title: Inflammasome activation drives inflammation in hidradenitis suppurativa skin

status: Public on Oct 01 2023

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

summary: Treatment for the debilitating, chronic skin disease hidradenitis suppurativa (HS) is grossly inadequate. A better understanding of its pathogenesis is required to design new therapeutic strategies. Despite an incidence of approximately 1 in 200, HS is underrecognized and underdiagnosed, with a high morbidity and poor quality of life, which may last decades. In this study we first employed single cell RNA sequencing to analyse gene expression in immune cells isolated from HS lesions compared with healthy control skin. We identified 30 unique immune cell clusters, with a significant enrichment in the frequency of plasma cells, Th17 cells and a subset of dendritic cells (DC) in HS skin. These findings were validated by flow cytometry, which revealed a significant increase in infiltrating immune cells in HS skin, including T cells, B cells, neutrophils, dermal macrophages and DC. The sequencing analysis revealed that the immune transcriptome in HS skin was distinct and much more heterogenous, when compared with healthy skin. Genes and pathways associated with Th17 cells and IL-17, IL-1β, and the NLRP3 inflammasome were enhanced in HS skin, particularly in samples with a high inflammatory load. Inflammasome constituent genes principally mapped to Langerhans cells and a subpopulation of DC. A skin explant model showed that culture of HS skin with an NLRP3 inflammasome inhibitor reduced the inflammatory response, with significant reduction of IL-1β and IL-17A as well as other key mediators of inflammation. These data provide a rationale for targeting the IL-17 pathway in HS, particularly upstream at the NLRP3 inflammasome.

overall_design: Skin samples from HS or healthy control skin was digested into a single cell suspension. Samples were resuspended in CryoStor cyropreservation media and frozen at -80 degrees. Once thawed, live cells were FACS sorted into CD45+ cells and 10X Genomics scRNA-seq was performed.

first: Barry

last: Moran

first: Conor

last: Smith

first: Alexandra

last: Zabarowski

first: Mark

last: Ryan

first: Jozsef

last: Karman

first: Robert

middle: W

last: Dunstan

first: Kathleen

first: Roisin

last: Hambly

first: Jana

last: Musilova

first: Andreea

last: Petrasca

first: Aurelie

last: Fabre

first: Margaret

last: O'Donnell

first: Kingston

last: Mills

first: William

last: Housley

first: Desmond

last: Winter

first: Brian

last: Kirby

first: Jean

last: Fletcher


title: Metabolic Model of Streptococcus suis reveals the Indispensability of catabolic ornithine carbamoyltransferase ArcB for Adapting to Anaerobiosis

city: Wuhan,Hubei

first: Hao

last: Tang

address: Shizishan Street 1

country: China

institute: Huazhong Agriculture University

type: Expression profiling by high throughput sequencing

summary: Pathogenic microorganisms have evolved various strategies to sense and respond to stress in order to establish infection and ensure survival within the host's complex environment. Hypoxia, a metabolic stress factor encountered by aerobic microorganisms during rapid growth, remains poorly understood in terms of pathogen adaptation. Streptococcus suis, a zoonotic pathogen causing meningitis and sepsis, exhibits remarkable adaptability to anaerobic conditions. Transcriptomic analysis reveals that anaerobic conditions significantly suppress carbohydrate metabolism in S. suis SC19 while differentially regulating genes related to toxins, metal uptake systems, and adhesion. A reconstructed genome-scale metabolic network (GSMM), constrained by transcriptomic information, was used to explore metabolic changes in SC19 under hypoxia. Anaerobic metabolism of SC19 is characterized by activation of the arginine deiminase (ADI) pathway and biosynthesis of branched-chain amino acids (BCAA). Enzymes ArcB and IlvH from these pathways were identified as potential targets and docked with drugs from the DrugBank database. Among the candidate inhibitors targeting ArcB, simvastatin and cis-(Z)-flupentixol demonstrated significant hypoxia-dependent inhibition of SC19 survival. Simvastatin was also found to attenuate virulence of SC19, proliferation, and pro-inflammatory capabilities in mice by inhibiting ArcB during the late stage of infection. This study unveils how Streptococcus suis adapts to low oxygen limitations by rewiring amino acid metabolism. A targeted antimicrobial strategy based on metabolic adaptability of pathogen is proposed to alleviate the pressure of developing new drugs against multidrug-resistant bacterial infections.

overall_design: To characterizing the impact of hypoxia on streptococcus suis SC19 growth, RNA-seq was utilized to monitor the global transcriptional regulation of SC19 at the mid-log phase (6 h) under oxygen limitation. A comparative analysis of gene expression between aerobic and anaerobic-cultivated SC19 cells revealed a global regulation of the transcriptome in response to hypoxia.

first: Lu

last: Li


title: A safety screening platform for individualized cardiotoxicity assessment

city: Enschede

first: Carla

last: Cofiño Fabrés

address: Drienerlolaan 5

country: Netherlands

institute: University of Twente

summary:
Cardiotoxicity remains a major cause of drug withdrawal, partially due to lacking predictability of animal models. Additionally, risk of cardiotoxicity following treatment of cancer patients is treatment limiting. It is unclear which patients will develop heart failure following therapy. Human pluripotent stem cell (hPSC)-derived cardiomyocytes present an unlimited cell source and may offer individualized solutions to this problem. We developed a platform to predict molecular and functional aspects of cardiotoxicity. Our platform can discriminate between the different cardiotoxic mechanisms of existing and novel anthracyclines Doxorubicin (DOXO), Aclarubicin (ACLA) and Amrubicin (AMR). DOXO and ACLA unlike AMR substantially affected the transcriptome, mitochondrial membrane integrity, contractile force and transcription factor availability. Cardiomyocytes recovered fully within two or three weeks, corresponding to the intermittent clinical treatment regimen.
Our system permits the study of hPSC-cardiomyocyte recovery and the effects of accumulated dose after multiple dosing, allowing individualized cardiotoxicity evaluation, which effects millions of cancer patients treated with anthracyclines annually.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hiPSC-CMs in Engineered Heart Tissues treated with DMSO (control), Doxorubicin (DOXO), Aclarubicin (ACLA) or Amrubicin (AMR) for 24h. 3 tissues per condition

first: Verena

last: Schwach

last: Cofiño-Fabres

first: Rolf

last: Slaats

last: Passier


title: Bulk RNA sequencing of total lung cells from 14 dpi of high-dose mtb on Atg14f/f and Atg14f/f-LysM-cre mice.

status: Public on Oct 13 2023

city: Beijing

first: Siwei

last: Feng

address: No.30,Shuangqing street

institute: Siwei Feng

summary: We found that several autophagy genes in myeloid cells are required to protect against high-dose Mtb (~1000cfu) infection. To understand the immune cell population in these mice after high-dose Mtb infection and what may contribute to the susceptibility, we did bulk RNAseq on mice infected with high-dose of Mtb strain Erdman.

overall_design: Lung cells from 14 dpi of high-dose mtb on Atg14f/f and Atg14f/f-LysM-cre mice. Cells pooled from 4 mice each, age 8-10 wks


title: An Amygdalar Local Oscillator Coordinates Cellular and Behavioral Rhythms

status: Public on Oct 08 2023

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

country: USA

institute: Johns Hopkins University

summary: Purpose: scRNA-Seq and snRNA were performed to characterize mWake-expressing neurons in the lateral amygdala

overall_design: The lateral amygdalae were collected from 7-8 wk old male mWake(Cre/+) mice at ZT0-2 using a previously published protocol.  Briefly, the coronal plane (350 um) containing the LA was sliced using a vibratome in bubbling aCSF.  LA were dissected into Hibernate-A media with a 2% B-27 and GlutaMAX supplement (0.5 mM final concentration).  Both LA from 2 mice were used for scRNA-Seq analysis, which was repeated with 2 additional mice.  This procedure was also performed for snRNA-Seq analysis (in total, 8 mice were used).

first: Qiang

last: Liu

first: Jiali

last: Xiong

first: Dong

first: Sang

middle: S

last: Lee

first: Benjamin

middle: J

last: Bell

first: Chloe

last: Alexandre

first: Seth

last: Blackshaw

first: Alban

last: Latremoliere

first: Mark

middle: N

last: Wu


title: MoTrPAC - Endurance Exercise Training Study In 6 Months Old Rats [RRBS]

status: Public on Sep 30 2023

city: Stanford

first: Euan

last: Ashley

state: CA

address: 870 Quarry Road

institute: Stanford University

type: Methylation profiling by high throughput sequencing

summary: The goal of the endurance exercise training study in young adult rats was to perform exercise training studies in young adult (6-month-old) F344 rats, and from these rats collect multiple tissues in order to provide high quality samples for detailed analysis by chemical analysis sites.  Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups.  The 8-week training group and controls were from the same cohort and same age at euthanasia. For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program.  Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max and training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31.  This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved.  If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized.  It is important to note that the starting treadmill speed varied depending on the sex and age of the rat.  The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats.  Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.

overall_design:
Regular exercise promotes whole-body health and prevents disease, yet the underlying molecular mechanisms throughout a whole organism are incompletely understood. Here, the Molecular Transducers of Physical Activity Consortium (MoTrPAC) profiled the temporal transcriptome, proteome, metabolome, lipidome, phosphoproteome, acetylproteome, ubiquitylproteome, epigenome, and immunome in whole blood, plasma, and 18 solid tissues in Rattus norvegicus over 8 weeks of endurance exercise training. The resulting data compendium encompasses 9466 assays across 19 tissues, 25 molecular platforms, and 4 training time points in young adult male and female rats.

Contributor: Molecular Transducers of Physical Activity Consortium (MoTrPAC)


title: Effect of depletion of FXR1 on gene expression in head and neck squamous cell carcinoma (HNSCC) cells

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street, BE208

institute: MUSC

summary: FXR1 is an essential RNA-binding protein. This chromosome 3q26-28 gene is overexpressed in many epithelial tumors. FXR1 controls the turnover and translation of multiple mRNAs and is involved in cellular transformation. We identified critical residues in the protein that are post-translationally modified. These regulate the stability of FXR1 protein, its RNA-binding function, cell growth, and proliferation. Here we show that PRMT5-mediated arginine methylation of FXR1 increases the protein's binding to G-quadruplex RNAs in vivo and controls their expression in cancer cells. Independent point mutations of specific arginine residues in the nuclear export signal (R386, R388) and arginine-glycine rich (R453, R455, R459) domains of FXR1 abrogate the RNA-binding in vitro. Genetic and small molecule inhibition of PRMT5 minimizes methylation and levels of FXR1 and suppresses oral tumor growth and proliferation. RNA-seq analyses of FXR1 KD cells show an increase in the expression of PLK2, TCN2, and TRAF4 along with FXR1’s well-known target CDKN1A. Like CDKN1A, these targets possess strong G4 sequences. FXR1 and G4-RNA interactions provide new insights into the molecular mechanism of FXR1 and its interaction with target mRNAs. Furthermore, an increased expression of FXR1 and PRMT5 is colocalized in cancer tissues, leading to a poor patient prognosis. Thus, our data demonstrate that PRMT5-mediated arginine methylation of FXR1 arginine residues in the NES and RGG domains plays a critical role in binding and controlling G4-RNAs, which encode tumor suppressors and promote cancer cell growth and proliferation.

overall_design: To investigate the cooperative functionFXR1 in the HNSCC cell lines in which FXR1 has been knocked down by shRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of control and KD cells with Biological triplicates.

first: Mrinmoyee

last: Majumder

first: Viswanathan

last: Palanisamy


title: MoTrPAC: Endurance Exercise Training Study In 6 Months Old Rats

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
MoTrPAC endurance exercise training study targets young adult (6-month-old) rats. Specifically, male and female Fischer 344 rats (n = 12) were subjected to progressive treadmill endurance exercise training for 1, 2, 4, or 8 weeks, with tissues collected 48 hours after the last exercise bout. Sex-matched sedentary, untrained rats were used as controls.
This study contributes to MoTrPAC's broader mission, which is to identify molecular changes occurring due to exercise. The ultimate goal is to understand how physical activity can improve and sustain health across various ages and fitness levels.
The program is supported by the NIH Common Fund. For additional information, visit the MoTrPAC Data Hub at https://motrpac-data.org/.

This SuperSeries is composed of the SubSeries listed below.

relation:
SuperSeries of: GSE242354
SuperSeries of: GSE242355
SuperSeries of: GSE242357

overall_design: 6-month-old young adult rats (Fischer 344) were subjected to progressive endurance exercise training for 1, 2, 4, or 8 weeks, with tissues collected 48 hours after the last training bout. Sex-matched sedentary, untrained rats were used as controls. Whole blood, plasma, and 19 solid tissues were analyzed using genomics, proteomics, metabolomics, and protein immunoassay technologies, with most assays performed in a subset of these tissues. Depending on the assay, between 3 and 6 replicates per sex per time point were analyzed.


title: MoTrPAC - Endurance Exercise Training Study In 6 Months Old Rats [ATAC-seq]


title: mRNA decapping activators Pat1 and Dhh1 regulate transcript abundance and translation to tune cellular responses to nutrient availability

status: Public on Sep 27 2023

city: Bethesda

first: Alan

middle: G

last: Hinnebusch

address: 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: Yeast mRNA decapping-activators Pat1 and Dhh1 have been implicated in repressing translation and mRNA degardation in glucose-deprived cells, but the specific mRNAs targeted by each factor and their functions in nutrient replete cells are poorly understood. To test this, we performed ribosome profiling and RNA-Seq in WT, pat1D and pat1Ddhh1D. Further, CAGE-Seq and Rpb1-ChIP Seq were employed to determine their role in decapping mediated degradation of mRNAs

overall_design: This study includes total 26 samples, 9 for ribosome profiling from triplicates of WT, pat1D and pat1Ddhh1D; 3 from  triplicates of WT. Separately, the same total RNA dhh1D, and pat1D in duplicates,  were subjected to CAGE-Seq (4 samples) and total RNA-Seq (4 samples). pat1D and dhh1D in triplicates were subjected to Rpb1-ChIP seq (6 samples).  All strains were grown in YPD at 30ºC till the OD600 ~0.6

first: Anil

last: Kumar Vijjamarri

first: Neha

last: Gupta

first: Chisom

last: Onu

first: Xiao

last: Niu

first: Fan

last: Zhang

first: Rakesh

last: Kumar

first: Zhenguo

last: Lin

first: Miriam

middle: L

last: Greenberg


title: cohesin spreads bi-directionally to form chromatin jets in C. elegans

city: New York

first: Jun

last: Kim

state: NY

address: 100 Washington Square East 1009 Silver Center

department: Biology

institute: NYU

summary: Inspection of Hi-C and ChIP-seq data suggests that cohesin spreads from putative loading sites form chromatin jets

overall_design: ChIP-seq and Hi-C data in auxin treated control, SMC-3 and WAPL-1 depletion conditions. All experiments were performed in two or more biological replicates. L2/L3 stage worms were used.

first: Sevinc

last: Ercan


title: Gene expression from HCT116 cells after LS 1 2 treatment

status: Public on Sep 01 2023

first: Haizhao

last: Yi

address: No. 52 Fucheng Rd., Haidian District

institute: Peking University Cancer Hospital & Institute

summary: To determine the signaling pathway involved in LS-1-2-mediated tumor inhibition, we performed genome-wide gene expression by comparing HCT116 cells with and without LS-1-2treatment.

overall_design: Differentially expressed genes total 2324 were identified between control vs 0.1 μM LS-1-2 6h, control vs 0.1 μM LS-1-2 12h, and control vs 0.1 μM LS-1-2 24h.

first: Dengbo

last: Ji


title: Quartet Methylomics

status: Public on Sep 04 2023

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

institute: Fudan University

type: Methylation profiling by genome tiling array

summary: The Quartet Project aims to provide resources for QC of multiple types of omic technologies and the effective integration of diverse datasets from various scenarios. Large quantities of multi-omics materials, datasets, and best practices for their QC utilities were developed for whole process QC of large-scale, multi-center, and longitudinal multi-omics profiling.

overall_design: Bisulphite converted DNA were hybridised to the Illumina Infinium MethylationEPIC BeadChip


title: MoTrPAC- Endurance Exercise Training Study In 6 Months Old Rats [RNA-seq]

first: Euan

last: Ashley

summary: The goal of the endurance exercise training study in young adult rats was to perform exercise training studies in young adult (6-month-old month) F344 rats, and from these rats collect multiple tissues in order to provide high quality samples for detailed analysis by chemical analysis sites.  Tissues were collected from 10-12 rats sedentary control rats concurrent with the collection of the 8-week training groups.  The 8-week training group and controls were from the same cohort and same age at euthanasia. For the older age group, an additional set of controls (n=5-6) were collected with the 1-2 week training group. Rats were either sedentary or underwent an exercise training program.  Rats were exercised on the rodent treadmill 5 days per week using a progressive training protocol designed to exercise the rats at approximately 70% of VO2max and training was performed no earlier than 10:00 am and no later than 5:00 pm over 5 consecutive days per week. Training was initiated with the treadmill set at 70% of VO2 max and 5 degrees grade for 20 minutes. The duration of exercise was increased by one minute each day until day 31 of training (start of week 7), when a duration of 50 min was reached. Speed and grade of each training session increased in larger increments due to treadmill parameters. The highest intensity and duration of training began on day 31.  This intensity was maintained for the final 10 days of the protocol to ensure steady state had been achieved.  If any rats were unable to perform at least 4 days of training per week they were removed from the study and euthanized.  It is important to note that the starting treadmill speed varied depending on the sex and age of the rat.  The initial and maximum speeds were based on VO2max measurements obtained during the pre-training testing of the compliant rats.  Rats assigned to the control group followed a schedule similar to the training group. They were placed in one lane on the treadmill for 15 minutes/day, 5 days per week. The treadmill was set at 0 m/min at an incline that corresponded to the incline being used by the training group.


title: 3D chromatin hubs as regulatory units of identity and survival in acute T-cell leukemia [hiChIP]

status: Public on Sep 25 2023

first: Javier

last: Rodriguez Hernaez

state: New York

address: East 30th Street. 8th Floor

institute: NYU Langone Health

summary: Cancer progression is associated with genetic and epigenetic aberrations that affect chromatin 3D organization in the nucleus. Changes in loop extrusion or phase separation alter the relationships between enhancer and promoter elements, defining novel gene expression programs that are selected to promote growth and survival. Here, we provide an integrative approach based on chromatin conformation, accessibility and transcription, further validated by CRISPR interference screenings in order to identify chromatin topologies relevant to different subtypes of T-cell leukemia, namely T-ALL and ETP-ALL. By focusing on highly interconnected elements, we characterized 3D hubs as headquarters of leukemia progression and identity, demonstrating that oncogenes and disease markers are regulated by multiple cis-regulatory regions.

overall_design:
Primary samples and prototypical cell lines of T cell acute lymphoblastic leukemia (T-ALL) and early T cell precursor leukemia (ETP-ALL) were collected and analyzed for H3K27ac HiChIP. To enrich for blast representation, samples were sorted based on clinical immune-phenotype, for CD2 and/or CD7 surface expression

Please note that the raw data files (SRR13492049,SRR13492050) for GSM5028231 (Jurkat HiChIP; SAMN17391130, GSE165207) sample were downloaded fron SRA and re-analyzed. The resulting processed data file is linked as Series supplementary file.

UPDATE: [11-04-2024] The title and treatment characteristic of Sample GSM7798271 was corrected.

first: Rodriguez-Hernaez

last: Javier

first: Boccalatte

last: Francesco

first: Gambi

last: Giovanni

first: Nadorp

last: Bettina

first: Aifantis

last: Ioannis

first: Tsirigos

last: Aristotelis


title: Transcriptomic response of Mycobacterium tuberculosis to artemisinin, Artemisia annua extract, and Artemisia afra extract

status: Public on Sep 28 2023

city: Worcester

first: Scarlet

last: Shell

state: Massachusetts

address: 60 Prescott St, WPI

department: Biology and Biotechnology

institute: Worcester Polytechnic Institute

summary: We sought to determine the transcriptomic impacts of artemisinin, Artemisia annua extract, and Artemisia afra extract on M. tuberculosis. Log phase cultures were treated with lethal doses for four hours or with inhibitory or sub-inhibitory doses for 24 hours. RNA was collected from untreated controls at the same timepoint.

overall_design: M. tuberculosis strain mc26230 (H37Rv ΔRD1 ΔpanCD) was treated with artemisinin or with dichloromethane extracts of A. annua or A. afra at three different doses. A lethal dose (2X MIC) was applied for four hours, and inhibitory (MIC or 1.33X MIC) and sub-inhibitory doses (0.5X MIC) were applied for 24 hours. Untreated cultures were harvested after 4 and 24 hours for comparison. All treatments were done in quadruplicate.

first: Maria

last: Alonso

first: Junpei

last: Xiao


title: Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis

status: Public on Sep 11 2023

city: Davis

first: Alex

middle: S.

last: Nord

address: 1544 Newton Court

department: Center for Neuroscience

institute: University of California Davis

summary: Transcription factors (TFs) bind combinatorially to genomic cis-regulatory elements (cREs), orchestrating transcription programs. While studies of chromatin state and chromosomal interactions have revealed dynamic neurodevelopmental cRE landscapes, parallel understanding of the underlying TF binding lags. To elucidate the combinatorial TF-cRE interactions driving mouse basal ganglia development, we integrated ChIP-seq for twelve TFs, H3K4me3-associated enhancer-promoter interactions, chromatin and transcriptional state, and transgenic enhancer assays. We identified TF-cREs modules with distinct chromatin features and enhancer activity that have complementary roles driving GABAergic neurogenesis and suppressing other developmental fates. While the majority of distal cREs were bound by one or two TFs, a small proportion were extensively bound, and these enhancers also exhibited exceptional evolutionary conservation, motif density, and complex chromosomal interactions. Our results provide new insights into how modules of combinatorial TF-cRE interactions activate and repress developmental expression programs and demonstrate the value of TF binding data in modeling gene regulatory wiring.

overall_design:
ChIP-seq, PLAC-seq
Peak files includes data from GSE124936, GSE85705, and GSE69724.

first: Rinaldo

last: Catta-Preta

first: Susan

last: Lindtner

first: Athena

last: Ypsilanti

first: James

last: Price

first: Linda

last: Su-Feher

first: Yurong

last: Wang

first: Armen

last: Abnousi

first: Yin

last: Shen

first: Axel

last: Visel

first: Len

last: Pennacchio

first: Diane

last: Dickel

first: John

last: Rubenstein


title: Active learning of enhancer and silencer regulatory grammar in photoreceptors

city: Saint Louis

first: Michael

middle: Aaron

last: White

state: MO

address: 660 South Euclid Ave

department: Genetics

institute: Washington University in St. Louis School of Medicine

summary: We performed iterative rounds of massively parallel reporter assay experiments in ex vivo retinas to generate training data for machine learning models of the photoreceptor cis-regulatory grammar.

sample_organism:
Escherichia coli
Mus musculus

platform_organism:
Escherichia coli
Mus musculus

overall_design: A series of libraries of barcoded reporter gene plasmids were transfected into mouse retinas in triplicate. We measured barcoded reporter gene activity by RNA-seq, normalized by the DNA-seq reads of the input plasmid pool.

middle: A

first: Ryan

middle: Z

last: Friedman

first: Barak

last: Cohen


title: Clinical subtyping of cancer from plasma based on comprehensive epigenomic profiling

status: Public on Sep 21 2023

city: Boston

first: Sylvan

middle: C

last: Baca

state: MA

address: 450 Brookline Ave

department: Center for Functional Cancer Epigenetics

institute: Dana Farber Cancer Institute

summary: While circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical decisions in cancer care, they have limited ability to identify the transcriptional programs that govern cancer phenotypes and their dynamic changes during the course of disease. To address these limitations, we developed a method for comprehensive epigenomic profiling of cancer from 1mL of patient plasma. Using an immunoprecipitation-based approach targeting histone modifications and DNA methylation, we measured 1,268 epigenomic profiles in plasma from 433 individuals with one of 15 cancers. Our assay provided a robust proxy for transcriptional activity, allowing us to infer the expression levels of diagnostic markers and drug targets, measure the activity of therapeutically targetable transcription factors, and detect epigenetic mechanisms of resistance. This proof-of-concept study in advanced cancers shows how plasma epigenomic profiling could unlock clinically actionable information that is currently accessible only via direct tissue sampling.

first: Matthew

last: Freedman

first: Brad

last: Fortunato


title: 3D chromatin hubs as regulatory units of identity and survival in acute T-cell leukemia [RNA-seq]

first: Javier

last: Rodriguez Hernaez

overall_design: Primary samples and prototypical cell lines of T cell acute lymphoblastic leukemia (T-ALL) and early T cell precursor leukemia (ETP-ALL) were collected and analyzed. To enrich for blast representation, samples were sorted based on clinical immune-phenotype, for CD2 and/or CD7 surface expression

last: Rodriguez-Hernaez

first: Francesco

last: Boccalatte

first: Giovanni

last: Gambi

first: Bettina

last: Nadorp

first: Ioannis

last: Aifantis

first: Aristotelis

last: Tsirigos


title: Genome-wide DNA methylation profiling of cell-free DNA in nipple aspirate fluid for breast cancer

status: Public on Sep 26 2023

city: Houston

first: Minsun

last: Jeon

address: 2121 W Holcombe Blvd

institute: Texas A&M Institute of Biosciences & Technology

summary: Nipple aspriate fluid (NAF) were obtained from 7 women including 3 breast cancer patients. Cell-free DNA (cfDNA) were isolated and bisulfite sequencing using Illumina HiSeq X Ten platform.

overall_design: cfDNA libraries of normal and breast cancer NAF samples were constructed and sequenced for genome-wide DNA methylation profiling.

first: Ke

last: Zhang


title: Effects of exercise on whole blood transcriptome profile in children with overweight/obesity

status: Public on Sep 19 2023

city: Irvine

first: ABEL

last: PLAZA FLORIDO

state: California

address: 101 Academy, Suite 150 Irvine

department: Department of Pediatrics, UC Irvine School of Medicine

institute: Pediatric Exercise and Genomics Research Center (PERC)

summary: Background:   The current knowledge about the molecular mechanisms underlying the health benefits of exercise is still limited, especially in the pediatric population. We set out to investigate the effect of a 20-week exercise intervention on whole blood transcriptome profile (RNA-seq) in children with overweight/obesity.  Methods:   Twenty-four pre-pubertal children (10.21 ± 1.33 years, 46% girls) with overweight/obesity, were randomized to either a 20-week exercise program (intervention group; n=10), or to a non-exercise control group (usual lifestyle, n=14). Whole blood transcriptome profile was analysed using RNA-seq STRT2 technique. Gene expression analysis was carried out with the Limma R/Bioconductor software package, and the gene ontology (GO) and pathway enrichment analyses were performed using R. Ingenuity Pathway Analysis (IPA) was performed for gene network detection. The transcriptome data were in silico validated using PHENOPEDIA and meta-analysis database extrameta.org.    Results:   161 genes were differentially expressed between the exercise and the control groups among boys, and 121 genes among girls (p-value < 0.05), while after multiple correction, no significant difference between groups persisted in gene expression profiles (FDR > 0.05). Based on non-corrected analyses, the enriched GO processes and molecular pathways highlighted the effect of exercise on different immune response related pathways in boys (antigen processing and presentation, infections, and T cell receptor complex) and girls (Fc epsilon RI signaling pathway) (FDR < 0.05). In silico data mining and validation analyses (using PHENOPEDIA and meta-analysis database extrameta.org)  highlight top genes regulated by exercise such as CD6, HLA-C, TNFRSF1A, MYD88, and NFKBIA genes in boys and RAC1, ANXA6, FYN, INPP5D, PIK3CD and SPARC genes in girls.  Conclusion:   These results suggest that 20-week exercise program influences different immune processes in children with overweight/obesity. The transcriptome differences between boys and girls could partly be explained, in addition to the gender differences, by the distinct intensity in the exercise intervention as boys had stronger exercise stimulus in training. Our findings should be considered exploratory and preliminary given the relatively small sample size. Larger and more powered randomized controlled trials should confirm or contrast our findings.

overall_design: Total whole blood mRNA profiles of 24 children with overweight/obesity were analyzed by 5’-end RNA sequencing at two different time points (before and after a 20-week exercise intervention).

first: Signe

last: Altmäe

first: Abel

last: Plaza-Florido

first: Francisco

last: Esteban

first: Augusto

last: Anguita-Ruiz

first: Kaarel

last: Krjutškov

first: Shintaro

last: Katayamah

first: Elisabet

last: Einarsdottir

first: Juha

last: Kere

first: Shlomit

last: Radom-Aizik

middle: B

last: Ortega


title: Gene expression profile at single cell level from the colorectal cancer (CRC)

first: Kangyu

last: Lin

address: 1515 Holcombe Blvd

department: Department of Gastrointestinal Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

summary: This study is part of MD Anderson Cancer Center CRC Moon Shot. We used single cell RNAsequencing (scRNA-seq) to analyze the diversity of CRC.

overall_design: Fresh colorectal cancer tissues and adjucent normal tissues from primary and liver/peritnoeum-Met patients were collected for scRNA-seq.

first: Scott

last: Kopetz

first: Shen

last: John Paul


title: Regulation of human interferon signaling by transposon exonization

status: Public on Sep 15 2023

city: Boulder

first: Edward

last: Chuong

state: Colorado

address: 3415 Colorado Ave., room E251

department: Molecular, Cellular and Developmental Biology

institute: University of Colorado Boulder

summary: Innate immune signaling is essential for clearing pathogens and damaged cells, and must be tightly regulated to prevent autoimmunity. Here, we found that the alternative splicing of exons derived from transposons is a key mechanism controlling immune signaling in human cells. By analyzing long-read transcriptome datasets, we identified numerous transposon exonization events predicted to generate functional protein variants of immune genes, including the type I interferon receptor IFNAR2. We demonstrated that the transposon-derived isoform of IFNAR2 is more highly expressed than the canonical isoform in almost all tissues, and functions as a decoy receptor that potently inhibits interferon signaling including in cells infected with SARS-CoV-2. Our findings uncover a primate-specific axis controlling interferon signaling and show how a transposon exonization event can be co-opted for immune regulation.

overall_design: Transcriptional profiling (RNA-seq) of HeLa cells cells (wild-type, IFNAR2-S KO, IFNAR2-L KO and IFNAR2-E7 KO) that were either untreated or stimulated with 10U/mL human recombinant interferon beta  (IFNb) for 4hrs.

first: Giulia

middle: I

last: Pasquesi


title: Endothelial cells differentiated from patient dermal fibroblast-derived induced pluripotent stem cells resemble vascular malformations of Port Wine Birthmark

status: Public on Sep 14 2023

city: Columbia

first: Wenbin

last: Tan

address: 6311 Garners Ferry Road

department: Cell Biology and Anatomy

institute: University of South Carolina School of Medicine

summary: Background:Port wine birthmark (PWB) is a congenital vascular malformation resulting from developmentally defective endothelial cells (ECs). Developing clinically relevant disease models for PWB studies is currently an unmet need. Objective: Our study aims to generate PWB-derived induced pluripotent stem cells (iPSCs) and iPSC-derived ECs that preserve disease-related phenotypes. Methods: PWB iPSCs were generated by reprogramming lesional dermal fibroblasts and differentiated into ECs. RNA-seq was performed to identify differentially expressed genes (DEGs) and enriched pathways. The functional phenotypes of iPSC-derived ECs were characterized by capillary-like structure (CLS) formation in vitro and Geltrex plug-in assay in vivo. Results: Human PWB and control iPSC lines were generated through reprogramming of dermal fibroblasts by introducing the “Yamanaka factors” (Oct3/4, Sox2, Klf4, c-Myc) into them; the iPSCs were successfully differentiated into ECs. These iPSCs and their derived ECs were validated by expression of a series of stem cell and EC biomarkers, respectively. PWB iPSC-derived ECs showed impaired CLS in vitro with larger perimeters and thicker branches as compared to control iPSC-derived ECs. In the plug-in assay, perfused human vasculature formed by PWB iPSC-derived ECs showed bigger perimeters and greater densities than those formed by control iPSC-derived ECs in severe combined immune deficient (SCID) mice. The transcriptome analysis showed that dysregulated pathways of stem cell differentiation, Hippo, Wnt, and focal adhesion persisted through differentiation of PWB iPSCs to ECs. Functional enrichment analysis showed that Hippo and Wnt pathway-related PWB DEGs are enriched for vasculature development, tube morphology, endothelium development, and EC differentiation. Further, members of the zinc finger (ZNF) gene family were overrepresented among the DEGs in PWB iPSCs. ZNF DEGs confer significant functions in transcriptional regulation, chromatin remodeling, protein ubiquitination, and retinoic acid receptor signaling. Furthermore, NF-kappa B, TNF, MAPK, and cholesterol metabolism pathways were dysregulated in PWB ECs as readouts of impaired differentiation. Conclusions: PWB iPSC-derived ECs render a novel and clinically-relevant disease model by retaining pathological phenotypes. Our data demonstrate multiple pathways, such as Hippo and Wnt, NF-kappa B, TNF, MAPK, and cholesterol metabolism, are dysregulated, which may contribute to the development of differentiation-defective ECs in PWB.

overall_design:
To investigate the molecular and pathway signatures in PWB iPSCs and their-derived MSCs and ECs as compared with controls during differentiation
Grant information:
Department of Defense (HT9425-23-10008), PI: Wenbin Tan
Grant title: Targeting of Photodynamic Therapy-Resistant Port Wine Birthmarks Affiliation: UNIVERSITY OF SOUTH CAROLINA

first: Vi

last: Nguyen

first: Chao

last: Gao

first: Marcelo

last: Hochman

first: Jacob

last: Kravitz

first: Elliott

middle: H

last: Chen

first: Harold

last: Friedman

first: Camilla

middle: F

last: Wenceslau

first: Dongbao

first: Yunguan

last: Wang

first: J

last: Nelson

first: Anil

last: Jegga


title: Human PSC-derived articular cartilage chondrocytes scRNA-seq

status: Public on Aug 24 2023

first: April

middle: M

last: Craft

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: Objectives Traditional approaches to study Progressive Pseudorheumatoid Arthropathy of Childhood (PPAC) failed to uncover how loss-of-function mutations in Wnt inducible secreted protein 3 (WISP3) cause premature cartilage failure in children. We developed a human induced pluripotent stem cell (hiPSC)-based model of cartilage development to elucidate pathological changes in WISP3-deficient articular cartilage tissues compared to WISP3-sufficient isogenic cartilage tissues.    Methods We generated iPSCs from 2 patients with PPAC, and we corrected the disease-causing mutation in one of these lines using CRISPR/Cas9. We also created a WISP3-knockout human embryonic stem cell line. We generated articular cartilage tissues from these hPSCs by established directed differentiation methods. Bioinformatic analyses were used to identify differentially expressed genes (DEGs) and cell type abundances, which were validated by quantitative RT-qPCR and in situ hybridization.  Results WISP3-deficient articular cartilage tissues exhibited significantly different transcriptomic profiles and cellular composition compared with their isogenic controls. WISP3-deficient cartilage transcriptomes exhibited enriched biological processes such as TGFb signaling and epithelial to mesenchymal transition. We validated increased expression of TGFb-related genes in WISP3-deficient cartilage, and determined that the abundance of chondrocyte subtypes was altered compared with isogenic controls.     Conclusions We developed a robust and reproducible model of iPSC-derived cartilage development to better understand the role of WISP3 in cartilage biology, and the pathology of cartilage failure associated with loss of WISP3 in patients with PPAC. We identified several altered biological processes and signaling pathways in WISP3-deficient cartilage that can be validated in the future with additional patient-derived cell lines, or large animal models.

overall_design:
comparative gene expression profiling of in vitro derived cartilage chrondrocytes from human PSCs

Please note: Raw data are not available for the PPAC iPSC samples due to patient privacy concerns.

first: Chaochang

last: Li

first: Mireia

last: Alemany Ribes

first: Rosanne

last: Raftery

first: Uzochi

last: Nwoko

first: Matthew

last: Warman


title: 3D chromatin hubs as regulatory units of identity and survival in acute T-cell leukemia.

first: Javier

last: Rodriguez Hernaez

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

overall_design: Refer to individual Series


title: NPAS4 controls cell type-specific circuit adaptations underlying drug-seeking behavior

status: Public on Aug 31 2023

first: Stefano

last: Berto

summary: Use of addictive substances often creates powerful and enduring associations with external cues that act as relapse triggers in individuals recovering from a substance use disorder (SUD). In the reward-associated brain region, the nucleus accumbens (NAc), drug use or drug-associated cue exposure activates a subset of D1 dopamine receptor-expressing medium spiny neurons (D1-MSNs), which typically promotes drug seeking, and a smaller subset of D2 dopamine receptor-expressing MSNs (D2-MSNs), which typically opposes drug seeking. The activity-regulated transcription factor, Neuronal PAS Domain Protein 4 (NPAS4), is activated in a small subset of NAc neurons during cocaine conditioning, and NAc NPAS4 is required for drug-context memories. Using a new Npas4-TRAP mouse combined with chemogenetics, we found that the during cocaine conditioning, the NPAS4-positive ensemble is required for drug-context associations. Single-cell transcriptomic analyses and in situ hybridization of NAc tissues from drug-conditioned mice revealed that NPAS4 is expressed predominantly in MSNs, and using cell type-specific molecular genetic approaches, we found that NPAS4 in D2-MSNs, but not D1-MSNs, was required for both drug-context associations and cue-reinstated cocaine seeking. Similarly, NPAS4 in NAc D2-MSNs, but not D1-MSNs, blocked cocaine experience-dependent strengthening of glutamatergic prefrontal cortical (PFC) inputs onto D2-MSNs. Analysis of differential gene expression in D2-MSNs revealed that NPAS4 and cocaine conditioning influence a gene expression program associated with synapses, dendrites, neuronal projections, dopamine, and cocaine. Together, our data reveal that NPAS4 functions during active cocaine use to maintain the imbalance of D1-MSN:D2-MSN activation and cue-induced drug seeking by suppressing excitatory drive onto relapse-opposing NAc D2-MSN circuits.

overall_design: We performed single nuclei RNA sequencing (snRNA-Seq) from NAc tissues isolated from mice expressing either AAV2-shNpas4 or AAV2-shScram virus. Mice were subjected to either cocaine or saline conditioning, and 24-hrs later (CPP test day), NAc tissues were rapidly extracted and processed for single nuclei RNA-sequencing (snRNA-seq)

first: Brandon

last: Hughes

first: Makoto

last: Taniguchi

first: Chirstopher

last: Cowan


title: Identification and subsequent validation of transcriptomic signature associated with metabolic status in endometrial cancer

city: Bialystok

first: Iwona

last: Sidorkiewicz

address: Sklodowska-Curie Street 24a

department: Clinical Research Centre

country: Poland

institute: Medical University of Bialystok

summary:
Metabolic status was successfully evaluated through Nanostring expression profiling of a total of 768 genes in 87 endometrial cancer (EC) cases.
The study revealed that 11 genes were deregulated in EC samples. Validation by qRT-PCR confirmed our findings. The results suggest that metabolic profiling can potentially be used as predictive biomarkers of EC.

overall_design:
In the study presented here, a consecutively operated, well-defined cohort of 87 EC cases was used to acquire expression profiles of a total of 768 unique metabolic-related genes.

** The submitter noted that the normalized data for the following samples are identical due to low expression of miRNA panel:
GSM5858294 Patient_229_FFPE
GSM5858297 Patient_250_FFPE

first: Maciej

last: Jóźwik

first: Adam

last: Krętowski

first: Magdalena

last: Niemira


title: An iPSC-based model of Progressive Pseudorheumatoid Arthropathy of Childhood identifies transcriptional changes in patient-iPSC-specific cartilage tissues

summary: Bulk RNA-seq is used to study transcriptomic differences between WISP3-deficient and WISP3-sufficient articular cartilage derived from hPSCs in vitro

overall_design:
Transcriptomic profiling of in vitro  chondrocyte populations

Please note: Raw data are not available for the PPAC iPSC samples due to patient privacy concerns.


title: Trained immunity of alveolar macrophages promotes injury resolution by enhancing KLF4-MERTK-mediated efferocytosis [RNA-seq]

status: Public on Aug 16 2023

city: Chicago

first: Jalees

last: Rehman

state: IL

address: 900 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC

summary: Recent studies suggest that training of innate immune cells such as tissue-resident macrophages by repeated noxious stimuli can heighten host defense responses. However, it remains unclear whether trained immunity of tissue-resident macrophages also comprises enhanced injury resolution capacity to counterbalance the heightened inflammatory responses. Here, we studied lung-resident alveolar macrophages (AMs) pre-challenged with either the bacterial endotoxin or with Pseudomonas aeruginosa and observed that these trained AMs showed greater resilience to pathogen-induced cell death. Transcriptomic analysis, and functional assays showed greater capacity of trained AMs to efferocytosis of cellular- debris, and facilitate injury resolution. Single-cell high-dimensional mass-cytometry analysis and lineage tracing demonstrated that training induces an expansion of a MERTKhiMarcohiCD163+F4/80low lung-resident AMs subset with pro-resolving phenotypes. Training epigenetically reprogrammed AMs to express a higher level of the transcription factor KLF4 which in turn upregulates the efferocytosis receptor MERTK. Adoptive transfer of these trained AMs restricted inflammatory lung injury in recipient mice exposed to lethal Pseudomonas aeruginosa. Thus, our study has identified a unique subset of tissue-resident trained macrophages which prevent hyper-inflammation and restore tissue homeostasis following pathogen challenge.

overall_design: Lung alveolar macrophage were isolated by flow sorting from naïve and LPS treated groups.  Three replicates for each group has been done.

first: Sreeparna

last: Chakraborty

first: Abhalaxmi

last: Singh

first: Li

last: Wang

first: Xinge

first: Mark

last: Sanborn

first: Zijing

last: Ye

last: Maienschein-Cline

first: Amitabha

last: Mukhopadhyay

first: Balaji

last: Ganesh

first: Asrar

last: Malik


title: Trained immunity of alveolar macrophages promotes injury resolution by enhancing KLF4-MERTK-mediated efferocytosis [ATAC-seq]

overall_design: Lung alveolar macrophage were isolated by flow sorting from naïve and 7day-LPS-trained mouse. Naïve macrophages were used for control and trained AM compared with naïve AMs. Two replicates with 200000 cells for each group has been done.


title: exoRNA-mediated Cell-to-cell Communications in E. coli are Supported by Dps Mobility

status: Public on Aug 30 2023

city: Pushchino

first: Konstantin

last: Shavkunov

address: Institutskaya street, 3

country: Russia

institute: Institute of Cell Biophysics RAS

type: Non-coding RNA profiling by high throughput sequencing

summary: Being a ferroxidase and a structural factor of the Escherichia coli nucleoid, Dps protein was recently encountered in the outer membrane and attracted attention as a potential partner for bacterial RNAs. Here, we show the first images visualizing Dps on the surface of bacteria and demonstrate that Dps produced by E. coli K-12 MG1655 or BL21(DE3) cells can cross bacteria-impermeable membrane and attach to the cell surface of a dps-null mutant. Using RNAseq and pull-down assays, we identified RNAs with specifically reduced secretion in the mutant and witnessed preferential interaction of Dps with tRNA and sRNA fragments. Upon analysis of their deviations from the genomic sequences, we selected one circular and six linear oligonucleotides with different folding as model RNAs and showed their ability to affect the growth of bacteria via Dps-dependent internalization by cells. This assumes Dps involvement in intercellular signal transduction within a bacterial population through participation in RNA secretion

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

overall_design: Secretion of E.coli RNAs in the presence or absence of Dps was studied using RNA-seq and pull-down assays

first: Olga

last: Ozoline

first: Natalia

middle: Y

last: Markelova

last: Glazunova

first: Uliana

last: Shvyreva

first: Nikolay

middle: P

last: Kolzhetsov

middle: V

last: Alikina

first: Valery

last: Panyukov

first: Sergey

last: Antipov

first: Elena

last: Shilova

first: Eleva

last: Preobrazhenskaya


title: Acid- and lactic acid-treated spleen-derived MDSCs in a mouse model of lung cancer transplantation tumor

status: Public on Aug 21 2023

city: 镇江市

first: 文信

last: 笪

state: 江苏省

address: 镇江市京口区学府路301号江苏大学

institute: 江苏大学医学院

summary: Transcriptome sequencing after treatment of spleen-derived MDSCs in a mouse model of lung cancer transplantation tumors using lactic and ph6.7 acids

overall_design: Euthanasia of mice; magnetic bead sorting of spleen-derived MDSCs in mice; treatment of MDSCs with acid at ph 6.7 and lactic acid for 24 hours


title: Palbociclib releases the latent differentiation capacity of neuroblastoma cells [RNA-seq PB and RA]

status: Public on Aug 15 2023

city: Cambridge

first: Sarah

last: Gillen

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute

summary: We have used RNA-seq to assess the global impact of palbociclib, retinoic acid and the combined treatment on the transcriptome.

overall_design: RNA-seq in SK-N-BE(2)C treated with DMSO, 10uM retinoic acid, 1uM palbociclib or 1uM palbociclib + 10uM retinoic acid

first: Kirsty

last: Ferguson

first: Anna

last: Philpott


title: Palbociclib releases the latent differentiation capacity of neuroblastoma cells [H3K27ac ChIP-seq palbociclib]

summary: We have used H3K27ac ChIP-seq to assess the global impact of palbociclib on the epigenetic H3K27ac landscape in three neuroblastoma cell lines.

overall_design: H3K27ac ChIP-seq in SK-N-BE(2)C, IMR-32 and SH-SY5Y following PB treatment for 5/7 days

first: Lewis

last: Chaytor

first: Laura

last: Woods


title: Palbociclib releases the latent differentiation capacity of neuroblastoma cells


title: Ahmed Scientific Advances 2023 data repository

status: Public on Aug 10 2023

city: Madison

first: Jack

last: Shireman

state: WI

address: 1500 Highland Ave

department: Neurological Surgery

institute: UW-Madison

summary: Understanding of TMZ therapy during and after treatment in a mouse model

overall_design: single cell sequencing was conducted on mice both after and during in Vivo TMZ treatment

first: Atique

middle: U

last: Ahmed


title: Gene regulatory networks underlying human microglia maturation

status: Public on Aug 14 2023

city: La Jolla

first: Christopher

last: Glass

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego


title: Palbociclib releases the latent differentiation capacity of neuroblastoma cells [RNA-seq PB]

summary: We have used RNA-seq to assess the global impact of palbociclib on the transcriptome at early and late time points in three neuroblastoma cell lines.

overall_design: RNA-seq in SK-N-BE(2)C, IMR-32 and SH-SY5Y following PB treatment for 24 hours and 5/7 days


title: Gene regulatory networks underlying human microglia maturation [ATAC-seq]

summary: Microglia, the tissue resident macrophages of the brain, are observed as early as the fourth week of human gestation and engage in a variety of processes essential for brain development and homeostasis. Microglia phenotypes are highly regulated by the brain environment but the transcriptional networks that specify their maturation remain poorly understood and the extent to which fetal or postnatal phenotypes can be modeled using iPSC-derived cells has not been systematically investigated. Here, we characterized stage-specific transcriptomes and epigenetic landscapes of fetal and postnatal human microglia ex vivo and acquired corresponding data in iPSC-derived microglia in vitro, in cerebral organoids, and as a function of time following engraftment into humanized mice.  By developing new computational approaches that integrate these data to predict state-specific transcription factor networks, we provide evidence that MiTF/TFE and MEF2 factors are key nodes in transcription factor networks associated with fetal microglia phenotypes, whereas MAFB, KLFs and IRF transcription factors are key nodes in the networks associated with postnatal phenotypes.  We further demonstrate that many features of the human fetal to postnatal transition in microglia gene expression are recapitulated in a time-dependent manner following the engraftment of iPSC-derived hematopoietic progenitor cells into humanized mice.  These studies thereby provide new computational and data resources enabling the elucidation of transcription factor networks underlying stage-specific human microglia phenotypes.

overall_design: Poly-A RNA-seq and ATAC-seq of iPSC-derived microglia, iPSC-derived microglia co-cultured with cerebral organoids, and iHPC xenografted into humanized mice and isolated at various time points.

first: Claudia

last: Han

first: Rick

last: Li

first: Emily

last: Hansen

first: Samantha

last: Trescott

first: Bethany

middle: R

last: Fixsen

first: Celina

middle: T

last: Nguyen

first: Hunter

last: Bennett

first: Nathanael

middle: J

last: Spann

first: Cristina

last: Mora

first: Olivier

last: Poirion

first: Justin

last: Buchanan

last: Warden

first: Bing

last: Xia

first: Johannes

last: Schlachetzki

first: Martina

last: Pasillas

first: Sebastian

last: Preissl

first: Gabriela

last: Ramirez

first: Jean

last: Challacombe

first: Samuel

last: Anavim

first: Avalon

last: Johnsonn

first: Mihir

last: Gupta

first: Michael

last: Levt

first: Sharona

last: Haim

first: David

middle: D

last: Gonda

first: Louise

last: Laurent

first: Mathew

last: Blurton-Jones

first: Nicole

last: Coufal

middle: K


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

status: Public on Aug 13 2023

city: Lund

last: Albinsson

address: BMC D12

country: Sweden

institute: Lund University

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

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


title: Selective modulation of gene expression in activated normal human peripheral blood mononuclear cells by store-operated calcium entry blocker BTP2

status: Public on Aug 07 2023

city: Ithaca

first: Iwijn

last: De Vlaminck

address: Weill Hall, 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

summary: Calcium is a critical signaling molecule in many cell types including immune cells. The calcium-release activated calcium channels (CRAC) responsible for store-operated calcium entry (SOCE) in immune cells are gated by STIM family members functioning as sensors of Ca2+ store content in the endoplasmic reticulum. We investigated the effect of SOCE blocker BTP2 on human peripheral blood mononuclear cells (PBMC) stimulated with the mitogen phytohemagglutinin (PHA).

overall_design: To investigate the effect of SOCE blocker BTP2 on human peripheral blood mononuclear cells (PBMC) stimulated with the mitogen phytohemagglutinin (PHA), we performed RNA sequencing (RNA-seq) to query gene expression at the whole transcriptome level and identified genes differentially expressed between PBMC activated with PHA and PBMC activated with PHA in the presence of BTP2.

first: Divya

last: Shankaranarayanan

first: Madhav

last: Mantri

first: Manikkam

last: Suthanthiran


title: EZH2 Mediated Metabolic Rewiring Promotes High-grade Serous Ovarian Cancer Progression Independently of Histone Methyltransferase Activity

status: Public on Aug 11 2023

city: Shanghai

first: Jianfeng

last: Chen

state: Shanghai

address: 270 Dong'an Road

institute: Fudan University Shanghai Cancer Center

summary: Despite EZH2 is overexpressed and exerts an oncogenic role in various cancer through catalytic-dependent or -independent manner, the mechanisms of EZH2 contributing to high-grade serous ovarian cancer (HGSOC) are incompletely understood. Here, we showed that a subgroup of HGSOC patients with high EZH2 expression but low H3K27me3 level exhibited worst prognosis. We demonstrated that EZH2 degradation but not catalytic inhibition profoundly lowered EZH2 protein and blocked cell proliferation and tumorigenicity in vitro and in vivo. Ectopic expression of EZH2 without SET domain (EZH2-∆SET), which is known to be essential for catalytic activity, restored the phenotypes of EZH2 degradation. Mechanistically, we identified that IDH2 was transactivated by EZH2 to impair metabolic rewiring by disrupting the TCA cycle, which contributed to the oncogenic role of EZH2 in OC. Together, these data reveal a novel carcinogenic role of EZH2 in HGSOC, and provide potential strategies in HGSOC by targeting EZH2 non-catalytic activity.

overall_design: RNA-seq for OVCAR8 treated with DZNep or doxycycline-induced EZH2 silence was performed (duplicate).

first: Jing

last: Tan


title: Palbociclib releases the latent differentiation capacity of neuroblastoma cells [H3K27ac ChIP-seq PB and RA]

first: Sarah

last: Gillen

summary: We have used H3K27ac ChIP-seq to assess the global impact of the combination of palbociclib and retinoic acid on the epigenetic H3K27ac landscape in three neuroblastoma cell lines.

overall_design: H3K27ac ChIP-seq in SK-N-BE(2)C cells following DMSO, RA, PB or PB+RA treatment for 5 days

middle: L

first: Roshna

last: Gomez

first: Fahad

last: Ali

first: Anna

last: Philpott


title: Transient naive reprogramming corrects hiPS cells functionally and epigenetically

city: Perth

first: Ryan

last: Lister

state: WA

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

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

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Th1/17 polarization and potential treatment by an anti-interferon-γ DNA aptamer in Hunner-type interstitial cystitis

status: Public on Jul 29 2023

city: Tokyo

first: Yoshiyuki

last: AKIYAMA

state: Please select...

department: Urology

country: Japan

institute: The University of Tokyo

summary: Hunner-type interstitial cystitis (HIC) is a rare, enigmatic inflammatory disease of the urinary bladder with no curative treatments. In this study, we aimed to characterize the unique cellular and immunological factors specifically involved in HIC by comparing with cystitis induced by Mycobacterium bovis bacillus Calmette–Guérin, which presents similar clinicopathological features to HIC. Here, we show that T helper 1/17 polarized immune responses accompanied by prominent overexpression of interferon (IFN)-γ, enhanced cGAS-STING cytosolic DNA sensing pathway, and increased plasma cell infiltration are the characteristic inflammatory features in HIC bladder. Further, we developed a novel mouse anti-IFN-γ DNA aptamer and observed that intravesical instillation of the aptamer significantly ameliorated bladder inflammation, pelvic pain and voiding dysfunction in a recently developed novel murine HIC mouse model with little migration into the blood. Our study provides the plausible basis for clinical translation of the anti-IFN-γ DNA aptamer in the treatment of human HIC.

overall_design: For 25 patients with HIC, paired cold-cup biopsy samples, one from a Hunner lesion and one from a background mucosal area without Hunner lesion, were obtained. For 13 patients with BCG, one cold-cup biopsy sample was obtained from a reddened mucosal flat lesion resembling a Hunner lesion. Biopsy samples were immediately frozen in liquid nitrogen and stored at -80°C for RNA extraction. We performed RNA-seq using these samples for comparative gene expression analyses of Hunner-type interstitial cystitis (lesion and non-lesion) and BCG cystitis.

last: Akiyama

first: Yi

last: Luo

first: Miyuki

last: Hori


title: RNA-seq of human prostate cancer cell line PC-3M trpv6 knockout versus wild type and PC3M-Luc-C6 wild type versus trpv6 overexpression.

status: Public on Jul 24 2023

city: Villeneuve d'Ascq

first: clement

last: cordier

address: Batiment SN3, cité Scientifique

country: France

institute: PhyCell

summary: TRPV6 is a membrane protein, a member of the transient receptor potential (TRP) ion channel family. The TRPV6 cation channel is highly selective for Ca2+, with PCa/PNa values greater than 100, playing a crucial role in calcium homeostasis in various cell types. Previous transcriptome analysis indicated that TRPV6 mRNAs were expressed in PCa and that channel expression correlates strongly with the pathology stage and metastasis status. The aim of the present study was to examine calcium-regulated signaling pathways in castration-resistant prostate cancers.

overall_design: Three biological replicates were analyzed for each of 2 conditions of PC3M cell line or two biological replicates were analyzed for each of 2 conditions of PC3M-Luc-C6 cell line with different trpv6 expression.

first: Clement

last: Cordier

first: V'yacheslav

last: Lehen'kyi


title: Large-scale map of RNA binding protein interactomes across the mRNA life-cycle

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

summary: RNA-binding proteins (RBPs) target RNA in a context-dependent manner to regulate gene expression. Protein-protein interaction (PPI) maps of RBP complexes and networks are critical for defining RBP function and RNA targeting. Yet, PPI networks under-represent RBP baits and need more information about RNA-driven interactions. Therefore, we generated an RNA-aware, RBP-interactome map combining two strategies that use systematic proteomic methods to identify 1) protein interactions using co-immunoprecipitation in the presence or absence of RNase treatment of a ~100 RBPs across the RNA life-cycle and 2) RNA-dependent complexes using Size Exclusion Chromatography. Together, this dataset provides proteome-wide, cell-type specific, and quantitative identification of RNA-protein interactions across multiple RNA processing events. In the resulting PPI network, several hundred database-supported interactions establish many complexes operating at each of these mRNA life-cycle stages. Nearly a thousand novel interactions imply new functions for RBPs across multiple steps of the RNA life cycle. Overlapping our network with eCLIP data, we find RNA targets between interactors and uncover complex-driven binding signatures. Betweenness-centrality scores identify multi-functional RBPs that participate across multiple mRNA life-cycle steps. We characterize the novel interactions and functions of different classes of multi-functional proteins. We find the scaffolding protein, ERH, interacts with numerous nuclear speckle proteins and facilitates splicing and mRNA export. Finally, we show that the splicing factor, SNRNP200, interacts with nuclear export, localization, and translation proteins and is an essential factor of RNA granule formation during stress. Our large-scale RBP interaction network provides new insights and a valuable resource for exploring new RBP complexes operating to control gene expression.

overall_design:
eCLIP-seq of human SNRNP200, CAPRIN, and G3BP1
eCLIP of RBP of interest. Each sample has an input and IP sample

first: Katherine

last: Rothamel

first: Lena

last: Street

first: Ahmed

last: Abdou

first: Wenhao

last: Jin

first: Kevin

last: Dong

last: Rhine

first: Assa

last: Madrigal

first: Norah

last: Al-Azzam

first: Kris

last: Brannan

first: Marko

last: Jovanovic

first: Gene

last: Yeo


title: Mineralized collagen induces phenotypic changes in MDA-MB-231

status: Public on Jul 19 2023

first: Claudia

last: Fischbach

address: 237 Tower Road

summary: We examine the transcriptional alterations induced by in vitro culture of MDA-MB-231 cells on microfabricated hydroxyapatite-mineralized collagen devices that simulate bone matrix (PMID 29759731). As a control, we additionally characterize the transcriptional activity of cells cultured on a collagen substrate. We find that mineralized collagen increases the expression of genes associated with stemness and metastasis while culture on collagen increased expression of genes associated with cell cycle progression.

overall_design: MDA-MB-231 were seeded onto collagen or mineralized collagen microwells and routinely cultured for 7 days. Cells were harvested using collagenase and RNA was isolated from each sample using an RNA isolation kit accourding to manufacturer's protocols. Library prep was done with Illumina TruSeq RNA stranded kit and samples were sequenced as 1 x 86 bp single-end reads on the NextSeq500.

first: Siyoung

last: Choi

first: Matthew

middle: A

last: Whitman

first: Adrian

last: Shimpi


title: Nucleosome-mediated competition of pioneer transcription factors

status: Public on Aug 02 2023

city: Freiburg

first: Daria

last: Onichtchouk

address: Hauptstrasse 1

country: Germany

institute: University of Freiburg

summary: Pioneer transcription factors Nanog, Pou5f3 and Sox19b  promote chromatin accessibility on the enhancers of the early zebrafish embryos. It is poorly understood how they act together; it is commonly assumed that they act additively or cooperatively to clear chromatin from the nucleosomes. We investigated this question by comparing chromatin accessibility (Omni ATAC-seq)  in seven mutant genotypes: single, double and triple maternal-zygotic mutants by Pou5f3, Sox19b and Nanog, and the wild-type embryos.  We found, that at most of the directly bound sites, either Pou or Nanog is required for chromatin accessibility; while at the minority of the sites two factors act additively. Further, on  the sites, where Pou5f3 promotes chromatin accessibility, Nanog often suppresses it, and vice versa. To explain this phenomenon,  we suggest a model of nucleosome-mediated competition between pioneer transcription factors: Pou5f3 and Nanog compete for the same binding motif on the DNA, but only one of the factors has a pioneer activity on this site. This entry contains only part fo the Omni-ATAC-seq experiments, the other part is in the previously released entry GSE188364.

overall_design: Omni-ATAC-seq on whole embryos

first: Aileen

last: Riesle


title: Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity

city: Santa Barbara

first: Alex

last: Chialastri

address: 2002 BioEngineering Bldg, CNTR for Bioengineering

institute: University of California Santa Barbara

summary: Transmission of 5-methylcytosine (5mC) from one cell generation to the next plays a key role in regulating cellular identity in mammalian development and diseases. While recent work has shown that the activity of DNMT1, the protein responsible for the stable inheritance of 5mC from mother to daughter cells, is imprecise; it remains unclear how the fidelity of DNMT1 is tuned in different genomic and cell state contexts. Here we describe Dyad-seq, a method that combines enzymatic detection of modified cytosines with nucleobase conversion techniques to quantify the genome-wide methylation status of cytosines at the resolution of individual CpG dinucleotides. We find that the fidelity of DNMT1-mediated maintenance methylation is directly related to the local density of DNA methylation, and for genomic regions that are lowly methylated, histone modifications can dramatically alter the maintenance methylation activity. Further, to gain deeper insights into the methylation and demethylation turnover dynamics, we extended Dyad-seq to quantify all combinations of 5mC and 5-hydroxymethylcytosine (5hmC) at individual CpG dyads to show that TET proteins preferentially hydroxymethylate only one of the two 5mC sites in a symmetrically methylated CpG dyad rather than sequentially convert both 5mC to 5hmC. To understand how cell state transitions impact DNMT1-mediated maintenance methylation, we scaled the method down and combined it with the measurement of mRNA to simultaneously quantify genome-wide methylation levels, maintenance methylation fidelity and the transcriptome from the same cell (scDyad&T-seq). Applying scDyad&T-seq to mouse embryonic stem cells transitioning from serum to 2i conditions, we observe dramatic and heterogenous demethylation and the emergence of transcriptionally distinct subpopulations that are closely linked to the cell-to-cell variability in loss of DNMT1-mediated maintenance methylation activity, with regions of the genome that escape 5mC reprogramming retaining high levels of maintenance methylation fidelity. Overall, our results demonstrate that while distinct cell states can substantially impact the DNA methylation maintenance machinery, there exists an intrinsic relationship between DNA methylation density, histone modifications and DNMT1-mediated maintenance methylation fidelity that is independent of cell state.

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design:
Bulk M-M-Dyad-seq, M-H-Dyad-seq, H-M-Dyad-seq, and H-H-Dyad-seq profiles of E14 mESC grown under multiple conditions for 48 hours.
Bulk M-M-Dyad-seq, M-H-Dyad-seq, and H-H-Dyad-seq profiles of E14 mESC grown with 0.05 µM of Decitabine for 24 hours.
scDyad-seq profiles of K562 grown with 0.6 µM DAC for 24 hours or DMSO vehicle control.
scDyad&T-seq profiles of E14 mESC grown in serum or in 2i for 3, 6, or 10 days (2iD3, 2iD6, or 2iD10 respectively).

first: Siddharth

middle: S

last: Dey


title: TGF-β signaling links early-life endocrine-disrupting chemicals exposure to suppression of nucleotide excision repair in rat myometrial stem cells

first: Qiwei

last: Yang

address: 5841 S. Maryland Avenue

department: Obstetrics and Gynecology

institute: University of Chicago

summary:
Environmental exposure to endocrine-disrupting chemicals (EDCs) is associated with uterine fibroids (UFs) development, the most common benign tumors in women of reproductive age. It has been shown that UFs originate from abnormal myometrial stem cells (MMSCs) and there is evidence that defective DNA repair capacity could be involved in the emergence of mutations with implications for tumorigenesis. Moreover, the multifunctional cytokine TGF-β1 has been related to UF progress and some works revealed its connection with certain DNA damage repair pathways. Eker rats develop spontaneous uterine tumors in adulthood, which makes it a useful model for the study of UFs emergence
The purpose of this study was to evaluate the impact of endocrine-disrupting chemicals (EDCs exposure on TGF-β1 pathway and nucleotide excision repair (NER) capacity, on Eker rat myometrial stem cells (MMSCs).

overall_design: MMSCs were isolated using Stro-1 and CD44 surface markers from 5-months old Eker rats exposed neonatally to Diethylstilbestrol (DES, an EDCs) or vehicle (VEH).  After the in vitro treatment of VEH-MMSCs with TGF-β1 or EDC-MMSCs with TGF-β Receptor I inhibitor, we performed RNA-seq to determine global gene expression profiles and identified altered genes and pathways.

first: Ayman

last: Al-Hendy

first: Maria

last: Bariani

first: Mohamed

last: Ali


title: Establishment of breast cancer PDX RNA-sequencing data library [bulk RNA-seq]

status: Public on Jul 18 2023

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

summary: Breast cancer is the most commonly diagnosed cancer among women. PDXs (patient-derived xenografts) are similar to cancer cell lines but differ in that they are maintained in a physiological setting as soon as they are isolated from the patient and for subsequent passages. These models are valuable for preclinical trials because PDX models have been shown to closely match their patient counterparts, both in genomic profile and response to treatment. Collection of RNA-expression data from multiple PDX models was performed to generate a library of RNA-sequencing data which may be utilized to compare tumors from different subtypes or treatment groups.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ER+ and triple negative mammary tumors were grown orthopedically in mice for 8 weeks. Tumor cells from each PDX were profiled by bulk RNA-sequencing to determine differentially expressed genes and gene signatures between models with the goal of furthering the fields of oncogenesis, metastasis and drug resistance.

first: J

middle: C

last: Harrell

first: Amy

last: Olex

first: Mikhail

last: Dozmorov

first: Julia

last: Altman

first: David

last: Boyd

first: Emily

last: Zboril


title: Single-cell RNA sequencing of CD11b+ Ly6C+ Ly6G- sorted bone marrow cells from radiation control and severe aplastic anemia mice

city: Albany

first: Katherine

last: MacNamara

address: 47 New Scotland Avenue

department: Immunology and Microbial Disease

institute: Albany Medical College

summary: During immune-mediated severe aplastic anemia (SAA) monocytes (CD11b+ Ly6C+ Ly6G-) signficantly increase by both frequency and number within the bone marrow. We isolated BM monocytes from F1 hybrid mice (C57BL/6;Balb/c) induced with SAA via the splenocyte-transfer model. We utilized single-cell RNA sequencing (scRNA-seq) to analyze the heterogenity of BM monocytes during SAA.

overall_design: CD11b+ Ly6C+ LyG- bone marrow (BM) cell were isolated from 3 radiation control and 3 SAA-induced mice by Flouresence-activated cell sorting (FACS). Mice in each group were pooled and then analyzed by scRNA-seq.

first: Grazda

last: Rachel

first: MacNamara

last: Katherine


title: The effect of Bcl-xL overexpression on H3K3me3

status: Public on Aug 04 2023

city: New York

first: Genomics-core-facility

last: WCM

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: To detect H3K4me3 histone modifications globally in HA-Bcl-xL overexpressing BON1 cells, we performed CUT&RUN assays.

overall_design: We used cells overexpressing HA-Bcl-xL (BON1/TGL/HA-Bcl-xL) and the control cells (BON1/TGL/pQ). CUT&RUN was performed from 500,000 cells per condition in triplicates.

first: Tiantian

last: Zhang

first: Adrian

last: Tan

first: Jenny

middle: Z

last: Xiang

first: Yi-Chieh

middle: N

last: Du


title: The role of stromal and immune cells in atrial disease [III]

status: Public on Jul 13 2023

city: Boston

first: I-Hsiu

last: Lee

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Mass General Hospital/Harvard University

summary: In atrial fibrillation, disturbed electrical conduction disrupts the coordinated contraction of the heart’s antechambers, increasing the risk of stroke and heart failure. The rising prevalence of this disease approaches 9% in patients >65 years. Studying freshly isolated human atrial tissue and a new mouse model, we here decipher how immune and stromal cells contribute to the structural tissue remodeling that underlies atrial fibrillation. Single-cell transcriptomes from control and diseased human atria documented macrophage doubling at the expense of endothelial and mural cells. An inflammatory monocyte and a pro-fibrotic SPP1+ macrophage cluster expanded in patients with atrial fibrillation. To experimentally perturb pathways observed in patients, we matched their risk factors Hypertension, Obesity and Mitral valvE Regurgitation (HOMER) in mice. Atrial single-cell transcriptomes obtained in HOMER mice, which developed enlarged, fibrillation-prone atria, recapitulated human cell composition and transcriptome variations. Recruitment drove the expansion of atrial macrophages; accordingly, inhibition of monocyte migration reduced arrhythmia in Ccr2-/- HOMER mice. Deleting Spp1 established macrophage-derived osteopontin as a pleiotropic signal that promotes atrial fibrillation through pro-fibrotic, inflammatory crosstalk with an arsenal of local immune and stromal cells. Taken together, we identify SPP1+ macrophages as targets for immunomodulatory therapy in atrial fibrillation.

overall_design: Single-cell mRNA sequencing was used to investigate the transcriptomic differences between non-cardiomyocytes FACS-purified from left ventricular tissues collected from 4 sham-operated mice and 4 mice exposed to Hypertension, Obesity and Mitral valvE Regurgitation (HOMER).

first: Maarten

last: Hulsmans

first: Maximilian

last: Schloss

first: Kamila

last: Naxerova

first: Matthias

last: Nahrendorf


title: Pregnane X receptor promotes ehtanol-induced hepatosteatosis in female mice

status: Public on Aug 09 2023

city: Seattle

middle: Yue

last: Cui

address: 4225 Roosevelt Way NE Suite #100

department: Occupational and Health Sciences

institute: University of Washington

summary:
The pregane X receptor (PXR), a xenobiotioc-sensing nuclear receptor has been implicated in alcohol-associated liver disease (ALD). The role of PXR signaling in potentiating ethanol (EtOH)-induced hepatotoxicty in male wild-type (WT) mice was reported previously, however, how PXR signaling modulated EtOH-induced hepatotoxicty in female is still unknown.
Several mRNAs that are involved in retinol and steroid hormone biosynthesis, chemical carcinogeneiss, and arachidonic acid metabolism were increased by EtOH in a PXR-dependent manner. Overall, female PXR-null mice are resistant against chronic EtOH-induced hepatotoxicity than their WT counterparts.

overall_design: The female WT and PXR-null mice were fed a 5% EtOH-containing diets or a paired-fed control diets for 8 weeks followed by gene expression (Affymetrix microarray)

first: Sarah

last: Kim

first: Maxwell

last: Gyamfi


title: To investigate the role of CXCL4 in activation of macrophages in vitro and in vivo

first: David

last: Oliver

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

summary: CXCL4 activates myeloid cells and augments endosomal TLR responses contributing to the pathogenesis of inflammatory and fibrotic diseases. However, the underlying mechanisms are not well defined because the receptor(s) that mediates CXCL4 inflammatory responses is not known and downstream signaling pathways leading to gene induction are not well characterized. Here we report that CXCL4 activates inflammatory and tissue repair/fibrotic gene expression in human primary macrophages ex vivo and regulates macrophage skin infiltration and promotes skin wound healing in vivo.

overall_design: In vitro experiment, human CD14+ monocytes were harvested from PBMCs and cultured with 20 ng/ml M-CSF overnight. The cells were then stimulated with 10 ug/ml CXCL4 for 1 h and 3 h. The cells were then harvested for RNA-seq. In vivo experiment, skin wound from WT littermates and Cxcl4-/- mice were harvested. Two to three wounds in each genotype were pooled together and digested. Then macrophages in the cell suspension were sorted based on Ly6C and F4/80 expression. The sorted cells were used for RNA-seq to investigate how CXCL4 affect macrophage activation in vivo.

first: Chao

last: Yang

first: Ruoxi

last: Yuan

first: Max

last: Chao

first: Franck

last: Barrat

first: Lionel

last: Ivashkiv


title: Expression of piRNAs and miRNAs in embryonic mouse ovary cells: dysregulation and apoptosis by exposure to Vinclozolin and MEHP

status: Public on Jul 17 2023

city: Madrid

first: Odei

last: Barreñada

address: C/ Ramiro de Maeztu 9

country: Spain

institute: CIB Margarita Salas - CSIC

summary: The early stages of embryonic development are critical for the proper formation of primordial germ cells. This process is tightly regulated by different cellular signals. Among others, small non-coding RNAs (sncRNAs) are involved in the regulation of these signals to carry out the embryonic development of germ cell linage. We analyzed the expression profiles of piRNAs and miRNAs after maternal exposure of embryos, during the first 13.5 days post-coitum, to two different endocrine disruptors (EDs) chemicals: vinclozolin and the main metabolite of phthalates (MEHP), in three successive generations after exposure only in the first generation. Our results indicate clear alterations in the expression of both piRNAs and miRNAs (including mitochondrial-related), concomitant with an increase in apoptotic cells in the female early folliculogenesis during this stage of development. However, the most drastic changes occur when the effect is generated by the exposure through both paternal and maternal pathways, rather than exclusively through the maternal exposure. Based on these findings, we hypothesize the existence of an "ovarian filtering" mechanism triggered by disruptor exposure and mediated by apoptotic mechanisms regulated by sncRNAs. This system, present only in the female germ cell lineage, could render a decrease in the follicle reserve in the adult life and would function as a defense mechanism to prevent the transmission of deleterious effects to subsequent generations.

overall_design: Briefly, a first generation of mice has been crossed, which are considered generation F0. When a successful mating is detected, they are randomly assigned to Control, VZN or MEHP group. From this moment on, they are exposed during the first 13.5 days of gestation to the endocrine disruptor or control. One part of these pregnant female mice was sacrificed at 13.5 dpc to obtain the fetal ovaries by dissection and differentiation of the sexes by gonadal morphology evident at this date of development, the other part of pregnant female mice was withdrawn from exposure to ED and allowed to finish gestation and birth, to analyze the effects of exposure to ED in the following generations, obtaining embryonic ovaries also at 13.5 dpc in each subsequent generation. This process was repeated two more generations to study both the F1 generation (directly exposed during their embryonic period to DEs) and the F2 and F3 (both indirectly exposed to DEs, since only their first- and second-degree female progenitors, respectively, have been exposed). Furthermore, an additional group was made ("-Sy" group or "paternal effect -PA- group")  evaluating the additive effect of the both progenitros (exposed to the same DE and dose).

first: Miguel

last: Brieño-Enriquez

first: Jesús

last: del Mazo


title: Evaluation of breast cancer PDX tumor heterogeneity

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

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


title: Dissociation Protocols used for Sarcoma Tissues Bias the Transcriptome observed in Single-cell and Single-nucleus RNA sequencing.

status: Public on Jul 21 2023

city: Houston

first: Danh

last: Truong

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

summary: To determine whether sarcomas – tumors of mesenchymal origin – are subject to the same technical artifacts, we profiled patient-derived tumor explants (PDXs) propagated from three aggressive subtypes: osteosarcoma, Ewing sarcoma (ES), desmoplastic small round cell tumor (DSRCT). Given the rarity of these sarcoma subtypes, we explored whether single-nuclei RNA-seq from more widely available archival frozen specimens could accurately be identified by gene expression signatures linked to tissue phenotype or pathognomonic fusion proteins.

overall_design: In this work, we studied sarcomas from varying tissue origins, including osteosarcoma (OS), Ewing’s sarcoma (ES), and desmoplastic small round cell tumor (DSRCT). We used different dissociation protocols: Miltenyi Tumor Dissociation Kit, cold-active protease derived from Bacillus licheniformis, and Nuclei EZ Prep. These three protocols are described herein as Warm, Cold, and Nuclei protocols. For the OS specimens, we used the same Nuclei protocol and a different Warm protocol optimized for OS. For DSRCT and ES specimens, we performed the additional Cold protocol, using the cold-active protease, as we had more specimens available. Each sarcoma subtype included three PDX specimens derived from different patients. In total, we analyzed 125,831 whole-cells and nuclei across the three sarcoma subtypes and three dissociation protocols.

first: Vidya

last: Gopalakrishnan

first: Nancy

last: Gordon

first: Najat

last: Daw

first: Joseph

last: Ludwig


title: The role of stromal and immune cells in atrial disease [II]

first: I-Hsiu

last: Lee

overall_design: Single-cell mRNA sequencing was used to investigate the transcriptomic differences between non-cardiomyocytes FACS-purified from left atrial tissues collected from 2 C57BL/6 bone marrow transplanted (BMT) and 2 Spp1-/- BMT mice exposed to Hypertension, Obesity and Mitral valvE Regurgitation (HOMER).

first: Maarten

last: Hulsmans

first: Maximilian

last: Schloss

first: Kamila

last: Naxerova

first: Matthias

last: Nahrendorf


title: Transient naive reprogramming corrects hiPS cells functionally and epigenetically [WGBS 2]

first: Ryan

last: Lister

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

overall_design: Examination of genome-wide DNA methylation in human embryonic stem cells and different classes of induced pluripotent stem cells

first: Sam

last: Buckberry

first: Xiaodong

last: Liu

first: Daniel

last: Poppe

first: Jia

last: Tan

first: Jose

middle: M

last: Polo


title: The role of stromal and immune cells in atrial disease [I]

overall_design:
Single-cell mRNA sequencing was used to investigate the transcriptomic differences between non-cardiomyocytes FACS-purified from left atrial tissues collected from 7 patients with persistent atrial fibrillation undergoing surgical mitral valve repair and from 5 control subjects. We also present single-cell transcriptomic data on FACS-purified, left atrial non-cardiomyocytes from 4 sham-operated mice and 4 mice exposed to Hypertension, Obesity and Mitral valvE Regurgitation (HOMER).

**Submitter declares that raw data have not been provided for the human samples due to privacy concerns**

first: I

middle: H

first: George

last: Tolis

first: Serguei

last: Melnitchouk


title: Sex-specific transcriptome of Anopheles gambiae during embryonic development

status: Public on Jul 25 2023

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

institute: Institute of Molecular Biology (IMB)

summary: In many species, males and females display differences in their physiology that are not limited to the gonads. Sex differences in adult insects can comprise body size and feeding behaviour, as only female, but not male mosquitoes are blood-feeding in order to produce eggs. This is relevant since the malaria-causing parasite Plasmodium is transmitted by a female mosquito through a previous blood meal from an infected individual. The initiation of sex-specific developmental programs can be often linked to heteromorphic sex chromosomes (XX/XY in Anopheles). In males, the X-linked genes are only present in a single copy. To counteract this hemizygosity, Anopheles, like other species, exhibits dosage compensation (DC). Anopheles DC manifests by upregulation of the single male X ensuring the equal expression of sex-chromosomal genes between males and females. To date, the sex-specific differences at the transcriptome level related to the X/Y chromosomes and DC have been characterized at post-embryonic stages. Their onset during embryogenesis, especially during the early stages where the embryo switches from the maternal to the zygotic transcriptome, is largely uncharacterized to date. Here, we generate a sex-specific transcriptome atlas across Anopheles embryogenesis ending at the first larval stage. Along with the transition from the maternal to the zygotic transcriptome, many transcripts switch isoform, where the 3’ untranslated regions (UTR) of zygotic transcripts are significantly extended compared to their maternal counterpart. We also identify stage- and sex-specific splicing events. Comparing male and female embryos, we identify 120 sexually dimorphic protein coding genes and non-coding RNAs, indicating that sexually dimorphic gene expression is not widespread during embryogenesis. Furthermore, the imbalance of X-linked genes between males and females after zygotic genome activation is corrected shortly after, where the majority of genes exhibit DC around 9 hours of embryogenesis with further fine-tuning later in development. Our atlas provides a framework to explore sex differences in development and evolution and thereby, enables future functional analyses of sex-specific expression patterns and isoform usage.

overall_design: Poly(A) stranded mRNA sequencing of single embryos of predetermined sex (males and females) collected at different time points of embryonic development and upon the completion of embryonic development (L1 larvae). Biological replicates are included.

first: Agata

middle: I

last: Kalita

first: Eric

last: Marois

first: Claudia

last: Keller Valsecchi


title: The role of stromal and immune cells in atrial disease

first: I-Hsiu

last: Lee

overall_design: Refer to individual Series


title: Single nuclei RNAseq of male rat area postrema and nucleus tractus solitarius after cisplatin treatment

status: Public on Jul 12 2023

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

state: PA

address: 125 S 31st St

institute: University of Pennsylvania

summary: We performed single-nuclei RNAseq of Sprague Dawley rat area postrema and nucleus tractus solitarius brain samples from animals treated with cisplatin to identify cellular subtype specific changes in the neural transcriptome.

overall_design: We performed the 10x Genomics 3' gene expression assay (v3.1) on nuclei isolated from frozen Sprague Dawley rat area postrema and nucleus tractus solitarius combined brain punches. At the onset of the dark cycle, rats (~400 g) were injected with cisplatin (6mg/kg, n=4) (i.p.). After six hours, rats were deeply anesthetized with a triple cocktail of ketamine, xylazine and acepromazine (180 mg/kg, 5.4 mg/kg and 1.28 mg/kg, respectively; i.p.) in the middle of the dark phase. Brains were removed and snap-frozen in dry ice-cold hexane. Three adjacent micro-punch samples (each ~1 cubic mm) containing the AP and left and right NTS were collected from coronally-prepared brains on a cryostat, pooled together, and stored at -80°C until further processing. Nuclei were isolated by differential centrifugation and microfluidically captured using the 10x Genomics Chromium controller. Sequencing libraries were constructed and sequenced on an Illumina NovaSeq 6000.

first: Richard

last: Crist

first: Matthew

last: Hayes

first: Bart

last: De Jonghe

first: Tito

last: Borner