title: Single-cell RNASeq analysis of human retinal organoids generated from hiPSC derived of a healthy donor patient

status: Public on Sep 01 2022

city: Bonn

first: Lisa

middle: Maria

last: Steinheuer

state: NRW

address: Venusberg Campus 1

department: Institute of Experimental Oncology

institute: University Hospital Bonn

summary:
Results: Our histologic studies indicated that human retinal organoids (HROs) at day 200 of differentiation in this system are postmitotic and thus completed retinogenesis. Further, HRO contain all major retinal cell types in a laminated structure. Notably, HROs are cone photoreceptor-rich, show a 1:1:1 ratio of Müller glia, rod and cone photoreceptor. Immunostaining and ultrastructural studies showed that photoreceptors neurons mature, including photoreceptor inner and nascent outer segment formation. Our transcriptome analysis at the single cell level supports these findings. Further, comparison with published datasets (Voigt et al. 2019 [PMID: 31075224]) indicate that the genotype of cone photoreceptors in this HRO system correlates more strongly with the foveal cones of the human primary retina than peripheral cones. Müller glia show a trend towards human fovea whereas rod photoreceptors were found to be nearly similar.
Conclusions: Single cell transcriptome analysis of HROs support and extend our findings at the histological level, indicating that HROs are cone photoreceptor-rich, and provide some characteristics of the human macula.

overall_design: Dissociated cells (n = 6665) of one human retinal organoid.

first: Manuela

last: Völkner

middle: M

first: Madalena

last: Carido

first: Sebastian

last: Canzler

first: Jörg

last: Hackermüller

first: Mike

last: Karl


title: Hi-C sequencing analysis of wild-type and nm1-knockout mouse embryonic fibroblasts

status: Public on Aug 25 2022

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: Hi-C sequencing of wild-type and nm1-knockout mouse embryonic fibroblasts to investigate the impact of nm1 loss on genome architecture

overall_design: Hi-C sequencing was performed for 6 samples (2 different cell types with three biological replicates each)

first: Tomas

last: Venit

first: Syed

middle: R

last: Mahmood


title: Single-cell analysis of bovine muscle-derived cell types for cultured meat production

status: Public on Sep 02 2022

city: Maastricht

first: Tobias

last: Messmer

address: Watermolen 28

department: Cell Biology

country: Netherlands

institute: Mosa Meat

type: Expression profiling by high throughput sequencing

summary: Cultured' or 'cultivated' meat technologies leverage the proliferation and differentiation of animal-derived stem cells ex vivo to produce edible tissues for human consumption in a sustainable fashion. However, skeletal muscle is a dynamic and highly complex tissue, involving the interplay of numerous mono- and multinucleated cell types, including muscle fibres, satellite cells (SCs) and fibro-adipogenic progenitors (FAPs), and accurate recreation of the entire tissue thus requires the identification, purification, proliferation and characterisation of a broad range of cell types. Here, we use a single-cell RNA sequencing approach to characterise transcriptional heterogeneity within bovine muscle and derived in vitro cultures over time. Using this data, we identify numerous distinct cell types, and develop robust protocols for the easy purification and proliferation of several of these populations. We note overgrowth of undesirable cell types within heterogeneous proliferative cultures as a barrier to efficient cultured meat production, and use transcriptomics to identify conditions that favour the growth of SCs in the context of serum-free medium. Combining RNA velocities computed in silico with functional data, we characterise dynamic subpopulations and transitions between active, quiescent and committed substates of SCs, and demonstrate methods for modulation of these states during long-term proliferative cultures. This work represents an important resource for advancing our knowledge of bovine skeletal muscle biology, and its application in the development of cultured meat technologies.

overall_design:
Five timepoints throughout long-term in vitro culture were selected for single-cell RNA sequencing (scRNA-seq), for each of which cells from all genotypes (donor animals) were pooled in equal ratios and washed with 1% BSA in PBS prior to injection. Timepoints 1 to 5 corresponded to unsorted cells directly after isolation (‘Muscle’) and after 72 h (‘passage 0’), and to cultured cells (unsorted cells (genotypes 1, 2, 9), SCs (genotypes 5, 6, 10) and FAPs (genotypes 4, 7, 8) at passages 2, 5, and 8 respectively.
Please note that processed data files generated from both run 1 and run2 are linked to the corresponding* run1 sample records.

first: Richard

middle: G

last: Dohmen

first: Lieke

last: Schaeken

first: Lea

last: Melzener

first: Rui

last: Hueber

first: Mary

last: Godec

first: Mark

middle: J

last: Post

first: Joshua

middle: E

last: Flack


title: ATAC-Seq analysis of wild-type and nm1-knockout mouse embryonic fibroblasts

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ATAC-Seq of wild-type and nm1-knockout mouse embryonic fibroblasts to investigate the impact of nm1 loss on chromatin accessibility

overall_design: ATAC sequencing was performed for 6 samples (2 different cell types with three biological replicates each)


title: Transcriptome Profiling Reveals Differential Expression of Circadian Behavior Genes in Peripheral Blood of Monozygotic Twins Discordant for Parkinson's Disease

status: Public on Aug 22 2022

city: Moscow

first: Ivan

middle: Nikolaevitch

last: Vlasov

address: Akademika Kurchatova square, 2

country: Russia

institute: National Research Center «Kurchatov Institute»

summary: This submission contains a result of a study of transcriptiomic profiles of blood, derived from Parkinson’s disease dicrodant twins

overall_design: Examination of transcriptiomic profiles of the blood, derived from Parkinson’s disease dicordant twins. Twins without PD were used as controls. Adjustments were made in the model to account for differences between twin pairs.

first: Ekaterina

middle: I

last: Semenova

middle: N

first: Suzanna

middle: A

last: Partevian

first: Anna

middle: V

last: Rosinskaya

last: Rybolovlev

first: Petr

last: Slominsky

first: Maria

last: Shadrina

first: Anelya

middle: K

last: Alieva


title: ChIP-Seq in Wild Type (WT),  and NM1-knockout (KO) Mouse Embryonic Fibroblasts

first: Piergiorgio

last: Percipalle

summary: Genome-wide ChIP-Seq of various epigenetic marks in WT and NM1-KO MEFs

overall_design: ChIP-Seq was performed for 2 replicates of WT and KO samples for each epigenetic mark

last: Raza Mahmood

first: Nadine

last: Hosny El Said

first: Tomas

last: Venit


title: Wild-type and nm1-knockout mouse embryonic fibroblasts

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

overall_design: Refer to individual Series


title: Expression analysis of RPE1-TP53KO cells with ESCO2mut, DDX11KO and PAXIP1KO

status: Public on Aug 19 2022

city: Amsterdam

first: Job

last: de Lange

address: Boelelaan 1117

department: Human Genetics

institute: Amsterdam UMC location Vrije Universiteit

summary: Identification of  the differential transcriptomic features of isogenic RPE1 cells via whole genome mRNA sequecing

overall_design: Differential expresison profiling of RPE1-TP53KO, RPE1-TP53KO-ESCO2mut, RPE1-TP53KO-DDX11KO and RPE1-TP53KO-PAXIP1KO cells

first: Janne

last: van Schie

first: Klaas

last: de Lint

first: Khashayar

last: Roohollahi


title: Effect of Bro40 and Bro40mut on gene expression of wild type H1299 non-small cell lung cancer cell line

status: Public on Aug 28 2022

city: Taipei

first: Nai Yang

last: Yeat

address: 128, Academia Road Sec. 2, Nankang

country: Taiwan

institute: Academia Sinica

summary: We previously discovered WDR4 as a Cullin 4 ubiquitin ligase substrate adaptor, which associates with poor cancer prognosis. With the help of ubiquitylome analysis, we uncovered PTPN23 as a substrate of WDR4. While PTPN23 is a component of ESCRT complex that facilitates EGFR lysosomal trafficking and degradation, the high expression of WDR4 and low expression of PTPN23 in patient sample suggesting that WDR4-mediated PTPN23 ubiquitination might contribute to PTPN23 proteasomal degradation and lead to poor patient survival rate. To prevent PTPN23 from WDR4-mediated ubiquitination, we used fine mapping to figure out the binding site of these two proteins and identified a 40-amino acid region on PTPN23 (Bro1 domain) can bind with WDR4, we named this 40-amino acid region as Bro40. Structural docking of WDR4 and Bro1 showed that the N-term of Bro40 is the favorable contact site. Thus, 6 amino acids at the N-term of Bro40 were mutated into alanine, so called Bro40mut. Bro40 and Bro40mut were fused on a GFP-tag plasmid for functional test and animal experiment. The tumor suppressing function of Bro40 was confirm by migration/invasion assays and animal model. To understand how Bro40 regulates cancer progression at RNA level, we transfected Bro40 and Bro40mut into H1299 cells followed by RNA sequencing.

overall_design: H1299 cells were transfected with Bro40 and Bro40mut for 24 hours, respectively. Comparative gene expression profiling analysis of high throughput RNA-seq data was obtained from 3 independent biological repeats. Bro40mut was set as control.

first: Nai-Yang

first: Ruey-Hwa

last: Chen


title: Effect of depletion or overexpression of CaSR on gene expression in BM-derived Lineage negative AML cells

status: Public on Aug 03 2022

city: Mainz

first: Pablo

last: Llavona

state: Rhineland-Palatinate

address: Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4

country: Germany

institute: IMB

summary: To investigate the effects of CaSR depletion or overexpression on gene expression in primary AML cells, we compared the gene expression profile of sorted lineage negative cells from the bone marrow of normal wildtype, CaSR knockout or CaSR overexpression mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for lineage negative cells isolated from the bone marrow of normal wildtype C57/BL6 mice (5 replicates), CaSR KO C57/BL6 mice (4 replicates) and CaSR OE C57/BL6 mice (4 replicates).

first: Raquel

middle: S

last: Pereira

first: Alessia

last: Cais

first: Rahul

last: Kumar

first: Lara

last: Paulini

first: Parimala

last: Godavarthy

first: Eric

last: Kowarz

first: Costanza

last: Zanetti

first: Fabian

last: Hoeller

first: Tabea

last: Stark

first: Georg

last: Tascher

first: Eshwar

last: Meduri

first: Christian

last: Münch

first: Francesco

last: Pampaloni

first: Rolf

last: Marschalek

first: Daniela

last: Krause


title: A compound directed against S6K1 hampers fat mass expansion and mitigates diet-induced hepatosteatosis

status: Public on Aug 01 2022

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

summary: Imbalanced mTORC1-S6K1 engages signalling cascades related to obesity and fatty liver. Here, we set up to assess the therapeutic blockage of the ribosomal protein S6 kinase 1 (S6K1) in diet-induced obese (DIO) mice challenged with LY2584702 (LY) tosylate, a specific oral S6K1 inhibitor initially developed for the treatment of solid tumours. To characterize the ability of LY in counteracting obesity and diet-induced disturbances, DIO male mice were challenged every 12 h by oral gavage with LY in treatments lasting 12 and 4 weeks. We show that diminished S6K1 activity in mice treated with LY hampers fat mass expansion and ameliorates dyslipidaemia and hepatic steatosis, while modifying transcriptome-wide gene expression programs relevant for adipose and liver performance. Accordingly, impaired mTORC1 signalling in fat (decreased) and liver (increased) co-segregated with defective epithelial-mesenchymal transition, being prominent a decreased expression of Cd36 (coding for a fatty acid translocase) and Lgals1 (Galectin 1) in both tissues. All these factors combined align with reduced adipocyte size and improved lipidomic signatures, while hypertriglyceridemia and hepatic steatosis were improved in treatments of 12 and 4 weeks. This study provides new insights into the therapeutic intervention of S6K1 signalling, and opens a promising avenue for prevalent metabolic diseases.

overall_design: Twelve (n=12) samples were analysed: liver (LIV, n=6) and subcutaneous adipose tissue (SAT, n=6) from HFD and HFD+LY male mice (1:1)

first: Francisco

last: Ortega

first: Sara

middle: C

last: Kozma


title: Ethanol exposure reveals persistent and categorizable astrocyte calcium response types and associated gene signatures

status: Public on Jul 27 2022

city: Philadelphia

first: Jai-Yoon

last: Sul

address: 89 John Morgan

country: USA

institute: University of Pennsylvania

summary: Various EtOH doses increased intracellular calcium in a subset of astrocytes, identifying three cellular response types categorized by response waveform properties S- (sustained), T- (transient), or M- (Mixed), along with non-responsive (NR) astrocytes. By single-cell RNA-seq analysis of astrocytes from the different response types, we report type-enriched discriminatory gene expression signatures and provide a basis for identifying the relationship between susceptibility to EtOH effects in the astrocyte subgroups and corresponding measurable markers of calcium signal and gene expression.

overall_design: Single-cell RNA-seq for primarily cultured astrocytes from cortex of single C57BL/6 mouse pups. In total, there are 22 cells including 5 No Response (NR), 6 S-type, 6 T-type and 5 M-type astrocytes.

first: Hyun-Bum

last: Kim

first: Youtao

last: Lu

first: Seonkyung

last: Oh

first: Jacqueline

last: Morris

first: Kevin

last: Miyashiro

first: Junhyong

first: James

last: Eberwine


title: In vitro transcriptomic analyses reveal pathway perturbations, estrogenic activities, and potencies of data-poor BPA alternative chemicals

status: Public on Aug 18 2022

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

summary: Since initial regulatory action in 2010 in Canada, bisphenol A (BPA) has been progressively replaced by structurally related alternative chemicals. Unfortunately, many of these chemicals are data-poor, limiting toxicological risk assessment. We used high-throughput transcriptomics to evaluate potential hazards and compare potencies of BPA and 15 BPA alternative chemicals in cultured breast cancer cells. MCF-7 cells were exposed to BPA and 15 alternative chemicals (0.0005 – 100 µM) for 48 hrs. TempO-Seq sequencing (BioSpyder Inc.) was used to examine general toxicological effects and estrogen receptor alpha (ERα)-associated transcriptional changes. Benchmark concentration (BMC) analysis was conducted to identify two global transcriptomic points of departure (tPODs): (a) the lowest pathway median gene BMC and (b) the 25th lowest rank-ordered gene BMC. ERα activation was evaluated using a published transcriptomic biomarker and an ERα-specific tPOD was derived. Genes fitting BMC models were subjected to upstream regulator and canonical pathway analysis in Ingenuity Pathway Analysis. Biomarker analysis identified BPA and eight alternative chemicals as ERα active. Global and ERα tPODs produced highly similar potency rankings with BPAF as the most potent chemical tested, followed by BPA, BPC, 4,4’-BPF, BPAP, BPS, BADGE, 2,4’-BPF, Pergafast201®, D-8, 2,4’-BPS, TGSA, and BPS-MAE. Further, BPA and transcriptionally active alternative chemicals enriched similar gene sets associated with increased cell division and cancer-related processes. These data provide support for future read-across applications of transcriptomic profiling for risk assessment of data-poor chemicals and suggest that several BPA alternative chemicals may cause hazards at similar concentrations to BPA.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: A total of 768 samples were sequenced for this toxicogenomics study on 16 bisphenol or bisphenol alternative chemicals, including technical controls (reference RNA; media only; cells with no treatment). The solvent controls were comprised of 0.1% DMSO. 10 concentrations of each bisphenol chemical were tested in quaduplicate, with a blocking design to avoid confounding across batches. Two reference chemicals, estradiol and dexamethasone, were also included in this study.

first: Geronimo

last: Matteo

first: Karen

last: Leingartner

first: Andrea

last: Rowan-Carroll

first: Andrew

last: Williams

first: Marc

last: Beal

last: Gagné

first: Reza

last: Farmahin

first: Shamika

last: Wickramasuriya

first: Anthony

last: Reardon

first: Tara

last: Barton-Maclaren

first: Chris

last: Corton

first: Carole

middle: L

last: Yauk

first: Ella

last: Atlas


title: Fate-resolved gene regulatory signatures of individual B lymphocytes in the early stages of Epstein-Barr Virus infection

status: Public on Aug 24 2022

city: Durham

first: Elliott

middle: Daniel

last: SoRelle

state: NC

address: 130 Research Drive (CARL Building)

department: Molecular Genetics & Microbiology

institute: Duke University

summary: Enriched human B lymphocyte sample were collected at key timepoints before and after infection with Epstein-Barr Virus (EBV) and analyzed to evaluate cellular heterogeneity with respect to gene expression and chromatin accessibility using single-cell multiomics library construction, sequencing, and analysis. These data were used to construct a multi-state model of post-infection dynamics and distinct B cell fate trajectories that arise from different cellular responses induced by EBV. These responses include antiviral interferon response induction, DNA damage responses and growth arrest, oncogene-induced senescence, B cell activation, and activation-induced differentiation into plasmablasts.

overall_design: Primary B cells were enriched from PBMCs from two donors

middle: D

first: Nicolas

last: Reinoso-Vizcaino

first: Ashley

middle: P

last: Barry

first: Cliburn

last: Chan

first: Micah

last: Luftig


title: Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq

status: Public on Jul 26 2022

city: San Francisco

first: Sara

last: Sunshine

address: 1700 4th Street

institute: University of California, San Francisco

summary: Numerous host factors of SARS-CoV-2 have been identified by screening approaches, but delineating their molecular roles during infection and whether they can be targeted for antiviral intervention remains a challenge. Here we use Perturb-seq, a single-cell CRISPR screening approach, to investigate how CRISPR interference of host factors changes the course of SARS-CoV-2 infection and the host response in human lung epithelial cells. Our data reveal two classes of host factors with pronounced phenotypes: factors required for the response to interferon, and factors required for entry or early infection, respectively. Among the latter, we have characterized the NF-κB inhibitor IκBα (NFKBIA), as well as the translation factors EIF4E2 and EIF4H as strong host dependency factors acting early in infection. Overall, our study provides high-throughput functional validation of host factors of SARS-CoV-2 and their roles during viral infection in both infected and uninfected bystander cells.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: We inactivated host factors in Calu-3 cells by CRISPR interference(CRISPRi), infected with an isolate of SARS-CoV-2, and performed single-cell RNA sequencing 24 hours after infection.

first: Jonathan

last: Weissman

first: Joseph

last: DeRisi

first: Marco

middle: Y

last: Hein


title: A single-cell transcriptomic inventory of murine smooth muscle cells

status: Public on Sep 26 2022

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet


title: DIS3L2 clears terminal-uridylated RNA to ensure oocyte maturation and female fertility

status: Public on Jul 22 2022

city: Ashburn

first: Di

last: Wu

state: Virginia

address: 19700 Helix Drive

institute: HHMI Janelia

summary: During mammalian oocyte development, transcriptome undergoes accumulation in the oocyte growth phase and elimination in the oocyte maturation phase. At the transition point between growth and maturation, which is the germinal vesicle intact oocyte (GV), terminal uridylation labels RNA for degradation. In our study, we show that a small cohort of RNA are polyadenylated after tail uridylation (defined as uridylated-poly(A) RNA). Upon genetic depletion of DIS3L2 (Dis3l2cKO) in mouse oocytes, uridylated-poly(A) RNA is extensively stabilized and dominates the oocyte transcriptome, which results in increased transcriptome in Dis3l2cKO oocytes. Consequently, Dis3l2cKO female mice are infertile and almost all oocytes are arrested at the GV stage. Uridylated-poly(A) RNA generally has shorter poly(A) tails and lower translation activity. The uridylated-poly(A) RNA in Dis3l2cKO oocytes not only generates from the insufficient RNA degradation, but also comes from the tail dynamics of RNA. Our study demonstrates more possibilities of RNA fates after being terminally uridylated, and highlights the role of DIS3L2 in safeguarding the transcriptome by degrading uridylated-poly(A) RNA.

overall_design: We performed transcriptome profiling using single oocyte RNA-seq (polyA RNA and total RNA) and single oocyte PAIso-seq. The single oocyte RNA-seq is done at GV and MII stages and the PAIso-seq is done at the GV stage.

first: Monique

last: Pedroza

last: Chang

first: Jurrien

last: Dean


title: Functional dissection of human cardiac enhancers and non-coding de novo variants in congenital heart disease

status: Public on Aug 05 2022

city: Boston

first: Seong Won

last: Kim

state: MA

address: 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: About 45% of congenital heart disease (CHD) is caused by rare gene mutations. Non-coding mutations that perturb cis-regulatory elements (CREs) likely contribute to CHD among the remaining cases without clear etiology. However, identifying CHD-causing non-coding variants has been problematic. We combined human induced pluripotent stem cell-derived cardiomyocyte (iPSC-CM) differentiation and a lentivirus-mediated massively parallel reporter assay (lentiMPRA) to create a high-throughput platform to measure human cardiac enhancer activity. We tested 2451 candidate human cardiac enhancers, identified 1185 with measurable activity, and functionally dissected 123 of these by systematic tiling mutagenesis. We functionally evaluated 6761 non-coding de novo variants (ncDNVs) prioritized from the whole genome sequencing (WGS) of 749 CHD trios. 397 ncDNVs significantly affected cardiac CRE activity. Remarkably, 53% of these ncDNVs increased enhancer activity, often at regions with undetectable enhancer activity in the reference sequence. We introduced 10 of these DNVs associated with CHD genes into iPSCs and found that 4 altered expression of neighboring genes. Moreover, these 4 DNVs also altered cardiomyocyte differentiation, as assessed by single nucleus RNA sequencing. Using the MPRA data, we developed a regression model to prioritize future DNVs for functional testing and demonstrate that this model finds enrichment of DNVs in a second, independent WGS cohort. Taken together, we developed a scalable system to measure the impact of non-coding DNVs on CRE activity and deployed this platform to systematically assess the contribution of non-coding DNVs to CHD.

overall_design: Control and the mutant hiPSC cells were differentiated into cardiomyocytes and frozen. Frozen cell pellets were individually barcoded with the CellPlex Kit from 10X Genomics. Nuclei from the barcoded cells were extracted and then pooled at equal amount. Single Nuclei RNAsequencing library was generated using 10X Genomics platform. Nuclei were demulitplexed using reads mapping to the barcodes.

first: Feng

last: Xiao

first: Xiaoran

last: Zhang

first: Sarah

last: Morton

first: Joshua

middle: M

last: Gorham

first: Christine

last: Seidman

first: William

middle: T

last: Pu


title: Inflammatory exposure drives permanent impairment of hematopoietic stem cell self-renewal activity and accelerated aging.

status: Public on Jul 19 2022

city: Heidelberg

first: Sina

last: Stäble

address: Im Neuenheimer Feld 280

department: Translational Cancer Epigenomics

institute: German Cancer Research Center (DKFZ)

summary: Hematopoietic stem cells (HSCs) mediate regeneration of the hematopoietic system following injury, as exemplified by the transient activation of HSCs out of dormancy upon exposure to infection or inflammation. Such challenges have been documented to impair HSC function. However, whether this functional impairment extends beyond the duration of inflammatory exposure is unknown. To assess the effects of repeated inflammatory challenge, wild-type C57BL/6J mice were subjected to a dose escalation regimen of polyinosinic:polycytidylic acid (pI:pC) treatment mimicking viral infection. Unexpectedly, we observed an irreversible depletion of functional HSCs and hallmarks of accelerated aging in LT-HSCs.

overall_design: Single cell RNA sequencing of purified LT-HSCs [Lin(-) c-kit(+) sca-1(+) CD150(+) CD48(-) CD34(-)] isolated from the bone marrow of individual C57BL/6J mice treated with PBS or pI:pC  (after 5 or 20 weeks recovery period). Single LT-HSC cells were subsequently captured on a small sized IFC using the Fluidigm C1 system.

first: Ruzhica

last: Bogeska

first: Florian

last: Buettner

first: Felix

last: Frauhammer

first: Michael

last: Milsom


status: Public on Jul 04 2022

city: Hangzhou

first: Xiaochun

last: Yu

state: Zhejiang

address: 18 Shilongshan Street

country: China

institute: Westlake University

summary: We report the BRCA1/BARD1 complex associated RNA in HEK293T cells using RNA-seq following PAR-Clip.

overall_design: Examination of BRCA1/BARD1 complex associated RNA in HEK293T cells

first: Duo

first: Qilin

last: Li

first: Huang

last: Huang


title: The Sub-ventricular Zone in Mild Traumatic Brain Injury at Single-cell Resolution

status: Public on Jun 28 2022

city: Chengdu

first: Weibo

last: Liang

address: Renmin South Road

institute: Sichuan University

summary: The subventricular zone (SVZ) is a neurogenetic niche that contributes to homeostasis and repair after brain injury. However, effects of mild traumatic brain injury (mTBI) on genomewide gene expression in the SVZ remain largely unexplored. To address this issue, we investigated the single-nucleus transcriptomic profiles of the SVZ after mTBI. 18 distinct clusters were yielded via unsupervised clustering of the transcriptomic profiles. Cell type specific gene expression responding to mTBI were revealed, some of which were closely associated with pathogenesis post-injury. Furthermore, the diverse cell to cell interaction networks uncovered an array of cellular processes under mTBI. Also, we reported novel lineage trajectories and molecular hallmarks that govern the neurogenesis. Our gene expression atlas provides extensive resources for future researches regarding mTBI induced pathogenesis, its therapeutic interventions or diagnostic tests.

overall_design: SVZ mRNA profiles of 8~10-week old mTBI and Sham mice were generated by  scRNA-Seq.

first: Xiameng

last: Chen

first: Manrui


title: Long and short-read transcriptome profiling of human lung cancer cell lines

status: Public on Jul 20 2022

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary:
Purpose: The aim of this study is to compare different long-read sequencing platforms using reference lung adenocarcinoma cell lines and spike-in controls.
Methods - Cell Culture: Lung adenocarcinoma cell lines NCI-H1975 and HCC827 from a range of passages (2-4) were grown on 3 separate occasions in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum and 1% penicillin-streptomycin.
Methods - RNA preparation: mRNA was extracted using a Qiagen RNA miniprep kit and purified using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490).
Purified mRNA spiked with sequins was used for Next Generation Sequencing library preparation using the NEBNext Ultra II Directional RNA Library Prep Kit (Illumina) and the cRNA-PCR Barcoding (SQK-PCS109 with SQK-PBK004) kit (ONT). Completed libraries were sequenced on NextSeq 500 (Illumina) and PromethION (ONT). Iso-Seq libraries were prepared and sequenced by Novogene on Sequel II (PacBio). Reads were mapped to known genomic features of the GRCH38 reference genome and RNA sequin decoy chromosome combined sequences at the gene-level and single reads were then summarized into gene-level counts using featureCounts software (Liao et al. 2014).

overall_design: Total RNA was extracted from lung adenocarcinoma cell lines NCI-H1975 and HCC827 (3 independent samples for each cell line). Both mRNA and Total RNA transcriptomes from these samples were profiled by RNA-Seq (Illumina NextSeq 500, Oxford Nanopore Technologies PromethION and PacBio Sequel II)

first: Luyi

last: Tian

first: Quentin

last: Gouil

first: Mei

middle: R

last: Du


title: Single-nucleus profiling of adult mice subventricular zone after blast-TBI

summary: To elucidate molecular features of the cells of Sub-ventricular Zone (SVZ), their progeny at each differentiation stage, and surrounding cells in SVZ under blast wave-induced changes, cells were profiled from matched SVZ of 3 mice that had received blast injury and 3 controls（The controls sequencing profile can be assessed in GEO at GSM5938054）.Cell type specific gene expression responding to (blast-related traumatic brain injury, bTBI) were revealed, some of which were closely associated with pathogenesis post-injury. Furthermore, the diverse cell to cell interaction networks uncovered an array of cellular processes under bTBI.  Our gene expression atlas provides extensive resources for future researches regarding bTBI induced pathogenesis, its therapeutic interventions or diagnostic tests.

overall_design: SVZ mRNA profiles of 7-week old bTBI mice were generated by  scRNA-Seq.


title: The human lncRNA GOMAFU suppresses neuronal interferon response pathways affected in schizophrenia

status: Public on Jun 24 2022

city: Atlanta

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

institute: Emory University

summary: Long noncoding RNAs (lncRNAs) play multifaceted roles in regulating molecular networks that underlie normal brain function and the complex etiology of neuropsychiatric disorders. One example is the human neuronal lncRNA GOMAFU, which was reported to display abnormal expression in schizophrenia (SCZ) postmortem brains, regulate alternative splicing of SCZ risk gene transcripts, and harbor genetic variates contributing to the risk of SCZ. However, functional targets and molecular networks regulated by GOMAFU have not been determined. How GOMAFU dysregulation contributes to SCZ pathogenesis remains elusive. Here we report that GOMAFU is a novel modulator of neuronal interferon (IFN) response pathways. We found ectopic changes of GOMAFU in a brain region-specific manner from transcriptomic profiling datasets derived from multiple SCZ cohorts. Using CRISPR-Cas9 to delete the GOMAFU promoter, we identified hundreds of human neuronal GOMAFU targets in various SCZ-affected molecular pathways, with the most striking effects on upregulation of numerous genes enriched in IFN signaling pathways. In addition, GOMAFU targets in the IFN pathways are differentially affected in SCZ postmortem brain regions and negatively associated with GOMAFU abundance. Furthermore, acute exposure to IFN- caused a marked decline of GOMAFU, leading to selective upregulation of a subclass of GOMAFU targets in stress and immune response pathways, which are also affected in SCZ brains and form a highly interactive molecular network. Together, our studies revealed novel roles of GOMAFU in governing the neuronal IFN pathways and suggest that GOMAFU dysregulation may contribute to the etiological neuroinflammatory responses in SCZ brain neurons.

overall_design: Untreated M17 and IFN-γ treated M17

first: Peng

last: Teng

first: Yangping

first: Yue

last: Feng


title: RNAseq analysis of GM-CSF and M-CSF polarized bone marrow derived macrophages cultured on TC or noTC dishes

status: Public on Jun 10 2022

city: qingdao

first: qiaoling

last: song

address: Xiang Gang East Road NO.23

institute: Ocean University of China

summary: Bone marrow cells were isolated, primed with M-CSF (M BMDM) or GM-CSF (GM BMDM) and cultured on tissue culture dishes (TC) or low adherent dishes (noTC) for 7 days. BMDMs were treated with LPS (100 ng/ml) for 3 hours. The difference between TC- and noTC-cultured BMDMs were analyzed to describe the phenotye and function of each population. Moreover, the influence of LPS treatment on GM-BMDMs and M-BMDMs were analyzed.

overall_design: GM-TC, M-TC, GM-noTC and M-noTC BMDMs with or without LPS treatment for 3 h

first: Qiaoling

last: Song

first: Chenyang

last: Zhao

first: Jinbo

last: Yang

first: Yazhuo

last: Zhang


title: Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions

status: Public on Jun 21 2022

city: Houston

first: Isaac

middle: B

last: Hilton

state: TX

address: 6500 Main St

department: Bioengineering

institute: Rice University

summary: Nuclease-inactivated CRISPR/Cas-based (dCas-based) systems have emerged as powerful technologies to synthetically reshape the human epigenome and gene expression. Despite the increasing adoption of these platforms, their relative potencies and mechanistic differences are incompletely characterized, particularly at human enhancer-promoter pairs. Here we systematically compared the most widely adopted dCas9-based transcriptional activators, as well as a novel activator consisting of dCas9 fused to the catalytic core of the human CBP protein, at human enhancer-promoter pairs. We find that these platforms display variable comparative expression levels in different human cell types and that their relative transactivation efficacies vary based upon the effector domain, effector recruitment architecture, targeted locus, and cell type. We also show that each dCas9-based activator can induce the production of enhancer RNAs (eRNAs), and that this eRNA induction is highly correlated with downstream mRNA expression from a cognate promoter. Additionally, we use dCas9-based activators to show that an intrinsic transcriptional and epigenetic reciprocity can exist between human enhancers and promoters and that contact frequencies between an enhancer and corresponding downstream promoter can be increased by targeting dCas9-based transcriptional activators to an enhancer. Collectively, our study provides new insights into the enhancer-mediated control of human gene expression and the use of dCas9-based activators.

overall_design: Cleavage Under Targets & Release Using Nuclease-sequencing (CUT&RUN-seq) for H3K27ac in HEK293T cells transfected with CRISPR activators (dCas9-CBP or dCas9-VPR) targeting HBG1 promoter or HS2 enhancer

first: Kaiyuan

last: Wang

first: Mario

last: Escobar

first: Jing

first: Barun

last: Mahata

first: Jacob

last: Goell

first: Spencer

last: Shaw

first: Madeleine

last: Cluck


title: VISTA targeting of T cell quiescence and myeloid suppression overcomes adaptive resistance

status: Public on Jun 26 2022

city: Lebanon

first: Evelien

last: Schaafsma

state: New Hampshire

address: One Medical Drive

institute: Dartmouth

summary: VISTA is a premier target for cancer treatment due to its broad expression in many cancer types and enhanced expression upon development of adaptive immune checkpoint resistance. Mechanisms of enhanced anti-tumor immunity were investigated using scRNAseq of the tumor immune infiltrate.

overall_design: CD45+, AH1-tetramer+ or Ly6G+ cells were sorted from CT26 tumors treated with IgG, anti-VISTA, anti-PD-1+anti-CTLA4, anti-PD-1+anti-CTLA4+anti-VISTA or untreated.

first: E

first: J

last: Lines


title: Microglia coordinate cellular interactions during spinal cord repair

status: Public on Jun 01 2022

city: Columbus

first: Phillip

middle: G.

last: Popovich

state: OH

address: 460 W 12th Ave

department: Department of Neuroscience

institute: The Ohio State University

summary: Traumatic spinal cord injury (SCI) triggers a neuro-inflammatory response dominated by tissue-resident microglia and monocyte derived macrophages (MDMs). Since activated microglia and MDMs are morphologically identical and express similar phenotypic markers in vivo, identifying injury responses specifically coordinated by microglia has historically been challenging. Here, we pharmacologically depleted microglia and use anatomical, histopathological, tract tracing, bulk and single cell RNA sequencing to reveal the cellular and molecular responses to SCI controlled by microglia. We show that microglia are vital for SCI recovery and coordinate injury responses in CNS-resident glia and infiltrating leukocytes. Depleting microglia exacerbates tissue damage and worsens functional recovery. Conversely, restoring select microglia-dependent signaling axes, identified through sequencing data, in microglia depleted mice prevents secondary damage and promotes recovery. Additional bioinformatics analyses reveal that optimal repair after SCI and likely other forms of neurological disease, might be achieved by co-opting key ligand-receptor interactions between microglia, astrocytes and MDMs.

overall_design: Bulk RNAseq of spinal cords from sham Vehicle (n=4), sham PLX5622 (n=4), 7dpi Vehicle (n=3), and 7dpi PLX5622 mice (n=3). Single cell RNAseq of spinal cords from sham, 7 dpi and 28 dpi Vehicle mice and sham, 7 dpi and 28 dpi PLX5622 mice.

first: Faith

middle: H

last: Brennan

first: Yang

last: Li

first: Cankun

first: Anjun

last: Ma

first: Qi

last: Guo

first: Yi

first: Nicole

last: Pukos

first: Warren

last: Campbell

first: Kristina

middle: G

last: Witcher

first: Zhen

last: Guan

last: Kigerl

first: Jodie

last: Hall

first: Jonathan

last: Godbout

first: Andy

middle: J

last: Fischer

first: Dana

last: McTigue

first: Zhigang

last: He

first: Qin


title: Inflammatory exposure drives permanent impairment of hematopoietic stem cell self-renewal activity and accelerated aging

first: Sina

last: Stäble

type: Methylation profiling by high throughput sequencing

summary: Hematopoietic stem cells (HSCs) mediate regeneration of the hematopoietic system following injury, as exemplified by the transient activation of HSCs out of dormancy upon exposure to infection or inflammation. Such challenges have been documented to impair HSC function. However, whether this functional impairment extends beyond the duration of inflammatory exposure is unknown. To assess the effects of repeated inflammatory challenge, wild-type C57BL/6J mice were subjected to a dose escalation regimen of polyinosinic:polycytidylic acid (pI:pC) treatment mimicking viral infection. Unexpectedly, we observed an irreversible depletion of functional HSCs and hallmarks of accelerated aging in LT-HSCs. In an effort to conclusively assess whether there was molecular evidence of accelerated aging of LT-HSC after sterile inflammation, we performed whole genome bisulfite sequencing and calculated the biological age by applying a multi-tissue DNA methylome clock. LT-HSCs from mice subject to inflammation demonstrated multiple cellular and molecular features of accelerated aging, including increased biological age.

overall_design: Tagmentation-based whole-genome bisulfite sequencing (TWGBS) of purified LT-HSCs [Lin(-) c-kit(+) sca-1(+) CD150(+) CD48(-) CD34(-)] isolated from the bone marrow of pooled untreated (8- to 12-week-old), PBS or pI:pC treated (32- to 36-week-old) C57BL/6J mice, and individual (111- to 130-week old) aged C57BL/6J mice. Lineage markers (Lin): CD5, CD8a, CD11b, B220, Gr1, Ter119). For each replicate, two to four separate TWGBS libraries were prepared and pools of four libraries were sequenced on one to three separate HiSeq2000 lanes using the 125bp paired-end mode.

first: Julia

last: Knoch

first: Stephen

last: Krämer

first: Matthias

last: Schlesner

first: Daniel

last: Lipka

first: Michael

last: Milsom


title: FUNCTIONAL SUBSETS OF PLASMA CELLS ASSOCIATED WITH AMYLOID PRODUCTION AND VENETOCLAX SENSITIVITY IN AL AMYLOIDOSIS

city: Beijing

first: Xuezhu

last: WANG

address: No.1 Shuaifuyuan Wangfujing Dongcheng District

institute: Peking Union Medical College Hospital

summary: Light chain amyloidosis (AL) is a life-threatening plasma cell dyscrasia manifested by irreversible damage of multiple organs caused by monoclonal immunoglobulin light chain, production of pathogenic bone marrow plasma cells (BMPCs). Although AL is featured by both misfolding of monoclonal protein and plasma cell proliferation, the functional subclones and molecular mechanism of BMPCs in AL remain elusive. Also, inter-individual heterogeneities of AL determine the chemotherapy response and organ tropism of light chains, which require well-defined molecular subtypes. To address these, we conducted single-cell RNA sequencing (scRNA-seq) of BMPCs donated by patients with AL, patients with monoclonal gammopathy of undetermined significance (MGUS), and healthy controls. Single-cell transcriptome revealed a continuity of bone marrow plasma cell (BMPC) functional subclones, delineating DNA repair, cell proliferation, immunoglobulin production, etc., with the gradient of signaling entropy and immunoglobulin production. The amyloidosis-associated genes, such as the amyloid-beta binding Apolipoprotein E (APOE), Cystatin 3 (CST3), and Complement C1q A Chain (C1QA), were up-regulated in a subclone enriched in AL. The speculated light chain-producing subclones in AL up-regulated neutrophil degranulation pathways, transport to and modifications in Golgi apparatus, and asparagine N-linked protein glycosylation. Cyclin D1 (CCND1)hi AL, consisted of larger main subclones which highly expressed Bcl-2 complex and B-cell differentiation genes, was sensitive to venetoclax that targets Bcl-2. A major subset of CCND1low AL harbored larger carbohydrate-synthesizing subclone and up-regulated CCND2 and the amyloidosis-associated genes. Collectively, our results provided frontier insights into the functional subclones and molecular mechanism of BMPCs in AL, associated with amyloidosis, light chain production and venetoclax sensitivity, as knowledge for the future research on AL pathogenesis, AL subtypes and AL-specific therapies.

overall_design: Single-cell RNA-seq of Homo sapiens: bone marrow of patients with light chain amyloidosis

last: Wang

first: Jian

last: Li

first: Yang

last: Chen


title: Normal and Sjogren’s syndrome models of the murine lacrimal gland studied at single-cell resolution

status: Public on Jun 07 2022

city: Baltimore

first: Jacob

last: Heng

state: MD

address: 725 North Wolfe Street

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

summary: The lacrimal gland is of central interest in ophthalmology both as the source of the aqueous component of tear fluid and as the site of autoimmune pathology in the context of Sjogren’s syndrome (SjS). To provide a foundational description of mouse lacrimal gland cell types and their patterns of gene expression, we have analyzed single-cell transcriptomes from wild-type (Balb/c) mice and from two genetically based SjS models, MRL/lpr and NOD (nonobese diabetic).H2b, and defined the localization of multiple cell-type-specific protein and mRNA markers. This analysis has uncovered a previously undescribed cell type, Car6+ cells, which are located at the junction of the acini and the connecting ducts. More than a dozen secreted polypeptides that are likely to be components of tear fluid are expressed by acinar cells and show pronounced sex differences in expression. Additional examples of gene expression heterogeneity within a single cell type were identified, including a gradient of Claudin4 along the length of the ductal system and cell-to-cell heterogeneity in transcription factor expression within acinar and myoepithelial cells. The patterns of expression of channels, transporters, and pumps in acinar, Car6+, and ductal cells make strong predictions regarding the mechanisms of water and electrolyte secretion. In MRL/lpr and NOD.H2b lacrimal glands, distinctive changes in parenchymal gene expression and in immune cell subsets reveal widespread interferon responses, a T cell–dominated infiltrate in the MRL/lpr model, and a mixed B cell and T cell infiltrate in the NOD.H2b model.

overall_design:
Single-cell RNAseq of BALB/cJ, MRL/MpJ-Fas(lpr/lpr), NOD.H2b lacrimal glands.

Processed and annotated data can also be accessed at: https://jacobheng.shinyapps.io/lacrimal/

first: Amir

last: Rattner

first: Briana

last: Winer

first: Loyal

middle: A

last: Goff

first: Jeremy

last: Nathans


title: Gene expression analysis of  mouse pancreas carrying Prox1 ectopic acinar expression

city: Chicago

first: Beatriz

last: Sosa-Pineda

state: IL

address: 303 E Superior SQI 8-520

department: Medicine

institute: Northwestern University

summary: RNA sequencing was used to identify gene expression changes in pancreatic acinar cells with ectopic expression of the homeodomain transcription factor Prox1

overall_design: The pancreas P7 control mice (Ptf1a cre/+) and P7 Prox1-AcOE transgenic mice (Ptf1a cre/+;CAG-loxP-STOP-loxP-Prox1-LacZ) was dissected and placed in RNA later reagent.  3 individual "control" pools and 3 individual "mutant" pancreata were processed for RNA extraction using TRIzol reagent and PueLinkTM RNA Mini Kit (Invitrogen). RNA quality was assesed using the Agilent 2100 bioanalyzer. Six sequencing libraries (3 "control" and 3 "mutant")  were made usingTruSeq mRNA-Seq library prep. NextSeq high througput was used for sequencng.

first: Angelica

last: Martinez Ramirez


title: Single Cell RNA-seq on Human PBMC

status: Public on May 27 2022

city: Durham

first: George

last: Fromm

address: 21 Parmer Way, Suite 200

institute: Shattuck Labs, Inc.

summary: To assess the impact of IgG1 and IgG4 variants of a TIGIT-Fc-LIGHT fusion protein on human PBMC expression, each fusion protein or an untreated control were incubated with human PBMC for 2 days in AIMV lymphoproliferative media.  Both IgG1 and IgG4 variants of TIGIT-Fc-LIGHT induced broad immune cell activation on T, NK, and myeloid cells.

overall_design: Human PBMC were purchased from StemCell Technologies and cultured either alone or with 150nM of human TIGIT-Fc(IgG1)-LIGHT or TIGIT-Fc(IgG4)-LIGHT fusion proteins for 2 days in AIMV media.  After 2 days, floating and adherent cells were isolated and processed using the 10x Genomics Chromium Handler.  Single cell libraries were generated using 10x Genomics Chromium Next GEM Single Cell 3’ v3.1: Dual Index reagents.  Libraries were sequenced on an Illumina NovaSeq 6000.


title: Rifampicin drug resistant Mycobacterium tuberculosis infection suppresses in vivo immune responses through a Type I Interferon response.

first: Luis

last: Barreiro

address: 900 E 57th Street

institute: University of Chicago

summary: Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), latently infects one quarter of the world’s population. The rise of multidrug resistant (MDR) Mtb infections worldwide presents a significant obstacle to curb TB globally. While human studies report dysregulated immune responses in MDR TB patients, there is a lack of clear understanding of the host-pathogen interactions following MDR Mtb infection. We recently showed that Mtb carrying a rifampicin drug resistance (RDR)-conferring single nucleotide polymorphism in the RNA polymerase-B gene (Mtb rpoB-H445Y) can modulate host macrophage metabolic reprogramming by production of Type I IFNs. Here, using a mouse model, we have characterized the host immune response in vivo following RDR Mtb infection. We show that despite establishment of Mtb infection in the lung and dissemination to the peripheral organs, lung myeloid and lymphoid immune responses to RDR Mtb is suppressed through a Type I IFN-dependent mechanism. These results coincide with a muted responses in the bone marrow hematopoietic stem and progenitor cells (HSPCs) and progenitors following RDR Mtb infection. These results suggest that host directed therapeutics and vaccines for drug resistant TB may need to be target specific host immune pathways for protection.

overall_design: Single cell RNA expression profiles of LKS+, cells of Control mice, and mice subject to an aerosol challenge with M.tuberculosis strains HN878 and rpoB-H445Y.

first: Suhas

last: Bobba

first: Nicole

last: Howard

first: Shibali

last: Das

first: Mushtaq

last: Ahmed

first: Nargis

last: Khan

first: Ignacio

last: Marchante

last: Barriero

first: Barun

last: Mathema

first: Joaquín

last: Sanz

first: Maziar

last: Divangahi

first: Shabaana

last: Khader


title: Investigation of bone marrow microenvironment-induced drug resistance in acute lymphoblastic leukemia (ALL)

status: Public on May 31 2022

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

summary: Bulk RNA-seq of B-ALL cells cocultured with bone marrow-mesenchymal stem cells (BM-MSC) identified that B-ALL acquire epithelial-mesenchymal transition (EMT) properties by interacting with primary bone marrow-mesenchymal stem cells (BM-MSC) and scRNA-seq dissected the hybrid cluster of adherent B-ALL (Adh B-ALL) harboring B-ALL and BM-MSC features induced by EMT program

overall_design: Integrative analysis of transcriptome in ALL cells interacting with BM-MSC using bulk RNA-seq and single cell RNA-seq

first: Chun

last: Park

first: Hiroki

last: Yoshihara

first: Qingsong

last: Gao

first: Chunxu

last: Qu

first: Charles

last: Mullighan


title: Gene expression analysis of E13.5 Prox1-deficient mouse embryonic pancreas

first: Beatriz

last: Sosa-Pineda

summary: RNA sequencing was used to identify gene expression changes in the pancreas of E13.5 Prox1-nullyzygous mouse embryos.

overall_design: The pancreas E13.5 control embryos (wildtype) and Prox1-nullyzygous embryos (Prox1 GFPCre/D) was dissected and pooled (each sample pool contained 5-6 individual pancreata; 3 "control" pools and 3 "mutant" pools were processed for RNA extraction using an RNAeasy Micro Kit (Qiagen). RNA quality was assesed using the Agilent 2100 bioanalyzer. Six sequencing libraries (3 "control" and 3 "mutant")  were made usingTruSeq mRNA-Seq library prep. NextSeq high througput was used for sequencng.


title: Inactivation of the histone H3 K36 methyltransferase NSD1 confers resistance to EZH2 inhibition [RNA-Seq]

status: Public on May 09 2022

city: Memphis

first: Jacquelyn

last: Myers

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children’s Research Hospital

summary: Disruption of antagonism between SWI/SNF chromatin remodelers and Polycomb repressor complexes drives the formation of numerous cancer types. Recently, an inhibitor of Polycomb protein EZH2 was approved for treatment of sarcomas mutant in SWI/SNF subunit SMARCB1, but resistance occurs.  Here we sought to identify additional contributors to SWI/SNF-Polycomb antagonism and potential resistance mechanisms. We performed CRISPR screens and found that NSD1 loss caused resistance to EZH2 inhibition. NSD1 loss reduced H3K36me2 and impaired transcriptional activation of targets inhibited by EZH2 or activated by SMARCB1. Further, inhibiting the H3K36me2 demethylase KDM2A restored EZH2 inhibition in cells lacking NSD1. Our results expand the mechanistic understanding of SWI/SNF and Polycomb interplay and identify NSD1 as key for coordinating this transcriptional control.

overall_design: To investigate how loss of NSD1 affects SWI/SNF mediated control of gene expression, we induced SMARCB1 in the presence and absence of NSD1 and RNA sequencing (RNA-seq) after 24 hours. Furthermore, to study whether NSD1 is essential for the transcriptional activation that occurs following loss of EZH2-mediated silencing, we performed RNA-seq of G401 control (shCTRL) and NSD1 knockdown (shNSD1) cells treated with DMSO or GSK126 for 72 hours.

first: Yiannis

last: Drosos

middle: W

last: Roberts


title: Inactivation of the histone H3 K36 methyltransferase NSD1 confers resistance to EZH2 inhibition

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

overall_design: Refer to individual Series


title: Immune Transcriptome Study of Human Nucleated Erythroid Cells from Different Tissues by Single-Cell RNA-Sequencing

status: Public on May 04 2022

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

summary:
Purpose: studying of immunity-related genes in CD235a erythroid cell in order to validate previous findings on the subject using single cell RNA sequencing (scRNA-seq) and its benefits such as mRNA co-localization in a single cell and cell specific marker gating of populaions of interest.
Methods: we extracted mononuclear cells from the fetal liver, the fetal thymus, the cord blood and the adult bone marrow, performed magnetic separation of CD235a (Erythroid) cells, marked magnetically separated cells with BD Sample Tags, loaded the cells on a BD Rhapsody cartridge, lysed the cells, performed reverse transcription, cDNA library preparation, QC of final cDNA libraries by BioAnalyzer 2000 and Qubit 4, pooled the final cDNA libraries, sequenced them on a Illumina NextSeq 550 sequencer. Then, we processed FASTQ R1 and R2 files using the BD Pipeline V1.9 and got final metrics in a mols_per_cell.tsv file.
Results: in this work, we investigated other possible immunity-related functions on a single cell level using RNA sequencing of adult bone marrow, cord blood and fetal liver NECs and found that NECs from every studied origin expressed ARG1, CXCL5, CXCL8, DEFA3, DEFA4, IL1B, IL15, IL18, IGHE (secreted), LGALS3, LAGLS9, TGFB3 and VEGFA.
Conclusions: our study allows to access new potential immunological roles of CD235a erythroid cells, both validated and discarded previous results regarding cytokine and chemokine gene expression in erythroid cells.

overall_design:
Single cell immunity-related gene profiles of CD235a Erythroid cells from the adult bone marrow, from the cord blood, from the fetal thymus and from the fetal liver.
Sample Tag 1-3 = Cord Blood, n=3, 1620 cells were called in total (Sample_ID 1 in the dataset).
Sample Tag 3-6 = Fetal liver parenchyma, n=3, week 20-22 of development, 3690 cells were called in total (Sample_ID 2 in the dataset).
Sample Tag 7-9 = Fetal thymus parenchyma, n=3, week 20-22 of development, this sample was discarded (only 37 single cells were called in total).
Sample Tag 10-12 = Adult bone marrow, n=3, 24-26 years old males, 3799 cells were called in total (Sample_ID 4 in the dataset).


title: DIS3 ribonuclease degrades Pou6f1 to promote mouse pre-implantation cell differentiation

status: Public on Apr 28 2022

city: Ashburn

first: Di

last: Wu

address: 19700 Helix Drive

institute: HHMI Janelia

summary: Mammalian early embryonic development involves precisely regulated cell differentiation. Discovering new regulators and profiling their crosstalk have been extensively studied and remain open questions. To identify novel developmental repressors, we established the knockout mouse model of Dis3, an RNA exosome associated RNase. Homozygous Dis3 null embryos have morula-to-blastocyst transition arrest and they lack cell differentiation. By single embryo RNA-seq, we identified Pou6f1 accumulation by DIS3 depletion. Sustained POU6F1 binds and represses the transcription of Nanog and Cdx2. In addition, a broader role of POU6F1 in cell fate transition is also revealed from derived mouse embryonic stem cells. We also tested DIS3 mutations and discovered their effects in causing cell transformation. Our findings uncover a new regulatory pathway of DIS3-POU6F1 in regulating pre-implantation cell differentiation in early mammalian embryogenesis.

overall_design: 1. Single embryo RNA-seq of mouse embryos derived from Dis3 hetereozygous mating, including wildtype, Dis3 heterozygotes and Dis3 null embryos at embryonic day 2.5 and 2.75. Multiple biological replicates are included. 2. ChIP-seq of derived mouse embryonic stem cells transfected with either mCherry or Pou6f1-mCherry. Each has two biological replicates.

first: Jurrien

last: Dean


title: The effect of NEIL3 on CA1 DNA methylation

status: Public on May 02 2022

city: Trondheim

first: Jing

last: Ye

address: Høgskoleringen 1

department: Department of Clinical and Molecular Medicine (IKOM)

country: Norway

institute: Norwegian University of Science and Technology (NTNU)

summary: CA1-specific brain tissue from the hippocampal formation was isolated at baseline (homecage condition). DNA was extracted and sequenced after bisulfite conversion to determine differentially methylated regions

overall_design: Wildtype (C57Bl6) and NEIL3-deficient (Neil3-/-, C57Bl6-background) were used. 3 wildtype and 3 mutant animals were included. Animals were exposed to the same housing conditions, food ad libitum and handled by the same experimenters.

first: Nicolas

last: Kunath

first: Anna

last: Bugaj

first: Tobias

last: Obermann

first: Marion

last: Fernandez

first: Ana

last: Vankova

first: Katja

last: Scheffler

first: Magnar

last: Bjørås


title: Transcriptomics of hypothalamic responses of broiler chickens fed L-citrulline supplemented diets under different ambient temperatures

city: Taian

first: Victoria

middle: Anthony

last: Uyanga

state: Please select

address: 61 Daizong Street, China

department: Animal Nutrition and Feed Science

institute: Shandong Agricultural University

summary: The above study is an original research that employs transcriptomics analysis to investigate the hypothalamic responses associated with dietary L-Citrulline treatment. L-Citrulline is a non-essential amino acid that is widely gaining research interest due to its role in thermoregulation and its efficiency as an arginine/nitric oxide precursor. Therefore, this study demonstrates that dietary supplementation of L-citrulline to broilers under different housing temperatures would stimulate regulatory pathways involved with brain development and feeding behavior. We have also identified potential candidate genes that would be beneficial in fostering further research on L-citrulline-induced hypothermia.

overall_design: Ross 308 broilers were raised from day-old and managed under standard conditions. Experimental diets were formulated to meet or exceed NRC requirements (Supplementary Data S1). Birds were fed two dietary treatments; basal diets or 1% L-Citrulline supplemented diets. At 28 days old. Birds were allocated to thermoneutral (TNZ- 24oC, 60% RH) or high temperature (HS-35oC, 60% RH) environments. The study had four (4) treatments comprising of CON (TNZ + basal diet); A (TNZ + L-Cit diet); B (HS + basal diet); C (HS+ L-Cit diet). Each treatment had 6 replicates of 12 chickens each. Weekly data was obtained for body weight and feed intake per replicate. At 42 days of age, 1 chicken per replicate was sacrificed and hypothalamic tissues were dissected and snap-frozen in liquid nitrogen and stored at -80 oC for further analysis

first: Semiu

middle: F

last: Bello

first: Ning

last: Chao

first: Haifang

last: Li

first: Jingpeng

last: Zhao

first: Xiaojuan

last: Wang

first: Hongchao

last: Jiao

first: Okanlawon

last: Onagbesan

first: Hai

last: Lin


title: Clinical Relevance of estrogen reactivity in the breast cancer microenvironment

status: Public on Apr 26 2022

city: Kumamoto

first: Takashi

last: Takeshita

address: 4 Chome-1-60 Higashimachi, Higashi Ward

country: Japan

institute: Kumamoto City Hospital

summary: Estrogen signals play an important role in the phenotype of estrogen receptor positive breast cancer. However, comprehensive analyses of the effect of estrogen signals on the tumor microenvironment and sur-vival in large cohorts of primary breast cancer patients have been lacking. We aimed to test the hypothesis that estrogen reactivity affects gene expression and immune cell infiltration profiles in the tumor microenvi-ronment and survival.

overall_design: A total of 3098 breast cancer cases were analyzed; 1904 from Molecular Taxonomy of Breast Cancer (METABRIC) cohort, 1082 from the cancer genome atlas (TCGA) cohort, and 112 from Hokkaido University hospital cohort. In Hokkaido University hospital cohot, Formalin-Fixed Paraffin-Embedded (FFPE) tissues were obtained from 112 breast cancer patients, who underwent breast surgery between 2005 and 2012 at Hokkaido University Hospital.

first: Yoshihisa

last: Tokumaru

first: Masanori

last: Oshi

first: Rongrong

last: Wu

first: Ankit

last: Patel

first: Wanqing

last: Tian

first: Yutaka

last: Hatanaka

first: Kanako

middle: C

first: Li

last: Yan

first: Kazuaki

last: Takabe


title: Cell fate roadmap of human primed-to-naive transition reveals preimplantation cell lineage signatures

status: Public on Apr 29 2022

city: Shanghai

first: Tu

middle: zhi

last: fen

address: Tongji University Siping Road Campus

department: life science and technology

institute: Tongji University

summary: We describe the global cell fate roadmap during primed-to-naive transition process by bulk mRNA-seq and ATAC-seq analysis among transition intermediates across different time points. We report that activation of ALPG is a landmark event  for naive state establishment. Further investigation into transitioning cells with dynamic fluorescence presents intermediates branching into TE-like subpopulations with capacities of TSC derivation.

overall_design: Analyzing mRNA-seq and ATAC-seq profiles of transitioning intermediates during primed-to-naive transition process.

first: Yan

last: Bi

first: Zhifen

last: Tu

first: Yixuan


title: The role of SWEET4 proteins in the post-phloem sugar transport pathway of Setaria viridis sink tissues

city: Philadelphia

first: Diep

last: Ganguly

state: PA

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

summary: In the developing seeds of all higher plants, filial cells are symplastically isolated from the maternal tissue supplying photosynthate to the reproductive structure. Photoassimilates must be transported apoplastically, crossing several membrane barriers; a process facilitated by sugar transporters. Sugars Will Eventually be Exported Transporters (SWEETs) have been proposed to play a crucial role in apoplastic sugar transport during phloem unloading and the post-phloem pathway in sink tissues. Evidence for this is presented here for developing seeds of the C4 model grass Setaria viridis. Using immunolocalisation, SvSWEET4 was detected in various maternal and filial tissues within the seed along the sugar transport pathway, in the vascular parenchyma of the pedicel and the xylem parenchyma of the stem. Expression of SvSWEET4a in Xenopus laevis oocytes indicated that they function as high-capacity glucose and sucrose transporters. Carbohydrate and transcriptional profiling of Setaria seed heads showed that there were some developmental shifts in hexose and sucrose levels and consistent expression of SvSWEET4 homologues. Collectively, these results provide evidence for the involvement of SWEETs in the apoplastic transport pathway of sink tissues and allow a pathway for post-phloem sugar transport into the seed to be proposed.

overall_design: Setaria viridis A.10 was grown in a PGC Flex growth chamber (Conviron, Winnipeg, Canada, https://www.conviron.com). The day/night lengths and temperatures were 16 h/8 h and 28 °C /20 °C, respectively, with 55% humidity and light at an intensity of approximately 600 μmol m−2 s−1 was supplied by halogen incandescent lamps (42W 2800K warm white clear glass 630 lumens, CLA, Brookvale, NSW, Australia, http://www. clalighting.com.au) and Pentron Hg 4ft fluorescent tubes (54W 4100K cool white, Sylvania, Wilmington, MA, USA, https://www.osram.us). Plants were grown in 1.7 L pots filled to 90% capacity using Green Wizard Premium Potting mix (Debco, Bella Vista, NSW, Australia, https://www. lovethegarden.com/), and the remaining 10% filled with Debco Seed Raising and Superior Germinating Mix, both supplemented with 1g kg-1 of slow-release fertiliser (Osmocote, Scotts, Bella Vista, Australia, https://www. lovethegarden.com/). As the seed itself is very small in Setaria, whole seed heads were harvested at the base of each from four developmental stages: 50% seed head emergence, anthesis, 8 DAA and 16 DAA (Figure S1). Both A.10 and ME034V ecotypes were sampled since most research has been done on the former, but transformation is conducted in ME034V. Each stage has four biological replicates where each biological replicate is made up of four individual plants. Samples were harvested into 10 mL vials and immediately snap-frozen in liquid nitrogen. Samples were homogenised cryogenically with the TissueLyser II (QIAGEN, Hilden, Germany, https://www.qiagen.com).

first: Lily

last: Chen

first: Robert

middle: E

last: Sharwood

last: Furbank


title: Epigenetic and Transcriptional Dysregulation in T cells of patients with Atopic Dermatitis [WGS]

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

summary: Atopic dermatitis (AD), the start of the atopic march, is one of the most common skin disorders in children. Immunologically, AD involves skin barrier defects and CD4+ T cells that localize to the skin, producing inflammatory cytokines and amplifying epidermal dysfunction. To understand the gene regulatory activity differences in peripheral blood T cells in AD, we measured chromatin accessibility (ATAC-seq), NFKB1 binding (ChIP-seq), and gene expression (RNA-seq) in stimulated CD4+ T cells from subjects with active moderate-to-severe AD and age-matched healthy, non-allergic controls. Chromatin accessibility in stimulated CD4+ T cells were highly enriched for AD genetic risk variants. The vast majority of ATAC-seq peaks were shared, consistent with those sections of chromatin being equally available between matched pairs; however, NFKB DNA binding motifs were enriched in chromatin accessible in an AD-dependent manner. NFKB1 ChIP-seq identified peaks that were stronger in AD cases, enriched in controls, or shared between cases and controls. The ChIP-seq peaks that were statistically stronger in AD were more strongly enriched for NFKB DNA binding motifs. Chromatin that was more strongly accessibe and bound by NFKB1 in AD were enriched for genetic variants that increase risk for AD. Using whole genome sequencing data, we identified wide-spread genotype-dependent chromatin accessibility and allelic NFKB1 binding at AD and allergic disease genetic risk loci.

overall_design: Whole genome sequencing (WGS) was performed in stimulated CD4+ T cells from 6 subjects with active moderate-to-severe AD and 6 age-matched healthy, non-allergic controls.

first: Leah

last: Kottyan


title: Epigenetic and Transcriptional Dysregulation in T cells of patients with Atopic Dermatitis [RNA-Seq]

overall_design: RNA-seq was performed in stimulated CD4+ T cells from 6 subjects with active moderate-to-severe AD and 6 age-matched healthy, non-allergic controls.


title: Analysis of circulating miRNAs altered in the acute respiratory distress syndrome related to SARS-CoV-2 infection

status: Public on Apr 12 2022

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

institute: Hospital del Mar Research Institute

type: Non-coding RNA profiling by high throughput sequencing

summary: Circulating miRNAs in patients who underwent ARDS and needed mechanical ventilation were analyzed by next generation sequencing (NGS) in comparison with patients who had COVID-19 poor symptoms but without intensive care unit requirement.

overall_design: SmallRNAs  were analyzed by NGS from 28  serum samples of COVID-19 patients with requirement or not of mechanical ventilation (MV): MV- (n=13); MV+ (n=15)

first: Natalia

last: Garcia-Giralt

first: Roberto

last: Güerri


title: Transcriptomically-guided pharmacological experiments in neocortical and hippocampal NPY-positive GABAergic interneurons

status: Public on Apr 20 2022

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

summary: Cortical GABAergic interneurons have been shown to fulfil important roles by inhibiting excitatory principal neurons. Recent transcriptomic studies have confirmed seminal discoveries that used anatomical and electrophysiological methods highlighting the existence of multiple different classes of GABAergic interneurons. However, individual studies have rarely addressed regional specific differences in gene expression in a given subclass of neuron. Using single-cell Patch-RNAseq, we characterised neuropeptide Y (NPY)-positive GABAergic interneurons in superficial layers of the primary auditory cortex and in distal layers of area CA3. We found that more than 300 genes are differentially expressed in NPY-positive neurons between these two brain regions. For example, the AMPA receptor auxiliary subunit Shisa9/CKAMP44 and the 5-HT2a receptor are significantly higher expressed in auditory NPY-positive neurons. These findings guided us to perform pharmacological experiments that revealed a role for 5-HT2a receptors in auditory NPY-positive neurons. Specifically, although the application of 5-HT led to a depolarisation of both auditory and CA3 NPY-positive neurons, the 5-HT2a receptor antagonist ketanserin only reversed membrane potential changes in auditory NPY-positive neurons. Our study demonstrates the potential of single-cell transcriptomic studies in guiding directed pharmacological experiments.

overall_design: 8 NPY-EGFP mice were analyzed for a total of 46 NPY positive cells and 1 NPY negative cell. For NPY positive cells, 21 were from the Hippocampal CA3, 20 from ACTX (auditory cortex), 3 from the Hippocampal CA1, and 2 from the Hippocampal DG. The NPY negative cell was from the Hippocampal CA3.

first: Sanna

last: Beerens

first: Jochen

last: Winterer

first: David

last: Lukacsovich

first: Christian

last: Wozny


title: Atlas of the aging mouse intestine

status: Public on Apr 25 2022

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

summary: Colon cancer is one of the leading causes of death within the western world and is linked to the aging of the colon. The disease presents differently between men and women, developing in different parts of the colon and often with a different morphology. The colonic epithelium is a rapidly renewing tissue, tasked with absorption of water and nutrients, interacting with a wide array of intestinal microbes. The gut-associated lymphoid tissue houses the majority of all immune cells. These immune cells interact with and help regulate the activity of epithelial cells. However, not much is known whether compartment-specific changes occur during aging and how said changes could impact the epithelium. Here we show that both epithelial and immune cells differ significantly between colonic compartments and experience age-related changes, with the possible causal interactions. We found a shift in the absorptive-secretory cell balance, the decrease in colonocytes possibly linked to age-associated malabsorption and intestinal disturbances. We demonstrate marked changes in the aging of the immune cells with regard to populations and interactions with epithelial cells, linking aged immune cell produced cytokines (Ifn-γ, Il1B) and the aging of colonic epithelium, which lines up with observations of inflammation causing or exacerbating age-associated gut disfunctions, such as colon cancer. Our results provide new insights into the normal and age-associated states of the colon. We anticipate our work will provide a foundation for further inquiry not only into diseases of the colon (even outside the realm of aging research) but developmental research as well.

overall_design: Single-cell RNA seq on immune cells from the mouse intestine

first: Jing

last: Lu

first: Omid

last: Omrani

first: Lisa

last: Adam

first: Francesco

last: Neri


title: Frac-Seq Analysis of ZFC3H1 Knockdown U2OS Cells

status: Public on Mar 31 2022

city: Ipswich

first: Eric

last: Wolf

email: ewolf@neb.com, ericjwolf1@gmail.com

address: 240 County Road

department: RNA Division

institute: New England Biolabs

summary: We have found that depletion of the zinc finger protein ZFC3H1 inhibits the nuclear retention of these RNAs. ZFC3H1 forms a complex with MTR4 and PABPN1 (the PolyAdenylation EXosome Targeting complex (Meola et al 2016, Ogami et al 2017) and likely recruits the nuclear exosome for RNA degradation. Recently, we found that depletion of U1-70K, one protein component of the U1 snRNP spliceosomal complex, inhibits nuclear retention of 5’SS motif containing RNAs. The U1 snRNP complex recognizes and binds to the 5’SS motif and in vitro studies showed that U1-70K directly interact with a similar 5’SS motif through U1 snRNA binding (Gunderson et al 1999). Interestingly, we found that U1 snRNP is involved in targeting 5’SS motif containing mRNAs to nuclear speckles shortly following RNA transcription. In contrast, ZFC3H1 is involved in nuclear speckle localization post-transcriptionally and actively retain RNAs in these structures. Together, our results suggest a model where U1 snRNP interacts with the RNA via the 5’SS motif and targets mature mRNAs to nuclear speckles. Specifically, it suggests that misprocessed RNAs can be targeted to speckles (or other nucleoplasmic foci) and that these foci serve as a platform to recruit the nuclear exosome via ZFC3H1. Our results highlight a splicing independent role of U1 snRNP and how mRNA nuclear export function in nuclear surveillance to prevent the translation of aberrant proteins.

first: Alexander

last: Palazzo

first: Eliza

last: Lee


title: Epigenetic and Transcriptional Dysregulation in T cells of patients with Atopic Dermatitis

first: Matthew

last: Weirauch


title: RNA-seq analysis of the chromosome-associated RNAs

status: Public on Mar 01 2022

city: Hangzhou

first: Kai

last: Ma

address: No.18 Shilongshan Road，Cloud Town, Xihu District

institute: Westlake University

summary: The goals of this study are to discover the RNAs associated with the condensed chromosomes during mitosis. RNA from the soluble and pellet fraction of the lysed mitotic HCT116 cells were extracted, RNA profiles of soluble and pellet RNA were generated by deep sequencing, using MGISEQ2000. The sequence reads that passed quality filters were analyzed by STAR (v2.7.8a). Using an optimized data analysis workflow, we found that the pre-rRNAs were significantly enriched in the pellet fraction of the mitotic HCT116 cells.

overall_design: Analyze the RNA from the soluble and pellet fraction of lysed mitotic HCT116 cells

first: Xiaochun

last: Yu


title: Analysis of transcriptional differences between TER cells, B lymphocytes and embryonic liver nucleated erythrocytes

status: Public on May 03 2022

city: Yangzhou

first: Zhe

last: Yang

state: Jiangsu province

address: No.88, South University Road, Yangzhou

department: medical college

institute: Yangzhou university

summary: To verify the origin of TER cells from B lymphocytes，we profiled the differentially expressed genes in CD19+/TER119+/CD45+ cells by RNA-sequencing, with fetal liver-derived CD71+/TER119+/FSChigh cells (CECs) as erythroblast control and CD19+/TER119- cells as B-cell control.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TER cells, B lymphocytes and embryonic liver nucleated erythrocytes


title: In vitro methylation studies in multiple human cell types

status: Public on Mar 03 2022

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

type: Methylation profiling by genome tiling array


title: Single-cell RNA sequencing reveals the link between axonal regeneration and neuropathic pain by modified analysis of a novel peripheral nerve injury rat model

status: Public on Mar 19 2022

city: Beijing

first: Xi-Yin

last: Zhang

address: College Road

department: Neuroscience Research Institute

institute: Peking University

summary: Severe peripheral nerve injury (PNI) often causes significant movement disorders and intractable pain. Therefore, promoting nerve regeneration while avoiding neuropathic pain, a problem that remains unsolved, is key to the clinical treatment of PNI patients. Here, we establish a novel spared nerve crush (SNC) rat model that successfully reproduces axonal regeneration and neuropathic pain after PNI. Subsequently, we obtained single-cell RNA sequencing (scRNA-seq) data from rat directly injured and indirectly injured rat dorsal root ganglion (DRG) neurons at various time points after SNC and found that the PEP1 neuronal subtype in directly injured DRG is of particular interest. Through experimental design, sc-RNA sequence processing (EDSSP) and functional verification, we identified a potential key gene, Adcyap1, that encodes a key molecule linking nerve regeneration and pain after PNI. Our study sheds new light on the intrinsic link between axonal regeneration and neuropathic pain following PNI and provides new molecular targets and ideas for therapeutic intervention.

overall_design: Single-cell RNA sequencing was performed on dorsal root ganglia neurons from male SD Rat, total 1446 sc-RNA seq cell data, 23 batches, sorted into 19 libraries, 2 surgical status (directly injured & indirectly injured) and 4 post-surgical time point (Sham, 1 day, 3 days and 7 days after SNC).

first: Qi

last: Chen

first: Yu-Pu

last: Wang

first: Yun


title: Epigenetic and Transcriptional Dysregulation in T cells of patients with Atopic Dermatitis [ChIP-seq]

overall_design: NFKB1 ChIP-seq was performed in stimulated CD4+ T cells from 6 subjects with active moderate-to-severe AD and 6 age-matched healthy, non-allergic controls.

first: Leah

last: Kottyan


title: In vitro methylation studies in multiple human cell types [HumanMethylation450 array]

summary: An Infinium microarray (Illumina HumanMethylation450 BeadChip) was used to generate DNA methylation data from human tissue samples.

overall_design:
n=27 samples. Endothelial Cell (n=13), keratinocyte (n=8), fibroblast (n=6).
Genome annotations of the array can be downloaded from https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html

first: Ken

last: Raj


title: METTL16 promotes translation and lung tumorigenesis by sequestering cytoplasmic eIF4E2

status: Public on Mar 07 2022

city: nanjing

first: Zhang

last: Jun

state: jiangsu

address: longmiandadao

institute: China Pharmaceutical University

summary: METTL16 was previously identified as an m6A methyltransferase. In this study, we validated the cytoplasmic location of METTL16 and explored its function in the cytoplasm. We found that METTL16 promoted translation by sequestering eIF4E2, a translation initiation repressor, from the 5' cap structure.

overall_design: Overall design: One sgRNA against METTL16 groups with two hybrid clones, one shRNAs against METTL16 groups, one shRNA against EIF4E2 groups with two bio-replicates, one sgNS group and two shNS group were subjected to ribosome profiling and both the input RNA and footprint RNAs were used for sequencing.

first: Fei

first: Xianrong

last: Lin

first: Jun


title: In vitro methylation studies in multiple human cell types [HumanMethylation850 array]

summary: An Infinium microarray (Illumina Infinium HumanMethylation850 BeadChip) was used to generate DNA methylation data from human tissue samples.

overall_design:
n=317 samples. Different sources of human DNA: skin, basal cell carcinoma, keratinocytes, fibroblasts, endothelial cells, keratinocyte stem cells, induced pluripotent stem cells, HUVEC, HCAEC, neural progenitor. These cells were exposed to different conditions and treatments: CCCP (Mitochondrial oxidative phosphorylation uncoupler), bezafibrate, hTERT immortalization, chronic radiation, rapamycin.
Genome annotations of the array can be downloaded from https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html


title: Rank pathway activation attenuates mammary tumorigenesis by inducing senescence

status: Public on Feb 24 2022

first: Júlia

last: Perera-Bel

department: MARData-BU

summary: Rank overexpression attenuates mammary tumorigenesis by inducing senescence in mammary epithelial cells but enhances tumor aggressiveness by increasing stemness.

overall_design: Examination of sorted mammary epithelial cells isolated from WT and MMTVRANK mice.

first: S

last: Benítez

first: E

last: González-Suarez


title: Dnase1l3 enhances antitumor immunity and suppresses tumor progression [scRNAseq]

status: Public on Feb 07 2022

city: Durham

first: Leping

last: Li

state: NC

address: 111 TW Alexander Dr.

department: Biostatistics and Computational Biology

institute: NIEHS

summary: For the chronic inflammation-related colon cancer model (AOM/DSS-colon cancer model), 3-month-old Dnase1l3 WT and KO mice were injected with AOM (8 mg/kg, body weight). One week later, mice were challenged with 2.5% DSS water for 7 days followed by a 14-day recovery with regular drinking water for three cycles. Body weight, rectal bleeding and diarrhea were monitored during the entire experiment. Mice with more than 25% weight loss were removed during the experiment. For the AOM model, 2-month-old Dnase1l3 WT and KO mice were injected intraperitoneally with AOM (8 mg/kg, body weight). Colon tissues were isolated 9 hours, or five days after injection. All animal experiments were conducted in accordance with guidelines of NIEHS/NIH Animal Care and Use Committee.

overall_design: Tumor associated DCs and total leukocytes were isolated and enriched. Cell surface antigens were stained with following fluorochrome-conjugated Abs together with eFluor780-conjugated Live/Dead dye (ThermoFisher Scientific). PerCP-Cy5.5-anti-mouse CD11c (N418, eBio 45-0114-82), APC-anti-mouse CD26 (H194-112, BL 137807), BV711-anti-mouse CD45.2 (104, BL 137807), PE-anti-mouse CD88 (20/70, BL 135806), eFluor450-anti-mouse MHC class-II I-Ab (AF6-120.1, eBio 48-5320-82), BV510-anti-mouse Ly-6G (1A8, BL 127633). Among stained cells, cDCs (CD11c+ CD26+ CD45.2+ CD88– I-A+ Ly-6G– Live/Dead–) or leukocytes (CD45.2+ Live/Dead–) were purified using a cell sorter FACS ARIA-II (BD Biosciences). The cells were counted and examined for viability using a TC-20 cell counter (Bio-Rad). About 8000-9900 live cells at 2×10^5 cells/mL concentration with 70% or higher viability were loaded into the Single Cell Chip followed by forming single cell emulsion in Chromium Single Cell Controller (10x Genomics, Chromium Single Cell 3’ Library & Gel Bead Kit v3.1). The mRNA reverse transcription, cDNA generation and amplification, and single cell gene expression library construction were carried out according to the protocols provided by the manufacture. The libraries were then sequenced by the NIEHS Epigenomics and DNA Sequencing Core Laboratory on NovaSeq 6000 (Illumina) with paired-end sequencing (Read 1: 28; Read 2: 90). A total of 8.7×10^8 reads were obtained for the four samples


title: Single cell multi-omic sequencing (CITEseq) of human peripheral blood mononuclear cells (PBMCs)

status: Public on Feb 02 2022

city: La Jolla

first: Vasantika

last: Suryawanshi

state: CALIFORNIA

address: 9420 Athena Circle

institute: La Jolla Institute of Immunology

summary: We utilized CITESeq to investigate changes in immune cell frequencies and their transcriptomic signatures in PBMCs obtained from subjects with low and high coronary artery disease (CAD) severity quantified using gensini scoring system as well as subjects with and without IgE to alpha-gal sensitization

overall_design:
We compared changes in immune cell subtypes between subjects with low and high CAD severity or with and without IgE to alpha-gal sensitization
Raw data files include reads for both gene expression and antibody-derived tags

first: Coleen

last: McNamara

first: Klaus

last: Ley

first: Catherine

last: Hedrick

first: Yury

last: Miller


title: Transdifferentiation of B lymphocyte line ER1 into ter cells in vitro

first: Zhe

last: Yang

summary: CD19 + ER1 (B lymphocyte line) cells differentiated into CD45 + Ter119 + ter cells in vitro, we selected CD19 + ER1 cells (CD19+CD45+TER119-CD11b+), intermediate ER1 cells (CD19-CD45+TER119-CD11b+) and Ter119 + CD45 + CD19 - ER1 cells (CD19-CD45+TER119+CD11b+) for transcriptome analysis. We then performed gene expression profiling analysis using data obtained from RNA-seq of those 3 cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD19 + ER1 cells (CD19+CD45+TER119-CD11b+), intermediate ER1 cells (CD19-CD45+TER119-CD11b+) and Ter119 + CD45 + CD19 - ER1 cells (CD19-CD45+TER119+CD11b+).


title: Potent stimulation of the androgen receptor instigates a viral mimicry response in prostate cancer [ChIP-seq]

status: Public on Feb 01 2022

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

institute: Flinders University

summary: Inhibiting the androgen receptor (AR), a ligand-activated transcription factor, with androgen deprivation therapy is a standard-of-care treatment for metastatic prostate cancer (PCa). Paradoxically, activation of AR can also inhibit the growth of PCa in some patients and experimental systems, but the mechanisms underlying this phenomenon are poorly understood. This study exploited a potent synthetic androgen, methyltestosterone (MeT), to investigate AR agonist-induced growth inhibition. MeT strongly inhibited growth of PCa cells expressing AR, but not AR-negative models. Genes and pathways regulated by MeT were highly analogous to those regulated by DHT, although MeT induced a quantitatively greater androgenic response in PCa cells. MeT potently down-regulated DNA methyltransferases, leading to global DNA hypomethylation. These epigenomic changes were associated with dysregulation of transposable element expression, with long-term MeT treatment resulting in upregulation of endogenous retrovirus (ERV) transcripts. Increased ERV expression led to accumulation of double-stranded RNA and a “viral mimicry” response characterised by activation of interferon signalling, upregulation of MHC Class I molecules and enhanced recognition of murine PCa cells by CD8+ T cells. Positive associations between AR activity and ERVs/anti-viral pathways were evident in patient transcriptomic data, supporting the clinical relevance of our findings. Collectively, our study reveals that the potent androgen MeT can increase the immunogenicity of PCa cells via a viral mimicry response, a finding that has potential implications for the development of strategies to sensitize this cancer type to immunotherapies.

overall_design: Androgen receptor ChIP-seq following androgen treatment in LNCaP prostate cancer cells

first: L

first: M

last: Alizadeh-Ghodsi

first: W

middle: D

last: Tilley


title: Potent stimulation of the androgen receptor instigates a viral mimicry response in prostate cancer

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

overall_design: Refer to individual Series


title: Comorbidity between Alzheimer’s disease and Major Depression: a behavioural and transcriptomic characterization study in mice

status: Public on Jan 17 2022

summary: Background: Major Depression (MD) is the most prevalent psychiatric disease in the population and is considered a prodromal stage of the Alzheimer’s disease (AD). Despite both diseases having a robust genetic component, the common transcriptomic signature remains unknown. Method: In this regard, we investigated the cognitive and emotional behavioural responses in 3- (n=16 per group) and 6-month-old (n=14 per group) in APP/PSEN1-Tg mutant mice, before -amyloid plaques were detected in comparison with non-transgenic mice. Then, we studied the deregulation of genes and pathways in prefrontal cortex, striatum, hippocampus and amygdala of mice at both ages, using transcriptomic and functional data analysis. Results: We found that depressive-like and anxiety-like behaviours, as well as memory impairments are already present at 3-month-old APP/PSEN1-Tg mutant mice together with the deregulation of several genes such as Ciart, Chrm5, Aldh1a, Grin3b, Nr1d1 and Mc4r, and gene sets, including components of the circadian rhythms, electronic transport chain, neuroinflammation and neurotransmission. Then, we extended these results to human data performing GSEA analysis using DisGeNET database, which is specific for diseases and disease-related phenotypes and provides translational support for common deregulated gene sets related to MD and AD. Conclusion: The present study shed further light on the genetic bases shared between MD and AD, illustrating a wide characterization from the behavioural to transcriptomic level in APP/PSEN1-Tg mutant mouse model. These findings could indicate that late MD could be an early manifestation of AD.

overall_design: Transcriptomic analysis comparison between APP/PSEN1 and non-transgenic mice in four different brain regions at two different ages.

first: Ana

last: Martin-Sanchez

first: Olga

last: Valverde


title: Dnase1l3 enhances antitumor immunity and suppresses tumor progression


title: Lentiviral-mediated small hairpin RNAs (shRNAs)-based knockdown of OLFM2 or PKP2 in human adipocytes

status: Public on Dec 28 2021

summary: We introduced into subcutaneous fully-differentiated human adipocytes from the same subject small hairpin RNAs (shRNAs) against two genes, thus enabling the study of functional consequences of sustained OLFM2 (shOLFM2; n=3 biological replicates) and PKP2 (shPKP2; n=3) knockdown in these cells. The lentiviral-based transfection was used to provide a long-lasting, convenient, reliable and efficient knockdown into in vitro cultured and fully differentiated adipocytes maintained for 6 d after reaching fully differentiation. A non-targeting shRNA was used as control (shCTRL; n=4) and reference for both modifications.

overall_design: 10 samples were analysed (shOLFM2=3, shPKP2=3, shCTRL=4)

first: Francisco

last: Ortega


title: Liver sexual dimorphism in key signaling pathways across the rat life course

status: Public on Jan 14 2022

city: Mexico

first: CONSUELO

last: LOMAS

state: MEXICO

address: Vasco de Quiroga 15, Belisario Domínguez Sección XVI,

department: REPRODUCTIVE BIOLOGY

country: Mexico

institute: INCMNSZ

summary: Introduction: At the molecular level, cellular aging involves changes in multiple gene pathways, which can produce many aging phenotypes. In the liver, senescence changes lead to impaired hepatic function. We hypothesized that the natural hepatic aging process is driven by sex-dependent mechanisms. Purpose: We studied our well-established model of aging in which we have previously determined aging of metabolism, reproduction and endocrine systems. We performed liver transcriptomics (RNA-seq) on male and female rats at 110 and 650 days (d) fed with normal rat chow to determine changes key signaling pathways related to senescence processes. Methods: To identify the functional F1 liver changes due to natural aging processes, we evaluated the differentially expressed genes (DEGs) between 650d and 110d in males and females, with separate pairwise comparisons due to the marked differences. Genes were filtered based on ?1.4 fold change (FC) and nominal P value <0.05 (Studentｴs t-test). Results: We found that the natural liver aging process shows sex-differences. RNA-seq revealed more male (3,967) than female (283) differentially expressed genes (DEG) and pathways over the 110d to 650d period studied. Cell cycle pathway signaling in males was accompanied by decreased protein and gene expression of key genes (CDK2, CDK4, Cycd and PCNA) and an increase of p57 at 650d vs. 110d. In females, protein and gene expression of cell growth regulators such as p15 and p21, that inhibit cell cycle G1 progression were increased. Moreover, additionally the cell senescence pathway showed sexual dimorphism in liver gene regulation. Conclusions: Our results demonstrate how the natural aging process affects the liver transcriptome signature in a sex-dependent manner, specifically in cell cycle and cell senescence pathways, pathways that contribute in a major fashion to the development of aging-induced liver diseases. Understanding cellular senescence pathways involved in the natural aging process will aid evaluation of mechanisms associated with altered aging and frailty trajectories.

overall_design: Liver transcriptomic profiles from 110d and 650d male and female Wistar rats were analyzed by RNA-seq. 24 samples, 6 animals per group: 1) 110 d MALE n=6, 2) 650d MALE,n=6; 3) 110d FEMALE, n=6 and 4) 650d FEMALE n=6

first: Consuelo

last: Lomas Soria

first: Peter

last: Nathanielsz

first: Laura

last: Cox

first: Elena

last: Zambrano


title: Short interfering RNAs (siRNAs)-based knockdown of OLFM2 or PKP2 in human adipocytes

first: Júlia

last: Perera-Bel

summary: We introduced into subcutaneous fully-differentiated human adipocytes from the same subject short interfering RNAs (siRNAs), thus enabling the study of functional consequences of OLFM2 (siOLFM2; n=3 biological replicates) and PKP2 (siPKP2; n=3) knockdown in these cells. A lipid-based transfection reagent (i.e. Lipofectamine 3000 reagent) was used to provide a transient (72h), convenient, reliable and efficient transfection into in vitro cultured and fully differentiated adipocytes. A non-targeting siRNA was used as control (siCTRL; n=4) for both modifications.

overall_design: 10 samples were analysed (siOLFM2=3, siPKP2=3, siCTRL=4)


title: Epigenetic and Transcriptional Dysregulation in T cells of patients with Atopic Dermatitis [ATAC-seq]

status: Public on Apr 26 2022

first: Matthew

last: Weirauch

summary: Atopic dermatitis (AD), the start of the atopic march, is one of the most common skin disorders in children. Immunologically, AD involves skin barrier defects and CD4+ T cells that localize to the skin, producing inflammatory cytokines and amplifying epidermal dysfunction. To understand the gene regulatory activity differences in peripheral blood T cells in AD, we measured chromatin accessibility (ATAC-seq), NFKB1 binding (ChIP-seq), and gene expression (RNA-seq) in stimulated CD4+ T cells from subjects with active moderate-to-severe AD and age-matched healthy, non-allergic controls. Chromatin accessibility in stimulated CD4+ T cells were highly enriched for AD genetic risk variants. The vast majority of ATAC-seq peaks were shared, consistent with those sections of chromatin being equally available between matched pairs; however, NFKB DNA binding motifs were enriched in chromatin accessible in an AD-dependent manner. NFKB1 ChIP-seq identified peaks that were stronger in AD cases, enriched in controls, or shared between cases and controls. The ChIP-seq peaks that were statistically stronger in AD were more strongly enriched for NFKB DNA binding motifs. Chromatin that was more strongly accessibe and bound by NFKB1 in AD were enriched for genetic variants that increase risk for AD. Using whole genome sequencing data, we identified wide-spread genotype-dependent chromatin accessibility and allelic NFKB1 binding at AD and allergic disease genetic risk loci.

overall_design: ATAC-seq was performed in stimulated CD4+ T cells from 6 subjects with active moderate-to-severe AD and 6 age-matched healthy, non-allergic controls.

first: Leah

last: Kottyan