title: Durable Alterations of Hematopoiesis and Chromatin post-COVID-19 [snATAC-seq]

city: New York

first: Jin-Gyu

last: Cheong

address: 1300 York Avenue

institute: Weill Cornell Medicine

summary: Acute SARS-CoV-2 infection is often highly inflammatory and protracted. Recent advances have established that inflammation can trigger innate immune memory and a persistent influence on hematopoietic development, through epigenetic mechanisms. However, these phenotypes and their molecular and cellular features are poorly described in humans. Here we reveal epigenomic alterations in innate immune and hematopoietic stem and progenitor cells (HSPC) post-COVID-19, with distinct molecular programs across disease severities. Enabled by novel approaches to study hematopoiesis from peripheral blood, we find persisting HSPC epigenetic programs conveyed, for months to a year, to short-lived progeny monocytes. These epigenetic changes are associated with increased myeloid cell differentiation and inflammatory and antiviral programs. We provide insights into post-infectious HSPC and innate immune cell epigenetic alterations that are broadly relevant.

overall_design: To discover changes in chromatin post-SARS-CoV-2 infection, ATAC-seq was performed on CD34+ HSPCs and CD14+ monocytes sorted from PBMC of healthy, non-COVID-19 post-ICU pateitns, mild convalescent, and severe convalescent COVID-19 patients.

first: Arjun

last: Ravishankar

first: Siddhartha

last: Sharma

first: Christopher

last: Parkhurst

first: Steven

middle: Z

last: Josefowicz

first: Duygu

last: Ucar


title: Chromatin organization in 3D distinguishes the influences of dMes-4/NSD and Hypb/dSet2 in protecting genes from H3K27me3 silencing

status: Public on Jul 01 2023

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

country: France

institute: CNRS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Maintenance of gene expression programs requires cell-type specific barcoding of genomes through euchromatin interspaced with facultative heterochromatin domains where PRC1/2 hinder chromatin accessibility thereby repressing genes inside such domains. At heterochromatin-euchromatin borders, regulation of heterochromatin spreading may depend on transcriptional activity, histone modifiers, and chromatin barrier insulators or the borders of topological associated domain (TADs). Here we show that depletion of H3K36 di- or tri-methyl histone methyl transferases dMes-4/NSD or Hypb/dSet2 induces H3K27me3 spreading at H3K27me3 borders, accounting for the repression of hundreds of genes upon depletion of these enzymes. dMes-4/NSD influences genes within active chromatin hubs and flanked by H3K27me3 borders demarcated by a TAD border, unlike dHypb/dSet2 that protects genes near H3K27me3 borders in absence of a TAD border. Insulator mutants that disrupt 3D chromatin hubs recapitulate only the H3K27me3 spreading observed upon depletion of dMes-4/NSD, and not of Hypb/dSet2. Hi-C data demonstrate how dMes-4/NSD directly block the propagation of the long-range interactions marking the inactive TADs, onto neighbor active regions, unlike Hypb/dSet2. Our data thus show a division of labor between dMes-4/NSD and Hypb/dSet2 to protect genes against H3K27me3 silencing, highlighting a direct influence of H3K36me marks on the demarcation of H3K27me3 domains within repressive TADs.

overall_design: We used the technology of ChIP-seq to quantifiy occupancy of histones modifications in presence or absence of H3K36 HMTs.Chromatin extracted from cells in wild-type or after a knock-down of HypB or Mes4

first: Depierre

last: David

first: Perrois

last: Charlène

first: Lhoumaud

last: Priscillia

first: Abdi-Galab

last: Mahdia

first: Fosseprez

last: Olivier

first: Heurteau

last: Alexandre

first: Cuvier


title: Proximity-dependent recruitment of Polycomb Repressive Complexes by the lncRNA Airn [ChIP-Seq]

city: Chapel Hill

first: Joseph

middle: Mauro

last: Calabrese

state: NC

address: 120 Mason Farm Rd

department: Pharmacology

country: USA

institute: UNC Chapel Hill

summary: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) in mouse F1-hybrid trophoblast stem cells for PRC subunits and PRC-induced chromatin modifications.

overall_design: ChIP-Seq

first: Aki

middle: K

last: Braceros

first: J

middle: M


title: Durable Alterations of Hematopoiesis and Chromatin post-COVID-19 [MultiomeATAC-seq]

first: Jin-Gyu

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

middle: N


title: Durable Alterations of Hematopoiesis and Chromatin post-COVID-19 [MultiomeRNA]

type: Expression profiling by high throughput sequencing

overall_design: To discover changes in chromatin post-SARS-CoV-2 infection, RNA-seq was performed on CD34+ HSPCs and CD14+ monocytes sorted from PBMC of healthy, non-COVID-19 post-ICU pateitns, mild convalescent, and severe convalescent COVID-19 patients.

first: Arjun


overall_design: mRNA profiles of Mes-4-depleted, HypB-depleted or wild-type control Drosophila S2 cells by RNA-seq (Illumina)


title: Proximity-dependent recruitment of Polycomb Repressive Complexes by the lncRNA Airn [Hi-C]

summary: In the developing mouse embryo, expression of the lncRNA Airn induces gene silencing and recruits Polycomb Repressive Complexes (PRCs) to varying extents over a 15 megabase domain, but the mechanisms remain unclear. Using high-resolution approaches, we show in mouse trophoblast stem cells that Airn expression induces long-range changes to chromatin architecture centered around a network of CpG islands occupied by PRCs and SMC1A/Cohesin. Extent of contact with Airn predicts underlying intensity of Polycomb-directed chromatin modifications and Airn-induced changes to chromatin architecture. Deletion of individual CpG islands alternately increase or decrease gene silencing and PRC activity over the domain in a manner predicted by changes in chromatin architecture. We conclude that Airn is a potent repressive lncRNA whose effects are controlled by an equilibratory network of DNA regulatory elements that modulate its frequency of contact with target chromatin.

overall_design: HiC in TSCs

first: Arima

last: Omer

first: Erez

middle: L

last: Aiden


title: Characterizing control of memory CD8 T cell differentiation by BTB-ZF transcription factor Zbtb20 using single cell RNA-sequencing

status: Public on Jun 30 2023

city: Lebanon

first: Edward

last: Usherwood

state: NH

address: Rubin Building, Level 7, 710-53

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth College

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

overall_design: Refer to individual Series


title: The NTCP receptor inhibitor Ezetimibe reduces the toxicity of α-amanitin: in vitro and in vivo study.

city: Kunming

first: Jinfang

last: Xue

address: No 157 Jinbi Road, Xishan District, Kunming

country: China

institute: Kunming University of Science and Technology

summary: Background and Aims: To verify the protective effect of Ezetimibe, an sodium taurocholate co-transporting polypeptide (NTCP) inhibitor, on α-amanitin poisoning in vitro and in vivo by inhibiting NTCP to prevent α-amanitin into hepatocytes. Approach and Results: In animal experiments, the survival rate was significantly improved in the treatment group. The pathomorphological characteristics of liver and kidney in the treatment group were significantly improved. In cell experiments,The cell viability of the treatment group was significantly improved, and the expression of NTCP in the treatment group was significantly decreased by immunofluorescence. In molecular docking simulations, we demonstrated the potential of NTCP to bind Ezetimibe and α-amanitin, respectively. Transcriptomics in high-throughput sequencing was used to detect the differential metabolic genes between α-amanitin poisoning group and the treatment group, and signal pathway enrichment was used to analyze the significantly different signal pathways. Conclusions: Ezetimibe, as an inhibitor of NTCP, can reduce the entry of α-amanitin into hepatocytes to play a protective role and improve the cell viability and survival rate of mice.

overall_design: Compare the control group using high-throughput sequencing Differences in mRNA gene expression in L-02 cell lines between  α-amanitin poisoning group and Ezetimibe treatment group after poisoning

first: Jiinfang

first: Xiran

last: Lou

first: Deyuan

last: Ning

first: Guobing

last: Chen


title: Genome wide CRISPR screen in AML chemotherapy resistance.

city: Jinan

first: Chunyan

last: Ji

address: Wenhua West Road

institute: Qilu Hospital

summary: Chemoresistance is the leading cause of acute myeloid leukemia (AML)-related deaths, and elucidation of the mechanisms of AML chemoresistance is necessary to effectively target this process. Here, we performed genome wide CRISPR-Cas9 screening to identify key molecules regulating AML chemoresistance.

overall_design: sgRNA counts from THP-1 hCas9 cells infected with two lentiviral gRNA libraries challenged with IDA treatment (1.5 ng/mL) or kept in regular medium.

first: Guangqiang

last: Meng

first: Tao

last: Sun

first: Mingying

last: Li


first: Olivier

last: Cuvier


title: Target capture bisulfite sequencing (tcBS-seq) to evaluate clonal methylation inheritance [BiSulfite-seq]

city: Cambridge

first: Anne

last: Ferguson-Smith

address: 20 Downing Place

department: Genetics

country: United Kingdom

institute: Cambridge University

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is considered a stable epigenetic mark due to its presumed long-term inheritance through cell divisions. Here, we perform high-throughput bisulfite sequencing on clonally derived cell lines to quantitatively measure mitotic methylation inheritance at the nucleotide level. We find that although DNA methylation is generally faithfully maintained at hypo- and hypermethylated sites, this is not the case at intermediately methylated CpGs. Low fidelity intermediate methylation is interspersed throughout the genome and within genes with no or low transcriptional activity. Moreover, we determine that the probabilistic changes that occur at intermediately methylated sites are due to DNMT1 rather than DNMT3A/3B activity. The observed lack of clonal inheritance at intermediately methylated sites challenges the concept of DNA methylation as a consistently stable epigenetic mark.

overall_design: To test whether DNMT3A/3B are mechanistically responsible for the probabilistic gain of methylation at intermediately methylated CpG sites, we generated four MEF lines (A, B, C, and D) from sibling E13.5 Dnmt3aflox/flox3bflox/flox  mouse embryos and used recombinant TAT-CRE protein to induce the double knockout (DKO) in vitro. We subsequently performed tcBS-seq with four DKO and four matched control cell lines.

first: Amir

middle: D

last: Hay

first: Noah

middle: J

last: Kessler

first: Daniel

last: Gebert

first: Nozomi

last: Takahashi

first: Hugo

last: Tavares

first: Felipe

last: Teixeira

middle: C


title: Target capture bisulfite sequencing (tcBS-seq) to evaluate clonal methylation inheritance [BiSulfite-seq 2]

overall_design: We devised an experiment to directly assess the fidelity of DNA methylation through cell divisions at the genome-scale, by subcloning populations of cells and performing target DNA capture followed by high-throughput bisulfite sequencing (tcBS-seq) on both the subclones (14 cell lines) and the parent population of cells (2 cell lines). To do so, we established mouse embryonic fibroblasts (MEFs) from two sibling E13.5 mouse embryos and immortalised the cell lines. From these parental lines, we randomly sampled fourteen single cells to establish clonal populations of around 1-2 million cells on which we profiled DNA methylation using tcBS-seq.


title: Target capture bisulfite sequencing (tcBS-seq) to evaluate clonal methylation inheritance


title: Spleens from mice exposed to either 9 Gy of whole-body ionizing radiation (WBIR) and WBIR combined with a 20% total body surface area burn (RCI) and treated with mouse mesenchymal stem cell derived extracellular vesicles (MSC-EVs)

city: Gainesville

first: Robert

last: Maile

state: FL

address: 1600 SW Archer Road

department: Surgery

institute: University of Florida

summary: Mice were treated with 1x1010 MSC-EVs inravenously 72 hours after exposure to 9 Gys of WBIR or RCI. 48 hours later the spleens were isolated from these mice and processed for RNA. This analysis was completed in order to assess the impact of MSC-EV treatment on the immune gene expression.

overall_design: There are six groups that were compared. WBIR compared to Sham (uninjured), WBIR with MSC-EVs compared to Sham, WBIR with MSC-EVs compared to WBIR, RCI compared to Sham, RCI with MSC-EVs compared to Sham, and RCI with MSC-EVs compared to RCI.

first: Roland

last: Seim


title: Nanostring mouse immunology mRNA panel - EVs isolated following exposure to WBIR were exposed onto RAW 264.7

summary:
561 mouse mRNA immunology panel.
EVs isolated from mice 3 or 7 days after exposure to 2 or 9 Grays of WBIR and were exposed onto RAW 265.7 macrophages in the presence of LPS in order to assess the gene expression changes in order to analyze the effect of these EVs on the pro-inflammatory response of macrophages. All experimental groups were compared to the exposure of Sham EVs onto macrophages.

overall_design: There are four groups that were analyzed. The impact of EVs isolated 3 days after exposure to either 2 or 9 Grays of WBIR and EVs isolated after 7 days after exposure to 9 Grays of WBIR. These EVs were exposed onto RAW 264.7 macrophages for 24 and the gene expression changes were compared to RAW 264.7 macrophages exposed to Sham EVs.


title: Target capture bisulfite sequencing (tcBS-seq) to evaluate clonal methylation inheritance [RNA-seq]


title: Secondary bile acids function through the vitamin D receptor in myeloid progenitor cells to promote myelopoiesis

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

summary: Metabolic products of the microbiota can alter hematopoiesis. However, the contribution and site of action of bile acids is poorly understood. Here we demonstrate that the secondary bile acids, deoxycholic acid (DCA), and lithocholic acid (LCA) increase bone marrow myelopoiesis. Treatment of bone marrow cells with DCA and LCA preferentially expanded immunophenotypic and functional (CFU-GM) granulocyte-monocyte progenitors (GMPs). DCA treatment of sorted hematopoietic stem/progenitor cells (HSPCs) increased CFU-GMs, indicating that direct exposure of HSPCs to DCA sufficed to expand GMPs. We determined that the vitamin D receptor (VDR) was required for the DCA-induced increase in CFU-GMs and GMPs. Finally, single-cell RNA sequencing revealed that DCA significantly upregulated genes associated with myeloid differentiation and proliferation in GMPs. The action of DCA on HSPCs to expand GMPs in a VDR-dependent manner suggests a mechanism for how microbiome-host interactions may directly impact bone marrow hematopoiesis and the severity of infectious and inflammatory disease.

overall_design:
Pre-irradiated murine embryonic liver fibroblasts (AFT024; ATCC- SCRC 1007.1) were seeded to confluency in 24 well plates in DMEM + 10%FBS + 0.05mM 2-mercaptoethanol in a 33°c, 5% CO2 incubator. Long-term culture media was made by the addition of 0.22uM filter sterilized Alpha-MEM with nucleosides (StemCell Inc) containing 1mM hydrocortisone (StemCell Inc) to Myelocult M5300 (StemCell Inc) to a final concentration of 1uM hydrocortisone. AFT024 media was then removed from the wells and two hundred thousand whole bone marrow cells in one mL of complete media was added to each well. Cells were cultured for 1 week either in a media control or in the presence of deoxycholic acid (35uM) or lithocholic acid (18uM). After 1 week, media was removed and placed into a collection tube, cells were then washed with HBSS (StemCell Inc), and this wash was placed into the same collection tube. Cells were then treated with Trypsin-EDTA (0.05%, Fisher Scientific) briefly to detach any cells still adhering to the culture plate. Trypsinization was halted by washing cells with heat-inactivated FBS, followed by IMDM+2%FBS. This wash was taken and added to the same collection tube used prior. Cells in the collection tubes were then centrifuged to pellet them and the media was decanted via aspiration. Cells were resuspended in FACS buffer (PBS+1%FBS), and subsequently stained for spectral flow cytometry to assay the wells for the growth of myeloid populations. All data is shown and is derived from 2 experimental replicates.
contributor: Bioinformatics Core Uva (bioinformatics@virginia.edu)

first: Stacey

last: Burgess

first: Brandon

last: Thompson


title: Nanostring mouse miRNA panel: performed on extracellular vesicles isolated following exposure to radiation

summary: Plasma derived extracellular vesicles (EVs) have emerged as critical mediators of complications following traumatic injuries and after exposure to radiation. In response to injury, the cargo of these EVs is altered and can contain potent cargo that can influence cell function, including alterations in miRNA cargo. Here, we utilized NanoString's mouse miRNA panel to compare the alterations in miRNA content following exposure to 2 or 9 Gys of whole-body irradiation isolated 3 days after exposure and compared these changes to sham mice.

overall_design: Mice were exposed to either 2 or 9 Grays of whole-body irradiation and 3 days later the plasma EVs were isolated. These EVs were analyzed using NanoString's miRNA panel and the expression changes were compared to EVs isolated from sham mice.

first: Rob


title: Isotype-based plasma cell subsets display differential niches requirements in the bone marrow

city: PARIS

first: Marion

last: Espeli

address: 1 avenue Claude Vellefaux, Inserm U1160, Institut de Recherche Saint Louis

institute: Inserm U1160

summary: Bone marrow long-lived plasma cells are essential for long-term protection against infection and their persistence within this organ relies on interactions with Cxcl12-expressing stromal cells that are still not clearly identified. Here, using single cell RNAseq and in silico transinteractome analyses we identified LepR+ mesenchymal cells as the stromal cell subset most likely to interact with plasma cells within the bone marrow. Moreover, we demonstrated that depending on the isotype they express, plasma cells may use different set of integrins and adhesion molecules to interact with these stromal cells. Altogether, our results constitute an unprecedented characterization of plasma cell subset stromal niches and open new avenues for the specific targeting of bone marrow plasma cells based on their isotype.

overall_design: Comparative gene expression profiling analysis of single cell RNA-seq data for bone marrow plasma cells of un stimulated mice.

first: Amélie

last: Bonaud

last: Espéli


title: PTEN loss confers resistance to anti-PD-1 therapy in nonsmall cell lung cancer by increasing tumor infiltration of regulatory T cells

city: Pamplona

first: Francisco

last: Exposito

state: Navarra

address: Irunlarrea SN, Research Building

department: Department of Pathology, Anatomy and Physiology, School of Medicine

country: Spain

institute: University of Navarra

summary: Immunotherapy resistance in non-small cell lung cancer (NSCLC) may be mediated by an immunosuppressive microenvironment, which can be shaped by the mutational landscape of the tumor. Here, we observed genetic alterations in the PTEN/PI3K/AKT/mTOR pathway and/or loss of PTEN expression in >25% NSCLC patients, with higher frequency in lung squamous carcinomas (LUSCs). Patients with PTEN-low tumors had higher levels of PD-L1 and PD-L2 and showed worse progression-free survival when treated with immunotherapy. Development of a Ptennull LUSC mouse model revealed that tumors with PTEN loss were refractory to antiPD-1, highly metastatic and fibrotic, and secreted TGF-β/CXCL10 to promote conversion of CD4+ lymphocytes into regulatory T cells (Tregs). Human and mouse PTEN-low tumors were enriched in Tregs and expressed higher levels of immunosuppressive genes. Importantly, treatment of mice bearing Pten-null tumors with TLR agonists and anti-TGF-β antibody aimed to alter this immunosuppressive microenvironment led to tumor rejection and immunological memory in 100% of mice. These results demonstrate that lack of PTEN causes immunotherapy resistance in LUSC by establishing an immunosuppressive tumor microenvironment that can be reversed therapeutically.

overall_design:
We generated a PTEN mutant version of the murin lung squamous carcinoma UNSCC680 cells using CRISPR-Cas9 technology.
We performed RNAseq from in vitro cultured EVGFP control cells and PTEN mutant cells, at a single time-point.
Comparative gene-expression profiling of RNAseq between EVGFP (Control) and PTEN null cells.

first: Alfonso

last: Calvo


title: Electroacupuncture Alleviates Ulcerative Colitis by Targeting CXCL1: Evidence from the Transcriptome and Validation

city: chengdu

first: Zhang

last: RuiBin

address: No. 37, Shi Er Qiao Road, JinNiu District

institute: chengdu university of traditional chinese medicine

summary:
We aimed to use transcriptomics, bioinformatics analysis, and core gene validation to identify the core gene and potential mechanisms for electroacupuncture (EA) treatment of mice with ulcerative colitis (UC).
The Full-length transcriptome was used for sequencing and analysis

overall_design: Comparative gene expression profiling analysis of  Full-length transcriptome for colon tissue of mice(CON,DSS,EAST36).

first: Rui-Bin

last: Zhang

first: Long-Cong

last: Dong

first: Shu-Guang

last: Yu

first: Qiao-Feng

last: Wu


title: Natural variation in the consequences of gene overexpression during osmotic stress [BAR-Seq]

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

institute: University of Wisconsin

summary: Free-living cells live in fluctuating environments and must be able to respond rapidly in order to survive. Genetic background can influence how an individual responds to a changing environment, including stressful changes. Changes in gene copy number can influence stress tolerance and responses, presumably due to corresponding changes in gene expression.  However, we recently showed that strains vary in their ability to tolerate gene copy number differences; how this influences variation in stress tolerance is relatively unknown. Here we measured the tolerance to gene overexpression (OE) in four different Saccharomyces cerevisiae strains, including wild isolates, when strains were grown under osmotic and ionic stress induced by sodium chloride (NaCl). OE genes that were deleterious to most strains under NaCl stress were enriched for translation processes, similar to the enrichments of deleterious genes in rich, non-stress medium. We found that the West African NCYC3290 strain and the North American YPS128 strain are more sensitive to NaCl stress than other strains. These strains showed the greatest number of sensitivities to gene OE compared to other strains. Although most genes were deleterious in these strains, subsets of genes are highly beneficial when OE during NaCl stress. Many of these highly beneficial genes are functionally related and point to underlying differences in strain physiology. This work illustrates how tolerance to gene overexpression is influenced by genotype-environment interactions.

overall_design: We conducted a barcode sequencing experiment examining 4 yeast strains expressing a high copy number plasmid library. For each strain, we took samples at generation 0 (start of experiment) and generation 10  to quantify how plasmid abundance changes over time when strains were grown under osmotic and ionic stress induced by 0.7M of sodium chloride (NaCl). Each strain was measured in biological triplicate for a total of 24 samples.

middle: P

first: DeElegant

last: Robinson


title: Natural variation in the consequences of gene overexpression during osmotic stress


title: Pasteurization of human milk affects the miRNA EVs cargo decreasing its immune modulatory activity

first: Monica

middle: F

last: Torrez Lamberti

address: 2033 Mowry Rd

department: Microbiology and Cell Science

type: Non-coding RNA profiling by high throughput sequencing

summary: We hypothesize that the collection, pooling, pasteurization, and freezing storage of the DHM exerts chemical and biological changes besides depleting the beneficial microbes and inactivating bioactive components in MOM. In this report, we evaluated the effect of the pasteurization process of DHM on the miRNA content of MOM EVs and their impact on innate immune response in human cell lines.

overall_design: RNA was extracted from human milk exosomes

first: Leslie

middle: A

last: Parker

first: Claudio

last: Gonzalez

first: Graciela

last: Lorca


title: Effect of transcription inhibitor DRB on gene expression under KRASG12V induction of SAEC

city: Chuo-ku

first: Bunsyo

last: Shiotani

state: Tokyo

address: 5-1-1 Tuskiji

department: Research Institute

country: Japan

institute: National Cancer Center

summary: To investigate RNA expression sensitive to DRB, we induced KRASG12V in SAEC cells with or without DRB treatment. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SAEC cells  with or without DRB treatment.

first: Taichi

last: Igarashi

first: Yusuke

last: Yamamoto

first: Takaaki

last: Yasuhara


title: The Transcriptional Regulator Ume6 is a Major Driver of Gene Expression during Gametogenesis in Budding Yeast

city: Berkeley

first: Anthony

last: Harris

state: CA

address: 622 Barker Hall

department: Molecular and Cell Biology

institute: UC Berkeley

summary: Early meiotic genes (EMGs) encompass an important subset within the developmental program of gametogenesis. Regulation of EMGs is achieved through the recognition of a common regulatory element in their promoters by the transcription factor Ume6. Proper meiotic execution requires the timely expression of EMGs, which is achieved through the adoption of the meiotic regulator Ime1 by Ume6. While it is known that Ime1’s binding to Ume6 promotes EMG expression, the mechanism of EMG activation remains unclear. Two competing models have been proposed: (1) Ime1 converts Ume6 to a coactivator complex, and (2) Ime1 binding targets Ume6 for degradation. Using a combination of tools including meiotic synchronization, temporally controlled protein depletion, protein-protein interaction engineering, and transcriptomics, here we address this conundrum. We identify 160 genes that are directly regulated by Ime1-Ume6, including UME6 itself. Removal of Ume6 shortly before meiotic entry is detrimental to EMG activation and gamete formation, whereas tethering of Ume6 to a heterologous activation domain is sufficient to trigger EMG expression and to generate viable gametes in the absence of Ime1. We conclude that Ime1-Ume6 functions as a coactivator complex. While Ume6 is indispensable for EMGs expression, Ime1 primarily serves as an evolutionarily tuned activation domain for Ume6.

overall_design:
(Mitotic Depletion)  Gene expression profiling of RNA-seq data from a time series before (t = -30 and 0min) and after Ume6 depletion (TIR; 15, 30, 60, and 120min) compared to undepleted time matched samples (NoTIR). Then, comparing their expression profiles for wild-type UME6 (WT) and a UME6 null (Ume6Del). Three replicates are included for each.
(Meiotic Depletion)  Expression profiling of RNA-seq data from a time series comparing effects of Ume6 depletion (TIR) before (t = 0.5 and 2h) and post-IME1 induction (t = 2.5, 3, 4.5, and 6h). Expression profiles for TIR were then compared to time matched samples for a NoTIR control. Three replicates are included for each.
(Meiotic Rescue)  Comparative gene expression profiling from RNA-seq data for a time series (t = 0, 2, 4, 6h) of untagged IME1 or sfGFP-tagged IME1 with various UME6 alleles (UME6, UME6-3V5, UME6(T99N)-3V5, and UME6(T99N)-3V5-aGFP). Three replicates are included.
(Meiotic Rescue)  Comparative gene expression profiling from RNA-seq data for a time series (t = 0, 2, 4, 6h) of untagged or sfGFP-tagged activation domains (IME1 and B112) in the UME6(T99N)-3V5-aGFP background. Three replicates are included.

first: Elçin

last: Ünal


title: Natural variation in the consequences of gene overexpression during osmotic stress [RNA-Seq]

summary: We used RNA-Seq to measure transcript abundance in 4 Saccharomyces cerevisiae strains (BY4743, BC187, NCYC3290, and YPS128) from a diverse range of genetic lineages when growing in rich media (YPD) with 0.7M NaCl to characterize differential expression across strains in response to osmotic and ionic stress.

overall_design: RNA-seq and transcriptome analysis of 4 strains (BY4743, BC187, NCYC3290, and YPS128) that were grown in YPD+ 0.7M NaCl. For each strain, 3 samples were collected: T0 (unstressed cells), T30 (30 mins after cells placed in 0.7M NaCl), and T3h (3 hours after cells placed in NaCl). These strains were collected in 3 biological replicates. The library for sample YPS128 Rep 3 T30 failed so this sample is missing and there are a total of 35 samples in the dataset.


title: Twins: A deep learning method for replicate-based conformation contact map analysis.

city: London

first: Ediem

last: Al-jibury

address: Hammersmith Hospital

institute: MRC LMS

type:
Third-party reanalysis
Other

summary: The organisation of the genome in nuclear space is an important frontier of biology. Chromosome conformation capture methods such as Hi-C and Micro-C produce genome-wide chromatin contact maps that provide rich data containing quantitative and qualitative information about genome architecture. Most conventional approaches to genome-wide chromosome conformation capture data are limited to the analysis of pre-defined features, and may therefore miss important biological information. One constraint is that biologically important features can be masked by high levels of technical noise in the data. Here we introduce Twins, a replicate-based method for deep learning from chromatin conformation contact maps. Using a Siamese network configuration, Twins learns to distinguish technical noise from biological variation and outperforms image similarity metrics across a range of biological systems. Features extracted by Twins from Hi-C maps after perturbation of cohesin and CTCF reflect the distinct biological functions of cohesin and CTCF in the formation of domains and boundaries, respectively. Twins distance metrics are biologically meaningful, as they mirror the density of cohesin and CTCF binding. Taken together, these properties make Twins an powerful tool for the exploration of chromosome conformation capture data, such as Hi-C capture Hi-C, and Micro-C.

relation:
Reanalysis of: GSM4386027
Reanalysis of: GSM4386026
Reanalysis of: GSM4386029
Reanalysis of: GSM4386028
Reanalysis of: GSM2453279
Reanalysis of: GSM2453280
Reanalysis of: GSM2453281
Reanalysis of: GSM2453282
Reanalysis of: GSM2453283
Reanalysis of: GSM2453284
Reanalysis of: GSM3457018
Reanalysis of: GSM3457019
Reanalysis of: GSM5963426
Reanalysis of: GSM5963427
Reanalysis of: GSM5963425
Reanalysis of: GSM5963424
Reanalysis of: GSM6918008
Reanalysis of: GSM6918007

overall_design:
This submission contains reprocessing of four chromatin conformation datasets and the resulting fully trained convolutional Siamese networks trained on images extracted from this chromatin conformation data. Each Hi-C replicate file normalised using ICE from hyalocytes processed in GSE93431 and GSE122157 is compared across wildtype (WT), control (TAM), Nipbl-/- (NIPBL) and Ncaph2-/- mice in two Siamese convolutional neural networks (SCNNs) one trained only on the WT, TAM and Nipbl-/- conditions (liver_NIPBLKO) and the other including the Ncaph2-/- (Liver_all_10kb) at 10kb resolution in 2.56Mb windows. Processed Hi-C files are also extracted as individual replicates from GSE94452 for mouse neural progenitor cells depleted of CTCF (aux) and in control (ctl) conditions and a SCNN is trained to compare KR normalised windows along the diagonal at 10kb resolution in 2.56Mb windows (NPC_CTCFdegron_10kb).  Mouse CD69-CD4+CD8+ (DP) T-cells extracted from processed Hi-C files at GSE199059 were compared to CD69-CD4+ (CD4 SP) T-cells from GSE222211 at various resolutions (2kb, 5kb, 10kb, 25kb) with various normalisations (VC, ICE, VC_SQRT, KR). Trained SCNNs were produced comparing high (R3 and R4) and low (R1 and R2) resolution DP T-cells and through T-cell differentiation (DP R1 and R2 to CD4 SP R1 and R2) for each normalisation and resolution.
Pre-processed Hi-C files from each of the respective studies were transformed into Pytorch datasets compatible with the Twins code base (ea409/twins_hic) and a Siamese network training protocol. Samples were split into validation (chr18), test (chr 2) and train (all other chromosomes) sets. For each Hi-C map, overlapping windows were extracted from along the diagonal, with resolution R and size 256xR from normalised maps. For each window any nan values are set to 0 and it is re-normalised by dividing by the maximum value in the window. Some windows values where the number positions containing with no information (i.e. all 0 values) exceeds 10% of the window are filtered out to avoid training on empty data. Regions are then fed into Siamese convolutional neural networks with LeNet architectures adpated with GeLU activation terms and to fit 256x256 images and trained using contrastive loss learning with an early stop criteria based on a 10% increase in validation loss from its minimal value.
.mlhic are processed datasets containing the results of mapped Hi-C data in a format compatable with the Twins software. Each file contains images taken along the diagonal of the Hi-C map and processed into a format suitable for machine learning.
.ckpt files are trained models, trained using the Siamese Networks method described in the Twins publication and in the Twins code.

first: James

middle: W

last: King

first: Ya

last: Guo

first: Amanda

middle: G

last: Fisher

first: Matthias

last: Merkenschlager

first: Daniel

last: Rueckert


title: Prediction of subclinical endometritis in postpartum dairy cows from circulating cell-free miRNA profiles

city: JOUY-en-JOSAS

first: gilles

last: charpigny

state: ILe de France

address: domaine de Vilvert

department: Physiologie Animale Systeme Elevage

institute: INRAE

summary: We aim at identifying possible differences in miRNA profiles and individual circulating miRNA between healthy cows and cows with persistent inflammation as diagnosed by cytology and histology. Ultimately the miRNA profiles will be correslated with RNAseq results to be performed from endometrial biopsies (planned later on this year following laser  micro dissection). Samples have been taken from 6 "healthy  cows" with low presence of immune cells at 21 and 44 days post partum which were subsequently pregnant, and from 11 cows with high numbers of immune cells at 21 and 44 days post partum, all non pregnant.

overall_design: Healthy (H, n =6) and Subclinical-Endometritis (SCE, n =11) cows characterized by endometrial cytology and biopsy were blood sampled at 21 and 44 days postpartum. Following extraction of cell-free plasma miRNAs and RNA-seq analysis, differential abundance analysis of miRNAs was performed with the DESeq2 R package (adjusted p-value of 0.05), and discriminant analysis was used to combine the differently abundant miRNAs in a single variable and create a predictive model.

first: Gonçalo

last: Pereira

first: Gilles

last: Charpigny

first: Yongzhi

first: Elisabete

last: Silva

first: Marta

first: Tao

last: Ye

first: Luís

last: Lopes-da-Costa

first: Patrice

last: Humblot


title: Unique miRNome and Transcriptome Profiles Underlie Microvascular Heterogeneity in Mouse Kidney

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

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

overall_design: Refer to individual Series


title: mRNA data - Unique miRNome and Transcriptome Profiles Underlie Microvascular Heterogeneity in Mouse Kidney

summary:
Endothelial cells in the blood vessels in the kidney exert different functions depending on the (micro)vascular bed they are located in. These functional differences are likely a result of differential microRNA and mRNA transcription patterns, yet the identity of these molecules is not well known.
We zoomed in on the endothelial cells of microvascular compartments in mouse renal cortex by laser microdissecting the microvessels prior to (small) RNA sequencing analyses. By these means, we characterised microRNA and mRNA transcription profiles of arterioles, glomeruli, peritubular capillaries, and post-capillary venules. RT-qPCR, in situ hybridisation, and immunohistochemistry were used to validate sequencing results.
Unique microRNA and mRNA transcription profiles were found in all microvascular compartments, with dedicated marker microRNAs and mRNAs showing enriched transcription in a single microvascular compartment. In situ hybridisation validated localisation of microRNAs mmu-miR-140-3p in arterioles, of mmu-miR-322-3p in glomeruli, and of mmu-miR-451a in post-capillary venules. Immunohistochemical staining showed that von Willebrand Factor protein was mainly expressed in arterioles and post-capillary venules, while GABRB1 expression was enriched in glomeruli and IGF1 in post-capillary venules.
Our study shows that microvascular endothelial heterogeneity in mouse kidney is a result of a combination of differentially expressed microRNAs and mRNAs. The identified profiles provide important molecular information to take into account for future studies into microvascular engagement in health and disease.

overall_design: Gene expression analysis in microvascular compartments from healthy mouse kidney cortex (arterioles, glomeruli, peritubular capillaries, post-capillary venules) to reveal microvascular-compartment specific gene expression profiles

first: Matthijs

last: Luxen

first: Peter

last: Zwiers

first: Femke

last: Meester

first: Rianne

last: Jongman

first: Timara

last: Kuiper

first: Jill

last: Moser

first: Susanna

last: Skalicky

last: Hackl

first: Matijs

last: van Meurs

first: Grietje

last: Molema


title: smallRNA data - Unique miRNome and Transcriptome Profiles Underlie Microvascular Heterogeneity in Mouse Kidney

first: Matthias


title: Genome wide CRISPR screen for Venetoclax plus Ruxolitinib combination resistance in OCI-AML2 cells using Y. Kosuke library

city: Portland

first: Daniel

last: Bottomly

address: 3181 S.W. Sam Jackson Park Rd.

institute: Oregon Health and Science University

summary: 30 million OCI-AML2 cells were infected with CRISPR/Cas9 library, selected for puromycin resistance for integration events and exposed DMSO, venetoclax (0.5 uM) or venetoclax (0.1 uM) plus ruxolitinib (1 uM).  Cells were collected at day 14 and 21 , DNA was extracted and sgRNA barcodes were amplified. PCR library was deep sequenced using Novaseq 6000 high throughput Illumina platform.

overall_design: Performed comparisons of sgRNA read counts between DMSO and Venetoclax as well as Venetoclax plus Ruxolitinib  treated cells at corresponding time points.

first: Christopher

last: Eide

first: Stephen

middle: E

last: Kurtz

first: Andy

last: Kaempf

first: Nicola

last: Long

first: Sunil

last: Joshi

first: Tamilla

last: Nechiporuk

first: Ariane

last: Huang

first: Charles

last: Dibb

first: Akosha

last: Taylor

first: Shannon

last: McWeeney

first: Jessica

last: Minnier

first: Brian

last: Druker

first: Jeffrey

last: Tyner


title: A genome-wide functional study of 3’UTR mutations in advanced prostate cancer [RNA-seq]

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: Metastatic, castration-resistant prostate cancer (mCRPC) is an advanced form of prostate cancer with a high mortality rate due to a current lack of treatment options. While much is already known about how mutations in protein-coding sequences across the genome affect prostate cancer, somatic mutations occurring in the 3’ untranslated regions (3’UTRs) of genes are largely unstudied. The 3’UTR is a genomic region that controls post-transcriptional gene expression through its recruitment of trans-acting factors such as RNA-binding proteins (RBPs) and microRNAs (miRNAs), which themselves are known to be oncogenes and tumor suppressors in many cases. To better understand the role of 3’UTR mutations across prostate cancer, we have created a database of 3’UTR somatic mutations in 185 patients with mCRPC, discovering 14,497 single-nucleotide mutations throughout the 3’UTRome. In order to functionally assay these variants, we have developed a novel pair of massively parallel reporter assays (MPRA) able to determine the effect of thousands of patient somatic mutations on post-transcriptional gene expression. In this two-pronged approach, we are able to measure whether each of 6,892 mutations found in recurrently mutated 3’UTRs affect mRNA stability, steady-state transcript level, and translation efficiency. This deep functional assessment of thousands of 3’UTR mutations allows us to uncover patterns in mutation functionality, including their association with RNA motifs and sequence conservation. Investigation into how the resultant gene expression changes from 3’UTR mutations affect prostate cancer pathogenesis, such as cancer growth or response to treatment, is also underway. This work represents an unprecedented view of the extent to which disease-relevant 3’UTR mutations affect mRNA stability, translation efficiency, and cancer phenotypes, expanding the boundaries of functional cancer genomics and potentially uncovering novel therapeutic targets in previously unexplored regulatory regions.

overall_design: IVT RNASeq of samples

first: Samantha

last: Schuster

first: Bethany

last: Stackhouse

first: Cynthia

last: Wladyka

first: Lukas

last: Corey

first: Patrick

last: Paddison

first: Andrew

last: Hsieh


title: Combination treatment of sodium pentaborate pentahydrate, curcumin and piperine on hepatocellular carcinoma cells

city: Istanbul

first: Fikrettin

last: Sahin

state: Other (Not found in list)

address: Kayisdagi Cd

country: Turkey

institute: Yeditepe University

summary: The goal of this study is to determine the response of sodium pentaborate pentahydrate, curcumin and piperine and their combination on hepatocellular carcinoma cell lines, HepG2 and Hep3B

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells on combination of NaB, Curcumin and piperine treatment.

first: Zehra

middle: O

last: Ulu


title: Single-cell RNA-seq uncovers novel metabolic functions of Schwann cells beyond myelination

city: Ann Arbor

first: Mohamed

last: Noureldein

address: 109 Zina Pitcher Place

department: Neurology

institute: University of Michigan

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of SCs and the effects of different diets on these populations.

overall_design: SCs from sciatic nerves of the C57BL6/J mice fed with either SD or HFD were isolated by anti-O4 magnetic beads and analyzed using scRNAseq.

first: Stephanie

last: Eid

first: Eva

last: Feldman


title: Reversing lysosome-mTORC1-ribosome axis dysregulations to mitigate C9FTD/ALS neurodegeneration [snRNA-Seq]

city: los angeles

first: Guoping

last: Fan

state: ca

address: 695 Charles E Young Drive South

department: Human Genetics

institute: university of california, los angeles

summary: We report the application of snRNA-seq in the mouse cortex with C9FTD/ALS neurodegeneration

overall_design: Mouse cortex tissues were dissociated into single nucleus and subjected to snRNA-seq in WT and C9-BAC (BAC) mice without and with C9orf72 heterozygous (C9-BAC;C9orf72+/-) or homozygous deletion (C9-BAC;C9orf72-/-).

first: Jing

last: Wang

first: Li

last: Ma


title: GLUT1 is redundant in hypoxic and glycolytic nucleus pulposus cells of the intervertebral disc

city: Philadelphia

first: Shira

last: Johnston

state: PA

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

institute: Thomas Jefferson University

summary:
Glucose is critical to the development, homeostasis, and survival of nucleus pulposus cells. GLUT1 is a major glucose transporter, a NP phenotypic cell marker, and highly expressed in nucleus pulposus (NP) cells, however its level of importance in NP cell development and homeostasis is unknown.
We used microarrays to explore the transcriptomics of differentially expressed genes between wildtype and Glut1 cKO NP cells in 9-month-old mice.

overall_design: NP tissue were dissected from discs from control (n=6) and K19Cre; Glut1 cKO mice (n=6). Mice were injected with Tamoxifen at 3-months-old and aged until they became 9-months-old. RNA extraction was prefomed and hybridization on Affymetrix microarrays.

first: Elizabeth

last: Silagi

first: Vedavathi

last: Madhu

first: Irving

last: Shapiro

first: Makarand

middle: V

last: Risbud


title: Single-cell RNA-sequencing of mouse colonic monocytes and macrophages

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: We performed a single-cell transcriptome analysis of colon monocytes and macrophages in 2 control mice and 2 mice orally treated with diesel exhaust particles.

overall_design: Lamina propria cells positive for Cd11b and positive for Ly6c2 or Cd64 were sorted for each replicate mouse, and used for single cell RNA Seq (10x genomics platform)

first: Angela

last: Bosch

first: Claudia

last: Cavelti

first: Julien

last: Roux


title: A genome-wide functional study of 3’UTR mutations in advanced prostate cancer [DNA-seq]

first: Sonali

last: Arora

overall_design: small seq on plasmid library

first: Samantha

last: Schuster

first: Bethany

last: Stackhouse

first: Cynthia

last: Wladyka

first: Lukas

last: Corey

first: Patrick

last: Paddison

first: Andrew

last: Hsieh


title: A genome-wide functional study of 3’UTR mutations in advanced prostate cancer [Polysome-Seq]

overall_design: Polysome Profiling of PC3 cell samples


title: RNA sequencing of liver tissues from mice treated with or without ischemia

city: Boston

first: Chen

last: Chu

state: MA

address: 450 Brookline Ave, Smith 914

institute: Dana-Farber Cancer Institute

summary: RIPK1 is a critical regulator of cell death and inflammation implicated in a multitude of human inflammatory and degenerative diseases. However, it remains elusive mechanistically whether and how RIPK1 may be activated under ischemia conditions.   Methods: Total RNA from the total livers of mice ( WT, Ripk1D138N, TNFR1/2 KO)  was purified using Qiagen RNeasy mini (Qiagen) according to the manufacturer’s instructions. Library preparation and sequenceing analysis were performed by Quintara Biosciences.   Conclusions: Our study indicates that ischemia can induce RIPK1 kinase-dependent cell death and inflammation.

overall_design: Total RNA was extracted from liver tissues from the following genotypes:  WT, Ripk1D138N, TNFR1/2 KO.  Each group has three repeats.

first: Tao

last: Zhang

first: Wenyi

last: Wei


title: A genome-wide functional study of 3’UTR mutations in advanced prostate cancer


title: Siglec-9 acts as an immune checkpoint molecule on macrophages in glioblastoma, restricting T cell priming and immunotherapy response [scRNA-seq]

status: Public on Jun 29 2023

city: Guangzhou

first: Guangshuai

last: Jia

address: Dongfengxi Rd, Yuexiu Campus

institute: Guangzhou Medical University

summary: The neoadjuvant immune checkpoint blockade therapy only benefits a limited fraction of glioblastoma multiforme (GBM) patients. Thus, targeting other immunomodulators on myeloid cells is an attractive therapeutic option. Here, we performed single-cell RNA sequencing and spatial transcriptomics of GBM patients treated with neoadjuvant anti-PD-1 therapy. We identified unique monocyte-derived tumor-associated macrophage (TAM) subpopulations with functional plasticity that highly expressed the immunosuppressive SIGLEC9 gene and preferentially accumulated in the non-responders to anti-PD-1 treatment. Deletion of Siglece (murine homologue) resulted in significantly restrained tumor development and prolonged survival in mouse models. Mechanistically, targeting Siglece directly activated both CD4+ T cells and CD8+ T cells through antigen presentation, secreted chemokines and co-stimulatory factor interactions. Furthermore, Siglece deletion synergized with anti-PD-1/PD-L1 treatment to improve antitumor efficacy. Our data demonstrated that Siglec-9 is an immune checkpoint molecule on macrophages that can be targeted to enhance anti-PD-1/PD-L1 therapeutic efficacy for GBM treatment.

overall_design:
For the samples from Pt1-Pt18 and mouse samples, scRNA-seq was performed using Chromium Single Cell Library Kits (10x Genomics). For the samples from Pt19-Pt24, scRNA-seq was performed with GEXSCOPE Single Cell RNA Library Kits (Singleron, China)48. All steps were carried out following the standard manufacturer protocols. The concentrations of single-cell suspensions were adjusted to target a recovery of 7,000-10,000 cells per sample. The libraries were sequenced on an Illumina HiSeq X Ten sequencer.
We have uploaded all raw sequences to NGDC.  For human data, it is NGDC accession number HRA004677.  For mouse data, it is NGDC accession number CRA011176.


title: Siglec-9 acts as an immune checkpoint molecule on macrophages in glioblastoma, restricting T cell priming and immunotherapy response


title: Siglec-9 acts as an immune checkpoint molecule on macrophages in glioblastoma, restricting T cell priming and immunotherapy response [ST]

overall_design:
ST experiment was performed using Visium Spatial Gene Expression Kits (10x Genomics) following standard manufacturer protocols.
*** We have uploaded all raw sequences to NGDC.  For human data, it is NGDC accession number HRA004677. ***


title: Siglec-9 acts as an immune checkpoint molecule on macrophages in glioblastoma, restricting T cell priming and immunotherapy response [bulk RNA-seq]

overall_design:
Differentially expressed genes in tumors of Siglece KO vs WT mouse, bulk RNA-seq data
We have uploaded all raw sequences to NGDC.  For mouse data, it is NGDC accession number CRA011176.


title: Immunogenomic profile at baseline predicts host susceptibility to clinical malaria

city: Baltimore

first: Carrie

last: McCracken

state: MD

address: 670 W. Baltimore St

department: Institute for Genome Sciences

institute: Institute of Genome

summary: Host gene and protein expression impact susceptibility to clinical malaria, but the balance of immune cell populations, cytokines and genes that contributes to protection, remains incompletely understood. To identify determinants of host susceptibility to clinical malaria at a time when acquired immunity is developing, we analyzed peripheral blood mononuclear cells (PBMCs) collected from children who differed in susceptibility to clinical malaria, all from a small town in Mali. PBMCs were collected from children aged 4-6 years at the start, peak and end of the malaria season. We characterized the immune cell composition and cytokine secretion for a subset of 20 children per timepoint (10 children with no symptomatic malaria age-matched to 10 children with >2 symptomatic malarial illnesses), and gene expression patterns for six children (three per cohort) per timepoint. We noted higher frequency of HLA-DR+ CD4 T cells in protected children during the peak of the malaria season and comparable levels cytokine secretion after stimulation with malaria schizonts across all three time points. We also observed differences between the two groups of children in the expression of genes related to cell death and inflammation; in particular, inflammatory genes such as CXCL10 and STAT1 and apoptotic genes such as XAF1 were upregulated in susceptible children before the transmission season began. This suggests that differences in apoptotic and inflammatory gene expression patterns can predict susceptibility to clinical malaria.

overall_design: Peripheral Blood Mononuclear Cells (PBMCs) collected from Malian Children were stimulated with Plasmodium falciparum schizonts (Pfsz), a positive control, Staphylococcal enterotoxin B (SEB), and a negative control, media, prior to RNA extraction and bulk RNA sequencing. Each individual has samples from day 0, day 90, and day 150.

first: Gillian

last: Mbambo

first: Joana

last: Silva

first: Kirsten

last: Lyke

first: Ankit

last: Dwivedi

first: James

last: Munro

first: Robin

last: Bromley


title: Hdac1 and Hdac2 regulate the quiescent state and survival of hair-follicle mesenchymal niche

city: SAFED

first: David

last: Enshell-Seijffers

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: BAR ILAN UNIVERSITY

summary: While cell division is essential for self-renewal and differentiation of stem cells and progenitors, dormancy is required to maintain the structure and function of the stem-cell niche. Here we use the hair follicle to show that during growth, the mesenchymal niche of the hair follicle, the dermal papilla (DP), is maintained quiescent by the activity of Hdac1 and Hdac2 in the DP that suppresses the expression of cell-cycle genes. Furthermore, Hdac1 and Hdac2 in the DP promote the survival of DP cells throughout the hair cycle. While during growth and regression this includes downregulation of p53 activity and the control of p53-independent programs, during quiescence, this predominantly involves p53-independent mechanisms. Remarkably, Hdac1 and Hdac2 in the DP during the growth phase also participate in orchestrating the hair cycle clock by maintaining physiological levels of Wnt signaling in the vicinity of the DP. Our findings not only provide insight into the molecular mechanism that sustains the function of the stem-cell niche in a persistently changing microenvironment, but also unveil that the same mechanism provides a molecular toolbox allowing the DP to affect and fine tune the microenvironment.

overall_design: To determine whether Hdac1 and Hdac2 play a role in the DP in regulating the hair cycle, Hdac1 and Hdac2 were ablated specifically in the DP postnatally. Then we preformed gene expression profiling analysis using data obtained from RNA-seq of  Control and  Hdac1/Hdac2 double mutant at 4 time point (P20, P24, P28 and P60).

first: Hadas

last: Sibony-Benyamini

first: Emil

last: Aamar


title: A spatially resolved single cell genomic atlas of the adult human breast [snRNA_nuclei]

city: Houston

first: Nicholas

last: Navin

state: TX

address: 6767 Bertner Ave

department: System Biology

institute: MD Anderson Cancer Center

summary: The adult human breast comprises an intricate network of epithelial ducts and lobules that are embedded in connective and adipose tissue. While most previous studies have focused on the breast epithelial system, many of the non-epithelial cell types remain understudied. Here, we constructed a comprehensive Human Breast Cell Atlas (HBCA) at single-cell and spatial resolution.  Our single-cell transcriptomics data profiled 714,331 cells from 126 women, and 120,024 nuclei from 20 women, identifying 12 major cell types and 58 biological cell states.  These data revealed abundant pericyte, endothelial and immune cell populations, and highly diverse luminal epithelial cell states.  Spatial mapping using four different technologies revealed an unexpectedly rich ecosystem of tissue-resident immune cells, as well as distinct molecular differences between ductal and lobular regions.  Collectively, these data provide an unprecedented reference of the adult normal breast tissue for studying mammary biology and diseases such as breast cancer.

overall_design:
This data provides an unprecedented atlas of the normal cell types and cell states in the human breast, that will serve as an important reference for studying breast development and diseases such as breast cancer.
single nuclei gene expression profiling by high throughput sequencing

first: T

last: Kumar

first: K

last: Nee

first: R

last: Kessenbrock

first: N


title: Tumor-associated fibrosis impairs immune surveillance and response to immune checkpoint blockade in non-small cell lung cancer

city: St. Louis

last: DeNardo

email: johnbaer@wustl.edu, ddenardo@wustl.edu

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine

institute: Washington University in St. Louis

summary: Non-small cell lung cancer (NSCLC) is a leading cause of cancer-related deaths. Immune checkpoint blockade has improved survival for many patients with NSCLC, but most fail to obtain long-term benefit. Understanding the factors leading to reduced immune surveillance in NSCLC is critical in improving patient outcomes. Here, we show that human NSCLC harbors large amounts of fibrosis that correlates with reduced T cell infiltration. In murine NSCLC models, the induction of fibrosis led to increased lung cancer progression, impaired T cell immune surveillance, and failure of immune checkpoint blockade efficacy. Associated with these changes, we observed that fibrosis leads to numerically and functionally impaired dendritic cells and altered macrophage phenotypes that likely contribute to immunosuppression. Within cancer-associated fibroblasts, distinct changes within the Col13a1-expressing population suggest that these cells produce chemokines to recruit macrophages and regulatory T cells while limiting recruitment of dendritic cells and T cells. Targeting fibrosis through transforming growth factor-β receptor signaling overcame the effects of fibrosis to enhance T cell responses and improved the efficacy of immune checkpoint blockade but only in the context of chemotherapy. Together, these data suggest that fibrosis in NSCLC leads to reduced immune surveillance and poor responsiveness to checkpoint blockade and highlight antifibrotic therapies as a candidate strategy to overcome immunotherapeutic resistance.

overall_design: Examination of cancer-associated fibroblasts (CAFs) and immune cells in murine model of non-small cell lung cancer (NSCLC)

first: John

last: Baer

first: Brett

last: Herzog


title: sox1a:eGFP transgenic line and single-cell transcriptomics reveal the origin of zebrafish intraspinal serotonergic neurons

city: Eggenstein-Leopoldshafen

first: sepand

last: Rastegar

address: Hermann-von-Helmholtz-Platz 1

department: Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP)

country: Germany

institute: Karlsruhe Institute of Technology (KIT)

summary: The Sox family of transcription factors plays a crucial role in the development of the vertebrate nervous system. In the zebrafish embryo, sox1 genes are expressed in neural progenitor cells and neurons of the ventral spinal cord. We recently reported that the loss of function of sox1a and sox1b results in a significant decrease in a subtype of V2 neurons, called V2s, in zebrafish. Here a single-cell RNA sequencing (scRNA-Seq) approach was used to analyse the transcriptome of sox1a lineage progenitors and neurons in the zebrafish spinal cord at four different time points during the development of an earlier established Tg(sox1a:EGFP) line. In addition to the sox1a-expressing neurons described previously, we found that this gene is also expressed in late-developing intraspinal serotonin neurons (ISNs). Developmental trajectory analysis of single-cell data and morpholino knockdown of lateral floor plate (LFP) cells expressing the nkx2.9 gene suggest that ISNs are generated from LFP progenitor cells. Pharmacological inhibition of the Notch signalling pathway demonstrates the necessity of this pathway for the development of LFP progenitor cells into ISN populations. Our results confirm that the zebrafish LFP is a progenitor domain from which ISN neurons are generated in addition to the previously described KA" and V3.

overall_design: The trunk and tail of Tg(sox1a:eGFP) lines were and dissected at 1, 2 3 and 5 dpf. The tissue  was dissociated and GFP positive cells were sorted by FACS as described (Cosacak et al. 2019). The single-cell encapsulation, cDNA synthesis by 10X Genomics. The reads were aligned to zebrafish genom (GRChZ 11) and ensemble version 105 was used for gene annotation and assigning reads to genes. Genomics Kit, and Sequencing done by Illumina.

first: Fushun

last: Chen

first: Mehmet

middle: I

last: Cosacak

first: Sepand


title: scRNAseq Datasets Supporting Tumor Intrinsic Mechanisms of Antigen Escape to Anti-BCMA and Anti-GPRC5D Targeted Immunotherapies in Multiple Myeloma

city: Calgary

first: Nizar

last: Bahlis

state: Alberta

address: 3330 Hospital Dr NW HMRB328

department: Divisions of Hematology and Oncology

country: Canada

institute: University of Calgary

summary: Multiple myeloma (MM) immune escape resulting from B cell maturation antigen (BCMA) target loss is considered to be a rare event that mediates MM resistance to anti-BCMA chimeric antigen receptor T cell (CAR T) or bispecific T cell engager (TCE) therapies. Emerging clinical data also suggests that downregulation of G protein coupled receptor family C group 5 member D (GPRC5D), another promising target antigen expressed on MM cells, is observed in patients at relapse post anti-GPRC5D CAR T, but the genomic mechanisms that underlie GPRC5D loss has not been described. In order to examine the tumor intrinsic factors that promote MM antigen escape, we performed combined bulk whole genome sequencing and single cell copy number variation analysis on CD138+ cells from bone marrow aspirates of patients before and after relapse from anti-BCMA or -GPRC5D CAR T/ TCE. We describe five cases with distinct biallelic events on TNFRSF17 at MM relapse after CAR T/ TCE. In addition to focal biallelic deletions at the TNFRSF17 locus acquired at relapse, BCMA negative clones can emerge from the selective expansion of subclones with homozygous TNFRSF17 loss that exist prior to any anti-BCMA therapy exposure. Furthermore, we corroborate with functional data to demonstrate that three different non-truncating mutations in the extracellular domain of BCMA negates the efficacies of BCMA directed TCEs and mediate disease relapse in patients. With respect to GPRC5D, we report four cases of MM relapse with biallelic loss of GPRC5D following anti-GPRC5DxCD3ε. Our data support that immunoselection of BCMA negative or mutant clones post anti-BCMA therapies may be more frequent than currently accepted in the field, and that an all or none screening approach for BCMA expression is inadequate to detect pertinent mutations that affect patient response to targeted therapies. We also highlight the importance of developing immunotherapies targeting novel and non-redundant epitopes or antigens in MM

overall_design: Experiments were conducted on primary multiple myeloma patients bone marrow samples provided after informed consent, in accordance with the Declaration of Helsinki and following the approval by the Medical Center Institutional Review Board. Unbiased mRNA and DNA profiling were conducted by using scRNA-seq and sc-CNV-seq from the GemCode system (10x Genomics) accordingly to the manufacturer’s protocols. For single-cell DNA library generation for CNV single-cell suspensions of primary MM cells were processed according to 10X Genomics Reagent Kits User Guide (CG000153). Single cells were partitioned in a hydrogel matrix by combining with a CB polymer to form Cell beads (CBs) using a microfluidic chip. Post a first encapsulation, CBs were treated to lyse the encapsulated cells and denature the genomic DNA (gDNA). The denatured gDNAs in the CB were then accessible to amplification and barcoding. A second microfluidic encapsulation step was then required to partition the CB with 10x barcode Gel Beads (GBs) to generate GEMs. Immediately after barcoding and amplification, 10x barcoded fragments were pooled and attached to standard Illumina adaptors. For all the single cell methods, quality control and quantification was performed using a Kapa Library Quantification qPCR kit (Kapa Biosystems) on a BioRad qPCR instrument prior to preparing a single pool containing equal amounts of each library. This pool was then subjected to on-board cluster formation and sequencing on an Illumina NextSeq 500 sequencer with a high-output v2.5 150 sequencing kit for RNA-seq and  300 cycle sequencing kit for CNV-seq as per the standard Illumina protocols. After sequencing, the bcl data was converted to fastq data files using the Illumina BCL2FASTQ utility. Samples were processed with CellRanger suite v3.0 and downstream analyses were realized with Seurat, Loupe and custom R packages.

first: Holly

last: Lee

first: Sungwoo

last: Ahn

first: Ranjan

last: Maity

first: Noemie

last: Leblay

first: Bachisio

last: Ziccheddu

first: Marietta

last: Truger

first: Monika

last: Chojnacka

first: Anthony

last: Cirrincione

first: Michael

last: Durante

first: Remi

last: Tilmont

first: Elie

last: Barakat

first: Mansour

last: Poorebrahim

first: Sarthak

last: Sinha

last: McIntyre

first: Angela

last: Chan

last: Wilson

first: Shari

last: Kyman

first: Amrita

last: Krishnan

first: Ola

last: Landgren

first: Wencke

last: Walter

first: Manja

last: Meggendorfer

first: Claudia

last: Haferlach

first: Torsten

first: Hermann

last: Einsele

last: Kortüm

first: Stefan

last: Knop

first: Jean-Baptiste

last: Alberge

first: Andreas

last: Rosenwald

first: Jonathan

last: Keats

first: Leo

last: Rasche

first: Francesco

last: Maura

first: Paola

last: Neri


title: scCNVseq Datasets Supporting Tumor Intrinsic Mechanisms of Antigen Escape to Anti-BCMA and Anti-GPRC5D Targeted Immunotherapies in Multiple Myeloma

first: Nizar

last: Bahlis

first: Holly

last: Lee

first: Sungwoo

last: Ahn

first: Ranjan

last: Maity

first: Noemie

last: Leblay

first: Bachisio

last: Ziccheddu

first: Marietta

last: Truger

first: Monika

last: Chojnacka

first: Anthony

last: Cirrincione

first: Michael

last: Durante

first: Remi

last: Tilmont

first: Elie

last: Barakat

first: Mansour

last: Poorebrahim

first: Sarthak

last: Sinha

first: John

last: McIntyre

last: Chan


title: A spatially resolved single cell genomic atlas of the adult human breast [visium]

first: Nicholas

last: Navin

overall_design: This data provides an unprecedented atlas of the normal cell types and cell states in the human breast, that will serve as an important reference for studying breast development and diseases such as breast cancer.

first: T

last: Kumar

first: K

last: Nee

first: R

last: Wei

last: Kessenbrock

first: N


title: From methylation to myelination: epigenomic and transcriptomic profiling of chronic inactive demyelinated multiple sclerosis lesions

city: Hasselt

first: Tim

last: Vanmierlo

address: Martelarenlaan 40

country: Belgium

institute: Universiteit Hasselt

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Tumor Intrinsic Mechanisms of Antigen Escape to Anti-BCMA and Anti-GPRC5D Targeted Immunotherapies in Multiple Myeloma

first: Nizar

last: Bahlis

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

B cell maturation antigen (BCMA) target loss is considered to be a rare event that mediates multiple myeloma (MM) resistance to anti-BCMA chimeric antigen receptor T cell (CAR T) or bispecific T cell engager (TCE) therapies. Emerging data report that downregulation of G protein coupled receptor family C group 5 member D (GPRC5D) protein often occurs at relapse after anti-GPRC5D CAR T. To examine the tumor intrinsic factors that promote MM antigen escape, we performed combined bulk and single cell whole genome sequencing/ copy number variation analysis of 30 patients treated with anti-BCMA and/ or -GPRC5D CAR T/ TCE. In two cases, MM relapse post TCE/ CAR T was driven by BCMA negative clones harboring focal biallelic deletions at the TNFRSF17 locus at relapse or by selective expansion of pre-existing subclones with biallelic TNFRSF17 loss. In another five cases of relapse, newly detected non-truncating missense mutations or in-frame deletions in the extracellular domain of BCMA negated the efficacies of anti-BCMA TCEs, despite detectable surface BCMA protein expression. Here, we also report the first four cases of MM relapse with biallelic mutations of GPRC5D following anti-GPRC5D TCE, including two cases with convergent evolution where multiple subclones lost GPRC5D through somatic events. Immunoselection of BCMA or GPRC5D negative or mutant clones is an important tumor intrinsic driver of relapse post targeted therapies. Mutational events on BCMA confer distinct sensitivities towards different anti-BCMA therapies, underscoring the importance of considering the tumor antigen landscape for optimal design and selection of targeted immunotherapies in MM.


title: From methylation to myelination: epigenomic and transcriptomic profiling of chronic inactive demyelinated multiple sclerosis lesions [RNA-seq]

summary: We compared transcriptomic profiles between chronically demyelinated MS lesions and matched normal-appearing white matter (NAWM).

overall_design: Chronically demyelinated lesions and matched normal-appearing white matter from progressive MS patients (n=9)

first: Daniel

last: van den Hove

first: Assia

last: Tiane


title: Transcriptomic analysis of the livers of mice acutely challenge with IL1B

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

institute: CNRS

summary: Livers from mice subjected to a single IL1B injection were collected and used to prepare RNA for transcriptomics analysis.

overall_design: Male C57BL/6J wild-type (WT) mice were purchased from Charles River at 7 weeks of age and housed in standard cages in a temperature-controlled room (22–24°C) with a 12-h dark–light cycle. They had ad libitum access to tap water and standard chow and were allowed to acclimate for 2 weeks prior to initiation of the experimental protocol. Acute liver inflammation was induced by intraperitoneal injection of recombinant mouse IL1B using 0.5 µg/ mouse (BioLegend, 575102) or vehicle (PBS) for 3h. Livers were collected and used to prepare RNA which was then processed for analysis using MoGene-2_0-st Affymetrix microarrays according to standard procedures.

first: Vanessa

last: Dubois

first: Celine

last: Gheeraert

first: Jerome


title: Transcriptomic analysis of THRB-regulated genes in mouse liver

summary: RNA-seq analysis of mouse liver samples from either control mice or mice with hepatocyte-specific THRB deletion.

overall_design: Differential gene expression analysis in liver-specific THRB knockout mice and their wildtype littermates. Strategy used to delete Thrb in these mice has been described in Billon C et al. Endocrinology 2014.

first: Karine

last: Gauthier

first: Céline

first: Loïc

last: Guille

first: Julie

last: Dubois-Chevalier


title: From methylation to myelination: epigenomic and transcriptomic profiling of chronic inactive demyelinated multiple sclerosis lesions [methylation]

summary: We compared genome-wide DNA methylation profiles between chronically demyelinated MS lesions and matched normal-appearing white matter (NAWM).


title: Effect of glucose refeeding after short-term glucose withdrawal on gene expression of MCF7 cells

city: Shenzhen

first: FengFeng

last: Rao

address: 1088 Xueyuan Road

institute: Southern University of Science and Technology

summary: MCF7 is an epithelial cell line isolated from the breast tissue of a patient with metastatic adenocarcinoma. Growth factors are well-known stimulators of glycometabolism. Whether glucose autoregulates its own metabolism remains poorly understood. To probe this, we designed the glucose-refeeding experiment in MCF7 for RNAseq analysis.

overall_design: RNAseq-profile of MCF7 breast cancer cells refed with/without glucose after short-term glucose withdrawal.

first: Yifan

last: Luo

first: Siyue

last: Nie

first: Yang

last: Su

first: Feng


title: Effect of short-term glucose withdrawal and glucose refeeding after short-term glucose withdrawal on gene expression of MCF7 cells


title: Biglycan and reduced glycolysis are associated with breast cancer cell dormancy in the brain

city: Leeds

first: Mihaela

last: Lorger

address: Woodhouse

institute: University of Leeds

summary: To understand the mechanisms of breast cancer cell dormancy in the brain

overall_design: We used an in vivo model of triple negative breast cancer brain metastasis to identify differences between cell cycle-inactive (GFP+CV+) and proliferating (GFP+CV-) cancer cells in the brain

first: Ashley

last: Sunderland

first: Jennifer

last: Williams

first: Tereza

last: Andreou

first: Nora

last: Rippaus

first: Christopher

last: Fife

first: Fiona

last: James

first: Yolanda

last: Kartika

first: Valerie

last: Speirs

first: Ian

last: Carr

first: Alastair

last: Droop


title: Fibrosis induced by resident macrophages has divergent roles in pancreas inflammatory injury and PDAC

first: David

last: DeNardo

summary: Tissue-resident macrophages (TRMs) are long-lived cells that maintain locally and can be phenotypically distinct from monocyte-derived macrophages. Whether TRMs and monocyte-derived macrophages have district roles under differing pathologies is not understood. Here, we showed that a substantial portion of the macrophages that accumulated during pancreatitis and pancreatic cancer in mice had expanded from TRMs. Pancreas TRMs had an extracellular matrix remodeling phenotype that was important for maintaining tissue homeostasis during inflammation. Loss of TRMs led to exacerbation of severe pancreatitis and death, due to impaired acinar cell survival and recovery. During pancreatitis, TRMs elicited protective effects by triggering the accumulation and activation of fibroblasts, which was necessary for initiating fibrosis as a wound healing response. The same TRM-driven fibrosis, however, drove pancreas cancer pathogenesis and progression. Together, these findings indicate that TRMs play divergent roles in the pathogenesis of pancreatitis and cancer through regulation of stromagenesis.

overall_design: Examination of macrophage subsets in steady-state, pancreatitis, and PDAC tissue

first: John

last: Baer


title: RNA Methyltransferase METTL16's Protein Domains Have Differential Functional Effects on Cell Processes

city: Greenville

first: Kyle

middle: D.

last: Mansfield

state: NC

address: 600 Moye Blvd, MS622

department: Biochemistry and Molecular Biology

institute: East Carolina University, Brody School of Medicine

summary:
To investigate the cellular role of METTL16, we established HEK293 cell lines over expressing wild-type METTL16 or METTL16 methylation and RNA binding mutations.  We then removed endogenous METTL16 from the cells using CRISPR.
We then performed gene expression profiling analysis using data obtained from RNA-seq of the various cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for METTL16 knockout HEK293 cells rescued with Wild-type or various mutated versions of METTL16

first: Emily

middle: R

last: Satterwhite


title: Effect of short-term glucose withdrawal on gene expression of MCF7 cells

first: FengFeng

last: Rao

summary: MCF7 is an epithelial cell line isolated from the breast tissue of a patient with metastatic adenocarcinoma. Whether glucose autoregulates its own metabolism remains poorly understood. To probe this, we performed RNA-Seq analysis on MCF7 breast cancer cells cultured with/without short-term glucose withdrawal.

overall_design: RNAseq-profile of MCF7 breast cancer cells cultured with/without short-term glucose withdrawal.

first: Yifan

last: Luo

first: Siyue

last: Nie

first: Yang


title: Single-cell transcriptomic analysis links non-myelinating Schwann cells to pro-inflammatory response in the lung [scRNA-seq]

status: Public on Jun 28 2023

city: South San Francisco

first: Josh

last: Kaminker

address: 1 DNA Way

department: OMNI Bx, gRED

institute: Genentech Inc

summary: The lung is a barrier tissue with constant exposure to the inhaled environment. Therefore, innate immunity against particulates and pathogens is of critical importance to maintain tissue homeostasis. While the lung harbors both myelinating and non-myelinating Schwann cells (NMSCs), NMSCs represent the abundant Schwann cell (SC) population in the lung. However, their contribution to lung physiology remains largely unknown. Here, we used the human glial fibrillary acidic protein promoter (GFAP) driving tdTomato expression in mice to identify SCs in the peripheral nervous system (PNS) and determine their location within the lung. Single-cell transcriptomic analysis revealed the existence of two NMSC populations (NMSC1 and NMSC2) that may participate in pathogen recognition. We demonstrated that these pulmonary SCs produce chemokines and cytokines upon lipopolysaccharide (LPS) stimulation using in vitro conditions. Furthermore, we challenged mouse lungs with LPS and found that NMSC1 exhibits an enriched pro-inflammatory response among all SC subtypes. Collectively, these findings define the molecular profiles of lung SCs and suggest a potential role for NMSCs in lung inflammation.

overall_design: hGFAP-tdTomato mice were either untreated or treated with PBS (vehicle) or LPS for 2 hours via oropharyngeal aspiration route (3 replicates per treatment condition). Then SCs were sorted using Fluorescence activated cell sorting (FACS) by selecting for CD45-EPCAM-CD31-tdTomato high cells from lung tissues, and analyzed by single-cell RNA-seq.

first: Min

last: Jung

first: Jose

last: Heredia

first: Alessia

last: Balestrini

first: Joshua

middle: S

first: Ning

last: Ding


title: Increased body mass index is linked to systemic inflammation through altered chromatin co-accessibility in human preadipocytes [RNA-Seq]

city: Princeton

first: Kristina

middle: Marie

last: Garske

email: kmgarske@ucla.edu, kg8086@princeton.edu

state: New Jersey

address: Carl Icahn Lab, South Drive, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics; Ecology & Evolutionary Biology

institute: Princeton University

summary: Obesity-induced adipose tissue dysfunction can cause low-grade inflammation and downstream obesity comorbidities. Although preadipocytes may contribute to this pro-inflammatory environment, the underlying mechanisms are unclear. We used human primary preadipocytes from body mass index (BMI) -discordant monozygotic (MZ) twin pairs to generate epigenetic (ATAC-sequence) and transcriptomic (RNA-sequence) data for testing whether increased BMI alters the subnuclear compartmentalization of open chromatin in the twins’ preadipocytes, causing downstream inflammation. Here we show that the co-accessibility of open chromatin, i.e. compartmentalization of chromatin activity, is altered in the higher vs lower BMI MZ siblings for a large subset (~88.5Mb) of the active subnuclear compartments. Using the UK Biobank we show that variants within these regions contribute to systemic inflammation through interactions with BMI on C-reactive protein. In summary, open chromatin co-accessibility in human preadipocytes is disrupted among the higher BMI siblings, suggesting a mechanism how obesity may lead to inflammation via gene-environment interactions.

overall_design:
To investigate the effects of increased body mass index (BMI) on preadipocyte genomic programming, we isolated and cultured preadipocytes from the subcutaneous adipose biopsies of BMI-discordant monozygotic (MZ) twins.
We performed gene expression profiling analysis from RNA-seq data produced from the preadipocytes of 10 pairs (n=20) of BMI-discordant MZ twins.
*
Submitter declares that the raw data were not deposited due to privacy concerns

first: Paivi

last: Pajukanta


title: Increased body mass index is linked to systemic inflammation through altered chromatin co-accessibility in human preadipocytes


title: Increased body mass index is linked to systemic inflammation through altered chromatin co-accessibility in human preadipocytes [ATAC-Seq]

overall_design:
To investigate the effects of increased body mass index (BMI) on preadipocyte genomic programming, we isolated and cultured preadipocytes from the subcutaneous adipose biopsies of BMI-discordant monozygotic (MZ) twins.
We performed chromatin accessibility profiling analysis from ATAC-seq data produced from the preadipocytes of 10 pairs (n=20) of BMI-discordant MZ twins.
We initiated the adipogenic differentiation of the preadipocytes and collected ATAC-seq data from 9 pairs (n=18) of the same BMI-discordant MZ twins (one pair failed the differentiation).
*
Submitter declares that the raw data were not deposited due to privacy concerns


title: Transposable Elements Lose Methylation and Gain Expression During Malignant Transformation [RNA-seq]

city: Washington

first: Katherine

last: Chiappinelli

address: 800 22nd Street, NW

department: Molecular Immunology and Tropical Medicine

institute: George Washington University

summary: Transposable elements (TEs) are typically silenced by DNA methylation and repressive histone modifications in differentiated healthy human tissues. However, TE expression increases in a wide range of cancers and is correlated with global hypomethylation of cancer genomes. We assessed expression and DNA methylation of TEs in fibroblast cells that were serially transduced with hTERT, SV40, and HRASR24C to immortalize and then transform them, which models the different steps of the tumorigenesis process. RNA-sequencing and whole-genome bisulfite sequencing were performed at each stage of transformation. TE expression significantly increased as cells progressed through transformation, with the largest increase in expression after the final stage of transformation, consistent with data from human tumors. The upregulated TEs were dominated by endogenous retroviruses (LTRs). Most differentially methylated regions (DMRs) in all stages were hypomethylated, with the greatest hypomethylation in the final stage of transformation. A majority of the DMRs overlapped TEs from the RepeatMasker database, indicating that TEs are preferentially demethylated. Many hypomethylated TEs displayed a concordant increase in expression. Demethylation began during immortalization and continued into transformation, while upregulation of TE transcription occurred in transformation. Numerous LTR elements upregulated in the model were also identified in TCGA datasets of breast, colon, and prostate cancer. Overall, these findings indicate that transposable elements, specifically endogenous retroviruses, are demethylated and transcribed during transformation.

overall_design: Comparative gene/TE expression profiling analysis of RNA-seq data for BJ fibroblast (EP) and transformation model (hTERT, SV40, HRAS)

first: Tomas

last: Kanholm

first: Uzma

last: Rentia

first: Melissa

last: Hadley

first: Jennifer

last: Karlow

first: Olivia

middle: L

last: Cox

first: Noor

last: Diab

first: Matthew

last: Bendall

first: Tyson

last: Dawson

first: James

last: McDonald

first: Wenbing

last: Xie

first: Keith

last: Crandall

first: Kathleen

middle: H

last: Burns

first: Stephen

last: Baylin

first: Hari

last: Easwaran


title: Comparative transcriptomics of porcine conventional blood NK cells, conventional liver NK cells and liver resident NK cells

city: Merelbeke

first: Robert

last: Jansens

address: Salisburylaan 133

department: Department of Translational Physiology, Infectiology and Public Health

institute: Ghent University

summary:
Liver-resident NK (lrNK) cells have been studied in human as well as in mice.
In the current study, we compared the transcriptome of three porcine NK cell populations: CD8αhigh cNK cells from peripheral blood, CD8αhigh NK cells isolated from the liver and the liver-specific CD8αdim NK cells using RNA-seq, to gain new insights in the biology of these cells.
Overall, our data indicate that lrNK cells show an immature and anti-inflammatory phenotype.
We also observed that the CD8αhigh NK cell population present in the liver appears to represent a population with an intermediate phenotype.
While the transcriptome of these cells largely overlaps with that of cNK cells, they also express transcripts associated with liver residency, such as CXCR6.

overall_design:
We isolated porcine blood NK cells through MACS and FACS purification of porcine PBMC.
Porcine conventional liver NK cells and porcine liver-resident NK cells were obtained by flushing the portal vein of the liver with PBS, followed by isolation of lymphocytes from the collected flush fluid and purification via MACS and FACS as was done for the blood NK cells.

first: Leen

last: Hermans

first: Herman

last: Favoreel


title: Single-cell transcriptomic analysis links non-myelinating Schwann cells to pro-inflammatory response in the lung [bulk RNA-Seq]

first: Josh

last: Kaminker

overall_design: Lung SCs were sorted from hGFAP-tdTomato mice by selecting for CD45-EPCAM-CD31-tdTomato high cells, cultured for 8 days,  stimulated with either PBS or LPS for 2 hours, and analyzed by bulk RNA-seq.

first: Min

last: Jung

first: Jose

last: Heredia

first: Alessia

last: Balestrini

first: Joshua

first: Ning

last: Ding


title: MAPK-related gene signature predicting MAPKi sensitivity in pLGG - McGill cohort

city: Jena

first: Romain

last: Sigaud

address: Am Klinikum 1

department: Pediatrics and Adolescent Medicine

institute: UKJ

summary: MAPK inhibitor sensitivity scores (MSS) were developed to predict sensitivity to MAPK inhibitors in pediatric low-grade gliomas (pLGG). The scores were validated in pLGG cell lines in vitro and in the publicly  available Open Pediatric Brain Tumor Atlas dataset. Validation in independent datasets is warranted.

overall_design: Gene expression profiling from primary pLGG samples prior MAPKi therapy

first: Till

last: Milde

first: Augusto

last: Andrade

first: Nada

last: Jabado


title: Overexpression of human alpha-Synuclein leads to dysregulated microbiome/metabolites with ageing in a rat model of Parkinson disease

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

institute: Universitätsklinikum Tübingen

summary: Braak’s hypothesis stating that sporadic Parkinson’s disease follows a specific progression of the pathology from the peripheral to the central nervous system and can be monitored by detecting accumulation of the alpha-Synuclein protein. There is growing interest in understanding how the gut (commensal) microbiome can regulate alpha-Synuclein accumulation which can lead to PD.  We studied a transgenic rat model overexpressing the human alpha-Synuclein and found that the protein overexpression resulted in gut alpha-Synuclein expression and aggregation in the gut neurons with advancing age. A progressive gut microbial composition alteration characterized by the reduction of Firmicutes to Bacteroidetes ratio could be detected in the young transgenic rat model and interestingly this ratio was then increased with aging. This observation was accompanied in older animals by intestinal inflammation, increase gut permeability and a robust alteration in metabolites production characterized by the increase of succinate level in the feces and serum. Manipulation of the gut bacteria by short-term antibiotics treatment revealed a complete loss of short-chain fatty acids (SCFAs) and reduction in succinate levels. Although antibiotics treatment did not change alpha-synuclein expression in the enteric nervous system of the colon, it can reduce alpha-synuclein expression in the olfactory bulb of the transgenic rats. In summary, synchronous with ageing, our data emphasize that the gut microbiome dysbiosis leads to a specific alteration of gut metabolites which are reflected in the serum and can be modulated by the environment.

overall_design: To investigate the inflammatiory pathyways in colon epithelial - we used isolated RNA from mucosa and submucosal layer from 3 and >12M old WT and TG rats. First we compared the gene expression at 3M age and >12M age (TG/WT) individually. Later gene expression profiling was compared among 3M and >12M age TG rats. In a second experiment, WT and TG (2.5M) age were treated with an antibiotic cocktail for two weeks and RNA was isolated at age 3M from mucosa and submucosal layer and comparisons were made for control vs antibiotic treat TG rats.

first: Yogesh

last: Singh

first: Nicolas

last: Casadei

first: Olaf

last: Riess


title: Effect of DNA G-quadruplex binder on tumor cell line SAS

city: Kitakyushu

first: Shigeori

last: Takenaka

state: Fukuoka

address: 1-1 Sensui-cho, Tobataku

department: Department of Applied Chemistry

institute: Kyushu Institute of Technology

summary: A new group of G-quadruplex binder, cyclic anthraquinone derivative which named cAQ-mBen was developed for G-quadruplex specific recognition. We used RNA-Seq to explore the effect of cAQ-mBen and anthraquinone derivative which named AQ-ac on the whole-transcriptome profiles of tumor cell line SAS.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Tumor cell line SAS untreated or treated with cAQ-mBen and AQ-ac which are DNA G-quadruplex binder

first: Hikaru

last: Fukuda

first: Tingting

last: Zou

first: Satoshi

last: Fujii

first: Shinobu

last: Sato

first: Daiki

last: Wakahara

first: Sen

last: Higashi

first: Ting-Yuan

last: Tseng

first: Ta-Chau

last: Chang

first: Naomi

last: Yada

first: Kou

last: Matsuo

first: Manabu

last: Habu

first: Kazuhiro

last: Tominaga

first: Hiroshi

last: Takeuchi


title: Malignant Transformation Drives DNA Methylation Loss and Transcriptional Activation of Transposable Element Loci [WGBS]

first: Katherine

last: Chiappinelli

overall_design: Comparative methylation analysis using whole-genome bisulfite sequencing data for BJ fibroblast (EP) and transformation model (hTERT, SV40, HRAS)

first: Tomas

last: Kanholm

first: Uzma

last: Rentia

first: Melissa

last: Hadley

first: Jennifer

last: Karlow

first: Olivia

last: Cox

first: Noor

last: Diab

first: Matthew

last: Bendall

first: Tyson

last: Dawson

first: James

last: McDonald

first: Wenbing

last: Xie

first: Keith

last: Crandall

first: Kathleen

last: Burns

first: Stephen

last: Baylin

first: Hari

last: Easwaran


title: MAPK-related gene signature predicting MAPKi sensitivity in pLGG - Charite cohort

first: Romain

last: Sigaud

first: Till

last: Milde

first: David

last: Capper

first: Ulrichn

last: Thomale

first: Pablo

last: Hernaiz-Driever

first: Michele

last: Simon

first: Svea

last: Horn

first: Nina

last: Herz

first: Arend

last: Koch


title: Single-cell transcriptomics of Cxcl13+ LN stromal cells

city: London

first: Pavel

last: Tolar

address: Institute of Immunity and Transplantation, Rowland Hill St

institute: University College London

summary:
Purpose: The goal of this study is to characterise the follicular dendritic cells (FDCs) upon antigen-immunocomplex immunisation.
Methods: FACS sorting of Live/Death- Podoplanin+ CD31- CD45- CXCL13-TdTomato+ after LN disgregation of CXCL13-CreTdTomato mice. Mice has been previously immunised with antigen-Ics at different time-points. Cells were loaded into 10x Genomics Chromium Platform, and sequenced using Illumina HiSeq 4000.
Conclusions: Our study detects previously identified stromal cell populations and shows the heterogeneity present on the FDCs. We detect 3 different FDC clusters.

overall_design: FACS-sorted CXCL13-TdTomato+ stromal cells were used for single-cell RNA-sequencing (10x Genomics Chromium Platform), and sequenced using Illumina HiSeq 4000.

first: Ana

last: Martinez Riano

first: Stefan

last: Boeing


title: Microglial expression of CD83 governs cellular activation and restrains autoimmune neuroinflammation

city: Erlangen

first: Hashem

last: Mohammadian

address: Ulmenweg 18

department: Department of Medicine 3 - Rheumatology and Immunology

institute: University of Erlangen-Nürnberg

summary: Microglial activation during neuroinflammation is crucial for coordinating the immune response against neuronal tissue and the initial response of microglia determines the severity of neuroinflammatory diseases. CD83 has been associated with early activation of microglia in various disease settings albeit its functional relevance for microglial biology was still elusive. Thus, we conducted a thorough assessment of CD83 regulation in microglia as well as its impact on microglial mediated neuroinflammation. Here, we describe for the first time that CD83 expression in microglia is not only associated with cellular activation but also with pro-resolving functions. Conditional deletion of CD83 causes malfunctioning responses to myelin debris, which results in an over-activated state during autoimmune neuroinflammation. Subsequently, CD83-deficient microglia recruit more pathogenic immune cells to the central nervous system and deteriorate resolving mechanism, which exacerbates the disease. Thus, CD83 in microglia orchestrates cellular activation and consequently, also resolution of neuroinflammation.

overall_design: Conditional CD83 x CX3CR1-CreERT2  knock out mice and CX3CR1-CreERT2 control mice were subjected to experimental auto-immune encephalitis (EAE). Microglia was isolated by Fluorescence-activated cell sorting (FACS) according to the presence of CD45 (intermediate), CD11b, CX3CR1 and P2RY12 signal  and analyzed using scRNAseq.

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