetylspermidine, a pro-tumor metabolite, through upregulation of the expression of spermidine/spermine acetyl transferase 1 (SAT1). Inhibition of SAT1 expression suppressed the accumulation of intra- and extracellular N1-acetylspermidine at acidic pH. Conversely, overexpression 3 of SAT1 increased intra- and extracellular N1-acetylspermidine levels, supporting the proposal that SAT1 is responsible for accumulation of N1-acetylspermidine. While inhibition of SAT1 expression only had a minor effect on cancer cell growth in vitro, SAT1 knockdown significantly decreased tumor growth in vivo, supporting a contribution of the SAT1-N1-acetylspermidine axis to pro-tumor immunity. Immune cell profiling revealed that inhibition of SAT1 expression decreased neutrophil recruitment to the tumor, resulting in impaired angiogenesis and tumor growth. We showed that anti-neutrophil neutralizing antibodies suppressed growth in control tumors to a similar extent to that seen in SAT1 knockdown tumors in vivo. Further, a SAT1 signature was found to be correlated with poor patient prognosis. Our findings demonstrate that extracellular acidity stimulates recruitment of pro-tumor neutrophils via the SAT1-N1-acetylspermidine axis, which may represent a novel target for anti-tumor immune therapy.

overall_design: To investigate the function of SAT1 on immune cells within tumours, HeLa cells knocked down SAT1 with shRNA were transplanted into scid/scid mice and excised 21 days later.

first: Miki

last: Kato

first: Keisuke

last: Maeda

first: Haruka

last: Hirose

first: Ayano

last: Kondo

first: Sho

last: Aki

first: Maki

last: Sugaya

first: Sana

last: Hibino

first: Miyuki

last: Nishida

first: Hinano

last: Morita

first: Ritsuko

last: Ando

first: Rika

last: Tsuchida

first: Minoru

last: Yoshida

first: Tatsuhiko

last: Kodama

first: Hideyuki

last: Yanai

first: Teppei

last: Shimamura

first: Tsuyoshi

last: Osawa


title: A Human Post-Implantation Embryoid Model Derived Ex Utero Solely from Genetically Unmodified Naïve PSCs (Multiome scRNA-Seq)

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: Our ability to study early human post-implantation development remains highly limited due to the ethical and technical challenges associated with intrauterine development of the human embryo after implantation. Despite the great progress made on human blastoids or gastruloids, such elegant models do not constitute an integrated synthetic stem cell-derived embryoid models (SEMs) that includes all the key extra-embryonic tissues of the early pre-gastrulating implanted human conceptus (e.g. hypoblast, yolk-sac, trophoblasts, amnion and extraembryonic mesoderm), and thus, do not recapitulate post-implantation epiblast development within the context of these extra-embryonic compartments. Mouse naïve pluripotent stem cells (PSCs) have recently been shown to give rise to embryonic and extra-embryonic stem cells capable of self-assembling into post-gastrulation mouse SEMs, while bypassing the blastocyst-like stage, and eventually initiating organogenesis ex utero. Here, we implement critical adaptations to extend these finding in humans, using only genetically unmodified human naïve PSCs, circumventing the need for ectopic expression of lineage promoting transgenes. Such integrated human SEMs recapitulate all known compartments of early post-implantation stage human embryos, including epiblast, hypoblast, extra-embryonic mesoderm, and trophoblast surrounding the latter layers. The organized human SEMs recapitulate key hallmarks of post-implantation stage embryogenesis up to 13-14 days post-fertilization (dpf, Carnegie stage 6a), such as bilaminar disk formation, epiblast lumenogenesis, amniogenesis, anterior-posterior symmetry breaking, PGC specification, primary and secondary yolk sac formation, and extra-embryonic mesoderm expansion that defines a chorionic cavity and a connective stalk. This new platform constitutes a tractable stem cell-based model for experimentally interrogating previously inaccessible windows of human early peri- and post-implantation development.

overall_design: Four stem cell culture samples (two Naïve and two primed) were sequenced using 10X Multiome

first: Bernardo

last: Oldak

first: Emilie

last: Wildschutz

first: Tom

last: Shani

first: Vladyslav

last: Bondarenko

first: Jacob

middle: H

last: Hanna


title: Ultra-fast deep-learned pediatric CNS tumor classification

status: Public on Aug 08 2023

city: Utrecht

first: Carlo

last: Vermeulen

state: Nederland

address: Universiteitsweg 100

country: Netherlands

institute: UMC Utrecht

type: Methylation profiling by high throughput sequencing

summary: In this study nanopore sequencing was applied to obtain sparse DNA methylation profiles from pediatric CNS tumor samples. A neural network was used to classify the tumor based on the obtained methylation profile.

overall_design:
Samples are obtained during resection surgery for adult glioma patients, aiming to obtain a high tumor fraction.
*** Submitter declares that the raw data will be uploaded to EGA due to data privacy concerns. ***

first: C

first: M

last: Pages-Gallego

first: L

last: Kester

middle: E

last: Kranendonk

first: P

last: Wesseling

first: N

last: Verburg

last: de Witt Hamer

first: E

last: Kooi

last: Dankmeijer

first: J

last: van der Lugt

first: K

last: van Baarsen

middle: W

last: Hoving

first: B

middle: B

last: Tops

last: de Ridder


title: Expression data from primary human lung MVPC

city: Denver

first: Susan

last: Majka

email: majkas@njhealth.org, susanmajka@mac.com

state: co

address: 1400 Jackson St, Goodman Bldg K810a

department: Medicine

institute: NJH

summary:
MVPC isolated from explanted lung tissue at VUMC.; Control MVPC - 3 independent patients, mTOR activated MVPC - 3 lines 1 patient; Fetal 3 independent patients.  Fetal lung MSC 3 independent patients   LAM MVPC - 1 patient 3 different parts of lung; Fetal lung MVPC 3 independent patients; Control MVPC - 3 independent patients
To elucidate pathways in human MVPC that were affected by mTOR activation, transcriptome expression analysis via microarray comparing primary human lung MVPC from normal control, mTOR+ and fetal lung was performed. Following normalization, hierarchical clustering analyses were presented as a heatmap (Figure 2A; Supplemental Figure 4), illustrating significant differences between the mTOR activated MVPC and normal controls. Interestingly, mTOR activated MVPC patterns of gene expression overlapped approximately 33% with the fetal lung MVPC

overall_design: Human Affy 1.0 st chips; CU AMC Genomics Core 2016

first: Swapna

last: Menon


title: Aortic samples of inducible vascular smooth muscle specific KO of YAP/TAZ

city: Lund

first: Sebastian

last: Albinsson

address: BMC D12

country: Sweden

institute: Lund University

summary: YAP and TAZ are transcriptional co-activators and downstream effectors of the Hippo pathway, which play crucial roles in organ size control and cancer pathogenesis. Genetic deletion of YAP/TAZ has revealed their critical importance for embryonic development of the heart, vasculature and gastrointestinal mesenchyme. The aim of this study was to determine the long term role of YAP/TAZ in adult vascular smooth muscle in vivo. We used the novel Itga8-CreERT2 mouse for deletion of YAP/TAZ (i8-Y/T-KO).

overall_design: RNA was isolated from control and i8-Y/T-KO thoracic, two weeks and eight weeks after the first tamoxifen injection, using RNeasy Mini Kit (Qiagen, 85600) and a QIAcube (Qiagen) workstation as per the manufacturer’s recommendations. RNA concentration and purity was measured in a NanoDrop 2000c (Thermo scientific). RNA from Ctrl (n=4 at 2w and n=4 at 8w) and i8-YT-KO (n=4 at 2w and n=4 at 8w) thoracic aorta was sent to Novogene Europe (Cambridge, UK) for 150 bp paired-end sequencing on an Illumina platform. After cDNA library construction, sequencing, and filtering, reads were mapped to the Mus musculus reference genome (GRCm38/mm10) using Hisat2. Read numbers mapping to each gene were obtained using FeatureCounts and converted to Fragments Per Kilobase of transcript per Million mapped reads (FPKM). Differential gene expression analysis was done using DESeq2 in R. Enrichment analysis was performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) using clusterProfiler.


title: Next-generation sequencing facilitates quantitative analysis of CON and PMB treatment HepG2 cells transcriptomes

city: Bei Jing

first: Yang

last: Gao

address: Tiantan Xili 2

department: Institute of Medicinal Biotechnology

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analyse the differential genes and pathways in CTRL and PMB treatment cells by using RNA-seq.
Methods: CTRL and PMB treatment cells mRNA profiles were generated by deep sequencing, using Illumina Novaseq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2, IGV was used to view the mapping result by the Heatmap, histogram, scatter plot or other style, FPKM was then calculated to estimate the expression level of genes in each sample, EdgeR software was used for differential gene expression analysis and Function Enrichment Analysis including GO enrichment analysis and KEGG.
Conclusions: Our study represents detailed analysis of CTRL and PMB cells transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: CTRL and PMB cells mRNA profiles were generated by deep sequencing, in triplicate, using Illumina Novaseq 6000.

first: Ke

last: Li

first: Jiandong

last: Jiang

first: Feng

last: Wang

first: Situ

last: Xue


title: Transient naive reprogramming corrects hiPS cells functionally and epigenetically

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

summary:
Cells undergo a major epigenome reconfiguration when reprogrammed to human induced pluripotent stem cells (hiPS cells). However, the epigenomes of hiPS cells and human embryonic stem (hES) cells differ significantly, which affects hiPS cell function. These differences include epigenetic memory and aberrations that emerge during reprogramming, for which the mechanisms remain unknown. Here we characterized the persistence and emergence of these epigenetic differences by performing genome-wide DNA methylation profiling throughout primed and naive reprogramming of human somatic cells to hiPS cells. We found that reprogramming-induced epigenetic aberrations emerge midway through primed reprogramming, whereas DNA demethylation begins early in naive reprogramming. Using this knowledge, we developed a transient-naive-treatment (TNT) reprogramming strategy that emulates the embryonic epigenetic reset. We show that the epigenetic memory in hiPS cells is concentrated in cell of origin-dependent repressive chromatin marked by H3K9me3, lamin-B1 and aberrant CpH methylation. TNT reprogramming reconfigures these domains to a hES cell-like state and does not disrupt genomic imprinting. Using an isogenic system, we demonstrate that TNT reprogramming can correct the transposable element overexpression and differential gene expression seen in conventional hiPS cells, and that TNT-reprogrammed hiPS and hES cells show similar differentiation efficiencies. Moreover, TNT reprogramming enhances the differentiation of hiPS cells derived from multiple cell types. Thus, TNT reprogramming corrects epigenetic memory and aberrations, producing hiPS cells that are molecularly and functionally more similar to hES cells than conventional hiPS cells. We foresee TNT reprogramming becoming a new standard for biomedical and therapeutic applications and providing a novel system for studying epigenetic memory.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: A branching model of lineage differentiation underpinning the neurogenic potential of enteric glia (Bulk gene expression analysis of  small intestinal glia cells in BAC-treated mice.)

city: London

first: Vassilis

last: Pachnis

state: London

address: 1 Midland Road

department: Development and Homeostasis of the Nervous System Laboratory

institute: The Francis Crick Institute

summary: Glial cells have been proposed as an endogenous source of progenitors for the treatment of neural deficits. However, the cellular and molecular mechanisms underpinning the neurogenic potential of certain populations of adult glial cells, are not known. Previous studies have indicated that chemical injury of the gut by benzalkonium chloride (BAC) of the gut can activate neuronal markers. To examine whether gut injury can induce in EGCs neurogenic programs similar to those expressed by early ENS progenitors in vivo, we performed bulk RNA-seq of enteric glia isolated from mouse guts 48 hours after BAC treatment. We isolated tdT+ cells (=EGCs) and tdT- cells (=non-glia cells) from the TM of control and BAC-treated Sox10CreERT2;Rosa26tdTomato mice and subjected the samples to bulk RNAseq analysis.

overall_design: Tamoxifen-treated Sox10CreERT2;Rosa26tdTomato mice, which express the fluorescent reporter tdTomato (tdT) specifically in the intrinsic glia cell network of the gut, were treated with BAC. At 48 hours post treatment, we isolated enteric glia cells (EGCs, tdT+) and non-glia cells (tdT-) using FACS from four individual mice for each treatment condition (4x EGC Control = Chem_GliaCtrl, 4x non-glia Control = Chem_NonGliaCtrl, 4x EGC BAC = Chem_GliaBAC, 4x non-glia BAC = Chem_NonGliaBAC)

first: Franze

last: Progatzky

first: Stefan

last: Boeing


title: The  application of epiphenotyping approaches to DNA methylation array studies of the human placenta

first: Maitreyi

last: Mazumdar

state: MA

address: Department of Neurology

institute: Boston Children's Hospital & Harvard Medical School

type: Methylation profiling by genome tiling array

summary:
204 placentas from three cohorts were processed for DNAme arrays in Vancouver, Canada. The three cohorts consisted of: (i) V-NORM, a normative population of term pregnancies recruited at BC Women’s Hospital (BCWH) in Vancouver, Canada (n=35), as part of a study on Epigenetics in Pregnancy Complications (EPIC); ii) V-SSRI, a population of pregnant individuals recruited in Vancouver, Canada in the 20th week of gestation (n=64), with/without clinical depression, and with/without the use of selective serotonin reuptake inhibitors (SSRIs); and (iii) QF-2011, a population of term pregnancies that were exposed to sudden-onset stress during gestation due to catastrophic flooding in the Australian state of Queensland in early January 2011 (n=105).
DNA samples from all three cohorts were run on Illumina Infinium MethylationEPIC arrays in Vancouver, BC, Canada. Processing included DNA purification after extraction using the DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA, USA), bisulfite conversion using the EZ DNAme Kit (Zymo Research, Orange, CA, USA), and hybridization to and processing of the Illumina Infinium MethylationEPIC BeadChip arrays according to the manufacturer’s protocol (Illumina, San Diego, CA, USA). Samples from the three cohorts were randomized and run in 3 array batches across 44 eight-sample chips as illustrated in Supp Figure 5. In the case of the V-SSRI and QF-2011 cohorts, sample exposure groups (SSRI exposed/non-exposed and objective flood stress high/low) and infant sex were carefully distributed across array chips (1-44) and rows (1-8) to minimize potential batch effects.    DNAme data from raw IDAT files were read into R v4.2.2(54) and annotated with the Illumina Infinium MethylationEPIC v1.0 B4 Manifest. Several data quality control checks were undertaken using the R packages minfi(55,56), wateRmelon(57,58), and ewastools(59). First, each sample was assessed at 17 Illumina control probes to evaluate bisulfite conversion efficiency and array run quality; all samples passed the manufacturer-recommended thresholds at the control probes. Next, average total (methylated + unmethylated) fluorescence intensity was assessed between samples, and between array batches. All samples had similar total fluorescence, though samples run on the EPIC array in Batch 3 had slightly higher average intensities than those in Batch 1 and 2. Sample sex was assessed with the ewastools package(59), using the mean total fluorescence intensity (methylated + unmethylated) of the X and Y chromosome probes, normalized to the per-sample mean autosomal total fluorescence intensity, and was confirmed to match the clinically-reported sex of the infant in all cases. Sample genetic identity was assessed using the 59 SNP (‘rs’) probes on the EPIC array with the call_genotypes() and enumerate_sample_donors() functions (ewastools)(59). Finally, DNAme beta value density plots of all samples were visually assessed to determine overall similarity of the beta value distributions between samples, with no outliers identified.

overall_design: 204 placentas and 19 technical replicates were analyzed with the Illumina Infinium Methylation EPIC array. These samples came from 3 distinct collection cohorts but were processed for arrays at a single facility in Vancouver, Canada. The tools included in the PlaNET R package (https://www.bioconductor.org/packages/release/bioc/html/planet.html) were used to estimate epiphenotype variables of ancestry, gestational age, and cell type composition in these samples, and these estimates were evaluated for relationships with each other, and with technical and biological variables associated with these cohorts.

first: Almas

last: Khan

first: Amy

last: Inkster

first: Maria

middle: S

last: Penaherrera

first: Suzanne

last: King

first: Sue

last: Kildea

first: Cathy

last: Vaillancourt

first: Tim

middle: F

last: Oberlander

first: Ursula

last: Brain

first: Ella

middle: O

last: Beraldo

first: Alexander

last: Beristain

first: Vicky

last: Clifton

first: Giulia

last: Del Gobbo

first: Wan

last: Lam

first: Gerlinde

last: Metz

first: Jane

last: Ng

first: David

last: Olson

last: Price

first: Johanna

last: Schuetz

first: Victor

last: Yuan

first: Elodie

last: Portales Casamar

first: Wendy

middle: P

last: Robinson


title: Next-generation sequencing facilitates quantitative analysis of CreAlbMYC and CreAlbScarb2F/FMYC mice liver tissue transcriptomes

first: Yang

last: Gao

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analyse the differential genes and pathways in liver tissue of CreAlbMYC and CreAlbScarb2F/FMYC mice by using RNA-seq.
Methods: CreAlbMYC and CreAlbScarb2F/FMYC liver tissue mRNA profiles were generated by deep sequencing, using Illumina Novaseq 6000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2, IGV was used to view the mapping result by the Heatmap, histogram, scatter plot or other style, FPKM was then calculated to estimate the expression level of genes in each sample, DEGseq was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG.
Conclusions: Our study represents the first detailed analysis of CreAlbMYC and CreAlbScarb2F/FMYC liver tissue transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: CreAlbMYC and CreAlbScarb2F/FMYC liver tissue mRNA profiles were generated by deep sequencing using Illumina Novaseq 6000.

first: Ke

last: Li

first: Jiandong

last: Jiang

first: Feng

last: Wang

first: Situ

last: Xue


title: CUT&Tag analysis genome-wide maps of chromatin state in CTRLcas9 and SCARB2cas9 HepG2 cells

summary: We report the application of CUT&Tag sequencing technology for high-throughput profiling of c-Myc with core promoters of its target genes in mammalian cells. We performed CUT&Tag sequencing with antibody to total c-Myc with core promoters of its target genes in CTRLcas9 and SCARB2cas9 group. Inspection of multiple individual traces and global analyses showed that SCARB2cas9 globally reduced association of c-Myc with core promoters of its target genes.

overall_design: HepG2 cells and HepG2 SCARB2Cas9 cells were harvested, and then the CUT&Tag assay was performed according to the manufacturer’s protocol using Hyperactive Universal CUT&Tag Assay Kit for Illumina. SCARB2cas9 reduced association of c-Myc with core promoters of its target genes.


title: Chromatin and gene expression changes during female Drosophila germline stem cell development.

city: Baltimore

first: Allan

middle: C

last: Spradling

state: Maryland

address: 3520 San Martin Drive

department: HHMI Lab at Embryology

institute: Carnegie Institution for Science

summary: The maintenance and differentiation of highly potent animal stem cells generates an epigenetic cycle that underlies development.  Drosophila female germline stem cells (GSC) produce cystoblast daughters that differentiate into nurse cells and oocytes. Developmental chromatin analysis profiling the differentiation of GSCs into cystoblasts and NCs of increasing ploidy shows that cystoblasts start developing by forming heterochromatin while in a transient syncytial state, the germline cyst, reminiscent of early embryonic cells. The open GSC chromatin state is further restricted by Polycomb repression of targets that include testis expressed genes briefly active in early female germ cells. Like other highly potent stem cells, GSC metabolism is reprogrammed and Myc-dependent growth is upregulated by altering mitochondrial membrane transport, gluconeogenesis and other processes. Thus, the animal generational cycle comprises similar but distinct maternal and zygotic stem cell epigenetic cycles. We propose that the pluripotent stem cell state and daughter cell differentiation were shaped by the pressure to resist transposon activity over evolutionary time scales. In this GEO submission, we present data and analyses pertaining to H3K27ac, H3K27me3, and H3K9me3 ChIPseq, ATACseq, and RNAseq of Germline Stem Cells (GSCs) and Nurse Cells (NCs) from Drosophila melanogaster ovaries.

overall_design:
H3K27ac ChIP-seq, H3K27me3 ChIP-seq, H3K9me3 ChIPseq, ATAC-seq, and RNA-seq of Germline Stem Cells (GSCs) and Nurse Cells (NCs) from Drosophila melanogaster ovaries.

Please note that this study includes third-party reanalysis of the previously published GSE145282 (Deluca et al, 2020), PRJNA466150 (Greenblatt and Spradling, 2018). The full details of the third-party reanalysis (including the GSM accession of the Samples reanalyzed, their associated GSE Series, data processing strategy, etc.) are provided in the readme_third-party_reanalysis.txt and the re-analyzed data is linked below as a supplementary files.

first: Liang-Yu

last: Pang

first: Steven

middle: Z

last: Deluca

first: Haolong

last: Zhu

first: John

last: Urban


title: Next-generation sequencing facilitates quantitative analysis of CON and PMB treated HepG2 cells and CreAlbMYC and CreAlbScarb2F/FMYC mice liver transcriptomes, and CUT&Tag analysis genome-wide maps of chromatin state in CTRLcas9 and SCARB2cas9 HepG2 cells

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Next Generation Sequencing Facilitates Quantitative Analysis of CON and PMB treatment HepG2 cells Transcriptomes

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in  CON and PMB treatment cells by using RNA-seq
Methods: CON and PMB treatment cells mRNA profiles were generated by deep sequencing, using Illumina Novaseq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2 , IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, EdgeR software was used for differential gene expression analysis and Function Enrichment Analysis including GO enrichment analysis and KEGG .
Conclusions: Our study represents detailed analysis of CON and PMB cells transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: CON and PMB cells mRNA profiles were generated by deep sequencing, in triplicate, using Illumina Novaseq 6000.


title: Single-Cell RNA-Sequencing reveals cellular heterogeneity and traiectories of lineage specification of human primary HCC tumorspheres

summary: We report the application of Single-Cell RNA-Sequencing technology for high-throughput profiling in human primary HCC tumorspheres. By obtaining human primary HCC cells isolated from tumor tissues of PDX mice, we proceeded sphere-forming culture and then performed Single-Cell RNA-Sequencing of human primary HCC cells. The scRNA-Seq libraries were prepared with Single Cell 3′ Reagent Kit v2 (10×Genomics) following the user guide provided. We found that SCARB2 positive cells accounted about 11.3% of total tumorspheres and were enriched with MYC target genes. We conclude that Single-Cell RNA-Sequencing would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: one sample from human primary HCC tumorspheres


title: Next Generation Sequencing Facilitates Quantitative Analysis of the effects of compound 5D on ILC2 transcriptome

status: Public on Aug 10 2023

city: Los Angeles

first: Emily

last: Howard

state: Ca

address: 1450 Biggy St

department: MMI

institute: University of Southern California

summary: Blocking Orai channels inhibits ILC2 effector function

overall_design: mRNA profiles of sorted mouse lung ILC2s from WT mice cultured with compound 5D or vehicle were generated by deep sequencing, in duplicates, using a NextSeq 500 (Illumina) system.


title: Single-cell RNA sequencing of liver fine-needle aspirates captures immune diversity in the blood and liver in chronic hepatitis B patients

city: Toronto

first: Adam

last: Gehring

state: ON

address: 101 College St

country: Canada

institute: UHN

summary: The objective of this study is to identify immunological differences between blood and liver in chronic hepatitis B (CHB) patients using Seq-well and 10x Chromium scRNAseq

overall_design:
Blood and liver FNAs were collected, and cellular and molecular capture were compared between the Seqwell S picowell-based and the 10x Chromium reverse-emulsion droplet based scRNAseq
This dataset represents SeqWell data only.
***Raw data for human samples not available due to patient privacy concerns***

first: Alex

last: Genshaft

first: Sonu

last: Subduhi

first: Arlin

last: Keo

first: Juan

middle: D

last: Sanchez Vasquez

first: Nádia

last: Conceição-Neto

first: Deeqa

last: Mahamed

first: Lauke

middle: L

last: Boeijen

first: Nadia

last: Alatrakchi

first: Chris

last: Oetheimer

first: Mike

last: Vilme

first: Riley

last: Drake

first: Ira

last: Fleming

first: Nancy

last: Tran

first: Constantine

last: Tzouanas

first: Jasmin

last: Joseph-Chazan

first: Martin

last: Arreola Villanueva

first: Harmen

last: van de Werken

first: Gertine

last: van Oord

first: Zwier

last: Groothuismink

first: Boris

last: Beudeker

first: Zgjim

last: Osmani

first: Shirin

last: Nkongolo

first: Aman

last: Mehrotra

first: Kurt

last: Spittaels

first: Jordan

last: Feld

first: Raymond

middle: T

last: Chung

first: Robert

last: de Knegt

first: Harry

last: Janssen

first: Jeroen

last: Aerssens

first: Jacques

last: Bollekens

first: Nir

last: Nacohen

first: Georg

last: Lauer

first: Andre

last: Boonstra

last: Shalek


title: Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation

status: Public on Aug 07 2023

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

institute: Blizard Institute

summary: Vitamin C (vitC) enhances the activity of 2-oxoglutarate-dependent dioxygenases, including TET enzymes, which catalyse DNA demethylation, and Jumonji-domain histone demethylases. The epigenetic remodelling promoted by vitC improves the efficiency of induced pluripotent stem cell derivation, and is required to attain a ground-state of pluripotency in embryonic stem cells (ESCs) that closely mimics the inner cell mass of the early blastocyst. However, genome-wide DNA and histone demethylation can lead to upregulation of transposable elements (TEs), and it is not known how vitC addition in culture media affects TE expression in pluripotent stem cells. Here, we show that vitC increases the expression of evolutionarily young LINE-1 (L1) elements in mouse ESCs. We find that TET activity is dispensable for these effects, as and that instead L1 upregulation occurs largely as a result of H3K9me3 loss mediated by KDM4A/C histone demethylases. Despite increased L1 levels, we find no evidence of substantially higher retrotransposition rates, suggesting that downstream mechanisms restrict L1 mobility. Notably, treatment of human ESCs with vitC also increases L1 protein levels, which could impact the genetic and epigenetic stability of human pluripotent stem cells.

overall_design: RNA-seq on mouse or human embryonic stem cells treated with vitamin C

first: Kevin

last: Cheng

first: Jennifer

last: Frost

first: Francisco

middle: J

last: Sánchez-Luque

first: Marta

last: García-Canãdas

first: Darren

last: Taylor

first: Wan

last: Yang

first: Branavy

last: Irayanar

first: Swetha

last: Sampath

first: Hemalvi

last: Patani

first: Kristian

last: Helin

first: Gabriella

last: Ficz

first: Kathleen

last: Burns

first: Adam

last: Ewing

first: Jose

last: García-Pérez


title: CD8+ cells and small viral reservoirs facilitate post-ART SIV control in MHC-M3+ Mauritian cynomolgus macaques

city: Madison

first: Shelby

last: O'Connor

state: WI

address: 555 Science Drive

institute: University of Wisconsin-Madison

summary: Sustainable HIV remission after antiretroviral therapy (ART) withdrawal, or post-treatment control (PTC), remains a top priority in the HIV field. We observed surprising PTC in an MHC-haplomatched cohort of SIVmac239+ Mauritian cynomolgus macaques (MCMs) initiated on ART at two weeks post-infection (wpi). For six months after ART withdrawal, we observed undetectable or transient viremia in seven of eight MCMs. In vivo CD8α depletion induced rebound in all animals, indicating the PTC was mediated by CD8α+ cells. We found that MCMs had a smaller acute viral reservoir than a cohort of identically infected rhesus macaques, a population that rarely develops PTC. The mechanisms by which unusually small viral reservoirs and CD8α+ cell-mediated virus suppression enable PTC can be investigated using this model of PTC in MHC-haplomatched MCMs. If the immunological mechanisms that can engender PTC are defined, this model could designate therapeutic targets for HIV remission strategies in humans.

overall_design: Comparative gene expression proifiling analysis of RNA-seq data for CD8+ T cells isolated from peripheral blood mononuclear cells (PBMCs) of SIV+ Mauritian Cynomolgus macaques.

first: Olivia

last: Harwood

first: Lea

middle: M

last: Matschke

first: Ryan

middle: V

last: Moriarty

first: Alexis

last: Balgeman

first: Abigail

last: Weaver

first: Amy

last: Ellis-Connell

first: Andrea

last: Weiler

first: Lee

last: Winchester

first: Courtney

last: Fletcher

first: Thomas

last: Friedrich

first: Brandon

last: Keele

first: David

last: O’Connor

first: Jessica

last: Lang

first: Matthew

last: Reynolds


title: Multimodal transcriptomic profiling of the embryonic palate enables novel in utero cleft therapy [scRNA-Seq]

city: Bethesda

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: Cleft palate is a common disorder of development resulting from failure of growth, migration, elevation, and osteogenic fusion of embryonic cranial neural crest-derived palatal shelves. Despite progress in recent decades, the molecular pathways involved in this failure are not well understood. Here, we present a multimodal, spatiotemporal transcriptomic profiling of the developing palate through integrated, unbiased single-cell and bulk RNA-sequencing and multiplexed in situ mRNA mapping of osteogenic cell lineages. We then show that loss of Pax9, a critical transcription factor orchestrator of Wnt signaling in palate development, results in increased expression of sclerostin (Sost), a known antagonist of Wnt signaling. Finally, we reveal that a single dose of sclerostin-neutralizing monoclonal antibody restores Wnt signaling and corrects cleft palate defects in utero in Pax9-/- mouse embryos.

overall_design: Herein, we begin to unveil the complex transcriptomic milieu driving morphogenetic gradients of expression and development of the secondary palate. The primary aims were three-fold: (1) define the temporospatial transcriptomic profile of the embryonic secondary palate; (2) assess the Wnt-dependent mechanisms driving palate morphogenesis and failure of palate fusion in Pax9-/- embryos; and (3) explore the potential role of a well-known Wnt antagonist protein, sclerostin, in the pathogenesis of cleft palate through the testing of a novel drug delivery approach targeting this protein for the treatment of cleft palate in utero.

first: Jeremie

last: Oliver

first: Resmi

last: Raju

first: Parna

last: Chattaraj

first: Fahad

last: Kidwai

first: Rena

last: D'Souza


title: Scavenger Receptor SCARB2 Drives Hepatic Carcinoma Initiation by Enhancing MYC Transcriptional Activity and Supporting Cancer Stem Cell Traits.

first: Yang

last: Gao

address: Dongcheng District, Tiantan Xili

institute: Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College


title: Multimodal transcriptomic profiling of the embryonic palate enables novel in utero cleft therapy [bulk RNA-Seq]

first: Ryan


title: Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation

status: Public on Aug 04 2023

city: Shenzhen

first: Yueyuan

last: Zheng

state: China

address: Zhenyuan Road, 628

institute: The Seventh Affiliated Hospital of Sun Yat-sen University


title: Effects of ginkgetin on nonalcoholic steatohepatitis (NASH) by single-cell RNA Sequencing (scRNA-Seq).

status: Public on Aug 03 2023

city: Wuhan

first: Chaoyang

last: Wang

address: Jiefang Avenue #1277

institute: Wuhan Union Hospital

summary: Ginkgetin could significantly attenuate NASH in a mouse model induced by high-fat diet, including reducing lipid accumulation in the liver and inhibiting hepatic inflammtion and fibrosis, which was supported by scRNA-Seq.

overall_design: To investigate the effect of ginkgetin on NASH and the underlying mechanism, we performed scRNA-Seq on the liver tissues from NASH mcie treated with vehicle (control group) or ginkgetin (10mg/kg/day) (ginkgetin group).

first: Bin

last: Xiong


title: Beneficial effects of ginkgetin on nonalcoholic steatohepatitis (NASH) by bulk RNA Sequencing

first: Huanzhang

last: Niu

address: Jiefang Avenue 1277#

summary: Ginkgetin could significantly attenuate NASH in a mouse model induced by high-fat diet, including reducing lipid accumulation in the liver and inhibiting hepatic inflammtion and fibrosis. In addition, the related signaling pathways and gene expression were also downregulated by ginkgetin by bulk RNA Sequencing analysis.

overall_design: To investigate the effect of ginkgetin on NASH and the underlying mechanism, we performed bulk RNA Sequencing on the liver tissues from NASH mcie treated with vehicle (control group) or ginkgetin (10mg/kg/day) (ginkgetin group).


title: "Immunogenic subtype" characterised by macrophages infiltration predominantly comprise meningiomas in neurofibromatosis type 2 patients

city: Bunkyo-ku

first: Satoru

last: Miyawaki

state: Tokyo

institute: The University of Tokyo

summary:
Aims: Whereas recent molecular analysis has revealed that sporadic meningioma has various genetic, epigenetic, and transcriptomic profiles, those of meningioma in NF2 patients are not fully elucidated. This study probed meningiomas' clinical, histological, and molecular characteristics in NF2 patients.
Methods: A long-term retrospective follow-up (13.5 ± 5.5 years) study involving 159 meningiomas in NF2 patients was performed. We assessed their characteristics by performing immunohistochemistry (IHC), bulk-RNA sequencing, and copy number analysis. All variables of meningiomas in NF2 patients were compared with those of 189 sporadic NF2-altered meningiomas.
Results: Most meningiomas in NF2 patients were stable, and the mean annual growth rate was 1.0 ± 1.8 cm3/yr. Twenty-eight meningiomas (17.6%) in 25 patients (43.1%) were resected during the follow-up period. WHO grade 1 meningiomas in NF2 patients` were more frequent than in sporadic NF2-altered meningiomas (92.9% vs 80.9%). Transcriptomic analysis for NF2 patients`/sporadic NF2-altered WHO grade 1 meningiomas (n = 14 versus 15, respectively) showed that tumours in NF2 patients had still higher immune response and immune cell infiltration than sporadic NF2-altered meningiomas. Furthermore, RNA-seq/IHC-derived immunophenotyping corroborated this higher immune response by identifying myeloid cell infiltration, especially macrophages.
Conclusions: Clinical, histological, and transcriptomic analyses for meningiomas in NF2 patients demonstrated that meningiomas in NF2 patients showed less aggressive behaviour than sporadic NF2-altered meningiomas and elicited marked immune response by identifying myeloid cell infiltration, especially macrophages.

overall_design:
Clinical analysis, retrospective
***The submitter declares that raw data files are not provided according to the ethical approval of the study ***

first: Yu

last: Teranishi

first: Masahiro

last: Nakatochi


title: Elucidating the Cellular and Molecular Dynamics of Sebaceous Gland Self-Renewal and Regeneration

city: Irvine

first: Scott

last: Atwood

state: CA

address: 4238 McGaugh Hall

department: Department of Developmental and Cell Biology

institute: University of California, Irvine

summary: We isolated murine sebaceous gland (SG) cells and performed highly targeted single cell RNA-sequencing (scRNA-seq) to identify novel cell subpopulations and to infer lineage relationships.

overall_design: Fluorescently labeled SG cells were flow-sorted from dorsal skin harvested from a PPARG;YFP label-on male mouse, 8 weeks of age. Four replicate low-throughput libraries (LT-1, LT-2, LT-3, LT-4) were prepared in parallel from the same animal and analyzed by scRNA-seq.

first: Natalia

middle: A

last: Veniaminova

first: Yunlong

middle: Y

last: Jia

middle: X

first: Sunny

last: Wong


title: In vitro cross-talk between metastasis-competent circulating tumor cells and platelets in colon cancer: a malicious association during a harsh journey in the blood.

city: Leiden

first: Danijela

last: Koppers-Lalic

address: Albinusdreef 2

department: Medical Oncology & Medical Microbiology

institute: Leiden University Medical Center

summary: Platelets are active players in hemostasis, coagulation, and tumorigenesis. The cross-talk between platelets and circulating tumor cells (CTCs) has been suggested to have a myriad of pro-cancerous effects including promoting tumor growth, epithelial-mesenchymal transition (EMT) induction, aiding metastatic cells for survival, adhesion, arrest, setting up the pre-metastatic niche and metastasis. These interactions might cause alterations on the transcriptome of the platelets. However, as CTCs are rare events, the cross-talk between CTCs and platelets is poorly understood. Taking advantage of established colon CTC lines, we aim to explore the reciprocal interaction of colon CTCs and platelets in vitro.

overall_design: Platelets total RNA profiling by high throughput sequencing

first: Zahra

last: Eslami-S

first: Luis

middle: E

last: Cortés-Hernández

first: Ilias

last: Glogovitis

first: Mafalda

last: Antunes-Ferreira

first: Silvia

last: D’Ambrosi

first: Keerthi

last: Kurma

first: Françoise

last: Garima

first: Laure

last: Cayrefourcq

first: Myron

middle: G

last: Best

first: Thomas

last: Wurdinger

first: Catherine

last: Alix-Panabières


title: Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation [ChIP-Seq]

first: Yueyuan

last: Zheng

summary:
As one of the most common malignancies, esophageal cancer has two subtypes, squamous cell carcinoma (ESCC) and adenocarcinoma (EAC), arising from distinct cells-of-origin. However, distinguishing cell-type-specific molecular features from cancer-specific characteristics has been challenging. Here, we analyze whole-genome bisulfite sequencing (WGBS) data on 45 esophageal tumor and nonmalignant samples from both subtypes. We develop a novel sequence-aware method to identify large partially methylated domains (PMDs), revealing profound heterogeneity at both the methylation level (depth) and genomic distribution (breadth) of PMDs across tumor samples. We identify subtype-specific PMDs, which are associated with repressive transcription, chromatin B compartments and high somatic mutation rate. While the genomic locations of these PMDs are pre-established in normal cells, the degree of loss is significantly higher in tumors. We find that cell-type-specific deposition of H3K36me2 may underlie the genomic distribution PMDs. At a smaller genomic scale, both cell-type- and cancer-specific differentially methylated regions (DMRs) are identified for each subtype. Using binding motif analysis within these DMRs, we show that a cell-type-specific transcription factor such as HNF4A can maintain the binding sites that it establishes in normal cells, while being recruited to new binding sites with novel partners such as FOSL1 in cancer. Finally, leveraging pan-tissue single-cell and pan-cancer epigenomic datasets, we demonstrate that a substantial fraction of the cell-type-specific PMDs and DMRs identified here in esophageal cancer, are actually markers that co-occur in other cancers originating from related cell types. These findings advance our understanding of the DNA methylation dynamics at various genomic scales in normal and malignant states, providing novel mechanistic insights into cell-type- and cancer-specific epigenetic regulations.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone H3K36me2 in EAC OE19 cell line, ESCC KYSE70 and TE5 cell lines.

overall_design: De-Chen Lin, Benjamin P Berman

first: Benjamin

last: Ziman

last: Berman


title: Androgen Receptor is a Determinant of Melanoma BRAFi/MEKi Resistance [Clariom_2]

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

summary: The majority of BRAFV600 mutant melanomas regress in response to BRAF/MEK inhibitors (BRAFi/MEKi). Yet nearly all relapse within the first two years. Most BRAFi/MEKi-resistant tumors are cross-resistant to immunotherapies, highlighting the need to prevent and circumvent resistance.  We recently showed that androgen receptor (AR) activity is required for sustained melanoma cells proliferation and tumorigenesis. Here we find that AR expression is markedly increased in BRAFi resistant melanoma cells as well as in sensitive cells already at very early times of BRAFi exposure. Proliferation and tumorigenicity of BRAFi resistant melanoma cells are blunted by genetic or pharmacologic suppression of AR activity, while AR overexpression is by itself sufficient to rendersmelanoma cells BRAFi/MEKi-resistant. Increased AR elicits transcriptional changes linked with AXL-positive BRAFi resistant subpopulations and induces expression of PAI-1 and EGFR, two determinants of melanoma progression that associate with elevated AR expression in clinical cohorts. Our results point to increased AR signaling as a determinant of melanoma BRAFi resistance, which can be counteracted by AR as well as PAI-1 and EGFR inhibitors.

overall_design:
Five different BRAF resistant (BR) melanoma cell lines were established from the parental (P) cells (A375, M121224, M160915, UACC903  and WM9) by continuous culturing in Dabrafenib for a period of 4 weeks, with weekly multistep increases in concentration from 0.5 to 3uM. Parental (P) and BRAF resistant (BR) melanoma cells were collected for transcriptoomic analysis from confluent 10cm dishes. mRNA was extracted using Direct-Zol RNA MiniPrep kit.
Cell line identifier followed by a indication of BRAF resisitant (BR) or parental (P) conditions.

first: Anastasia

last: Samarkina

first: Markus

middle: K

last: Youssef

first: Gian

last: Dotto


title: Androgen Receptor is a Determinant of Melanoma BRAFi/MEKi Resistance [ChIP-Seq]

overall_design: A375 melanoma cells  were treated with Dabrafenib (0.5uM) versus vehicle control (DMSO) for 48 hours. In addition, A375 melanoma cells were transduced with AR overexpression (AR OE) virus. Following untreated AR OE cells and the drug treated untransduced A375 cells, cells were collected simultaneously for ChIP-seq


title: The effect of Histone H3.3 knockdown on DNA methylation in HepG2 cells

status: Public on Aug 02 2023

city: Hefei

first: Pengfei

last: Zhang

address: 443 Huang-Shan Road

department: School of Life Sciences

institute: University of Science and Technology of China

summary: Whole genome bisulfite sequencing (WGBS) is performed to study the effect of H3.3 on DNA methylation in HepG2 cells.

overall_design: The expression of Histone H3.3 was knocked down by lentiviruses-mediated shRNA in HepG2. The control and H3.3-deficient HepG2 cells were subjected to WGBS and genome-wide DNA methylation analyzing.

first: Danlei

last: Chen

first: Lianxin

last: Liu


title: mRNA transcript levels in E15.5, E17.5 and P1 Crb1KOCrb2ΔRPC against Crb1KO neuroretina, and in E15.5 Crb1KOCrb2ΔRPC against wild type neuroretina

status: Public on Aug 01 2023

first: Jan

last: Wijnholds

department: Ophthalmology

summary: mRNA transcript levels in embryonic day 15.5 (E15.5), E17.5 and postnatal day 1 (P1) mouse Crb1KOCrb2ΔRPC against mouse Crb1KO neuroretina (Run1), and in E15.5 mouse Crb1KOCrb2ΔRPC against wild type neuroretina (Run2) were analyzed. A comparison between Crb1KOCrb2ΔRPC and Crb1KO retina, at E15.5, or E17.5, or P1 on 100% C57BL/6JOlaHsd, yielded only subtle persistent changes at the transcriptional level over time (Figure 1 G-I, respectively), despite significant differences in morphology. As inter-nal positive control at E15.5, E17.5 and P1 we used ATP-binding cassette, sub-family D (ALD), member 4 (Abcd4), which is substantially upregulated in mouse retina expressing the Cre recombinase fused to the Chx10 promoter, with the Abcd4 gene immediately adja-cent to the Chx10Cre locus in the mouse genome. To further examine potential transcriptional changes at E15.5, we compared Crb1KOCrb2ΔRPC mice in 100% C57BL/6JOlaHsd genetic background against wild type C57BL/6JRccHsd mice. In this setting, we observed 40 differentially expressed genes (DEGs) compared to the previously 0 DEGs (E15.5; adj. p-val < 0.01 & log2FC > 1.5). The Crb1KOCrb2ΔRPC mice on C57BL/6JOlaHsd genetic background, due to mutations in the synuclein alpha (Snca), multimerin-1 (Mmrn1), and Crb1 gene, do not express Snca, Mmrn1, or Crb1 gene transcripts, and express high levels of Abcd4 due to the adjacent Chx10Cre transgene on chromosome 6. We made use of all 4 genes as negative and positive controls in the gene expression profiling, since the mice on C57BL/6JRccHsd genetic background have no mutations in Snca, Mmrn1 or Crb1 and express low levels of Abcd4. Analysis of the E15.5 data revealed upregulated expression of the WD repeat and FYVE domain-containing protein 1 (Wdfy1) gene also known as FYVE domain-containing pro-tein localized to endosomes (Fens-1), which encodes a phosphatidylinositol 3-phosphate binding protein that contains a FYVE zinc finger domain and multiple WD-40 repeat do-mains.

overall_design: Comparison of E15.5, E17.5 and postnatal day 1 (P1) mouse Crb1KOCrb2ΔRPC against mouse Crb1KO neuroretina (Run1) on exactly the same genetic background. Comparison of  E15.5, E17.5 mouse Crb1KOCrb2ΔRPC against wild type neuroretina (Run2) was on different genetic backgrounds of C57BL/6JOlaHsd versus C57BL/6JRccHsd, respectively. Sequencing was performed using Life Technologies SOLiD5500 with single-end, 50 bp reads. Two separate runs were performed. Run1 contained n=30 mice; n=5 Crb1KOCrb2F/F (Crb1KO) and n=5 Crb1KOCrb2ΔRPC (Tg) per development timepoint of the mouse embryo at E15.5, E17.5 and P1. Run2 contained n=9 mice; n=4 Crb1KOCrb2ΔRPC mice (C57BL/6JOlaHsd) and n=5 healthy mice (C57BL/6JRccHsd = wildtype, WT) at E15.5. Reads were aligned against mm10, using the 'whole.transcriptome.frag' workflow with bamgen.mqv.threshold set to 20 (Lifescope v2.5). Counts were obtained using the GTF as supplied by Lifescope (transformation of refGene.txt downloaded from UCSC at 25-06-2014) within this workflow.

first: Peter

last: Quinn


title: Deep scRNA sequencing reveals a universally applicable Regeneration Classifier and implicates antioxidant response in corticospinal axon regeneration

first: Hugo

middle: Jae Mun

last: Kim

address: 4760 Templeton St, Unit 3113

department: Neuroscience

institute: UNIVERSITY OF CALIFORNIA, SAN DIEGO

summary: Despite substantial progress in understanding the biology of axon regeneration in the CNS, our ability to promote the regeneration of the clinically important corticospinal tract (CST) after spinal cord injury remains limited. To understand regenerative heterogeneity, we conducted patch-based single cell RNA sequencing on rare regenerating CST neurons at high depth following PTEN and SOCS3 deletion. Supervised classification with Garnett gave rise to a Regenerating Classifier, which can be broadly applied to predict the regenerative potential of diverse neuronal types across developmental stages or after injury. Network analyses highlighted the importance of antioxidant response and mitochondrial biogenesis. Conditional gene deletion validated a role for NFE2L2 (or NRF2), a master regulator of antioxidant response, in CST regeneration. Our data demonstrate a universal transcriptomic signature underlying the regenerative potential of vastly different neuronal populations, and illustrate that deep sequencing of only hundreds of phenotypically identified neurons has the power to advance regenerative biology.

overall_design: Single Cell Patch-seq

first: H

first: B


title: PM2.5 leads to adverse pregnancy outcomes by inducing trophoblast oxidative stress and mitochondrial apoptosis via KLF9/CYP1A1 transcriptional axis

city: Jinan

first: Shuxian

last: Li

address: Jingshi 238 RD

institute: Maternal and Child Health Care Hospital of Shandong Province

summary: Epidemiological studies have demonstrated that fine particulate matter (PM2.5) is associated with adverse obstetric and postnatal metabolic health outcomes, but the mechanism remains unclear. This study aimed to investigate the toxicological pathways by which PM2.5 damaged placental trophoblasts in vivo and in vitro. We confirmed that PM2.5 induced adverse gestational outcomes such as increased fetal mortality rates, decreased fetal number and weight, damaged placental structure, and increased apoptosis of trophoblasts. Additionally, PM2.5 induced dysfunction of the trophoblast cell line HTR8/SVneo, including in its proliferation, apoptosis, invasion, migration and angiogenesis. Moreover, we comprehensively analyzed the transcriptional landscape of HTR8/SVneo cells exposed to PM2.5 through RNA-Seq and observed that PM2.5 triggered overexpression of pathways involved in oxidative stress and mitochondrial apoptosis to damage HTR8/SVneo cell biological functions through CYP1A1. Mechanistically, PM2.5 stimulated KLF9, a transcription factor identified as binding to CYP1A1 promoter region, which further modulated the CYP1A1-driven downstream phenotypes. Together, this study demonstrated that the KLF9/CYP1A1 axis played a crucial role in the toxic progression of PM2.5 induced adverse pregnancy outcomes, suggesting adverse effects of environmental pollution on pregnant females and putative targeted therapeutic strategies.

overall_design: PM2.5 was collected from the atmosphere in Jinan, Shandong Province, China, and RNA-Seq high-throughput sequencing was performed after stimulating the trophoblast cell line HTR8/SVneo for 24h at a PM2.5 concentration of 100ug/mL

first: Li

last: Shuxian

last: Lingbing

first: Zhang

last: Meihua

first: Wang

last: Xietong


title: High resolution landscape of an antibiotic binding site

city: NYC

first: Kevin

last: Yang

state: New York

institute: New York University Medical Center

summary: Antibiotic binding sites are located in important domains of essential enzymes and have been extensively studied in the context of resistance mutations, however their study is limited by positive selection. Using multiplex genome engineering1 to overcome this constraint, we generate and characterize a collection of 760 single residue mutants encompassing the entire rifampicin binding site of E. coli RNA polymerase (RNAP). By genetically mapping drug-enzyme interactions, we identify an alpha helix where mutations dramatically enhance or disrupt rifampicin binding. We find mutations in this region that prolong antibiotic binding, converting rifampicin from a bacteriostatic to bactericidal drug by inducing lethal DNA breaks. The latter are replication-dependent, indicating that rifampicin kills by causing detrimental transcription-replication conflicts at promoters. We also identify additional binding site mutations that greatly increase the speed of RNAP. Fast RNAP depletes the cell of nucleotides, alters cell sensitivity to different antibiotics, and provides a cold growth advantage. Finally, by mapping natural rpoB sequence diversity, we discover functional rifampicin binding site mutations that alter RNAP properties or confer drug resistance occur frequently in nature.

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

overall_design: ChIP-seq data from rifampicin hypersensitive mutants after treatment and recovery from rifampicin.

first: Yang

last: Kevin

first: Nudler

last: Evgeny


title: Role of Znf750 in skin development

city: Beer Sheva

first: Idan

last: Cohen

address: David Ben Gurion Blvd 1

department: Microbiology, Immunology and Genetics

institute: Ben-Gurion University

summary: The skin epidermis is a constantly renewing stratified epithelial tissue that provides essential protective barrier functions. The major barrier is at the outermost layers of the epidermis, formed by terminally differentiated keratinocytes reinforced by proteins and lipids of their cornified envelope (CE), and disruptions to this process characterizes common skin disorders. ZNF750 is an epithelial transcription factor essential for in vitro keratinocyte differentiation, whose autosomal dominant mutation in humans causes psoriasis-like skin disease.  Here, we report epidermal-specific Znf750 conditional knockout mouse model utilized to uncover the role of Znf750 in epidermal development. We show that deletion of Znf750 in the developing skin does not block epidermal differentiation, suggesting in vivo compensatory feedback mechanisms, yet results in impaired barrier function and perinatal lethality. Molecular dissection uncovered ultrastructural defects in the differentiated layers of the epidermis, accompanied by alterations in the expression of ZNF750-dependent genes encoding for key proteins and lipids involved in CE formation, including gene subsets known to be mutated in skin disease with impaired barrier function.

overall_design: Newborn mouse epidermal cells  were purified fromZnf750 knock out and control mice, and RNA was analyzed by RNA-seq.

first: Liat

last: Oss-Ronen


title: Vedolizumab efficacy is associated with decreased intracolonic dendritic cells, not memory T cells [P430]

city: Seattle,

first: Stephanie

last: Osmond

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Background: Vedolizumab, an antibody blocking integrin α4β7, is a safe and effective therapy for Crohn’s disease and ulcerative colitis. Blocking α4β7 from binding its cognate addressin MAdCAM-1 on intestinal blood vessel endothelial cells prevents T cells from migrating to the gut mucosa in animal models. However, data supporting this mechanism of action in humans is limited. Methods: We conducted a cross-sectional case-control study to evaluate the effect of vedolizumab on intestinal immune cell populations while avoiding the confounding effect resolving inflammation could have on the cellularity of the colonic mucosa in treatment-responsive patients. Colon biopsies from 71 case patients receiving vedolizumab were matched with biopsies from 71 control patients, similar in disease type, medications, anatomic location, and inflammation. Biopsies were analyzed by flow cytometry and full mRNA transcriptome sequencing of sorted T cells. Results: No difference was seen between vedolizumab recipients and controls in the quantity of any antigen-experienced lymphocyte subset, nor the quality of the transcriptome in any experienced T cell subset. Fewer naïve colonic B and T cells were seen in vedolizumab recipients than controls, regardless of response. The only immune population that was significantly reduced exclusively in the colonic mucosa of vedolizumab-responsive patients was CD1c+ (BDCA1+) dendritic cells. In blood, these dendritic cells ubiquitously express more α4β7 per cell than almost any other circulating leukocyte, but rapidly downregulate α4β7 expression upon vedolizumab exposure. Conclusions: The clinical efficacy of vedolizumab thus reveals integrin α4β7-dependent dendritic cell migration to the intestinal mucosa to be central to IBD pathogenesis.

overall_design: Cross-sectional case-control

first: Elisa

last: Boden

first: Ramya

last: Kongala

first: Duncan

last: Hindmarch

first: Donna

last: Shows

first: Julius

last: Juarez

first: James

last: Lord


title: PRMT5 and HP1𝛾 funtion as coregulators of glucocorticoid receptor in MDA-MB-231 cells

city: Lyon

first: Coralie

last: Poulard

address: 28 rue laennec

country: France

institute: CRCL

summary: Using a genome-wide analysis, we demonstrated that HP1𝛾 and PRMT5 are required for dexamethasone-regulated expression of glucocorticoid receptor (GR) target genes, implicated in cell migration

overall_design: Expression profiling by high throughput sequencing

first: Lara

last: Noureddine

first: Muriel

last: Le Romancer


title: Pou3f1 orchestrates a gene regulatory network controlling contralateral retinogeniculate projections [RNA-seq]

city: Montreal

first: Benoit

middle: Charles

last: Boulan

state: Quebec

address: 110, avenue des Pins Ouest

institute: IRCM

summary: POU3F1 as a key regulator of the cRGC transcriptional program

overall_design: RNA-seq analysis of POU3F1 over expression and Pou3f1 KO

first: Michel

last: Fries

first: Thomas

last: Brown

first: Benoît

first: Camille

last: Boudreau-Pinsonneault

first: Christine

last: Jolicoeur

last: Cayouette


title: Time course of measles infection in healthy human airway epithelial cell cultures

city: Iowa City

first: Alejandro

middle: A.

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

summary: The goal of this study was to examine changes in gene expression over time in healthy human airway epithelia infected with measles virus.

overall_design: Primary human airway epithelia were infected with measles, prepared for RNA sequencing, and sequenced on Illumina HiSeq 4000 system using 2x150bp paired end SBS chemistry.

first: Brajesh

last: Singh

first: Jennifer

last: Bartlett

first: Sateesh

last: Krishnamurthy

first: Andrew

last: Thurman

first: Patrick

last: Sinn


title: Transcription Across the H19/Igf2 Imprinting Control Region Initiates Paternally Methylated Imprinting in Mouse Prospermatogonia

city: Grand Rapids

first: Piroska

last: Szabó

state: MI

address: 333 Bostwick Ave NE

department: Department of Epigenetics

institute: Van Andel Insitute

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

overall_design: Refer to individual Series


title: STING-dependent inflammation and redox homeostasis maintained by ACSL4 in renal epithelial cells promotes hypertension-associated chronic kidney disease

city: Heifei

first: Gao

last: Li

address: Meishan Road

institute: The First Affiliated Hospital of Anhui Medical University

summary: To determine the function of STING in kidney epithelial cells, we constructed conditional STING knockout mice (CDH16KO mice).We then performed gene expression profiling analysis using data obtained from RNA-seq of renal tissues in AngII-induced mice and  AngII-induced CDH16KO mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for renal tissues in AngII-induced mice and  AngII-induced CDH16KO mice.

first: Yonggui

last: Wu

first: Li

last: Gao


title: Pou3f1 orchestrates a gene regulatory network controlling contralateral retinogeniculate projections


title: Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler

city: San Francisco

first: Megan

last: Ostrowski

address: 1700 Owens

institute: Gladstone Institutes

summary: SAMOSA, a method previously developed in the Ramani Lab, was employed to reveal nucleosome patterns from remodeling reactions in vitro with the Imitation Switch (ISWI) ATP-Dependent Remodeler ATPase, SNF2h. SAMOSA was further employed to reveal single-molecule nucleosome patterns in vivo from SNF2h knockout and re-expression murine embryonic stem cells.

sample_organism:
Mus musculus
unidentified plasmid

platform_organism:
Mus musculus
unidentified plasmid

overall_design: Investigating an ATP-Dependent Chromatin Remodeler ATPase via single-molecule chromatin profiling with m6A methyltransferase footprinting and SMRT long-read sequencing. 128 in vitro chromatin samples were analyzed (two replicates per condition), including the following controls: unremodeled methylated arrays and methylated/unmethylated unassembled template DNA. 35 in vivo samples were analyzed, including SAMOSA SNF2h KO/WT re-expression/E14 mESC SAMOSA samples (three biological replicates and technical replicates) and unmethylated/methylated mESC controls.

first: Nour

last: Abdulhay

first: Laura

last: Hsieh

first: Colin

middle: P

last: McNally

middle: S

last: Moore

first: Mythili

last: Ketavarapu

first: Sivakanthan

last: Kasinathan

first: Arjun

last: Nanda

first: Ke

first: Un

last: Chio

first: Ziling

last: Zhou

first: Hani

last: Goodarzi

first: Geeta

last: Narlikar

first: Vijay

last: Ramani


title: Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation [WGBS]

city: Shenzhen

first: Yueyuan

last: Zheng

address: Zhenyuan Road, 628

institute: The Seventh Affiliated Hospital of Sun Yat-sen University

summary:
As one of the most common malignancies, esophageal cancer has two subtypes, squamous cell carcinoma (ESCC) and adenocarcinoma (EAC), arising from distinct cells-of-origin. However, distinguishing cell-type-specific molecular features from cancer-specific characteristics has been challenging. Here, we analyze whole-genome bisulfite sequencing (WGBS) data on 45 esophageal tumor and nonmalignant samples from both subtypes. We develop a novel sequence-aware method to identify large partially methylated domains (PMDs), revealing profound heterogeneity at both the methylation level (depth) and genomic distribution (breadth) of PMDs across tumor samples. We identify subtype-specific PMDs, which are associated with repressive transcription, chromatin B compartments and high somatic mutation rate. While the genomic locations of these PMDs are pre-established in normal cells, the degree of loss is significantly higher in tumors. We find that cell-type-specific deposition of H3K36me2 may underlie the genomic distribution PMDs. At a smaller genomic scale, both cell-type- and cancer-specific differentially methylated regions (DMRs) are identified for each subtype. Using binding motif analysis within these DMRs, we show that a cell-type-specific transcription factor such as HNF4A can maintain the binding sites that it establishes in normal cells, while being recruited to new binding sites with novel partners such as FOSL1 in cancer. Finally, leveraging pan-tissue single-cell and pan-cancer epigenomic datasets, we demonstrate that a substantial fraction of the cell-type-specific PMDs and DMRs identified here in esophageal cancer, are actually markers that co-occur in other cancers originating from related cell types. These findings advance our understanding of the DNA methylation dynamics at various genomic scales in normal and malignant states, providing novel mechanistic insights into cell-type- and cancer-specific epigenetic regulations.
Whole-genome bisulfite sequencing (WGBS) for EAC ESO26 cell line and ESCC TE5 cell line.

overall_design: De-Chen Lin， Benjamin P Berman

first: Benjamin

last: Ziman

last: Berman


title: Genome wide (GW) and validation CRISPR screens on encephalitogenic CD4+ T cell migration into the CNS

city: Planegg

first: Anneli

last: Peters

address: Großhaderner Str. 9

institute: Institute for Clinical Neuroimmunology, Biomedical Center, University Hospital of the Ludwig-Maximilians University Munich

summary:
To identify genes driving encephalitogenic CD4+ T cell migration into the CNS, we performed a genome-wide CRISPR screen and a subsequent validation screen
For the genome-wide CRISPR screen, up to 4 sgRNA per gene and 800 non targeted controls were included, for a total of 87690 individual sgRNAs, and for the validation screen, up to 6 sgRNA per gene and 241 non targeted controls for a total of 12000 individual sgRNAs

sample_organism:
Rattus norvegicus
synthetic construct

platform_organism:
Rattus norvegicus
synthetic construct

overall_design: Comparison of sgRNA distribution by pairwise comparisons across blood, spleen, spinal cord leptomeninges and spinal cord parenchyma

first: Arek

last: Kendirli

first: Clara

last: de la Rosa

first: Katrin

middle: F

last: Laemmle

first: Martin

last: Kerschensteiner

first: Naoto

last: Kawakami


title: scRNAseq of blood and CSF CD4+ T cells from MS patients and controls

summary:
To study the regulation of candidate genes from our study in human cells, we analyzed CD4+ T cells from blood and CSF of MA patients and age and sex matched idiopathic intracranial hypertension controls
We analyzed 40845 cells in control blood, 807 cells in control CSF, 29749 cells in MS blood and 15768 cells in MS CSF

overall_design:
Analysis of overlapping TCR sequences in blood and CSF CD4+ T cells of the same transcript, transcriptomic characterization of the cell clusters and analysis of the behaviour of individual genes that came out as candidates from the CRISPR screen
---------------------
Author state:
Fastq raw data files from humans are not updated due to data protection concerns

first: Klara

last: Eglseer

first: Eduardo

last: Beltran


title: CD4+ T cell

sample_organism:
Homo sapiens
Rattus norvegicus
synthetic construct


title: HIF-1 regulates pathogenic T cells in lupus skin disease (bulk RNA-Seq)

city: New Haven

first: Alicia

last: Little

state: CT

address: 333 Cedar St, PO Box 208059

department: Dermatology

institute: Yale University

summary: Using a mouse model of lupus skin disease, we find that skin-infiltrating CD4+ and CD8+ T cells express high levels of HIF-1 and demonstrate a strong cytotoxic signature.

overall_design: We performed bulk RNA seq of sorted CD4+ and CD8+ T cells from MRL/lpr spleen and skin to understand the role of HIF1 in promoting lupus skin disease.

first: Joe

last: Craft

first: Ping-Min

last: Chen


title: Effect of Grk2 (spleen, rat) or Ets1 (spleen and spinal cord parenchyma, rat; in vitro, human) KOs on gene expression of CD4+ T cells

summary:
To study the effect of the Grk2 or Ets1 KOs in rat and human CD4+ T cells, in vivo or in vitro respectively, we generated KO CD4+ T cell lines by CRISPR-RNP nucleofection (with an gRNA targeting the gene locus) or control (with a non-targeting gRNA)
3' bulk RNAseq was conducted on CD4+ T-MBP rat cells isolated form spleen or spinal cord parenchyma three days after co-transfer of control and KO cells into the animal. Cells were FACS sorted based on their fluorescent protein reporters, BFP for control, and GFP for KOs. For human experiments, CD4+ T cells were isolated from buffy coats, KOed and restimulated in vitro, and 3' bulk RNAseq was performed. For rats, three biological replicates were used from three different animals, for humans, four biological replicates were used from four different donors

overall_design: Comparison of KO vs control

first: Stephan

last: Winklmeier

first: Christian

last: Wichmann


title: Androgen Receptor is a Determinant of Melanoma BRAFi/MEKi Resistance

first: Paola

last: Ostano


title: Genomic and transcriptomic landscape of a mouse model for immunotherapy in oral squamous cell carcinoma

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

summary: We examined the 4-nitroquinoline-1-oxide (4NQO)-induced oral squamous cell carcinoma (OSCC) model for genetic aberrations, transcriptomic profile, and immune cell compositions at different pathological stages.

overall_design: Transcriptome profiling

first: Y

last: Lee

middle: H

first: C

middle: T

last: Tan

first: D

middle: L

last: Ou


title: Chromosome-level organization of the regulatory genome in the Drosophila nervous system

city: Princeton

first: Michael

last: Levine

state: New Jersey

address: Icahn lab, Princeton University

institute: Princeton University

summary: Past studies have identified topologically associating domains (TADs) as basic units of genome organization.  Here, we present evidence for a new level of genome folding, whereby distant TAD pairs megabases apart interact to form meta-domains. Within meta-domains, gene promoters and structural intergenic elements present in distant TADs are specifically paired. The associated genes encode neuronal determinants, including those engaged in axonal guidance and adhesion. These long-range associations occur in a large fraction of neurons but support transcription in only a subset of neurons. Meta-domains are formed by diverse transcription factors that are able to pair over long and flexible distances. We present evidence that two such factors, GAF and CTCF, play direct roles in this process. The relative simplicity of higher-order meta-domain interactions in Drosophila, compared with those previously described in mammals, allowed the demonstration that genomes can fold into highly specialized cell type-specific scaffolds that enable megabase-scale regulatory associations.

overall_design: Testing chromosomal level genome organization with Micro-C

first: Xiao

last: Li

first: Maria

last: Gambetta


title: Effect of IL-15 culture +/- anti-NK1.1 stimulation on splenic NK cells [mNK_IL-15_RNA-seq]

city: SAINT LOUIS

first: Megan

last: Cooper

state: MISSOURI

address: MPRB, 6th floor, 4905 Childrens Place

department: Pediatrics

institute: Washington University in St Louis

summary:
Splenic NK cells were enriched and cultured in either low dose (5-10 ng/ml) or high dose (100 ng/ml) IL-15. Naïve NKs are freshly enriched NKs, obtained the day of the anti-NK1.1 stimulation.
Cells were either left unstimulated or were stimulated via plate-bound anti-NK1.1

overall_design: RNA-seq

last: Cimpean

first: Amanda

last: Swain

first: Prabhakar

last: Pandhey


title: Effect of IL-12+IL-18 or anti-NK1.1 stimulation on splenic NK cells [mNK_Activation_RNA-seq]

summary:
We stimulated freshly enriched splenic NK cells with either IL-12+IL-18 (1ng/ml each) or plate-bound anti-NK1.1. NKs from several C57Bl/6 mice were pooled.
We then performed gene expression profiling analysis using data obtained from RNA-seq at two time points: 3 or 6 hours.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for unstimulated versus IL-12+IL-18 or anti-NK1.1 stimulated NK cells

first: Molly

last: Keppel

first: Anastasiia

last: Gainullina


title: HIF-1 regulates pathogenic T cells in lupus skin disease (scRNA-Seq)

first: Alicia

middle: J

last: Little

summary: Using a mouse model of lupus skin disease, we find that skin-infiltrating CD4+ and CD8+ T cells express high levels of HIF-1, demonstrate a strong cytotoxic signature, and the cytotoxic signature decreases after pharmacologic HIF1 inhibition.

overall_design: We performed scRNA seq of MRL/lpr splenocytes and skin cells to understand the role of HIF1 in promoting lupus skin disease. We combined this technology to CITE-sequencing to obtain measurement at the protein and transcriptome level.

first: Joe

last: Craft

last: Chen


title: IL-15 priming alters IFN-g regulation in murine NK cells.


title: Telomerase upregulation induces progression of mouse BrafV600E-driven thyroid cancers and triggers non-telomeric effects

city: Boston

first: Iñigo

last: Landa

state: Massachusetts

address: 77 Avenue Louis Pasteur, 4BF Building, Room 645A

department: Medicine/Endocrinology

institute: Brigham and Women's Hospital, Harvard Medical School

summary: Mutations in the promoter of the telomerase reverse transcriptase (TERT) gene are the paradigm of a cross-cancer alteration in a non-coding region. TERT promoter mutations (TPMs) are biomarkers of poor prognosis in cancer, including thyroid tumors. TPMs enhance TERT transcription, which is otherwise silenced in adult tissues, thus reactivating a bona fide oncoprotein. To study TERT deregulation and its downstream consequences, we generated a Tert mutant promoter mouse model via CRISPR/Cas9 engineering of the murine equivalent locus (Tert-123C>T) and crossed it with thyroid-specific BrafV600E-mutant mice. We also employed an alternative model of Tert overexpression (K5-Tert). Whereas all BrafV600E animals developed well-differentiated papillary thyroid tumors, 29% and 36% of BrafV600E+Tert-123C>T and BrafV600E+K5-Tert mice progressed to poorly differentiated cancers at week 20, respectively. Tert-upregulated tumors showed increased mitosis and necrosis in areas of solid growth, and older animals displayed anaplastic-like features, i.e., spindle cells and macrophage infiltration. Murine Tert promoter mutation increased Tert transcription in vitro and in vivo, but temporal and intra-tumoral heterogeneity was observed. RNA-sequencing of thyroid tumor cells showed that processes other than the canonical Tert-mediated telomere maintenance role operate in these specimens. Pathway analysis showed that MAPK and PI3K/AKT signaling, as well as processes not previously associated with this tumor etiology, involving cytokine and chemokine signaling, were overactivated. These models constitute useful pre-clinical tools to understand the cell-autonomous and microenvironment-related consequences of Tert-mediated progression in advanced thyroid cancers and other aggressive tumors carrying TPMs. Implications: Telomerase-driven cancer progression activates pathways that can be dissected and perhaps therapeutically exploited.

overall_design:
Total RNA was isolated from up to 20,000 YFP+ cells sorted into TRIzol (range= 9,000-20,000 cells). Phase
separation in cells lysed in TRIzol reagent was achieved with chloroform. RNA was precipitated with
isopropanol, washed with 75% ethanol, and resuspended in RNase-free water following the
manufacturer’s protocol. RNAseq was performed at the Dana-Farber Cancer Institute Molecular Biology
Core Facility. RNA libraries were prepared following a low input mRNAseq protocol. RNA samples were
fragmented at 94°C for 8 min with 14 cycles of PCR post-adapter ligation, according to manufacturer’s
recommendation. The finished dsDNA libraries were quantified by Qubit fluorometer and Agilent
TapeStation 2200. Libraries were pooled in equimolar ratios. Final sequencing was performed on an
Illumina NovaSeq with paired-end 100 bp reads.

first: Caitlin

middle: M

last: Thornton

first: Bin

last: Xu

first: Jacob

last: Haase

first: Gnana

last: Krishnamoorthy

first: Jingzhu

last: Hao

first: Jeffrey

last: Knauf

first: Zachary

last: Herbert

first: Paula

last: Martínez

first: María

last: Blasco

first: Ronald

last: Ghossein

first: James

last: Fagin


title: Pou3f1 orchestrates a gene regulatory network controlling contralateral retinogeniculate projections [CUT&RUN]

first: Benoit

last: Boulan

overall_design: Cut&Run of  Pou3f1 at E14

first: Michel

last: Fries

first: Thomas

last: Brown

first: Benoît

first: Camille

last: Boudreau-Pinsonneault

first: Christine

last: Jolicoeur

last: Cayouette


title: Effect of IL-15 dose on cultured splenic NK cells [ATAC-seq]

first: Megan

last: Cooper

summary:
We cultured splenic NK cells in either low (10 ng/ml) or high (100 ng/ml) doses of IL-15 for ~72 hours.
We then performed ATAC-seq to compare differentially accessible regions.

overall_design: Comparison of differentially accessible chromatin regions between mouse NK cells cultured in low dose and high dose IL-15, in duplicate.

first: Maria

last: Cimpean

first: Changxu

last: Fan

first: Ana

last: Kolicheski

middle: A