title: Cell type specific gene expression analysis in pre-symptomatic huntington's disease.

city: Linköping

first: Susanne

last: Bauer

address: BKV, Cellbiologi Pl 10

department: BKV

institute: Linköpings universitet

summary: Selective neuronal vulnerability is a common, yet poorly understood characteristic of neurodegenerative diseases and is particularly prominent in Huntington's disease (HD). To determine how presence of mutant prion protein influences gene expression at pre-symptomatic stages, we used RiboTag to isolate cell type-specific, translating RNA from GABAergic, glutamatergic, somatostatin- (SST) and parvalbumin-expressing neurons of 9-month-old knock-in mice of heterozygous for a Q185 expansion in the endogenous Hdh gene or littermate controls.

overall_design: We analyzed four cell types (Gad2+, PV+, SST+, vGluT2+) in HD mice and littermate controls. Cell type-specific RNA was obtained from in two brain regions (cerebrum sans olfactory bulb, and cerebellum). For cerebellum, only Gad2+ and vGluT2+ were analyzed. For each analyzed RiboTag sample set (genotype_celltype_region) 5-7 biological replicates were prepared and sequenced. Cell type-specific RNA was obtained using the RiboTag Immunoprecipitation method from brain tissue homogenates (details below). For a subset of samples, total RNA was isolated from brian homogenates as input control. Differential expression anaysis was performed for each sample set, comparing HD vs. Control.

first: Bauer

last: Susanne

first: Jackson

last: Walker S


title: Aberrant expression and localization of the RAP1 shelterin protein contributes to age-related phenotypes [2019]

status: Public on Nov 04 2022

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

summary: Short telomeres induce a DNA damage response (DDR) that evokes apoptosis or senescence in human cells. An extant question is the contribution of this DDR to the phenotypes observed in telomeropathies. One exemplar is RAP1, a telomere-associated protein that also controls transcription at extratelomeric regions. To distinguish these roles, we generated a knock-in mouse containing a Rap1 variant unable to bind telomeres but which did not result in eroded telomeres or a DDR. Rap1 variant MEFs exhibited decreased RAP1 expression and re-localization away from telomeres, with an increased cytosolic distribution akin to that observed in aging human fibroblasts. Rap1 knock-in mice were viable, but exhibited transcriptional alterations, proinflammatory cytokine/chemokine signaling, decreased lifespans, increased body weight/fasting blood glucose levels, increased spontaneous tumor incidence, and behavioral deficits. Taken together, our data indicate that some of the underlying mechanisms that drive telomeropathies may arise from phenotypes distinct from a telomere-induced DDR.

overall_design: Gene expression profiles for wild-type (WT) and Rap1-variant mice (MUT) were assayed using Agilent gene expression microarrays for 14-15 months old female mice, examining four tissues (Brain, Heart, Liver, and Muscle), with N=3 per genotype/ and issue group for total of 24 microarray samples.

first: Amanda

middle: J

last: Stock

first: Ross

middle: A

last: McDevitt

first: Yongqing

last: Zhang

first: Kun

last: Wang

first: Yajun

first: Chandrakala

last: Puligilla

first: Chongkui

last: Sun

first: Kevin

last: Becker

first: Elin

last: Lehrmann

first: William

middle: H

last: Wood III

first: Yi

last: Gong

first: Myong-Hee

last: Sung

first: Victoria

last: Hoffman

first: Chengyu

last: Liu

first: Myriam

last: Gorospe

first: Lea

last: Harrington

first: Luigi

last: Ferrucci

first: Yie


title: Lipolysis-derived linoleic acid drives beige fat progenitor cell proliferation via CD36

city: Bronx

first: Kosaku

last: Shinoda

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

type: Expression profiling by high throughput sequencing

summary: To investigate what stimulates beige progenitor cell proliferation, we performed RNA-seq of primary isolated CD81+ cells (Lin-: Sca1+: CD81+) and CD81- cells (Lin-: Sca1+: CD81-) in the inguinal WAT of mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD81+ APCs and CD81- APCs.

first: Ichitaro

last: Abe

first: Yasuo

last: Oguri

first: Shingo

last: Kajimura


title: Drug screening identifies tazarotene and bexarotene as therapeutic agents in Multiple Sulfatase Deficiency

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: We analysed differences in gene expression upon treatment of MSD patient fibroblast lines with either tazarotene or adapalene and DMSO control (untreated condition)

overall_design: Comparative gene expression profiling analysis of RNA-seq data

first: Sophie

last: Schröder

first: Tonatiuh

last: Pena-Centeno

first: André

first: Lars

last: Schlotawa


title: Transcriptional effects of IL-6 on peptide-stimulated OT-I CD8 T cells after 2 or 7 days

city: SOUTH SAN FRANCISCO

first: Kobe

last: Yuen

state: California

address: 1 DNA WAY

department: Oncology Biomarker Development

institute: Genentech

summary: Interleukin 6 (IL-6) is a pleiotropic cytokine with diverse roles in homeostasis, inflammation, and cancer. To identify transcriptional patterns and differentiation states induced by IL-6 in CD8 T cells, we performed RNAseq profiling of  murine OT-I CD8+ T cells stimulated with SIINFEKL peptide in the presence of exogenous IL-6 (10 ng/ml) or anti-IL6R antibody (to block endogenous IL-6 signaling). Bulk OT-I splenocytes were stimulated with SIINFEKL peptide and CD8 T cells were FACS-sorted for RNA extraction after 2 and 7 days. We found that IL-6 potently repressed classical effector differentiation and promoted a gene expression pattern similar to that of memory precursor cells.

overall_design: Bulk splenocytes from OT-I mice (C57BL/6) were cultured with SIINFEKL peptide and  isotype control antibody (5 ug/ml), anti-IL6R antibody (clone MR16-1, 5 ug/ml) or recombinant mouse IL-6 (10 ng/ml) for 2 or 7 days. At each timepoint, CD8+ T cells were FACS-sorted for RNA extraction and RNAseq profiling.

first: Lifen

last: Wang

first: Yasin

last: Senbabaoglu

first: Nathaniel

last: West


title: Acute transcriptional effects of IL-6 on murine naive CD8 T cells

summary: Interleukin 6 (IL-6) is a pleiotropic cytokine with diverse roles in homeostasis, inflammation, and cancer. To identify genes regulated by short-term IL-6 treatment, we performed RNAseq profiling of naïve murine CD8+ T cells stimulated for 4 hours with recombinant mouse IL-6 in the presence or absence of anti-CD3/CD28 antibodies. We found that IL-6 controls expression of diverse regulators of T cell differentiation and function, including repression of co-stimulatory receptors, induction of co-inhibitory receptors, and induction of transcription factors important for memory formation and T cell quiescence.

overall_design: FACS-sorted naïve (CD62L+ CD44-low) CD8 T cells from female C57BL/6J mice were stimulated in vitro for 4 hours with recombinant mouse IL-6 (10 ng/ml), plate-bound anti-CD3/CD28 antibodies + IL-2, or IL-6 + plate-bound anti-CD3/CD28 antibodies + IL-2


title: Transcriptional profiling of IL6R-deficient CD8 T cells isolated from subcutaneous MC38 tumors treated with anti-PD-L1 therapy

summary: Interleukin 6 (IL-6) is a pleiotropic cytokine with diverse roles in homeostasis, inflammation, and cancer. In multiple syngeneic mouse tumor models, we found that  blockade of IL-6 signaling (using an IL6R-blocking antibody) synergized with anti-PD-L1 therapy to drive potent anti-tumor CD8 T cell responses and tumor rejection. To better characterize the cell-intrinsic effects of IL-6 signaling in tumor-reactive CD8+ T cells during anti-PD-L1 therapy, we generated mice with genetic IL6R deficiency restricted to CD8 T cells by crossing IL6R.loxp and E8i.CD8.Cre mice (CD8ΔIL6R mice). Compared to WT littermate controls, we found that CD8ΔIL6R mice had stronger respones to anti-PD-L1 therapy in terms of improved CD8 T cell function (e.g. increased production of IFNγ and TNF, measured by flow cytometry) and enhanced tumor control, suggesting that direct IL-6 signaling in CD8 T cells is sufficient to impair anti-tumor immunity. In this study we aimed to characterize the phenotype of IL6R-deficient CD8 T cells in more detail via whole-transcriptome profiling. CD8ΔIL6R and WT littermates were implanted with MC38 tumors in the right flank; when tumors reached ~150mm3 in volume, animals were randomized to isotype control or anti-PD-L1 treatment. CD8 T cells were FACS-purified from tumor tissue 7 days later and profiled by bulk RNAseq. Compared to cells from WT mice, CD8 T cells from CD8ΔIL6R mice showed increased expression of interferon-driven gene signatures, increased expression of cell cycle genes, and increased expression of genes critical for oxidative phosphorylation. In contrast, WT cells had higher expression of genes associated with naive and memory precursor cells. Thus, IL-6 signaling in tumor-reactive CD8 T cells limits their capacity to differentiate into potent anti-tumor effectors.

overall_design: Total CD8 T cells from digested MC38 tumor tissue were sorted by FACS from mice with the following genotypes: IL6R.wt/wt_E8i.CD8.Cre+ (WT) and IL6R.loxp/loxp_E8i.CD8.Cre+ (IL6R.ko). Tumors were harvested 1 week after start of treatment with isotype control or anti-PD-L1 (clone 6E11) antibodies (10 mg/kg), dosed on day 0 and day 4. N=5 per group; each sample is from an individual mouse.

first: Beatrice

last: Breart


title: Transcriptomic analysis reveals rescue of dysregulated genes in SBMA muscle upon silencing of AR co-factors

city: Trento

first: Alessandro

last: Romanel

state: TN

address: Via Sommarive 9

country: Italy

institute: University of Trento

summary:
Purpose: The goal of this study is to evaluate the rescue of SBMA phenotype upon modulation of AR co-factors expression
Results: NGS analysis of the transcriptome of quadriceps isolated from SBMA mice upon treatment reveal the rescue (partial or total) of assemblies of genes involved in SBMA pathogenesis
Conclusion: targeting overexpressed AR co-regulators is a new therapeutic approach for SBMA to attenuate the toxic GOF without exacerbating AR LOF

overall_design: RNA from quadriceps of wt and AR100Q (mouse model of SBMA) +/- silencing of AR co-factors

first: Maria

last: Pennuto

first: Manuela

last: Basso


title: RNAseq data for mouse mammary tumors from three novel genetically engineered mouse models combining loss of Brca1, p53 and Rb supression

city: Frederick

first: Ludmila

last: Szabova

state: MD

address: 1050 Boyles Street

department: CAPR

institute: Frederick National Laboratory for Cancer Research

summary: We have developed novel genetically engineered mouse  mammary cancer models that develop hormone receptor-positive or -negative tumors depending on the combination of genetic abrrations induced in tumors. Tumors with loss of Brca1 and Trp53 are hormone receptor (HR) negative and tumors with or without Brca1 loss together with concomitant loss of Trp53 and inhibition of proteins of Rb family (Rbf) are HR positive. Transcriptome analysis revealed that HR-positive and -negative mammary tumors recapitulated human luminal and basal-like breast cancer expression signatures, respectively, confirming the histology-defined subtypes.

overall_design: Five tumors from each of the three genotypes were sequences together with 3 normal strain-matched mammary glands that served as controls.

first: Melanie

last: Gordon

first: Lucy

last: Lu

first: Nathan

last: Pate

first: Laura

last: Bassel

first: Anthony

last: Iacovelli

first: Baktiar

last: Karim

first: Philip

last: Homan

first: Deborah

last: Householder

first: Theresa

last: Guerin

first: Sandra

last: Burkett

first: Amanda

last: Day

first: Wendi

last: Custer

first: Zoe

middle: W

last: Ohler


title: DNA methylation landscape and transcriptome of tumor-associated macrophages reveals pathways, transcription factors, and prognostic value relevant for breast cancer patients.

city: Heidelberg

first: Joschka

last: Hey

state: Deutschland

address: Im Neuenheimer Feld 280

department: Cancer epigenomics

institute: DKFZ

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: DNA methylation landscape and transcriptome of tumor-associated macrophages reveals pathways, transcription factors, and prognostic value relevant for breast cancer patients [methylation]

summary: DNA methylation profiling of tumor-associated macrophages (TAMs), mammary gland macrophages (MGMs), bone marrow-derived monocytes from healthy (BMDM-Hs), and tumor-bearing mice (BMDM-Ts).

overall_design: 4t1 cells were injected orthotopically into the mammary fat pad of balb\c mice. Tumors were harvested and digested after reaching a size of 1 cm. TAMs were collected by enrichment for CD45 positive cells following fluorescence-activated cell sorting (FACS) based on CD11b+ Gr1-and F4/80+. from tumor-bearing mice, Tibia and Femur leg bones were dissected flushed, and BMDM-Ts were facs sorted by CD11b+, Gr1+ and F4/80 low. MGMs were collected by harvesting the mammary fat pad of age-matched Balb\c mice, facs sorting was performed with CD11b and F/80 markers same procedure were also done for the Tibia and Femur leg bones of healthy mice and BMDM-Hs were collected as the BMDM-Ts.

first: Coral

last: Halperin

first: Ruth

middle: S

last: Shouval

first: Christoph

last: Plass


title: Aberrant expression and localization of the RAP1 shelterin protein contributes to age-related phenotypes

first: Supriyo

last: De


title: IL-6 signaling in CD8 T cells promotes resistance to anti-PD-L1 immunotherapy

first: Kobe

last: Yuen


title: RNA Sequencing facilitates quantitative analysis of differently expressed genes with negative control (NC), siHASML, and siHuR treatment in rheumatoid fibroblast-like synoviocytes

city: Guangzhou

first: Siqi

last: Xu

state: Guangdong

address: Zhongshan 2nd Road

country: China

institute: Department of Rheumatology and Immunology, The First Affiliated Hospital, Sun Yat-sen University

summary: To determine the mechanism of abnormal activity of RA FLS, we have done some research and found out that lncRNA HASML and protein HuR have some effects on migration and invasion of RA FLS. To more deeply explore how HASML and HuR regulate the functions of RA FLS, RNA sequencing analysis was used to evaluate the transcriptome of siHASML and siHuR treatment and negative control (NC) group. A P-value less than 0.05 was considered significant.

overall_design: Firstly, to detect differentially expressed genes (P<0.05) by RNA sequencing in NC, siHASML, and siHuR treated RA FLSs from three different patients. Secondly, to analyze the shared genes regulated both by HASML and HuR.

first: Ruiru

last: Li

first: Di

last: Liu


title: Skeletal Muscle Transcriptome Is Affected By Age In Severely Burned Mice

city: Galveston

first: Juquan

last: Song

state: TX

address: 301 University Blvd.

institute: University of Texas Medical Branch at Galveston

type: Non-coding RNA profiling by high throughput sequencing

summary: Severe burn results in muscle wasting affecting quality of life in both children and adults. Biologic metabolic profiles are noticeably distinctive in childhood. We posit that muscle gene expression profiles are differentially regulated in response to severe burns in young animals. Twelve C57BL6 male mice, including young (5 weeks-old) and adults (11 weeks-old), received either scald burn, or sham procedure. Mouse muscle tissue was harvested 24 hours later for Next Generation Sequence (NGS) analysis. Our results showed 662 downregulated and 450 upregulated genes in gastrocnemius of young mice compared to adults without injury. After injury, we found 74/75 downregulated genes and 107/128 upregulated genes in both burned groups compared to respective uninjured age groups. VEGFA-VEGFR2, focal adhesion, and nuclear receptor meta-pathways were the top 3 gene pathways undergoing a differential change in response to age. Of note, the proteasome degradation pathway showed the most similar changes in both adult and young burned animals. This study demonstrates the characteristic profile of gene expression in skeletal muscle in young and adult burned mice. Prominent age effects were revealed in transcriptional levels with increased alterations of genes, miRNAs, pathways, and interactions.

overall_design: Twelve C57BL6 male mice (six 4-weeks-old, young; and six 10-weeks-old, adult) received either a 25% body surface area (TBSA) scald burn, or sham burn procedure. There are 3 animals  per group. Gastrocnemius tissues were harvested from euthanized animals 24 hours after injury.mRNA and miRNA were examined by Next Generation Sequence (NGS) analysis.

first: Steven

middle: G

last: Widen

middle: E

last: Wolf

first: Amina

last: EI Ayadi


title: Spatial transcriptomics profiling of the developing mouse embryo

status: Public on Nov 03 2022

city: Stockholm

first: Margherita

last: Zamboni

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

summary: We profiled the gene expression landscape of the developing mouse embryo across three ages (E12.5, E13.5, and E15.5) using fresh frozed tissue sections processed with 10X Genomics's Visium platform.

overall_design: Spatially resolved gene expression profile mouse embryos at E12.5, E13.5, and E15.5

first: Enric

last: Llorens-Bobadilla


title: Chromatin accessibility profiling of the developing mouse embryo at the single nulceus level

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We profiled the epigenetic landscape of the developing mouse embryo across three ages (E12.5, E13.5, and E15.5) using single nuclei processed with 10X Genomics's Single Cell ATAC platform.

overall_design: snATAC-seq of mouse embryos at E12.5, E13.5, and E15.5


title: Spatially-resolved chromatin accessibility profiling of the developing mouse embryo

summary: We profiled the epigenetic landscape of the developing mouse embryo across three ages (E12.5, E13.5, and E15.5) using fresh frozen tissue sections processed with 10X Genomics's OMNI ATAC, which allows to record regions of open chromatin while retaining spatial resolution.

overall_design: Spatial ATAC-seq of mouse embryos at E12.5, E13.5, and E15.5. Each developmental age was profiled in two replicates (i.e., two neighbouring tissue slices of the same embryo)


title: Multi-modal characterization and simulation of human epileptic circuitry

city: Seattle

first: Anatoly

last: Buchin

state: Washington

address: 1616 Eastlake Ave E

institute: Cajal Neuroscience Inc

summary: Temporal lobe epilepsy is the fourth most common neurological disorder with about 40% of patients not responding to pharmacological treatment. Increased cellular loss in the hippocampus is linked to disease severity and pathological phenotypes such as heightened seizure propensity. While the hippocampus is the target of therapeutic interventions such as temporal lobe resection, the impact of the disease at the cellular level remains unclear in humans. Here we show that properties of hippocampal granule cells change with disease progression as measured in living, resected hippocampal tissue excised from epilepsy patients. We show that granule cells increase excitability and shorten response latency while also enlarging in cellular volume, surface area and spine density. Single-cell RNA sequencing combined with simulations ascribe the observed electrophysiological changes to gradual modification in three key ion channel conductances: BK, Cav2.2 and Kir2.1. In a bio-realistic computational network model, we show that the changes related to disease progression bring the circuit into a more excitable state. In turn, we observe that by reversing these changes in the three key conductances produces a less excitable, “early disease-like” state. These results provide mechanistic understanding of epilepsy in humans and will inform future therapies such as viral gene delivery to reverse the course of the disorder.

overall_design:
Estimated the gene expression in 4 human hippocampus samples in dentate gyrus region: NW_TX0011-5, NW_TX0012-1, NW_TX0014-1, NW_TX0014-3
*** Submitters declare that raw data is not provided because no previous agreements have been signed with the patients***

first: Costas

last: Anastassiou


title: Developing mouse embryo


title: Aberrant expression and localization of the RAP1 shelterin protein contributes to age-related phenotypes [2017]

overall_design: Gene expression profiles for wild-type (WT) and Rap1-variant mice (MUT) were assayed using Agilent gene expression microarrays for 2-5 month old male mice, examining four tissues (Brain, Heart, Liver, and Muscle), with N=3 per genotype/tissue group for total of 24 microarray samples.

first: Amanda

last: Stock

first: Ross

last: McDevitt

first: Yongqing

last: Zhang

first: Kun

last: Wang

first: Yajun

first: Chandrakala

last: Puligilla

first: Chongkui

last: Sun

first: Kevin

last: Becker

first: Elin

last: Lehrmann

first: William

last: Wood III

first: Yi

last: Gong

first: Myong-Hee

last: Sung

first: Victoria

last: Hoffman

first: Chengyu

first: Myriam

last: Gorospe

first: Lea

last: Harrington

first: Luigi

last: Ferrucci

first: Yie


title: PAHSAs reduce cellular senescence and protect pancreatic beta cells from metabolic stress through regulation of Mdm2/p53

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: Senescence in pancreatic beta cells plays a major role in beta cell dysfunction which leads to impaired glucose homeostasis and diabetes. Therefore, prevention of beta cell senescence could reduce the risk of diabetes.  Treatment of NOD mice, a model of Type 1 autoimmune diabetes (T1D), with Palmitic acid hydroxy stearic acids (PAHSAs), a novel class of endogenous lipids with antidiabetic and anti-inflammatory effects, delays the onset and reduces the incidence of T1D from 82% with vehicle treatment to 35% with PAHSAs. Here we show that a major mechanism by which PAHSAs protect islets of the NOD mice is by directly preventing and reversing the initial steps of metabolic stress-induced senescence. In vitro PAHSAs increased Mdm2 expression, which decreases the stability of p53, a key inducer of senescence-related genes. In addition, PAHSAs enhanced expression of protective genes, such as those regulating DNA repair and glutathione metabolism, and promoting autophagy. We demonstrate the translational relevance by showing that PAHSAs prevent and reverse early stages of senescence in metabolically-stressed human islets by the same Mdm2 mechanism. Thus, a major mechanism for the dramatic effect of PAHSAs to reduce the incidence of Type 1 diabetes in NOD mice is by decreasing cellular senescence; PAHSAs may have a similar benefit in humans.

overall_design: 4 mice treated with PAHSA and 4 mice treated with vehicle control.

first: Maria

middle: F

last: Rubin de Celis

first: Ruben

last: Garcia‐Martin

first: Ismail

last: Syed

first: Jennifer

last: Lee

first: Cristina

last: Aguayo‐Mazzucato

first: Susan

last: Bonner‐Weir

first: Barbara

middle: B

last: Kahn


title: DNA methylation landscape and transcriptome of tumor-associated macrophages reveals pathways, transcription factors, and prognostic value relevant for breast cancer patients [RNA-seq]

first: Joschka

last: Hey

summary: We performed RNA-seq to characterize the transcriptome of tumor-associated macrophages  (TAMs), bone marrow-derived monocytes from healthy and tumor-bearing mice (BMDM-Ts/BMDM-Hs) and, macrophages from healthy mammary fat pad (MGMs).

first: Coral

last: Halperin

first: Ruth

last: Shouval

first: Christoph

last: Plass


title: Sex differential gene expression in macrophages and osteoclasts

city: Cheney

first: Jason

last: Ashley

state: WA

address: Eastern Washington University, SCI154

department: Biology

institute: Eastern Washington University

summary: To determine differences in gene expression during osteoclastogenesis, we performed sequencing on RNA extracted from MCSF-differentiated bone marrow macrophages and MCSF+RANKL differentiated osteoclasts from male and female C56Bl/6 mice

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bone marrow derived macropahges and osteoclasts from female and male C57Bl/6 mice.

first: Abigail

middle: L

last: Keever

first: Kathryn

last: Collins

first: Rachel

last: Clark

first: Amber

last: Framstad


title: DNA methylation profiling in blood of OSA patients and controls

city: Columbia

first: Rene

middle: Gabriel

last: Cortese

state: MO

address: 1 Hospital Dr. MA104E

department: Child health Research Institute

institute: University of Missouri

type: Methylation profiling by genome tiling array

summary: Obstructive sleep apnea (OSA) is associated with increased risk for cardiovascular morbidity and mortality. Epidemiological and animal models studies generate hypotheses for innovative strategies in OSA management by interfering intermediates mechanisms associated with cardiovascular complications. In this study, we interrogated DNA methylation profiles in 16 polysomnographically evaluated OSA patients (Apnea Hypopnea Index, AHI > 30) and 8 controls (AHI<5 events/h sleep). Blood samples were collected at initial visit (V1) and a year later (V2). OSA patients received Continuous Positive Air Pressure (CPAP) therapy with high adherence (> 4 hours/night). Control individuals did not receive CPAP therapy. Genomic DNA was treated with sodium bisulfite. Converted DNA was analyzed using Illumina’s Infinium Human Methylation 450 BeadChip assay. DNA methylation profiles enabled the prospective evaluation of inflammatory and epigenetics mechanism involved in cardiovascular complication of OSA patients compared with non OSA subjects, as well as the variation of epigenetic profiles in OSA patients after one year of high-adherence CPAP therapy.

overall_design: This case-control study includes 16 polysomnographically evaluated OSA patients and 8 controls. Blood samples were collected at initial visit (V1) and one year later (v2). Microarray data set consisted of n=48 microarrays, including one microarray per sample at visit 1 (n=24 arrays) and one microarray per sample at visit 2 (n=24 arrays). Microarray data was analyzed using Illumina Genome Studio v2011.1. Data was processed with background normalization.

first: David

last: Sanz-Rubio

first: Jose

last: Marin

last: Gozal


title: An inflammatory state remodels the immune microenvironment and improves risk stratification in acute myeloid leukemia

city: New York

first: Bettina

last: Nadorp

address: 500 1st Ave

department: Medicine/Pathology

institute: NYU Langone Health

summary: Acute myeloid leukemia (AML) is a hematopoietic malignancy with poor prognosis and limited treatment options. Here we provide a comprehensive census of the bone marrow immune microenvironment in adult and pediatric AML patients. We characterize unique inflammation signatures in a subset of AML patients, associated with inferior outcomes. We identify atypical B cells, a dysfunctional B cell subtype enriched in high-inflammation AML patients, as well as an increase in CD8+ GZMK+ and regulatory T cells, accompanied by a reduction in T cell clonal expansion. We derive an inflammation-associated gene score (iScore) that associates with poor survival outcomes in AML patients. Addition of the iScore refines current risk stratifications for AML patients and may enable identification of patients in need of more aggressive treatment. This work provides a framework for classifying AML patients based on their immune microenvironment and a rationale for consideration of the inflammatory state in clinical settings.

overall_design: Single-cell RNAseq, CITEseq and TCRseq

first: Audrey

last: Sandler

first: Zhengxi

last: Sun

first: Iannis

last: Aifantis


title: Differential Methylation of CircRNA m6A in the APP/PS1 Alzheimer's Disease Mouse Model [cirRNA-seq]

city: Jinan City

first: song

last: han

state: ShanDong province

address: Tianqiao District

institute: The Second Hospital of Shandong University， Cheeloo College of Medicine，Shandong University

summary: Alzheimer's disease (AD) is a chronic neurological disease which characterized as memory loss and progressive cognitive impairment. The characteristic of AD pathologies include extracellular senile  plaques formed by β-amyloid protein deposition, neurofifibrillary tangles formed byhyper-phosphorylation of tau protein, and neuronal loss caused by glial cell proliferation. However, the pathogenesis of AD is still unclear. Resent research have shown that the dysregulation of RNA methylation is related to many biological processes, including neurodevelopment and neurodegenerative diseases. N6-methyladenosine (m6A) is the mainly modification in eukaryotic RNA, and it may be associated with the pathophysiology of AD. Circular RNA (circRNA) is a new type of evolutionarily conserved non-coding RNA without 5’cap and 3’polyadenylic acid tail. Recent studies suggested that circRNA may involved in the pathogenesis of AD. m6A RNA methylation is also found in circRNAs. In this study, we performed high-throughput sequencing on the degree of circRNA m6A methylation in APP/PS1 AD and C57BL/6 mice. The results suggest that circRNA m6A methylation degree in AD mice is different compared to the control group. In addition, using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to predict related pathways, the results showed that the genes with different circRNA m6A methylation in AD mice is associated with axon guidance, long-term potentiation, glutama tergic synapse, cholinergic synapse, gabaergic synapse and long-term depression. The MeRIP-qPCR results showed that among the 8 selected circRNA m6A genes, there are 5 genes with increased methylation and others with decreased methylation. In summary, the results of this study indicate that circRNA m6A methylation may related to the pathogenesis of AD.

first: Xiao

last: Zhang

first: Suge

last: Yang

first: Song

last: Han

first: Yuan

first: Min

first: Xiaolei

last: Zheng

first: Fan

last: Li

first: Yan

last: Wei

first: Yun

last: Wang

first: Jianzhong

last: Bi


title: Effect of IL-6 on antigen-specific CD8+ T cell activation in vitro

first: Kobe

last: Yuen

summary: Interleukin 6 (IL-6) is a pleiotropic cytokine with diverse roles in homeostasis, inflammation, and cancer. Here we performed transcriptional profiling of OT-I CD8+ T cells activated in the presence or absence of IL-6. In this study, splenocytes from wild type C57BL/6J mice were incubated with SIINFEKL peptide for two days to activate OT-I CD8+ T cells. SIINFEKL was then withdrawn, T cells were rested in medium with IL-2 for three days, and CD8+ T cells were restimulated with anti-CD3 + anti-CD28 antibodies and purified by FACS for RNA sequencing analysis on day 7. Throughout this culture period, some cells were treated with anti-IL6R antibody (clone MR16-1, 5 ug/ml), isotype control antibody (5 ug/ml), recombinant IL-6 (10 ng/ml), or recombinant hyper-IL-6 (IL-6 linked to IL6R; 20 ng/ml). Experimental conditions were run in triplicate, for a total of 15 samples. Conclusion: Neutralization of endogenous IL-6 signaling (with anti-IL6R antibody) enhances effector differentiation of CD8+ T cells, while addition of exogenous IL-6 or hyper-IL-6 suppresses effector differentiation.

overall_design: Activation of TCR-transgenic T cells in vitro with cognate peptide in the presence or absence of IL-6 signaling inhibitors or recombinant IL-6.

first: Lifen

first: Yasin

last: Senbabaoglu

first: Zora

last: Modrusan

first: Nathaniel

last: West


title: Gene expression profile at single cell level of Medicago truncatula roots in response to rhizobia infection

city: Tucson

first: Sergio Alan

last: Cervantes-Perez

state: Arizona

address: 1140 E South Campus Dr

department: School of Plant Sciences

institute: University of Arizona

summary: The nuclei of Medicago truncatula root seedlings exposed to rhizobia were isolated at single-cell resolution with single-nuclei RNA-seq applying 10x Genomics technology.

overall_design: The nuclei of the 6 days-old roots of Medicago truncatula seedlings inoculated for 48h with water (mock) or Ensifer meliloti were isolated for sNucRNA-seq libraries construction. The pre-processing and processing of the datasets were performed with Cell Ranger and Seurat.

first: Sergio

first: Sandra

last: Thibivilliers

first: Carole

last: Lafont

first: Andrew

middle: D

last: Farmer

first: Florian

last: Frugier

first: Marc

last: Libalult


title: Patterns of heterochromatin distribution alterations linked to transcriptional changes at Plasmodium falciparum clonally variant gene loci

city: Barcelona

first: Lucas

last: Michel-Todó

state: Barcelona

address: Roselló, 149

department: Malaria Epigenetics

country: Spain

institute: ISGlobal


title: Patterns of heterochromatin distribution alterations linked to transcriptional changes at Plasmodium falciparum clonally variant gene loci [gene expression]

summary:
The survival of malaria parasites in the changing human blood environment largely depends on their ability to alter gene expression by epigenetic mechanisms. The active state of Plasmodium falciparum clonally variant genes is associated with euchromatin characterized by the histone mark H3K9ac, whereas the silenced state is characterized by H3K9me3-based heterochromatin. However, the localization of the euchromatin-heterochromatin transitions associated with expression switches in different clonally variant genes has not been characterized. Here we compared the distribution of heterochromatin between subclones of the same genetic background with different patterns of expressed and silenced clonally variant genes to identify at a genome-wide level the patterns associated with the different transcriptional states. We found that de novo heterochromatin formation or complete disruption of a heterochromatin domain are relatively rare events, and in the majority of loci expression switches can be explained by expansion or retraction of heterochromatin. We describe different modalities of heterochromatin changes linked to transcriptional differences, revealing a complex scenario. Despite this complexity, heterochromatin distribution patterns generally enable prediction of the transcriptional state of clonally variant genes. Some subclones expressed and had in an active chromatin state several var genes simultaneously. We also found that heterochromatin levels in the putative regulatory region of the gdv1-as non-coding RNA, previously involved in sexual commitment, varied between parasite lines with different sexual conversion rates.
Gene expression data for subclones A7, E5 and B11 (3D7-B stock).

overall_design: Time-course analysis for 3D7-B subclones: A7, E5 and B11. Samples for transcriptomic analysis of A7, E5 and B11 lines were obtain from tightly synchronized cultures (0-5 h window) achieved by Percoll purification of erythrocytes infected with mature stages followed by 5% sorbitol lysis 5 h later. RNA was extracted from samples collected at 10-15, 20-25, 30-35, 37-42, 40-45 and 43-48 h post-invasion (hpi) using the Trizol method. The reference pool consisted of a mixture of equal amounts of cDNA from rings, trophozoites and schizonts from 3D7-A and 3D7-B stocks. Samples were hybridized oncustom Agilent microarrays (AMADID no. 085763) modified from design  AMADID no. 037237.

first: Núria

last: Rovira-Graells

last: Casas-Vila

first: Alfred

last: Cortés


title: Epigenome analysis of human gastroesophageal junction (GEJ) organoids TP53/CDKN2A KO

status: Public on Nov 02 2022

city: Shenzhen

first: Yueyuan

last: Zheng

state: China

address: Zhenyuan Road, 628

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

summary: Inactivation of the tumor suppressor genes TP53 and CDKN2A occurs early during GEJ tumorigenesis. However, due to a paucity of GEJ-specific disease models, cancer-promoting consequences of TP53 and CDKN2A inactivation at the GEJ have been incompletely characterized. Here we report the development of the first wild-type primary human GEJ organoid model, as well as a CRISPR-edited transformed GEJ organoid model. CRISPR/Cas9 engineering to inactivate TP53 and CDKN2A (TP53/CDKN2A KO) in GEJ organoids induced morphologic dysplasia as well as pro-neoplastic features in vitro and tumor formation in vivo. Notably, lipidomic profiling identified several Platelet-Activating Factors (PTAFs) among the most upregulated lipids in CRISPR-edited organoids; and importantly, PT AF/PT AFR abrogation by siRNA knockdown or a pharmacologic inhibitor (WEB2086) significantly blocked proliferation and other pro-neoplastic features of TP53/CDKN2A KO GEJ organoids in vitro and tumor formation in vivo. In addition, murine xenografts derived from Eso26, an established esophageal adenocarcinoma (EAC) cell line, were suppressed by WEB2086. Mechanistically,  TP53/CDKN2A dual inactivation disrupted both the transcriptome and the DNA methylome, likely mediated by key transcription factors, particularly Forkhead Box M1 (FOXM1). Importantly, FOXM1 activated PTAFR transcription by binding to the PTAFR promoter, further amplifying  the PTAF-PTAFR pathway. In summary, we established a robust model system for investigating early GEJ neoplastic events, identified crucial metabolic and epigenomic changes occurring during GEJ model tumorigenesis, and discovered a potential cancer-therapeutic strategy, while providing insights into pro-neoplastic mechanisms associated with TP53/CDKN2A inactivation in early GEJ neoplasia.

overall_design: Examination of DNA methylation in human gastroesophageal junction organoids with or without knockout of TP53/CDKN2A

first: Hua

last: Zhao

first: Stephen

last: Meltzer

first: De-Chen

last: Lin


title: The helicase domain of Dicer ensures essential accuracy of miRNA biogenesis in mice

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

summary: Dicer ribonucleases, which generate small RNAs for the RNA interference (RNAi) and microRNA (miRNA) pathways, often have an N-terminal DExD helicase subdomain (also called HEL1). In the mammalian Dicer, HEL1 inhibits RNAi while it appears unnecessary for miRNA biogenesis. To determine its functional significance, we genetically eliminated HEL1 from Dicer in mice. We observed embryonic growth retardation, defects in the cardiopulmonary system, and perinatal lethality. HEL1 suppresses biogenesis of mirtrons, a non-canonical low-abundant class of miRNAs, and is required for high-fidelity cleavage and strand selection during biogenesis of canonical miRNAs. The HEL1 domain itself is essential rather than its helicase activity, because mutations of critical catalytic amino acids do not affect mouse viability or fertility and have minimal impact on miRNA biogenesis. Therefore, HEL1 is a critical structural component of the mammalian Dicer, supporting its role of a conserved structural “mold” that ensures high-fidelity processing and adaptive evolution of mammalian miRNA precursors.

overall_design: Bulk small RNA-seq of 6 mouse E15.5 embryo samples:  - 3x WT  - 3x DicerGNT homozygotes

first: Petr

last: Svoboda

first: Radek

last: Malik

first: Valeria

last: Buccheri


title: Usp22 is an intracellular regulator of systemic emergency hematopoiesis

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

summary: Emergency hematopoiesis is a concerted response geared towards enhanced protection from infection, involving multiple cell types and developmental stages across the immune system. Despite its importance, the underlying molecular regulation remains poorly understood. The deubiquitinase USP22 regulates the levels of monoubiquitinated histone H2B (H2Bub1), which is involved in intracellular interferon responses. Here we show that, in the absence of infection or inflammation, mice lacking Usp22 in blood and immune cells display profound systemic emergency hematopoiesis, evident by increased hematopoietic stem cell proliferation, myeloid bias, and extramedullary hematopoiesis. Functionally, loss of Usp22 results in elevated phagocytosis by neutrophilic granulocytes, and enhanced innate protection against Listeria monocytogenes infection. At the molecular level, we find this state of emergency hematopoiesis associated with transcriptional signatures of myeloid priming, enhanced mitochondrial respiration, as well as innate and adaptive immunity and inflammation. Augmented inflammatory gene expression was linked to elevated locus-specific H2Bub1 levels. Collectively, a tunable epigenetic state promotes systemic emergency hematopoiesis in a cell-autonomous manner and enhances innate protection, paving potential ways towards immune enhancement.

overall_design: To uncover potential cell-intrinsic and systemic functions of Usp22 in hematopoiesis and immunity in vivo, we analyzed conditional Usp22 KO mice, with multiple omics approaches, including bulk and single-cell transcriptomics analysis, and epigenome profiling using ATAC and ChIP sequencing.

first: Nikolaus

last: Dietlein

first: Jonas

last: Metz

first: Thomas

last: Höfer

first: Hans-Reimer

last: Rodewald


title: ChIP-seq H3K9ac in sea cucumber

city: Qingdao

first: Dongxue

last: Xu

address: Changcheng road No.700

institute: Qingdao Agricultural University

summary: We presented a genome-wide characterization for H3K9 acetylation (H3K9ac) binding regions in normal temperature and heat-stress conditions via ChIP-seq. The results revealed H3K9ac was an extensive epigenetic modulation in A. japonicus. We further identified differentially acetylated regions (DARs) under heat stress.

overall_design: Examination of H3K9ac in control and heat-stress groups  in intestine tissue of Apostichopus japonicus

first: Bin

last: Xia


overall_design: Bulk long RNA-seq of 4 mouse ESC samples:  - 2x WT  - 2x DicerX homozygotes

first: Eliska

last: Taborska


title: Cancer immunotherapies transition endothelial cells into HEVs that generate TCF1+ T lymphocyte niches through a feed-forward loop [10X Genomics]

city: Leuven

first: Gabriele

last: Bergers

address: Herestraat 49

department: Department of Oncology

country: Belgium

institute: KU Leuven-VIB CCB

summary: The lack of T cell infiltrates is a major obstacle to effective immunotherapy in cancer. Conversely, the formation of tumor-associated tertiary-lymphoid-like structures (TA-TLLSs), which are the local site of humoral and cellular immune responses against cancers, is associated with good prognosis, and they have recently been detected in immune checkpoint blockade (ICB)-responding patients. However, how these lymphoid aggregates develop remains poorly understood. By employing single-cell transcriptomics, endothelial fate mapping, and functional multiplex immune profiling, we demonstrate that antiangiogenic immune-modulating therapies evoke transdifferentiation of postcapillary venules into inflamed high-endothelial venules (HEVs) via lymphotoxin/lymphotoxin beta receptor (LT/LTβR) signaling. In turn, tumor HEVs boost intratumoral lymphocyte influx and foster permissive lymphocyte niches for PD1- and PD1+TCF1+ CD8 T cell progenitors that differentiate into GrzB+PD1+ CD8 T effector cells. Tumor-HEVs require continuous CD8 and NK cell-derived signals revealing that tumor HEV maintenance is actively sculpted by the adaptive immune system through a feed-forward loop.

overall_design: Single-cell RNA sequencing of mouse tumor endothelial cell (EC) and immune cell (IC) from untreated (UT) or DPAg treated, PyMT/E0771 breast tumor model by 10X.


title: Cancer immunotherapies transition endothelial cells into HEVs that generate TCF1+ T lymphocyte niches through a feed-forward loop [SmartSeq2]

overall_design: Single-cell RNA sequencing of mouse lymph node (LN) HEV, tumor (TU) HEV and TU endothelial cell (EC) by SmartSeq2.


title: JAK-STAT signaling in inflammatory breast cancer enables chemotherapy-resistant cell states  [single-cell RNA-seq]

first: Kornelia

last: Polyak

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Inflammatory breast cancer (IBC) is a difficult-to-treat disease with poor clinical outcomes due to high risk of metastasis and resistance to treatment. We previously described a CD44+CD24-pSTAT3+ breast cancer cell subpopulation with stem cell-like features that is dependent on JAK2/STAT3 signaling. Here we report that CD44+CD24- cells are the most frequent cell-type in IBC and are commonly pSTAT3+. Combination of JAK2/STAT3 inhibition with paclitaxel decreased IBC xenograft growth more than either agent alone. We developed and characterized IBC cell lines resistant to paclitaxel and doxorubicin to mimic therapeutic resistance in patients. Multi-omic profiling of parental and resistant cells revealed genes associated with lineage identity and inflammation were enriched in chemotherapy resistant derivatives. Integrated pSTAT3 ChIP-seq and RNA-seq analyses showed pSTAT3 regulates genes related to inflammation and epithelial to mesenchymal transition (EMT) in resistant cells, as well as PDE4A, a cAMP-specific phosphodiesterase. Metabolomic characterization identified elevated cAMP signaling and CREB as a candidate therapeutic target in IBC. We also investigated cellular dynamics and heterogeneity at the single cell level during chemotherapy and acquired resistance by CyTOF and single cell RNA-seq. We identified mechanisms of resistance including a shift from luminal to basal/mesenchymal cell states through selection for rare pre-existing subpopulations or an acquired change. Lastly, we showed that combination treatment with paclitaxel and JAK2/STAT3 inhibition prevented the emergence of this more mesenchymal chemo-resistant subpopulation. Our results provide mechanistic rational for combination of chemotherapy with inhibition of JAK2/STAT3 signaling as a new more effective therapeutic strategy in IBC.

overall_design: scRNA-seq of parental and paclitaxel resistant inflammatory breast cancer cell lines

first: Guillermo

last: Peluffo

first: Laura

last: Stevens

first: Xintao

last: Qiu

first: Anne

last: Trinh

first: Daniel

last: Temko

last: Fassl

first: Renee

middle: C

last: Geck

first: Shaokun

last: Shu

first: Natalie

last: Kingston

first: Nicholas

last: Harper

first: Vanessa

last: Almendro

first: Alanna

last: Pyke

first: Shawn

last: Egri

first: Malvina

last: Papanastasiou

first: Kendell

last: Clement

first: Sarah

last: Walker

first: Jacqueline

last: Salas

first: So

middle: Y

last: Park

first: David

last: Frank

first: Alexander

last: Meissner

first: Jacob

last: Jaffe

first: Piotr

last: Sicinski

first: Franziska

last: Michor

first: Alex

last: Toker

first: Henry

last: Long

first: Beth

last: Overmoyer


title: Cancer immunotherapies transition endothelial cells into HEVs that generate TCF1+ T lymphocyte niches through a feed-forward loop

first: Gabriele

last: Bergers

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

overall_design: Refer to individual Series


title: JAK-STAT signaling in inflammatory breast cancer enables chemotherapy-resistant cell states [RNA-seq]

first: Kornelia

last: Polyak

summary: We developed and characterized derivates of inflammatory breast cancer (IBC) cell lines resistant to paclitaxel and doxorubicin to mimic therapeutic resistance in patients. Comprehensive molecular characterization of gene expression, genetic, epigenetic, and metabolomic profiles of parental and resistant cells revealed a central role for STAT3 in regulating genes associated with inflammation and resistance to chemotherapy, which we also validated in clinical patient samples. Our results suggest a combination of chemotherapy with inhibition of JAK/STAT signaling could be a more effective therapeutic strategy in IBC.

overall_design: RNA-seq: Gene expression analysis of SUM149 and FCIBC02 Parental, Paclitaxel-Resistant, and Doxorubicin-resistant cell lines. Cells were treated with either vehicle or the indicated drug combinations of Paclitaxel, Doxorubicin, and INC424. SUM149 Paclitaxel-resistant cells were also sorted for EpCAM high and low populations and treated with either vehicle or Paclitaxel. All samples were sequenced in duplicates.

first: Guillermo

last: Peluffo

first: Laura

last: Stevens

first: Xintao

last: Qiu

first: Anne

last: Trinh

first: Daniel

last: Temko

last: Fassl

first: Renee

last: Geck

first: Shaokun

last: Shu

first: Natalie

last: Kingston

first: Nicholas

last: Harper

first: Vanessa

last: Almendro

first: So-Yeon


title: Stromal inflammation is a targetable driver of hematopoietic aging [droplet-based scRNAseq]

first: Emmanuelle

last: Passegue

department: Columbia Stem Cell Initiative

institute: Columbia University Irving Medical Center

summary: To investigate global changes in the structure of the bone marrow niche with age, we performed droplet-based scRNAseq (10X Genomics) of unfractionated endosteal and central marrow stromal cells (Ter119-/CD45-). 8,735 cells passed QC, and hematopoietic clusters of cells were excluded based on marker gene expression, leaving 2359 cells distributed across 9 distinct clusters for final presentation.

overall_design: Endosteal and central marrow stromal cells from the bone marrow of young (10 weeks) and old (24 months) wild-type C57BL/6 mice were isolated by flow cytometry and subjected to droplet-based scRNAseq (10X Genomics).

first: Evgenia

middle: V

last: Verovskaya

first: Carl

last: Mitchell

first: Fernando

last: Calero-Nieto

first: Xiaonan

last: Wang

first: Berthold

last: Gottgens


title: Combination treatment of PTUPB with enzalutamide in C4-2B MDVR cells

city: Sacramento

first: Chengfei

last: Liu

state: CA

address: 4645 2nd Ave Research III building, suite2300

institute: University of California, Davis

summary:
To explore the gene regulatory mechanisms underlying PTUPB treatment in drug-resistant prostate cancer cells.
We performed RNA sequencing analyses using PTUPB-treated C4-2B MDVR cells with or without enzalutamide treatment to identify the gene programs affected by the treatments.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C4-2B MDVR cells and its treatments (20 μM enzalutamide, PTUPB 10 μM to PTUPB 20 μM and their combination).


title: JAK-STAT signaling in inflammatory breast cancer enables chemotherapy-resistant cell states  [ChIP-seq]

first: Kornelia

last: Polyak

overall_design: ChIP-seq: Examination of pSTAT3 in SUM149 Parental or Paclitaxel resistant and FCIBC02 Parental, Paclitaxel or Doxorubicin resistant cell lines. Samples were either treated with vehicle, Paclitaxel, or Doxorubicin and sequenced without replicates.

first: Laura

last: Stevens

first: Guillermo

last: Peluffo

first: Alanna

last: Pyke

first: Shawn

last: Egri

first: Malvina

last: Papanastasiou

first: Kendell

last: Clement

first: Sarah

last: Walker

first: Jacqueline

last: Salas

last: Park

first: David

last: Frank

first: Alexander

last: Meissner

first: Jacob

last: Jaffe

first: Piotr

last: Sicinski

first: Franziska

last: Michor

first: Alex

last: Toker

first: Henry

last: Long

first: Beth

last: Overmoyer

first: Zheqi

last: Li

first: Ningxuan

last: Zhou

first: Marco

last: Seehawer

first: Bojana

last: Jovanovic


title: Stromal inflammation is a targetable driver of hematopoietic aging [Microarray analysis]

first: Emmanuelle

last: Passegue

state: NY

summary:
We performed integrated analyses of hematopoietic stem and progenitor cells as well as bone marrow stromal cells to better understand the underlying mechanisms of blood aging.
To determine how the molecular state of multipotent progenitor (MPP) cells change with age we performed transcriptomic analyses of myeloid-biased MPP3 and lymphoid-biased MPP4 populations from young and old mice.

overall_design: Microarray analysis of 3-5 biological replicated of the indicated MPP populations were isolated from young (8-10 weeks) and old (24 months) wild-type C57BL/6 mice. MPP3s are identified as Lin-/cKit+/Sca-1+/Flk2-/CD48+/CD150-, and MPP4s are identified as Lin-/cKit+/Sca-1+/Flk2+. Young controls listed here are also available under GSE68529.

first: Evgenia

last: Verovskaya

first: Carl

last: Mitchell

first: Eric

last: Pietras


title: Patterns of heterochromatin distribution alterations linked to transcriptional changes at Plasmodium falciparum clonally variant gene loci [ChIP-seq]

first: Lucas

last: Michel-Todó

summary: The survival of malaria parasites in the changing human blood environment largely depends on their ability to alter gene expression by epigenetic mechanisms. The active state of Plasmodium falciparum clonally variant genes is associated with euchromatin characterized by the histone mark H3K9ac, whereas the silenced state is characterized by H3K9me3-based heterochromatin. However, the localization of the euchromatin-heterochromatin transitions associated with expression switches in different clonally variant genes has not been characterized. Here we compared the distribution of heterochromatin between subclones of the same genetic background with different patterns of expressed and silenced clonally variant genes to identify at a genome-wide level the patterns associated with the different transcriptional states. We found that de novo heterochromatin formation or complete disruption of a heterochromatin domain are relatively rare events, and in the majority of loci expression switches can be explained by expansion or retraction of heterochromatin. We describe different modalities of heterochromatin changes linked to transcriptional differences, revealing a complex scenario. Despite this complexity, heterochromatin distribution patterns generally enable prediction of the transcriptional state of clonally variant genes. Some subclones expressed and had in an active chromatin state several var genes simultaneously. We also found that heterochromatin levels in the putative regulatory region of the gdv1-as non-coding RNA, previously involved in sexual commitment, varied between parasite lines with different sexual conversion rates.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histonemodifications H3K9me3 and H3K9ac in different P.Falciparum strains/subclones.

first: Cristina

last: Bancells

first: Núria

last: Casas-Vila

first: Alfred

last: Cortés


title: Stromal niche inflammation mediated by IL-1 signaling is a targetable driver of hematopoietic aging


title: JAK-STAT signaling in inflammatory breast cancer enables chemotherapy-resistant cell states

first: Kornelia

last: Polyak


title: Sentinel p16INK4a+ cells in the basement membrane form a reparative niche in the lung

city: San Francisco

first: Peng

last: Tien

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco


title: Selective advantage of epigenetically disrupted cancer cells via phenotypic inertia [RNA-seq]

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: Identification of gene expression changes induced by glutamine deprivation in melanoma cells lacking various epigenetic regulators

overall_design: RNA-seq analysis of melanoma cells expressing 4-7sgRNAs targeting members of the PRC2 complex (EED, EZH2, SUZ12), histone H1B (HIST1H1B), the chromatin remodeller SMARCD1 and a non-expressed control gene (TNP2), and grown in either unperturbed conditions (d0) or under glutamine deprivation (d12).

first: Ioannis

last: Loukas

first: Harshil

last: Patel

first: Philip

last: East


title: DNA methyltransferases 3A and 3B target specific sequences during mouse gastrulation

city: Rehovot

first: Amos

last: Tanay

address: Herzl

country: Israel

institute: Weizmann Institute of Science

summary: We performed single-cell transcriptome analysis (using MARS-seq) of mouse embryonic stem cells, embryiod bodies and mouse embryos. Additionally, we performed methylation analysis of bulk and single cells of this source (using whole-genome PBAT and PBAT capture).

overall_design: The ESCs lines that were used are J1 (SCRC1010, ATCC), Dnmt3a-/- clone 6aa, Dnmt3b-/- clone 8bb, Dnmt1-/- Dnmt3a -/- Dnmt3b-/- clone 19 (TKO) (Cell Bank Riken BioResource Research Center) , Dnmt3a -/- Dnmt3b-/- clones 7aabb and 16aabb (DKO) (kindly provided by Dr. Masaki Okano), Wild type,  Dnmt3a and Dnmt3b knockout ES line, passages 3 or 5 in 2i/L, respectively (N15, kindly provided by Dr. Masaki Yagi). Embryiod bodies were generated by hanging drop protocol . Cells  and embryos were collected dissociated  and FACS-sorted into single-cell methylation or scRNA profiling or were collected as a bulk a long time points.

first: Zohar

last: Mukamel


title: JAK-STAT signaling in inflammatory breast cancer enables chemotherapy-resistant cell states [RNA-seq II]

overall_design: RNA-seq: Gene expression analysis of SUM190 Parental, Paclitaxel-Resistant, and Doxorubicin-resistant cell lines. Cells were treated with either vehicle or the indicated drug combinations of Paclitaxel and Doxorubicin. All samples were sequenced in duplicates.

first: Guillermo

last: Peluffo

first: Laura

last: Stevens

first: Xintao

last: Qiu

first: Anne

last: Fassl

first: Natalie

last: Kingston

first: Nicholas

last: Harper

first: Daniel

last: Temko

first: Vanessa

last: Almendro

first: Alanna

last: Pyke

first: Shaokun

last: Shu

first: Kunihiko

last: Hinohara

first: Shawn

last: Egri

first: Malvina

last: Papanastasiou

first: Kendell

last: Clement

first: Sarah

last: Walker

first: So

last: Park

first: David

last: Frank

first: Alexander

last: Meissner

first: Jacob

last: Jaffe

first: Franziska

last: Michor

first: Piotr

last: Sicinski

first: Henry

last: Long

first: Beth

last: Overmoyer


title: Trans-interaction of risk loci 6p24.1 and 10q11.21 is associated with endothelial damage in coronary artery disease

city: Singapore

first: Christine

last: Cheung

state: Singapore

address: Experimental Medicine Building 59 Nanyang Drive, Level 3

country: Singapore

institute: Nanyang Technological University

summary: The variant rs6903956 has been identified as one of the Asian-specific genetic risk factors for coronary artery disease (CAD). However, rs6903956 lies in a non-coding locus on chromosome 6p24.1, hampering efforts of functional annotation. We produced induced pluripotent stem cells (iPSCs) from CAD patients (AA risk genotype at rs6903956) and normal controls (GG non-risk genotype at rs6903956). CRIPSR-Cas9-based deletions (Δ63-89bp) on 6p24.1 including rs6903956 were performed to generate isogenic iPSC-derived endothelial cells. Edited CAD endothelial cells exhibited a global transcriptional downregulation of pathways relating to abnormal vascular physiology and activated endothelial processes. Surprisingly, deletions on either risk or non-risk 6p24.1 locus had minimal influence on cis gene expressions. Instead, a CXC chemokine ligand on chromosome 10q11.21, CXCL12, was uncovered as a potential effector gene in CAD endothelial cells. Underlying this effect was the preferential inter-chromosomal interaction of 6p24.1 risk locus to a weak promoter of CXCL12, confirmed by chromatin conformation capture assays on our iPSC-derived endothelial cells. Functionally, risk genotypes AA/ AG at rs6903956 were associated significantly with elevated levels of circulating damaged endothelial cells in CAD patients. Circulating endothelial cells isolated from patients with risk genotypes AA/ AG were also found to have 10 folds higher CXCL12 transcript copies/ cell than those with non-risk genotype GG. Our study reveals the trans-acting impact of 6p24.1 risk locus, involving the atherosclerosis-implicated gene CXCL12, and is associated with intensified endothelial injury.

overall_design: RNA-seq of endothelial cells differentiated from patient derived induced pluripotent stem cells (iPSCs) with CRISPR-Cas9 based deletions (63-89bp) on 6p24.1 including rs6903956

first: Kai

last: Tay


title: Stromal inflammation is a targetable driver of blood aging [droplet-based scRNAseq - Batch 2]

first: Emmanuelle

last: Passegue

summary: To investigate the role of IL1 signaling in hematopoietic aging, we performed droplet-based scRNAseq (10X Genomics) of hematopoietic stem and progenitor cells (LK/LSK) and unfractionated endosteal and central marrow stromal cells (Ter119-/CD45-) from young wild type and young and old wild type and IL1R1-/- C57BL/6 mice.

overall_design: Hematopoietic stem and progenitor cells (lineage negative, cKit positive (LK) and lineage negative, cKit positive, Sca-1 positive (LSK)) and endosteal and central marrow stromal cells from the bone marrow of young (10 weeks) and old (24 months) wild-type C57BL/6 mice were isolated by flow cytometry and subjected to droplet-based scRNAseq (10X Genomics).

first: Carl

last: Mitchell

first: Oakley

last: Olson

first: Fernando

last: Calero-Nieto

first: Berthold

last: Gottgens


title: Transcriptome-wide analysis of gene expression regulated by YB-1 in glioblastoma multiforme (GBM)

city: Shanghai

first: Wei

middle: Kang

last: Wang

state: Shanghai

address: 320 Yueyang Road

department: State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences

institute: Chinese Academy of Sciences

summary: YB-1 is a cold shock domain (CSD)-containing RNA binding protein. It is involved in virtually all steps of RNA metabolism. In this study, we detected the gene expression profiles of control or YB-1 knockdown in U251 and U87 cells by performing high-throughput RNA sequencing.

overall_design: RNA-seq was performed from U251 cells expressing control- or YB-1-specific shRNAs. RNA-seq was performed from U87 cells expressing control- or YB-1-specific shRNAs.

first: Jinzhu

first: Weikang

first: Jingyi

last: Hui


title: Tissue-specific regulation of lipid polyester synthesis genes controlling oxygen permeation into Lotus japonicus nodules

status: Public on Nov 01 2022

first: Lucas

middle: Esteban

last: Wange

address: Dr. Aiguader 88

department: Institut de Biologia Evolutiva

institute: Universitat Pompeu Fabra

summary: Legumes establish endosymbiotic associations with nitrogen-fixing rhizobia, which they host inside root nodules. Here, specific physiological and morphological adaptations, such as the production of oxygen-binding leghemoglobin proteins and the formation of an oxygen diffusion barrier in the nodule periphery, are essential to protect the oxygen-labile bacterial nitrogenase enzyme. The molecular basis of the latter process remains elusive, as the identification of required genes is limited by the epistatic effect of nodule organogenesis over nodule infection and rhizobia accommodation. We overcame this by exploring the phenotypic diversity of Lotus japonicus accessions that uncouple nodule organogenesis from nodule infection when inoculated with a sub-compatible Rhizobium strain. Using comparative transcriptomics, we identified genes with functions associated with oxygen homeostasis and deposition of lipid polyesters on cell walls to be specifically upregulated in infected compared to uninfected nodules. As such hydrophobic modifications on cell walls are pivotal for creating diffusion barriers like the root endodermis, we focused on two Fatty acyl-CoA reductase genes that were specifically activated in the nodule or in the root endodermis. Mutant lines in a Fatty acyl-CoA reductase gene expressed exclusively in the nodule endodermis showed had decreased suberization of this cell layer and increased nodule permeability compared to wild type plants. Oxygen concentrations were significantly increased in the inner cortex of mutant nodules, which correlated with reduced nitrogen fixation rates, and impaired shoot growth. These results provide the first genetic evidence for the formation of the nodule oxygen diffusion barrier, a key adaptation enabling nitrogen fixation in legume nodules.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for different Lotus japonicus accessions that were either susceptible to rhizobium infection or not

first: Rafael

last: Venado

first: Macarena

last: Marin


title: Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features [dataset 4]

city: Chapel Hill

first: Marielle

last: Bond

state: North Carolina

address: 104 Manning Drive Thurston Building Room 4012

department: Genetics Curriculum

institute: UNC Chapel Hill

summary: 3D chromatin structure is thought to play a critical role in regulating gene transcription during cellular transitions. While our understanding of loop formation and maintenance is rapidly improving, much less is known about the mechanisms driving changes in looping and the impact of differential looping on gene transcription. One limitation has been a lack of well powered differential looping data sets. To address this, we conducted a deeply sequenced Hi-C time course of megakaryocyte development comprising 4 biological replicates and 6 billion reads per time point. Statistical analysis revealed 1,503 differential loops. Gained loops were enriched for AP-1 occupancy and correlated with increased expression of genes at their anchors. Lost loops were characterized by increases in expression of genes within the loop boundaries. Linear modeling revealed that changes in histone H3K27 acetylation, chromatin accessibility, and JUN binding in between the loop anchors were often just as predictive of changes in loop strength as changes to CTCF and/or cohesin occupancy at loop anchors. Finally, we built linear models and found that incorporating the dynamics of enhancer acetylation and loop strength increased accuracy of gene expression predictions. Together, our well-powered study has added to our understanding of the mechanisms that regulate looping, and the relationship of looping with gene expression.

overall_design: Hi-C of K562 cells treated with PMA to differenitate into a megakaryocyte-like state after 0, 6, or 72h

first: I

last: Quiroga

first: Michael

middle: I

last: Love

first: Hyejung

last: Won

first: Douglas

last: Phanstiel


title: Sentinel p16INK4a+ cells in the basement membrane form a reparative niche in the lung [RNA-Seq]

first: Peng

last: Tien

summary: We collected freshly sorted mesenchyme (live CD45-Epcam-CD31-PDGFRa+GFP- or GFP+) from dissociated lung tissue of INKBRITE animals to characterize the transcriptome difference between p16INK4a+ vs p16INK4a- cells at homeostasis and during injury. We used fluorescence activated cell sorting (FACS) to exclude immune (CD45+), epithelial (Epcam+), and endothelial (CD31+) cells and positively select for PDGFRa+ mesenchyme. Cells were sequenced at a depth of average of 45 million reads/sample. The results revealed an increase of senescence associated secretory phenotype (SASP) signature in p16INK4+ cells that becomes refined after injury. We found the expression of an epithelial growth factor epiregulin (ereg) increased in p16INK4a+ cells after injury suggesting a possible role of p16INK4a+ senescence during regeneration of lung epithelium.

overall_design: The INKBRITE animals we constructed by inserting a tandem cassette of H2B-GFP expressed in frame with the p16INK4A gene product in the murine Cdkn2a locus into a bacterial artificial chromosome (BAC). The expression of multiple copies of a stable fluorescent protein is driven by p16INK4A promoter. Whole adult murine lung tissue was dissociated to single cells stained with DAPI for live cells selection and subjected to FACS to select live CD45-Epcam-CD31-PDGFRa+GFP+ (p16INK4a+) and CD45-Epcam-CD31-PDGFRa+GFP- (p16INK4a-) cells. We collected p16INK4a+ and – cells from 3 INKBRITE  naphthalene injured animals and 3 solvent controls. The RNA was extracted and shipped to GENEWIZ company for sequencing o the Illumina HiSeq instrument. Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software

first: Nabora

last: Reyes

first: Tien

last: Peng


title: Inflammation of the Aged Bone Marrow Niche Drives Blood Aging

first: Xiaonan

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

summary: Hematopoietic aging is defined by a loss of regenerative capacity and skewed differentiation from hematopoietic stem cells (HSC) leading to dysfunctional blood production. Signals from the bone marrow (BM) microenvironment dynamically tailor hematopoiesis, but the effect of aging on the niche and the contribution of the aging niche to blood aging still remains unclear. Here, we show the development of an inflammatory milieu in the aged marrow cavity, which drives both niche and hematopoietic system remodeling. We find decreased numbers and functionality of osteogenic endosteal mesenchymal stromal cells (MSC), expansion of pro-inflammatory perisinusoidal MSCs, and deterioration of the central marrow sinusoidal endothelium, which together create a self-reinforcing inflamed BM milieu. Single cell molecular mapping of old niche cells further confirms disruption of cell identities and enrichment of inflammatory response genes. Inflammation, in turn, drives chronic activation of emergency myelopoiesis pathways in old HSCs and multipotent progenitors, which promotes myeloid differentiation at the expense of lymphoid and erythroid commitment, and hinders hematopoietic regeneration. Remarkably, both defective hematopoietic regeneration, niche deterioration and HSC aging can be improved by blocking inflammatory IL-1 signaling. Our results indicate that targeting the pro-inflammatory niche milieu can be instrumental in restoring blood production during aging.

overall_design: RNA sequencing of mesenchymal and endothelial populations isolated from both endosteum and central marrow of young and old mice

first: Evgenia

last: Verovskaya

first: Carl

middle: A

last: Mitchell

first: Fernando

middle: J

first: Aurélie

last: Hérault

first: Paul

last: Dellorusso

first: Si

last: Zhang

first: Arthur

last: Svendsen

first: Sietske

last: Bakker

first: Eric

last: Pietras

first: Theodore

middle: T

last: Ho

last: Göttgens

first: Emmanuelle

last: Passegué


title: RNA-seq analysis of mouse esophageal tissue following GITR agonism in a model of esophageal squamous cell cancer

city: Chicago

first: Marie-Pier

last: Tetreault

state: IL

address: 300 East Superior Street

department: Medicine/GI&Hep division

institute: Northwestern University

summary: Immune checkpoint modulation is an emerging therapeutic strategy for the treatment of esophageal squamous cell cancer (ESCC), but current strategies only benefit a fraction of patients. Glucocorticoid-induced TNFR-related protein (GITR) is a costimulatory immune checkpoint molecule that, upon engagement, can induce anti-tumor activity in solid tumor models. Here, we performed RNA sequencing analysis following targeting of GITR with an agonist antibody (clone DTA-1) or isotype control in the 4-nitroquinoline-1-oxide (4-NQO) mouse model of ESCC.

overall_design: Total RNA was isolated from 4-NQO treated mice injected with either GITR agonist antibody (DTA-1) or isotype control. Murine esophageal tissue was peeled off and enriched enriched for invading cells Three replicates of each group were studied.

first: Kelsey

middle: N

last: Wiles


title: RNA-seq on ES cells where DDX6 was knocked down by the AID method

city: Mishima

first: Yumiko

last: Saga

state: Shizuoka

address: 1111 Yata

department: Department of Gene Function and Phenomics

country: Japan

institute: National Institute of Genetics

summary: To degrade DDX6 acutely, we adopted an advanced protein degradation method, the auxin-induced degron (AID) system. For this purpose, we prepared an AID-tagged DDX6 and E3 ligase subunit of OsTIR1 in an engineered ES (D6AdP cell line). These deposited data are RNA-seq data on these D6AdP ES cells treated with the auxin analog (IAA) treatment for 0, 3, and 6 hours.

overall_design: Single-end RNA-seq of polyA RNAs originally from 500-1000 ng of total RNAs extracted from the D6AdP ES cells treated with the auxin analog (IAA) treatment for 0, 3, and 6 hours, processed with the Truseq Stranded mRNA Library Prep kit (Illumina).

first: Masafumi

last: Muraoka


title: Failure of diet-induced transcriptional adaptations in A30P alpha-synuclein transgenic mice

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

summary: Nutritional influences have been discussed as potential modulators of Parkinson’s disease (PD) pathology. In animal models, a high fat diet (HFD) with greater intake of lipid-derived calories leads to accelerated disease onset and progression. The underlying molecular mechanisms of HFD-induced aggravated pathology, however, remain largely unclear. In this study, we aimed to further illuminate the effects of a fat-enriched diet in PD by examining the brainstem and hippocampal transcriptome of alpha synuclein transgenic mice exposed to a life-long HFD. Investigating individual transcript isoforms, differential gene expression, and co-expression clusters, we observed that transcriptional differences between wildtype and transgenic animals intensified in both regions under HFD. Both brainstem and hippocampus displayed strikingly similar transcriptomic perturbation patterns. Interestingly, expression differences resulted mainly from responses in wildtype animals to HFD, while these genes remained largely unchanged or were even slightly oppositely regulated by diet in transgenic animals. Genes and co-expressed gene groups exhibiting this dysregulation were linked to metabolic and mitochondrial pathways. Our findings propose failure of metabolic adaptions as potential explanation for accelerated disease unfolding under exposure to HFD. From the identified clusters of co-expressed genes, several candidates lend themselves to further functional investigations.

overall_design: Four experimental groups in brainstem and hippocampus each: [Wildtype, Transgenic] x [standard diet, high fat diet]

first: Thomas

last: Hentrich


title: HuR-dependent expression of Wisp1 is necessary for TGFbeta-induced cardiac myofibroblast activity

city: Columbus

first: Michael

last: Tranter

state: OH

address: 2255 Kenny Road

department: Molecular Medicine and Therapeutics

institute: The Ohio State University

summary: We show that activity of the RNA binding protein HuR is necessary for myofibroblast activation. This data set identifies directly bound HuR target genes in quiescent cardiac fibroblasts and active myofibroblasts.

overall_design: RNA-sequencing of eluted HuR-bound targets following photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) in primary isolated murine cardiac fibroblasts treated with vehicle control or 10 ng/ml TGFbeta

first: Tranter

last: Michael


title: Knockdown of circular RNAs using LNA-modified antisense oligonucleotides

city: Copenhagen

first: Marianne

middle: Bengtson

last: Løvendorf

address: Frederikskaj 10b, 2. floor

department: Clinical Medicine

country: Denmark

institute: Center for RNA Medicine, Aalborg University

summary: Circular RNAs (circRNAs) constitute an abundant class of covalently closed non-coding RNA molecules that are formed by backsplicing from eukaryotic protein-coding genes. Recent studies have shown that circRNAs can act as microRNA or protein decoys as well as transcriptional regulators. However, the functions of most circRNAs are still poorly understood. Because circRNA sequences overlap with their linear parent transcripts, depleting specific circRNAs without affecting host gene expression remains a challenge. Here, we assessed the utility of LNA-modified antisense oligonucleotides (ASOs) to knock down circRNAs for loss-of-function studies. We identified 5807 circRNAs in total RNA sequencing data from 4 liver cancer cell lines and used the back splice junction (BSJ) sequences of 7 validated circRNAs as target sites for designing different LNA-modified ASOs for circRNA knockdown. We found that while most RNase H-dependent gapmer ASOs mediate effective knockdown of their target circRNAs, some gapmers reduce the levels of the linear parent transcript and may also cause degradation of unintended off-targets. The circRNA targeting specificity can be enhanced using design-optimized gapmer ASOs or LNA/DNA mixmer ASOs, which display potent and specific circRNA knockdown with a minimal effect on the host genes or predicted off-targets. In summary, our results demonstrate that LNA-modified ASOs complementary to BSJ sequences mediate robust knockdown of circRNAs in vitro and, thus, represent a useful tool to explore the biological roles of circRNAs in loss-of-function studies in cultured cells and animal models.

overall_design: Analysis of circular RNA expression in four liver cancer cell lines (Hep3B, HepG2, Huh-7D12, SK-Hep-1) using total RNA sequencing (100-bp, paired end)

first: Andreas

last: Petri

first: Anja

last: Holm

first: Tsinat

last: Berhane

first: Charlotte

last: Thrue

first: Sakari

last: Kauppinen


title: Deletion of small GTPase H-Ras rescues memory deficits and ameliorates amyloid pathology in transgenic Alzheimer’s mice

city: MINNEAPOLIS

first: Ling

last: Li

state: MN

address: Mcguire Translational Research Facility, 4-419

department: Experimental and Clinical Pharmacology

institute: University of Minnesota

summary: This study aimed to invistigate the impact of H-Ras depletion on cognitive function and pathological features of AD.

overall_design: We performed bulk mRNA-seq to examine the transcriptome changes associated with Hras knockout in APP/PS1 mice. RNA-Seq data was collected from 6 mice (3 males & 3 female) from each genotype group (APP/PS1, APP/PS1/Hras-/-) at 9 months of age. Sequencing was performed using Illumina NovaSeq 6000 platform, generating 20 million reads per sample on a 150-bp paired-end run.

first: Wenhui

last: Qu


title: Expression data from mouse bone marrow derived macrophages

city: Suita

first: Tomohiko

last: Murakami

state: OSAKA

address: 1-8 Yamada-Oka

institute: Osaka University

summary: To understand the effect of LPS on macrophages, macrophages were stimulated with LPS and the gene expressions were analyzed by microarray.

overall_design: Bone marrow derived macrophages were stimulated with or without LPS. Total RNAs were analyzed by microarray using an Affymetrix Mouse Genome 430 2.0 Array.


title: RNA-seq data from mouse articular chondrocytes

summary: To understand the effect of semaphorin 4D on articular chondrocytes, articular chondrocytes were stimulated with semaphorin 4D. Total RNA was analyzed by RNA-seq.

overall_design: mRNA profiles of primary articular chondrocytes stimulated with or without semaphorin 4D


title: Transcriptomic analysis of HepG2 cells treated with BDE-47, BDE-99, BDE-209 and their ternary mixture at 1nM as a dietary relevant concentration

status: Public on Oct 28 2022

city: Rome

first: Sabrina

last: Tait

state: Italy

address: Viale Regina Elena 299

department: Dpt. Infectious Diseases

institute: Istituto Superiore di Sanità

summary: Polybrominated diphenyl ethers (PBDEs) are persistent organic chemicals implied as flame re-tardants. Humans are mainly exposed to BDE-47, -99 and -209 congeners by diet. PBDEs are metabolic disruptors with liver as main target organ. To investigate their mode of action at a human relevant concentration, we exposed HepG2 cells to these congeners and their mixture at 1 nM for 72h, analyzing their transcriptomic and proteomic profiles. KEGG pathways and GSEA Hallmarks enrichment analyses evidenced that BDE-47 disrupted the glucose metabolism and Hypoxia pathway; all the congeners and the MIX affected lipid metabolism and signaling Hallmarks regulating metabolism as mTORC1 and PI3K/AKT/MTOR. These results were confirmed by glucose secretion depletion and increased lipid accumulation, especially in BDE-47 and -209 treated cells. These congeners also affected the EGFR/MAPK signaling; further, BDE-47 enriched the Estrogen pathway. Interestingly, BDE-209 and the MIX increased ERα gene expression, whereas all the congeners and the MIX induced ERβ and PPARγ. We also found that PBDEs modulated several lncRNAs and that HNRNAP1 represented a central hub in all the four interaction networks. Overall, despite the low concentration used, the PBDEs investigated affected glucose and lipid metabolism with different underlying modes of action, as highlighted by the integrated omics analysis. These results may support the mechanism-based risk assessment of these compounds in relation to liver metabolism disruption.

overall_design: Five conditions experiment: Control (medium alone); BDE-47 1 nM; BDE-99 1 nM; BDE-209 1 nM; MIX (BDE-47 1nM+BDE-99 1nM+BDE-209 1nM). Biological replicates: three replicates per condition. Technical replicates: 2 (dye swap) per biological replica


title: Early life provision of 12-HETE by neutrophils imprints self-renewing capacity on alveolar macrophages

city: Montreal

first: Jun

last: Ding

state: QC

address: 1001 Decarie Blvd.

department: Department of Medicine

country: Canada

institute: McGill University

summary: The goal of this study is to determine the effect of the 12/15-lipoxygenase deficiency on transcriptomic profile of alveolar macrophages.

overall_design: Expression profiling by bulk RNA-Seq. Alveolar macrophages were obtained by bronchoalveolar lavages of adult (6-8 weeks) wild-type or Alox15-deficient mice using PBS.

first: Erwan

last: Pernet

first: Sarah

last: Sun

first: Nicole

last: Sarden

first: Saideep

last: Gona

first: Angela

last: Nguyen

first: Nargis

last: Khan

first: Martin

last: Mawhinney

first: Kim

last: Tran

last: Chronopoulos

first: Dnyandeo

last: Amberkar

first: Mina

last: Sadeghi

first: Alexandre

last: Grant

first: Shradha

last: Wali

first: Renaud

last: Prevel

first: James

middle: G

last: Martin

first: Ajitha

last: Thanabalasuriar

first: Bryan

last: Yipp

first: Luis

last: Barreiro

first: Maziar

last: Divangahi


title: Nuclear condensates of YAP fusion proteins as a critical driver for ependymoma

status: Public on Oct 27 2022

city: Cincinnati

first: Zaili

last: Luo

address: 3333 Burnet Ave.

institute: CCHMC

summary: To further determine chromatin conformation and long-range enhancer/promoter interactions altered by YAP-M, we performed a whole-genome chromatin capture assay using Hi-ChIP.

overall_design: Neural progenitor cells and tumor cells isolated from YAP-M tumor tissue were analyzed using HiChIP

first: Xiaohua

last: Hu

first: Richard

last: Lu

first: Chuntao

last: Zhao


title: Leveraging the Epigenomic Landscape to identify Histology-Specific Master transcription factors and to functionally annotate risk loci in renal cell carcinoma

city: Boston

first: Elio

last: Adib

address: 20 Shattuck Street

institute: Brigham and Women's Hospital

summary: We performed histone (ChIP-seq, the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), and RNA sequencing (RNA-seq) on 42 fresh frozen RCC tumor samples (24 ccRCC, 6 pRCC, 12 chRCC). We integrated 153 unique data sets  to gain a holistic view of gene regulation in RCC subtypes and 50 candidate histology-specific master transcription factors (TF) to define RCC histologic subtypes. We also integrated RCC GWAS risk SNPs with H3K27ac ChIP-seq and ATAC-seq data and revealed that risk variants were significantly enriched in allelically imbalanced peaks

overall_design:
We performed histone ChIP-seq, ATAC-seq, and RNA sequencing (RNA-seq) to annoate the epigenetic landscape then untegrate that data to nominate candidate master TFs important to maintain cellular identity. We manipulated the expression of two of these candidate TFs and evaluated RNA expression as a readout. We also GWAS risk loci with epigenetically marked peaks.
This submission corresponds to ChIP-seq component of study.
The RNA-seq samples were included on Dec 13, 2022.

first: Matthew

last: Freedman

first: David

last: Kwiatkowski

first: Toni

middle: K

last: Choueiri


title: Phase separation of YAP fusion proteins drives supratentorial ependymoma

address: 3333 BURNET AVENUE

department: Brain Tumor Center

institute: Cincinnati Children's Hospital Medical Center

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

overall_design: Refer to individual Series


title: A Transcriptomic Map of EGFR-induced Epithelial-to-Mesenchymal Transition Identifies Prognostic and Therapeutic Targets for Head and Neck Cancer

status: Public on Oct 26 2022

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary:
Purpose: We aim to identify transcriptomic changes associated with EGFR-mediated epithelial to mesenchymal transition in carcinoma cells of the upper aerodigestive tract
Method: Kyse30 and FaDu (ATCC, Manassas, VA, USA) were passaged in DMEM or RPMI, 10% FCS, 1% penicillin/streptomycin, 5% CO2 atmosphere at 37°C. Treatment with EGF (PromoCell PromoKine, Heidelberg, Germany), EpEX-Fc (Pan et al. PMID: 30261040) were conducted under serum-free conditions for 6h and 72h.
Results:  Kyse30 cells: At 6h/72h of treatment high-dose EGF (9nM) induced 612/1208 genes; low-dose EGF (1.8nM) induced 397/0 genes; EpEX-Fc (50nM) induced 137/2 genes; high-dose EGF (9nM) + EpEX (50nM) induced 291/0 genes  FaDu cells: At 6h/72h of treatment high-dose EGF (9nM) induced 994/1536 genes; low-dose EGF (1.8nM) induced 671/4 genes; EpEX-Fc (50nM) induced 36/0 genes; high-dose EGF (9nM) + EpEX (50nM) induced 911/103 genes
Conclusion: High- and low-dose EGF treatment in Kyse30 and FaDu cells differ with respect to short-term and long-term gene regulation. High-dose EGF, which is associated with induction of EMT, induces a higher number of differentially regulated genes (DEGs) after 6h and has a sustained strong regulatory capacity at 72h, when other treatmernts showed no DEGs.

overall_design: RNAseq analysis of human Kyse30 and FaDu cell lines treated with different concentrations of EGF and the extracellular domain of EpCAM termed EpEX as a fusion with Fc (EpEX-Fc)

first: Olivier

last: Gires

first: Henrik

last: Schinke

first: Min

last: Pan


title: Transcriptomic profiles of porcine PBMC from nonimmune and ASFV-immune pigs upon in vitro stimulation

status: Public on Oct 24 2022

city: Cerdanyola del Vallès (Bellaterra)

first: Jordi

last: Argilaguet

state: Spain

address: Campus de la Universitat Autònoma de Barcelona, Edifici CReSA s/n

department: CReSA

institute: IRTA

summary: We describe the transcriptomic recall response to African swine fever virus (ASFV) upon in vitro stimulation in porcine peripheral blood mononuclear cells (PBMC) obtained three weeks after receiving an intranasal dose of 106 pfu of the live attenuated BA71ΔCD2 vaccine prototype. PBMC from 4 unvaccinated and 4 vaccinated pigs were stimulated with BA71ΔCD2 or left untreated for 10 hours, RNA was extracted, and bulk RNA-sequencing was performed. Major transcriptional changes were found in BA71ΔCD2-stimulated samples from vaccinated pigs. Indeed, compared to unvaccinated control pigs, cells from vaccinated animals showed an upregulation of genes corresponding to a robust Th1 response. Together with this adaptive immune response, we also distinguished an innate immune response characterized by the expression of macrophage-related inflammatory genes. Altogether, our results demonstrate that intranasal vaccination of pigs with BA71ΔCD2 induce a systemic Th1 memory response that is concomitant with a rapid enhancement of innate immunity upon in vitro activation.

overall_design: Transcriptomic profiles of PBMC from 4 control unvaccinated pigs and 4 pigs vaccinated with the live attenuated BA71ΔCD2 prototype (three weeks after vaccination), in vitro stimulated with BA71ΔCD2 or left untreated for 10 hours.

first: Anna

last: Esteve-Codina

first: Beatriz

last: Martín-Mur

first: Marc

last: Dabad

first: Laia

last: Bosch-Camós

first: Uxía

last: Alonso

first: Boris

last: Gavrilov

first: Fernando

last: Rodríguez


title: M6A-seq & RNA-seq analysis of wild type and Mettl3-cKO liver tissues' or hepatocytes' transcriptomes

status: Public on Oct 29 2022

city: Xi'an Shaanxi

first: Xiang

last: Zhang

address: Changle West Road 169

institute: The Fourth Military Medical University

summary: To investigate the role of METTL3-mediated m6A modification in liver, we performed m6A-sequencing and RNA-seq to map the m6A modification and gene expression in liver tissues or hepatocytes of wild type (WT) and liver-sepcific Mettl3-KO mice.

overall_design: m6A-seq and transcriptome profiles of liver in 8 weeks wild type (WT) and liver-sepcific Mettl3-KO mice were generated by deep sequencing,with biologic replicates. In addtion, m6A-seq and transcriptome profiles of hepatocytes in 8 weeks wild type (WT) and liver-sepcific Mettl3-KO mice were generated by deep sequencing,too.

first: Zhang

last: Xiang

last: Rui


title: Sensory nerve niche regulates mesenchymal stem cell homeostasis via FGF/mTOR/autophagy axis [scRNA-seq]

city: Los Angeles

first: Fei

last: Pei

address: 2250 Alcazar St

institute: USC

summary: In this study, using the mouse molar as a model, we took advantage of single-cell transcriptome profiling, lineage tracing and transgenic mouse models to interrogate the cellular heterogeneity and gene regulatory networks (GRNs) of postmigratory CNCCs.In this study, we have put together a dynamic spatiotemporal single-cell regulatory atlas and revealed the landscape of transcriptional heterogeneity and defined the cellular domains during the progression of cranial neural crest cell (CNCC)-derived dental lineage diversification. Importantly, we identified cell type-specific gene regulatory networks (GRNs) during CNCC-derived dental lineage development.

overall_design: Single-nuclei transcriptomes were obtained from trigemial ganglion of one-month-old mice


title: Functional role of GATA3 and CDX2 in lineage specification during bovine early embryonic development

city: Hangzhou

first: Kun

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: Current understandings of the initiation of the trophectoderm (TE) program in mammalian embryonic development lacks evidence of how TE-associated factors such as CDX2 and GATA3 participate in bovine lineage specification. In this study, we describe the effects of TE-associated factors on lineage specification marker genes such as SOX2, OCT4, NANOG, GATA6 and SOX17, assisted by a cytosine base editor system. Interestingly, GATA3 downregulates the NANOG expression in bovine blastocysts. Further analysis of the blastocyst mosaic shows that GATA3 is required for NANOG in TE cells of bovine blastocysts. It is worthy to notice that, unlike mouse embryos where GATA3 and CDX2 did not reciprocally affect each other in bovine embryos.

overall_design: PolyA RNA profiles of  bovine embryos

first: Huanan

last: Wang

first: Yan

last: Shi

first: Bingjie

last: Hu


title: Drug screening identifies tazarotene and bexarotene as therapeutic agents in Multiple Sulfatase Deficiency II

status: Public on Oct 31 2022

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: We analysed differences in gene expression upon treatment of MSD patient fibroblast lines and control fibroblast lines with tazarotene and bexarotene or DMSO control (untreated condition)

overall_design: Comparative gene expression profiling analysis of RNA-seq data

first: Sophie

last: Schröder

first: Tonatiuh

last: Pena-Centeno

first: André

first: Lars

last: Schlotawa

first: Tea

last: Berulava


title: HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia

status: Public on Oct 25 2022

first: Ayse

middle: Selen

last: Yilmaz

address: 1800 Cannon Drive

department: Biomedical Informatics

institute: OSU


title: HDAC1 regulates the chromatin landscape to control transcriptional dependencies in chronic lymphocytic leukemia [miRNA-seq]

summary: Chronic lymphocytic leukemia (CLL) is a quiescent B-cell malignancy that depends on transcriptional dysregulation for survival.  The histone deacetylases are transcriptional regulators whose role within the regulatory chromatin and consequence on the CLL transcriptome is poorly characterized.  Here, we profiled and integrated the genome wide occupancy of HDAC1, BRD4, H3K27Ac and H3K9Ac signals with chromatin accessibility, Pol2 occupancy and target expression signatures in CLL cells. We identified that when HDAC1 was recruited within super-enhancers (SEs) marked by acetylated H3K27 and BRD4, it functioned as a transcriptional activator that drove the de novo expression of select genes to facilitate survival and progression in CLL. Targeting HDACs reduced BRD4 and Pol2 engagement to downregulate the transcript and proteins levels of specific oncogenic driver genes in CLL such as BLK, a key mediator of the B-cell receptor pathway, core transcription factors such as PAX5 and IKZF3 and the anti-apoptotic gene, BCL2. Concurrently, HDAC1, when recruited in the absence of super-enhancers repressed target gene expression. HDAC inhibition reversed silencing of a defined set of protein coding and noncoding RNA genes. We focused on a specific set of microRNA genes and show that their upregulation was inversely correlated with the expression of CLL specific survival, transcription factor and signaling genes. Our findings identify that the transcriptional activator and repressor functions of HDACs cooperate within the same tumor to establish the transcriptional dependencies essential for survival in CLL.

overall_design: miRNA-seq

middle: S

first: Hatice

last: Ozer

first: Deepa

last: Sampath

first: Tzung-Hueim

last: Lai


title: Sensory nerve niche regulates mesenchymal stem cell homeostasis via FGF/mTOR/autophagy axis.


title: AhR-mediated lipid peroxidation contributes to TCDD-induced cardiac injury in zebrafish

status: Public on Oct 30 2022

city: Jinan

first: Ping

last: Mi

address: Wenhuaxi 44

institute: Shandong University

summary: 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a persistent environmental contaminant. Previous reports revealed TCDD activating aryl hydrocarbon receptor (AhR) pathway and causing cardiac damage. However, the mechanism of AhR-induced cardiac defect in response to TCDD exposure remains unclear. In this study, we characterized the impacts of TCDD exposure on heart morphology and cardiac function in zebrafish. To investigate the differentially expressed genes under TCDD exposure, we collected the zebrafish larave heart from the control and TCDD treatment groups. We then performed gene expression profiling analysis using data obtained from RNA-seq. Transcriptomic profiling showed that, along with an upregulation of the AhR signaling pathway by TCDD, the expression of pro-ferroptosis genes was upregulated, while genes implicated in glutathione metabolism were downregulated. Consistently, lipid peroxidation, as indicated by malonaldehyde (MDA) production, increased in TCDD-exposed cardiac tissue. Accordingly, inhibiting lipid peroxidation with Liproxstatin-1 reversed the adverse cardiac effects under TCDD treatment. Together, our findings demonstrate that AhR-mediated lipid peroxidation contributes to the cardiac developmental defects of TCDD during zebrafish early development.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the zebrafish heart of the control and TCDD treatment groups.

first: Detian

last: Yuan

first: Lei

last: Li

first: Kang

last: Ai