title: DNA polymerase POLD1 promotes proliferation and metastasis of bladder cancer by stabilizing MYC

status: Public on Apr 22 2022

first: Yu

last: Xiao

summary:
Hitherto, most studies on DNA polymerase δ (POLD1) have mainly focused on the effect of POLD1 inactivation mutation in tumors. Nonetheless, the mechanism underlying high POLD1 expression in tumorigenesis remains elusive. Herein, we substantiated the pro-carcinogenic role of POLD1 in bladder cancer (BLCA) and found that POLD1 expression is related to malignancy and prognosis of BLCA. Next, we demonstrated that POLD1 could promote proliferation and metastasis of BLCA via MYC in vivo and in vitro.
Furthermore, POLD1 and MYC were colocalized in the nucleus and co-expressed during the cell cycle. Mechanistically, we validated that POLD1 could interact directly with MYC, and POLD1 could stabilize MYC by counteracting GSK3β-mediated phosphorylation of threonine 58 and blocking the interaction between E3 ubiquitin ligase FBXW7 and MYC. Moreover, MYC could transcriptionally activate POLD1, forming a POLD1-MYC positive feedback loop to enhance the pro-carcinogenic effect of POLD1-MYC on BLCA. Overall, our study identified a novel MYC-driven oncogene POLD1, providing a potential diagnostic and therapeutic target for BLCA.

overall_design: To investigate the downstream mechanism of POLD1 regulation of bladder cancer, we performed RNA sequencing on three repeated siNC and siPOLD1-treated 5637 cells.

first: Yejinpeng

last: Wang

first: Xinghuan


title: Global gene-regulatory targets and Genome-wide binding sites of FOSL1, FOSL2 and BATF in human Th17 cells

status: Public on Apr 12 2022

city: Turku

first: Sini

last: Junttila

address: Tykistökatu 6 A

department: Turku Bioscience Centre

country: Finland

institute: University of Turku

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: MYBL2 promotes proliferation and metastasis of bladder cancer through transactivation of CDCA3

status: Public on May 02 2022

city: Wuhan

address: Donghu Road 169

department: Department of Urology

country: China

institute: Zhongnan Hospital of Wuhan University

summary: The transcription factor MYB proto-oncogene like 2 (MYBL2) plays a critical role in the regulation of gene expression and tumorigenesis. However, the biological function of MYBL2 in bladder cancer (BLCA) remains to be elucidated. Here, we first revealed that MYBL2 was elevated in BLCA tissues and was significantly correlated with clinicopathological parameters and cancer-specific survival of BLCA patients. Phenotypic assays showed that MYBL2 deficiency suppressed the proliferation and migration of BLCA cells in vitro and in vivo, whereas overexpression of MYBL2 contributed to the opposite phenotype. Mechanistically, MYBL2 could bind to the promoter of its downstream target gene cell division cycle-associated protein 3 (CDCA3) and transactivate it, which in turn promoted the malignant phenotype of BLCA cells. Further investigations revealed that MYBL2 interacted with forkhead box M1 (FOXM1) to co-regulate the transcription of CDCA3. In addition, MYBL2 and CDCA3 may activate the Wnt/β-catenin signaling by inhibiting the suppressor dickkopf-1 (DKK1), thereby regulating the malignant phenotype of BLCA cells. In conclusion, the current study has identified MYBL2 as an oncogene in BLCA. MYBL2 can accelerate the proliferation and metastasis of BLCA through the transactivation of CDCA3.

overall_design: To investigate the downstream target genes (signaling) regulated by MYBL2 in BLCA, RNA-seq was performed in 5637 cells treated by siNC/siMYBL2.

first: Wei

last: Liu


title: Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

status: Public on Mar 30 2022

city: Berkeley

first: Jessen

middle: V

last: Bredeson

state: CA

address: 545 Weill Hall #3200

department: Molecular and Cell Biology

country: USA

institute: University of California Berkeley

summary: Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus and Hymenochirus boettgeri.  Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., centric) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding, surrounded by pericentromeric LINE/L1 elements. We explored chromosome structure across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible association of centromeric chromatin, and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.

overall_design: Chromatin immunoprecipitation experiment to identify the centromeric sequence of X. tropicalis chromosomes that bind to CENP-A protein. The experiment is composed by a total of 11 samples (three biological replicates). CENP-A binding across the genome is compared against Histone H3 and H4. For each biological replicate there are input controls:  MNase treated mononucleosomes (input) and/or IgG controls.

first: Owen

middle: K

last: Smith

first: Guadalupe

last: Aguirre-Figueroa

first: Sofia

middle: M

last: Ruiz

first: Marko

middle: E

last: Horb

first: Gary

middle: J

last: Gorbsky

first: Aaron

middle: F

last: Straight


title: Genome-wide binding sites of FOSL1, FOSL2 and BATF in human Th17 cells [ChIP-seq]

summary: The aim of this study was to investigate the transciptional mechanisms governed by FOSL1, FOSL2 and BATF for regulation of human Th17 cell-function. To determine the genome-wide binding sites of these factors, ChIP-seq analysis was performed using in vitro derived Th17 cells at 72h of polarization.

overall_design: Analysis of of FOSL1, FOSL2 and BATF genome-wide binding sites. Altogether 12 ChIP-seq samples [4 - BATF ChIP, 4 - FOSL1 ChIP and 4 - FOSL2 ChIP] were analysed. Two biological replicates of each TF ChIP and their corresponding inputs were sequenced on Miseq Nano (Fasteris Life Sciences).

first: Ankitha

last: Shetty

first: Subhash

last: Tripathi

first: Tanja

last: Buchacher

first: Rahul

last: Biradar

first: Santosh

middle: D

last: Bhosale

first: Tapio

last: Envall

first: Asta

last: Laiho

first: Robert

last: Moulder

first: Omid

last: Rasool

first: Sanjeev

last: Galande

first: Laura

middle: L

last: Elo

first: Riitta

last: Lahesmaa


title: QuantSeq/3' targeted seq supporting study Probing 3’UTRs as modular regulators of gene expression

status: Public on Apr 09 2022

city: Edinburgh

first: Edward

last: Wallace

address: Waddington 2.18, Max Born Crescent, King’s Buildings

department: School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

summary: The goal of the study is to analyze the function of 3'-UTR motifs in the non-native context. Several 3'-UTR motifs predicted to have stabilizing or destabilizing effects on mRNA were inserted into terminators controlling the expression of reporter mCherry gene in following contexts: pRps3-mCherry-tRps3, pPgk1-mCherry-tRps3, pTsa1-mCherry-tTsa. 3'-end sequencing was used to measure the levels of expression of reporter gene and distribution of poly(A) sites.

overall_design: 3'-end sequencing of Saccharomyces cerevisiae strains expressing mCherry reporter controlled by different promoters as well as modified and non-modified terminators. mCherry reporter constructs are expressed from a low copy number plasmid. All modified constructs have three 9bp insertion sites with different combinations of the following motifs: N, a randomly generated sequence;  A, an ATATTC motif; H, a TTTCATTTC motif; and T, a TGTACAATA motif.

first: Sam

last: Haynes

first: Jamie

last: Auxillos

first: Weronika

last: Danecka


title: Molecular signature of cardiac remodeling associated with Polymerase Gamma mutation

city: Columbus

first: Matthew

last: Stratton

state: OH

address: 473 W 12th Ave

institute: Ohio State University

summary: Gene expression analysis of cardiac RV tissue in WT and POLG mutant mice.

overall_design: 4 WT and 4 POLG mutants were analyzed (all female)

middle: S


status: Public on Mar 15 2022

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: RNA sequencing was performed on differentiated airway epithelial cells that either remained untreated or were treated with IL-5 for 6 or 24 hours. Total RNA samples were sent to the DNA Sequencing Facility at the University of Wisconsin-Madison Biotechnology Center’s Gene Expression Center for library preparation and sequencing. RNA was quantified using NanoDrop and Agilent NanoChip. Library preparation was based on the TruSeq RNA Sample Preparation v2 Guide. cDNA libraries were assayed on Agilent DNA1000 Chip to verify library size. Genes were filtered to include those that had a trimmed mean of M values (TMM) normalization count of at least 1 in at least 10% of libraries and were classified as protein coding using BioMart, and then transformed to log2 counts per million along with observations level weights using voomWithQualityWeights from the limma R package.  Normalized voom counts were then used to compare among the 3 conditions by linear modeling (limma) including a random effect for donor. Multiple testing correction was by the Benjamini–Hochberg procedure controlling the false discovery rate (FDR) at level 0.05.

overall_design: IL-5 induced gene expression in human differentiated airway epithelial (ALI) culture. Sequencing was performed on differentiated airway epithelial cells that either remained untreated or were treated with IL-5 for 6 or 24 hours.

first: Karina

middle: T

last: Barretto

first: Rebecca

middle: A

last: Brockman-Schneider

first: Yury

last: Bochkov

first: James

last: Gern

first: Stephane

last: Esnault

middle: C

last: Altman


title: Single-Cell Transcriptomics of Human Substantia Nigra in Parkinson's Disease

status: Public on Mar 28 2022

city: New York

first: Bin

last: Zhang

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Parkinson’s disease (PD) is the most common neurodegenerative movement disorder with unknown etiology. Loss of neuromelanin-containing dopaminergic (DA) neurons in the substanstia nigra (SN) is the hallmark of PD neuropathology. Here we performed single-nucleus RNA sequencing (snRNA-seq) of nuclei from the postmortem SN of control and idiopathic PD patients across various disease stages. The resulting transcriptomic atlas revealed a landscape of cellular alterations associated with disease progression in PD.

overall_design: The SN from postmortem brains were requested from NIH Neurobiobank (www.neurobiobank.nih.gov) and fulfilled by Brain Endowment Bank at Miller School of Medicine, University of Miami. Specifically, frozen punches of substantia nigra were obtained and then pulverized in a liquid-nitrogen-chilled mortar and aliquoted. Approximately 50mg tissues were used for snRNA-seq. Single nucleus gene expression sequencing was performed on the samples using the Chromium platform (10x Genomics, Pleasanton, CA) with the Next GEM Single cell 3’GEX Reagent kit, and an input of ~10,000 nuclei from a debris-free suspension.

first: Qian

last: Wang

first: Minghui

first: Insup

last: Choi

first: David

last: Davis

first: Xiaoyan

last: Sun

first: Zhenyu

last: Yue


title: Mettl3-dependent m6A modification and mRNA expression in postnatal liver

status: Public on Mar 09 2022

city: Jinan

first: Detian

last: Yuan

address: Wenhuaxi 44

institute: Shandong University

first: Shiguan


title: Identification and characterization of human CD34+ and CD34dim/- neutrophil-committed progenitors [Bulk RNA-seq]

status: Public on Mar 11 2022

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

country: Italy

institute: University of Verona

summary: Here we report the identification of human CD66b-CD64dimCD115- neutrophil-committed progenitor cells (NCPs) within the SSCloCD45dimCD34+ and CD34dim/- subsets in the bone marrow. NCPs were either CD45RA+ or CD45RA-, and in vitro experiments showed that CD45RA acquisition was not mandatory for their maturation process. NCPs exclusively generated human CD66b+ neutrophils in both in vitro differentiation and in vivo adoptive transfer experiments. Single-cell RNA-sequencing analysis indicated NCPs fell into four clusters, characterized by different maturation stages and distributed along two differentiation routes. One of the clusters was characterized by an interferon-stimulated gene signature, consistent with the reported expansion of peripheral mature neutrophil subsets that express interferon-stimulated genes in diseased individuals. Finally, comparison of transcriptomic and phenotypic profiles indicated NCPs represented earlier neutrophil precursors than the previously described early neutrophil progenitors (eNePs), proNeus and COVID-19 proNeus. Altogether, our data shed light on the very early phases of neutrophil ontogeny.

overall_design: Examination of the gene expression profiles of neutrophil-committed progenitors (NCPs), promyelocytes (PMs), myelocytes (MYs) metamyelocytes (MMs), band cells (BCs) and segmented neutrophils (SNs) from BMs as well as peripheral blood neutrophils (PMN), isolated by cell sorting by using a Becton Dickinson FACS Aria Fusion (BD Biosciences)

last: Bianchetto

first: Nicola

last: Tamassia

first: Marco

last: Cassatella

first: Federica

last: Calzetti

first: Giulia

last: Finotti


title: RNA-seq analysis of abdominal and gulteofemoral adipose derived stem cells isolated form PCOS and control women

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

summary: RNA-seq experiments revealed an ABD-and GF-ASC selective gene expression signature between PCOS and control women.

overall_design: ASC isolated and cultured from Abominal and Gluteo-Femoral adipose tissue obtained from premenopausal apple-shaped women with or without PCOS were used to perform transcriptome analysis by RNA-seq

first: Steven

middle: R

last: Smith

first: Timothy

last: Osborne


title: Identification and functional prediction of long noncoding RNA and mRNA related to connective tissue disease-associated interstitial lung diseases

status: Public on Jan 05 2022

city: Nanchong City

first: daifei

last: dai

state: Sichuan Province

address: No. 234, Fujiang Road, Shunqing District

institute: North Sichuan Medical College

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: LncRNA microarray analysis was used to identify the pattern of lncRNA and mRNA dysregulation between connective tissue disease-associated interstitial lung diseases (CTD-ILD) and connective tissue disease without associated interstitial lung disease (CTD-NILD). Differential genes were identified by bioinformatic analysis. Relative expression levels of five differentially expressed lncRNAs and one mRNA in 120 CTD patients with or without ILD were detected by quantitative reverse-transcription PCR (qRT-PCR). The differential gene expression analysis revealed 46 lncRNAs and 133 mRNAs were upregulated while 194 lncRNAs and 85 mRNAs were downregulated in the CTD-ILD group compared to the CTD-NILD group. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses identified several significant biological processes and signaling pathways, including NF-kappa B signaling pathway, IL-17 signaling pathway, Toll-like receptor signaling pathway, B cell receptor signaling pathway. QRT-PCR confirmed that the selected target genes were differentially expressed in different groups. In particular, the ENST00000604692 expression level was significantly higher in the ILD than the NILD group. This research has demonstrated, for the first time, the specific profile of lncRNA in PBMCs of CTD-ILD patients and the potential signal pathways related to the pathogenesis of CTD-ILD, which may provide newfound insights for the diagnosis and treatment of CTD-ILD patients.

overall_design: Two-condition experiment：connective tissue disease-associated interstitial lung diseases (CTD-ILD) patients vs. connective tissue disease without associated interstitial lung disease (CTD-NILD)  patients peripheral blood mononuclear cells. Biological replicates: 4 CTD-ILD patients replicates, 3 CTD-NILD patients replicates.

first: Fei

last: Dai

first: Quanbo

first: Yixi

last: He

first: Yiping

last: Tang

first: Tianyi

last: Lei

first: Yi

last: Jiang

first: Yufeng

last: Qing


title: Transcriptional control of retinal ganglion cell death after axonal injury

status: Public on Mar 24 2022

city: Bar Harbor

first: Gareth

last: Howell

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary:
Purpose: This study aims to the downstream transcriptional networks controlled by JUN and DDIT which are critical for RGC death
Methods: RNA was isolated from the retinas of wild-type mice and mice deficient in Jun, Ddit3, and both Jun and Ddit3 three days after mechanical optic nerve crush injury (CONC), and was subjected to RNA-sequecing.
Results: This study identified downstream transcriptional changes after injury included both neuronal survival and pro-inflammatory signaling that were attenuated to differing degrees by loss of Ddit3, Jun, and Ddit3/Jun.
Conclusion: These data suggest pro-inflammatory signaling in the retina might be secondary to activation of pro-death pathways in RGCs after acute axonal injury. These results determine the downstream transcriptional networks important for apoptotic signaling which may be important for ordering and staging the pro-degenerative signals after mechanical axonal injury.

overall_design: Retina mRNA profiles of wild-type and mice deficient in Jun (Jun-/-), Ddit3 (Ddit3-/-), and both Jun and Ddit3 (Jun-/- Ddit3-/-) three days after mechanical optic nerve crush injury (CONC)

first: Stephanie

middle: B

last: Syc-Mazurek

first: Hongtian

last: Yang

first: Olivia

last: Marola

first: Richard

last: Libby


title: Arginase-1 is Required for Macrophage-Mediated Renal Tubule Regeneration

status: Public on Mar 23 2022

city: New Haven

first: Leyuan

last: Xu

state: CT

address: 300 Cedar Street, Ste S255B

department: Internal Medicine/Section of Nephrology

institute: Yale University

summary: In this study, we compared the transcriptomes of the kidney subjected to unilateral IRI with contralateral nephrectomy (IRI/CL-NX) and the normal healthy control kidney at the single cell level to identify major cell types in the kidney and the differential transcriptional response during kidney repair following IRI.

overall_design: Single cell mRNA profiling of kidneys from wild-type mouse subjected to IRI/CL-NX and normal healthy control mouse

first: Lloyd

middle: G

last: Cantley


title: Single-cell analysis reveals inter- and intra-tumor heterogeneity in metastatic breast cancer

status: Public on May 13 2022

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel

summary: The plasticity and heterogeneity of cancer cells are known to play a major role in malignant progression, yet the precise molecular drivers of metastases remain elusive. We performed single-cell RNA-Seq (scRNA-Seq) on tumours and matched lung macrometastases of patient-derived xenografts (PDXs) of breast cancer to identify molecular mechanisms of metastasis during colonization.

overall_design: Tumors and matched lung metastases from PDX models grown in NSG mice were dissociated and human cells purified by FACS . PDX models cells selection relied on the CD298 human-specific marker. Samples derived from a cell line MDA-MB-231 expressing a GFP-Luciferase construct were selected based on GFP expression. Single cell isolation was performed on the Fluidigm C1 platform. mRNA was isolated with the Takara SMART-Seq Ultra Low RNA kit. Libraries for Illumina sequencing were prepared with the Nextera XT DNA Library Preparation Kit.

first: Baptiste

last: Hamelin

first: Milan

last: Obradović

first: Atul

last: Sethi

first: Michal

last: Kloc


title: CD66b-CD64dimCD115- cells in the human bone marrow represent neutrophil-committed progenitors

first: Francisco

last: Bianchetto-Aguilera


title: Imbalance of Ly6Chi and Ly6Clo monocytes/macrophages worsens hyperoxia-induced lung injury and is rescued by IFN-gamma

status: Public on Feb 28 2022

last: Osmond

summary: This study is to examine the transcriptome of mononuclear cell populations in the neonatal lung.  We investigated how acute hyperoxia-induced lung injury changes gene expression within these mononuclear populations: dendritic cells, interstitial monocytes/macrophages, and alveolar macrophages.

overall_design: Litters of newborn C57BL/6 mice were identified within 6 hours of birth, mixed, and randomly assigned to hyperoxia conditions (FiO2 0.9) or normoxic control condition.  Pups were euthanized after 1.5 days of hyperoxia or normoxia exposure.  Mice were perfused and whole lungs were isolated then enzymatically and mechanically digested.  4 populations of mononuclear cells were identified by flow cytometry, including dendritic cell (DC, MHCIIhi CD11chi), Ly6Chi monocytes/macrophages (Ly6Chi CD11clo), Ly6Clo monocytes/macrophages (Ly6Clo CD11chi), and alveolar macrophages (AM, SiglecFhi CD11chi).

first: Laurie

last: Eldredge

first: Rane

last: Creasy

first: Shigeru

last: Tanaka

first: Jen-Feng

last: Lai

first: Mario

last: Rosasco

first: Steven

last: Ziegler


title: Effect of group IIA phospholipase A2 deletion on gene expression in the small intestine

status: Public on Jan 01 2022

city: Tokyo

first: Yoshitaka

last: Taketomi

address: 7-3-1 Hongo, Bunkyo-ku,

department: CDBIM, Graduate School of Medicine,

country: Japan

institute: The University of Tokyo

summary: Besides promoting inflammation by mobilizing lipid mediators, secreted phospholipase A2 group IIA (sPLA2-IIA) prevents bacterial infection by degrading bacterial membranes. Here we show that despite the restricted intestinal expression of sPLA2-IIA in BALB/c mice, its genetic deletion leads to amelioration of cancer and exacerbation of psoriasis in distal skin. Intestinal expression of sPLA2-IIA is reduced after antibiotics treatment or under germ-free conditions, suggesting its upregulation by gut microbiota. Metagenome, transcriptome and metabolome analyses have revealed that sPLA2-IIA deficiency alters the gut microbiota, accompanied by notable changes in the intestinal expression of genes related to immunity and metabolism as well as the levels of various blood metabolites and fecal bacterial lipids, suggesting that sPLA2-IIA contributes to shaping of the gut microbiota. The skin phenotypes in Pla2g2a–/– mice are lost when they are co-housed with littermate wild-type mice, resulting in mixing of the microbiota between the genotypes, or when they are housed in a more stringent pathogen-free facility, where Pla2g2a expression in wild-type mice is low and the gut microbial compositions in both genotypes are nearly identical. Thus, our results highlight a new aspect of sPLA2-IIA as a modulator of gut microbiota, perturbation of which affects distal skin responses.

overall_design: Groups, Pla2g2a knockout (–/–) and Pla2g2a wild-type (+/+) mice on BALB/c background; Tissue, small intestine; Age, 12-week-old; Condition, steady state; RNA, total RNA samples pooled from three mice.

first: Yuh

last: Kidoguchi

first: Yasumasa

last: Nishito

first: Makoto

last: Murakami


title: A single-cell landscape of human liver transplantation reveals a pathogenic immune niche associated with early allograft dysfunction

status: Public on Dec 16 2021

city: Hangzhou

first: Xin

last: Shao

state: Zhejiang

address: #866 Yuhangtang Rd.

institute: Zhejiang University

summary: Liver transplantation (LT) is the standard therapy for individuals afflicted with end-stage liver disease. Despite notable advancements in LT technology during recent decades, the incidence of early allograft dysfunction (EAD) remains a critical concern, exacerbating the current organ shortage and detrimentally affecting the prognosis of recipients. Unfortunately, the perplexing hepatic heterogeneity has impeded our comprehension of the cellular traits and molecular events that contribute to EAD. Herein, we constructed the pioneering single-cell transcriptomic landscape of human transplanted livers derived from non-EAD and EAD patients, with 12 liver samples from 7 donors collected at the stages of cold perfusion and portal reperfusion. By comparing 75,231 cells of non-EAD and EAD patients, we identified an EAD-associated immune niche comprising MAIT, GZMB+ GZMK+ NK cells, and S100A12+ neutrophils, which were significantly elevated in EAD patients. Moreover, we verified this immune niche and its association with EAD occurrence in two independent cohorts. Our findings clarified the cellular characteristics of transplanted livers and the EAD-associated pathogenic immune niche at the single-cell level, offering valuable insights into the EAD onset. The updated data see FigShare (https://figshare.com/articles/dataset/24521662)

overall_design: The complete database comprised the single-cell gene expression for samples taken from four patients,  wherein liver grafts berfore LT (Con) were sampled after cold perfusion and liver grafts after LT (IR) were sampled affer 2h portal reperfusion. Four donors were from the healthy after brain death. RNA was extracted from the 8 samples and analyzed using 10X Genomics and Illumina sequencing technology.

first: Kai

last: Wang

first: Xiao

last: Xu

first: Xiaohui

last: Fan


title: Identification of gene expression signatures for phenotype-specific drug targeting of cardiac remodeling

status: Public on Feb 24 2022

city: Vienna

first: Dominika

last: Lukovic

address: Waehringer Guertel 18-20

department: Internal Medicine II

country: Austria

institute: Medical University of Vienna

summary: Objectives  Transcriptome analysis of the left ventricle (LV) aimed to identify targets for prevention of myocardial fibrosis (MF).    Background  MF causing heart failure with reduced ejection fraction is generated by different pathological mechanisms. We have designed two types of MF by using translational animal models: reactive interstitial MF and replacement fibrosis.    Methods  Domestic pigs were treated with either doxorubicin (DOX, n=5) or a liposomal encapsulation of doxorubicin-citrate (Myocet®, MYO, n=5) to generate cardiotoxicity-induced MF. For pressure overload-induced MF, we used artificial isthmus stenosis with stepwise developing myocardial hypertrophy and final fibrosis (Hyper, n=3). Volume-overload MF was developed in adverse remodeled LV after myocardial infarction (RemoLV, n=3). Sham interventions served as controls (Control, n=3). Myocardial samples from the anterior wall of groups DOX, MYO, Hyper and Control, and from the non-ischemic remodeled posterior wall of animals in group RemoLV were subjected to RNA-sequencing following transcriptional analysis.

overall_design: Overall, 19 myocardial tissue samples were subjected to RNA-seq analysis with following groups: DOX (N=5), MYO(N=5), Hyper(N=3), RemoLV(N=3), Control (N=3).

first: Johannes

last: Winkler

first: Ena

last: Hasimbegovic

first: Julia

last: Mester-Tonczar

first: Katrin

last: Zlabinger

first: Katharina

last: Schefberger

first: Nina

last: Kastner

first: Andreas

last: Spannbauer

first: Denise

last: Traxler-Weidenauer

first: Jutta

last: Bergler-Klein

first: Noemi

last: Pavo

first: Georg

last: Goliasch

first: Sandor

last: Batkai

first: Thomas

last: Thum

first: Faiez

last: Zannad

first: Mariann

last: Pavone-Gyöngyösi


title: mRNA profiles of sorted CD4 T cells from wild-tye, T-bet-/-, and Rorc mutant mice infected with Chlamydia muridarum

status: Public on Jan 25 2022

city: Davis

first: Stephen

last: McSorley

address: One Shields Avenue

department: Center for Immunology and Infectious Diseases

institute: University of California Davis

summary: The purpose of this study was to compare CD4 T cell gene expression from the female reproductive tracts (FRTs) of mice infected vaginally with Chlamydia muridarum in wild-type, T-bet deficient, and RORgt mutant mice.

overall_design: 15 samples total were submitted, 5 for each genotype. Each sample was generated from a pool of three mice.

first: Jordan

last: Rixon


title: High affinity enhancer promoter interactions can bypass strong CTCF/cohesin-mediated insulation contributing to phenotypic robustness

status: Public on Dec 30 2021

city: Bethesda

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health

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

overall_design: Refer to individual Series


title: Single-cell RNAseq analysis of kidneys from RNLS knockout mice with chronic kidney disease treated with RNLS peptide encapsulated in mesonanoparticles

first: Leyuan

last: Xu

summary: We compared transcriptome profiles of kidneys from RNLS KO mice treated with RNLS peptide RP81 in mesonanoparticle (RP81-MNP) or with empty MNP (control). Our study provided some molecular mechanism of how RNLS peptide protected kidney from  cisplatin-induced CKD.

overall_design: RNLS KO mice were treated with either empty MNP or RNLS peptide RP81-MNP once a week for 4 weeks, and 2 doses of cisplatin at 15mg/kg, 2 weeks apart, for 4 weeks. Control mice kidneys were collected and digested into single cells, followed by next-generation sequencing analysis.

first: Xiaojia

last: Guo

first: Robert

last: Safirstein

first: Gary

last: Desir


title: Induction of T cell dysfunction and NK-like T cell differentiation in vitro and in patients after CAR T cell treatment [scRNA-seq]

status: Public on Dec 06 2021

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: Chimeric antigen receptor (CAR) T cell therapy has achieved remarkable success in hematological malignancies but remains largely ineffective in solid tumors. A major factor leading to the reduced efficacy of CAR T cell therapy is T cell dysfunction, and the mechanisms mediating this dysfunction are under investigation. Here we establish a robust in vitro model to study mesothelin-redirected CAR T cell dysfunction in pancreatic cancer. Continuous antigen exposure results in hallmark features of exhaustion including reduced proliferation capacity and cytotoxicity, and severe defects in cytokine production. Here we identified a transcriptional signature at both population and single-cell levels in CAR T cells after chronic antigen exposure. In addition, TCR lineage tracing revealed a CD8+ T-to-NK-like T cell plasticity that results in reduced antigen- dependent tumor cell killing. The transcription factors SOX4 and ID3 are specifically expressed in the dysfunctional CAR NK-like T cells and are predicted to be master regulators of the dysfunction gene expression signature and of the post-thymic acquisition of an NK-like T cell fate. Finally, we identified the emergence of CAR NK-like T cells in a subset of patients after infusion of CAR T cells. The findings gleaned from this study reveal new approaches to improve the efficacy of CAR T cell therapy in solid tumors by preventing or revitalizing CAR T cell dysfunction and shed light on the plasticity of human CAR T cells.

overall_design: Examines expression by single-cell RNA-seq in CD8+ T cells from three donors. One experimental variable: exposure (values: control day 0 and continuous antigen exposure).

first: Shunichiro

last: Kuramitsu

first: Charly

last: Good

first: Parisa

last: Samareh

first: Greg

first: Kenichi

last: Ishiyama

first: Yujie

last: Ma

first: Nils

last: Wellhausen

first: Lifeng

last: Tian

first: Sangya

last: Agarwal

first: Sonia

last: Guedan

first: M

last: Aznar

first: Katherine

last: Alexander

first: Zhen

last: Zhang

first: Nathan

last: Singh

first: Max

middle: W

last: Richardson

first: Keisuke

last: Watanabe

first: Janos

last: Tanyi

first: Mark

middle: H

last: O'Hara

first: Marco

last: Ruella

first: Simon

last: Lacey

first: Edmund

last: Moon

last: Schuster

first: Steven

last: Albelda

first: Lewis

last: Lanier

first: Regina

last: Young

first: Shelley

last: Berger

first: Carl

last: June


title: Generation of Allogeneic Hematopoietic Stem Cell-Engineered Invariant Natural Killer T cells for Off-the-Shelf Immunotherapy [RNA-seq]

status: Public on Dec 01 2021

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: While T cell-based immunotherapies have shown promising clinical responses, current cancer treatments are restricted to autologous cellular products due to the risk of graft-versus-host disease (GvHD) by allogeneic cell transfer. Invariant natural killer T (iNKT) cells are ideal cell carriers for developing off-the-shelf allogeneic cellular therapy because they are powerful immune cells targeting a broad range of cancers without causing GvHD. However, current immunotherapies using iNKT cells are impeded by their extremely low number in cancer patients. In this study, we aimed to overcome this limitation by generating a large number of iNKT cells through TCR engineering of human hematopoietic stem cells (HSCs) and differentiation of HSCs to iNKT cells in an in vitro cultured system. Additionally, Chimeric antigen receptor (CAR) engineering and the CRISPR-Cas9 gene editing tool were utilized to enhance the tumor killing efficacy of iNKT cells and eliminate HLA molecules on their surface, making the cellular product suitable for cancer therapy and allogeneic adoptive transfer. Our results demonstrated successful generation of the promising off-the-shelf B cell maturation antigen (BCMA)-CAR engineered iNKT cells for treating multiple myeloma, and the same strategy will be applied to multiple cellular products for treating other cancers.

overall_design: Examination of expression changes of different T cell and NK cell subtypes.

first: Yanruide

last: Li

first: Matteo

last: Pellegrini

first: Lili

last: Yang


title: Function analysis and characterisation of a novel chitinase, MdCht9, in Musca domestica

status: Public on Nov 30 2021

city: Guiyang

first: Wen-Jing

last: Zhao

state: Guizhou

address: Dongqing Road

department: School of Basic Medical Sciences

institute: Guizhou Medical University

summary: To investigate how MdCht9 contribute to the  development and digestion of Musca domestica, we silenced the chitinase gene 9 (MdCht9) by its dsRNA, while silenced  the GFP as the control. Then we compared  the differental expression genes between the test group  and the control group.

overall_design: Retinal mRNA profiles of silencing MdCht9 (dsMdCht9) and silencing GFP (dsGFP) toward to the 2nd-instar housefly larvae.

first: Guo

last: Guo

first: Yan

first: Long-Bin


title: KRAS allelic imbalance drives a MAPK dependent tumour initiation programme inefficient at rewiring the tumour microenvironment to provoke metastasis

status: Public on Jan 17 2022

city: Glasgow

first: Andrew

last: Campbell

address: Switchback Road

institute: CRUK Beatson Institute

summary: Murine small intestinal tumours, adjacent normal tissues and tumour organoids, following Kras mutation under the control of VilCreER, alone or in combination with p53 and Notch mutation, in the presence or absence of a wild type Kras allele.

overall_design: Expression data from whole intestinal tumours, normal intestine, or tumour derived organoids.

first: Arafath

last: Kaja Najumudeen

first: Owen

last: Sansom

first: Kathryn

last: Gilroy


title: Chronic AMPK inactivation slows SHH medulloblastoma progression by inhibiting mTORC1 and depleting tumor stem cell populations

status: Public on Dec 08 2021

city: Atanta

first: Tim

last: Gershon

state: GA

address: Emory University School of Medicine

department: Pediatrics

institute: Emory University

summary: We report scRNA-seq data showing the effect of Prkaa1/2 deletion  on medulloblastomas that form in Smo-mutant mice. We generate tumor-bearing mice by breeding hGFAP-Cre/Prkaa1fl/fl/Prk112fl/fl  and Prkaa1fl/fl/Prk112fl/fl/SmoM2 mouse lines to prodce tumor-prone progeny with homozygous, conditional deletion of Prkaa1 and Prkaa2 (G-SmoAMPK mice). We compared tumors from  G-Smo mice withintact Prkaa1 and Prkaa2 to tumors from G-SmoAMPK mice, using Drop-seq-based scRNA-seq.

overall_design: comparison of tumors in replicate Prkaa1/2-deleted mice versus tumors in Prkaa1/2 intact controls

first: Taylor

last: Dismuke

first: Daniel

last: Malawsky

first: Andrey

last: Tikunov

first: Timothy


title: High affinity enhancer promoter interactions can bypass strong CTCF/cohesin-mediated insulation contributing to phenotypic robustness [ChIP-seq]

first: Pedro

last: Rocha

summary: Transcriptional control by enhancers located at large genomic distances from their targets is a common and integral feature of gene regulation. To understand how tissue specific enhancer-promoter interactions arise and to assess their resilience to perturbation of chromatin architecture, we generated an allelic series of mouse mutants carrying modifications to the structure of the Sox2 locus. We show that in pre-implantation epiblast cells and in neuronal lineages, CTCF-mediated loops are neither required for the interaction of Sox2 with its long-distance enhancers nor for its expression. Sox2-enhancer interactions in these cells were also robust to the introduction of CTCF/cohesin-mediated loops of varying degrees of insulation. These loops led to reduced interactions and Sox2 expression but did not cause their full disruption and were compatible with implantation and neurogenesis. In contrast, Sox2 expression in the anterior foregut was highly susceptible to perturbation of local chromatin structure with mutant embryos failing to separate trachea from esophagus and dying perinatally. Thus, in addition to being locus-specific, the functional impact of nuclear organization on cell fate-decisions is also highly dependent on biological context. Our work highlights the need of studying nuclear organization mechanisms in vivo and suggests that high-affinity enhancer-promoter interactions can provide robustness to structural perturbations to ensure faithful phenotypic outcomes.

overall_design: ChIP-seq was performed in heads of pooled WT E11.5 embryos


title: Modular transcriptional repertoire analyses identify neutrophil signature as candidate biomarker for lupus nephritis

status: Public on Jan 02 2022

city: Seattle,

first: Stephanie

last: Osmond

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Gene expression profiling (compared to healthy controls) to identify a biomarker for lupus nephritis

overall_design: 157 “SLE”, 20 “Healthy controls of SLE,  25 Control of Kidney Disease, 21 Healthy control of sepsis, and kidney disease, and 15 ICU Controls, were followed up for up to 3 years. Clinical assessment, current treatment, laboratory results and SLEDAI score were collected at each visit (V1, V2...). SLE patients are compared to control groups.

first: Laurent

last: Chiche

first: Noemie

last: Jourde-Chiche

first: Elizabeth

last: Whalen

first: Scott

last: Presnell

first: Cate

last: Speake

first: Vivian

last: Gersuk

first: Bertrand

last: Dussol

last: Gondouin

first: Stephane

last: Burtey

first: Peter

last: Linsley

first: Virginia

last: Pascual

first: Damien

last: Chaussabel


title: Longitudinal single-cell RNA-seq data of metastatic ovarian cancer

status: Public on Dec 24 2021

city: Helsinki

first: Kaiyang

last: Zhang

state: Finland

address: Biomedicum Helsinki 1, Haartmaninkatu 8

department: Faculty of Medicine

institute: University of Helsinki

summary: We characterized transcriptional patterns of chemotherapy resistance in high-grade serous ovarian cancer (HGSOC) using patient-derived prospective tissue sample pairs before and after treatment at single-cell resolution. Our cohort consists of scRNA-seq data from treatment-naïve and post-neoadjuvant chemotherapy (post-NACT) pairs from 11 homogeneously treated HGSOC patients. After quality control, we obtained 51,786 cells, including 8,806 malignant epithelial (tumor), 8,045 stromal and 34,935 immune cells. Our unbiased analysis reveals how chemotherapy modulates cancer cell states by both subclonal selection and microenvironment boosted transcriptional induction across the homogeneously treated sample cohort. Our results define a cell state that allows biomarker-based prediction and targeting of chemoresistance.

overall_design:
Expression profiles of single cells from treatment-naïve and post-NACT patient-derived prospective tissue sample pairs from 11 homogeneously treated HGSOC patients.
Patients participating in this study are from the DECIDER cohort (NCT04846933), and treated at Turku University Hospital.
*** Raw data were deposited in EGA (EGAD00001006922) due to patient privacy concerns.

first: Erdogan

last: Erkan

first: Sampsa

last: Hautaniemi

first: Anna

last: Vähärautio


title: Thyroid hormone action in human hepatocytes and the Cistromes of TRB1 and ChREBP in liver of mice

status: Public on Nov 16 2021

city: new york

first: arturo

last: mendoza

state: ny

address: 1 east loop 15a

department: Division of Endocrinology, Diabetes and Metabolism

institute: weill cornell medicine

summary: Human iPSC were differentiated to hepatocytes and treated with T3 or vehicle then total RNA was sequenced. The cistrome of TRB1 or ChREBP was delineated in liver of hypothyroid and hyperthyroid mice.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 24 total ChREBP ChIP-Seq samples: 2 sequencing replicates of 2 biological samples in each of 3 conditions (wildtype treated with PTU, wildtype treated with PTU and T3, knockout model treated with PTU and T3), plus corresponding input controls for all.  8 total THRB ChAP-Seq samples: 2 biological samples in each of 2 conditions (hyper- and hypothyroidism) with corresponding controls.  9 total RNA-Seq samples: 5 treated (T3) and 4 controls.

first: Arturo

last: Mendoza

first: Anthony

middle: N

last: Hollenberg

first: Andrew

last: Wilson

first: Douglas

last: Forrest


title: Deep mutational scan of a drug efflux pump reveals its structure-function landscape

status: Public on Nov 25 2021

city: Zurich

first: Gianmarco

last: Meier

address: Gloriastrasse 28/30

department: Institute of medical microbiology

institute: University of Zurich

summary: Drug efflux is a common resistance mechanism found in bacteria and cancer cells. Although several structures of drug efflux pumps are available, they provide only limited functional information on the phenomenon of drug efflux. Here, we performed deep mutational scanning (DMS) on the bacterial ATP binding cassette (ABC) transporter EfrCD from Enterococcus faecalis to determine the drug efflux activity profile of more than 1400 single variants

overall_design: Plasmid libraries (triplicates rep1-3) of EfrCD variants were expressed in Lactococcus lactis NZ9000 ΔlmrCD ΔlmrA and subjected to one round of growth competition in the presence of drugs (Daunorubicin, Ethidium and Hoechst 33342). Plasmids from input library (t0) and after one round of growth competition (t1) were extracted. The coding region of EfrCD was sequenced by Illumina sequencing and reads for individual variants were counted.

first: Sujani

last: Thavarasah

first: Markus

last: Seeger


title: Single-cell RNAseq analysis of kidneys from Wild Type and RNLS knockout control mice and mice with chronic kidney disease

first: Leyuan

last: Xu

summary: We compared transcriptome profiles of WT kidneys with that of RNLS KO kidneys. We also compared transcriptome profiles of healthy kidneys to CKD kidneys. Our study represents the first detailed transcriptome analysis of kidneys from mice with cisplatin-induced chronic kidney disease and provides the dissection of renalase functions.

overall_design: WT and RNLS KO mice were treated with or without 2 doses of cisplatin at 15mg/kg, 2 weeks apart. After 4 weeks of cisplatin treatment, animals developed CKD as evidenced by elevated plasma creatinine levels. Kidneys were collected and digested into single cells, followed by next-generation sequencing analysis.

first: Xiaojia

last: Guo

first: Robert

last: Safirstein

first: Gary

last: Desir


title: High affinity enhancer promoter interactions can bypass strong CTCF/cohesin-mediated insulation contributing to phenotypic robustness [Capture Hi-C]

first: Pedro

last: Rocha

overall_design: Capture HiC (CHiC) was performed in the following tissues: blastocyst-derived mouse embryonic stem cells, heads of individual E11.5 embryos, sox2-expresssing anterior foregut cells. For ES and neural cells, 2 individual homozygous embryos were processed and anakyzed separately.  WT controls are littermates from isolated embryos. AFG cells were pooled from a WT embryo.


title: Kidney-targeted renalase agonist prevents cisplatin-induced chronic kidney disease by inhibiting regulated necrosis and inflammation


title: Generation of Allogeneic Hematopoietic Stem Cell-Engineered Invariant Natural Killer T cells for Off-the-Shelf Immunotherapy

first: Feiyang

last: Ma


title: Dual RNA-seq on Klebsiella pneumoniae infection to human epithelial cells

status: Public on Dec 14 2021

city: Groningen

first: Rieza

last: Aprianto

state: Groningen

address: Nijenborg 7

department: Molecular Genetics Department

country: Netherlands

institute: University of Groningen

summary: Klebsiella pneumoniae poses significant threat to global health. Detailed investigation to the nature of its interaction to human epithelial cells is still lacking. OmpR is an important regulator to the expression of major outer membrane protein genes, ompF and ompC. Here, we exploited the recently described dual RNA-seq to simultaneously measure genome-wide expression of host and pathogen two hours into infection. By comparing OmpR deleted strain to its wildtype parental strain, we, simultaneously, reconstructed OmpR regulon and deletion effect to host response.

sample_organism:
Klebsiella pneumoniae
Homo sapiens

platform_organism:
Klebsiella pneumoniae
Homo sapiens

overall_design: Five samples are analysed, categorized into two conditions: infection with wildtype and OmpR deletion strain

first: Jan-Willem

last: Veening

first: Michel

middle: M

last: Peren

first: Christian

last: Kemmer


title: Integrative tissue analysis of men with prostate cancer III

status: Public on Sep 30 2021

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

summary:
Prostate cancer is readily curable if detected early.
The overall goal of this study is to conduct integrative profiling of tumor and blood genomics and transcriptomics.

overall_design: To identify potential genomic drivers of tumor aggressivity, we conducted whole genome somatic copy number analysis using OncoScan CNV arrays.

first: Eytan

last: Ruppin

first: Kenneth

last: Aldape


title: Deciphering the fate of slan+-monocytes in tonsils by gene expression profiling

status: Public on Nov 19 2021

city: Verona

first: Francisco

last: Bianchetto-Aguilera

address: Strade le Grazie, 8

department: Department of Medicine

institute: University of Verona

summary: slan+-monocytes represent a subset of the “non-classical” CD14dim/-CD16++ monocytes, which are characterized by the expression of the so-called “slan” antigen, recognized by specific monoclonal antibodies. slan+-cells can be identified in peripheral tissues including tonsils. However, their origin from slan+-monocytes as well as their terminal differentiation state (toward macrophages/dendritic cells) were only partially resolved. In this study, we performed transcriptomic studies of tonsil slan+-cells,CD1c+DCs/DC2 and CD11b+ CD14+macrophages, as well as subsets of peripheral blood monocytes and we report that tonsil slan+-cells mainly represent macrophage-like cells with features distinct from those of tonsil CD11b+CD14+macrophages or CD1c+DCs/DC2.  Moreover we provide a number of molecular evidence indicating that tonsil slan+-cells derive from peripheral slan+-monocytes.

overall_design: Tonsil slan+-cells, CD1c+DCs/DC2 and CD11b+ CD14+macrophages, as well as peripheral DC2, “classical” (CL) CD14++CD16- monocytes, “intermediate” (INT) CD14++CD16+ monocytes, “non-classical” (NC) CD14dim/-CD16++ monocytes and slan+-monocytes were isolated by cell sorting. Total RNA was then extracted and subjected to Smart-seq2 protocol for transcriptomes analysis

first: Nicola

last: Tamassia

first: Marco

last: Cassatella


title: miR1908-5p primary hepatocytes

status: Public on Jul 14 2021

city: Ottawa

first: Ruth

last: McPherson

state: Ontario

address: 40 Ruskin

country: Canada

institute: UOHI

summary: Transfection experiments aimed at understanding the role of miR1908-5p in liver.

overall_design: Human primary hepatocytes  were transfected with a miR1908-5p mimic or its control mIRNA (miRIDIAN; Dharmacon). RNA was then isolated and the transcriptome analyzed by transcription array.  Two distinct lots of cryopreserved hepatocytes were used (Sigma and Thermofisher).

first: Sebastien

last: Soubeyrand


title: The chemokine receptor CXCR3 promotes CD8+ T cell dependent lung pathology during influenza pathogenesis

status: Public on Oct 31 2021

city: Grand Forks

first: Kai

last: Guo

state: ND

address: 1301 N Columbia Rd Stop 9037

institute: University of North Dakota

summary:
Purpose: A growing body of evidence highlights the association of exuberant CD8+ T cell responses with influenza acute lung injury. Given their indispensable role in viral clearance, we studied the double-edged function of CD8+ T cells as a bridge between infection resolution and lung pathology.
Methods: we performed scRNA-Seq to study the cellular heterogeneity and regulation of cellular response in CD8+ T cells during peak viral (day 7) and post-viral resolution phase (day 14).
Results: Our single-cell RNA-Seq data reveal significant differences in CD8+ T cell heterogeneity during different stages of influenza infection (peak viral load vs. infection resolved state). While CXCR3hi CD8+ T effector memory (Tem) was associated with a more robust cytotoxic response (compared to CXCR3low CD8+ T central memory, Tcm), both CD8+ Tem and Tcm exhibited equally potent effector function. The ablation of CXCR3 mitigates lung injury without affecting viral clearance. IFN-gamma was dispensable to the recruitment and regulation of cytotoxic response of CXCR3+ CD8+ T cells. Using scRNAseq, we identified unique regulons associated with regulating cytotoxic response in CXCR3hi CD8+ T cells.
Conclusions: Collectively, our data identify CXCR3 as a potential therapeutic target to curb lung injury during influenza pathogenesis.

overall_design: scRNAseq profiles of mock, 7 days and 14 days post-IAV infection

first: M

last: Khan


title: P220-1: CDK8 in Treg differentiation

status: Public on Jul 28 2021

first: Stephanie

last: Osmond

state: WA

summary: Immune health requires innate and adaptive immune cells to engage precisely balanced pro- and anti-inflammatory forces. A holistic understanding of how individual small molecules affect this balance is essential to anticipate immune-related side effects, select mitigating immunomodulatory therapies and highlight novel utility as immunomodulators. We previously showed that the high-specificity, low-toxicity cyclin dependent kinase 8 (CDK8) inhibitor DCA promotes tolerogenic effects in innate immune cells. Here, we demonstrate that DCA exerts a novel profile of tolerogenic activity on CD4+ T cells, promoting Treg and Th2 while inhibiting Th1 and Th17 differentiation. DCA enhances human Treg differentiation and our models demonstrate clear tolerogenic function of DCA-driven Tregs in the absence of confounding contribution from DCA-innate immune interactions. DCA engages unique mechanisms, including specifically enhancing early Foxp3 expression via regulating c-Jun phosphorylation, to promote Treg differentiation. CDK8 inhibitors are currently being developed to treat cancer; our findings suggest that the potential blunting of host-versus-tumor effects may warrant ancillary pro-inflammatory agents. Importantly, these results highlight novel utility of DCA as an immunomodulator, not only in vivo, but also in ex vivo cellular therapy.

overall_design: All cells from 4 sets of 2 B6.FOXP3GFP M mice. CD4+CD62L+GFP- cells were sorted for RNA and culture. Cells were cultured in Treg_lo (TGFb 1.5 ng/ml), Treg_DCA (TGFb 1.5 ng/ml + 100nM DCA) or Treg_hi (TGFb 10 ng/ml) conditions (1 ug/ml ea plate-coated anti-CD3/CD28). Aliquots were taken at d1, d2 and d4 post-stimulation. D1 and D2 samples were sorted for total, GFP+ and GFP- populations; D4 was sorted for GFP+ from Treg_DCA and Treg_hi conditions only. First analyses should compare naive vs D2 GFP+ and GFP- from Treg_lo/DCA. The goal would be to determine qualitative differences in FOXP3+ populations between Treglo, Treghi & TregDCA.

first: Azlann

last: Arnett

first: Keagan

last: Moo

first: Kaitlin

middle: J

last: Flynn

first: Thomas

last: Sundberg

first: Liv

last: Johannessen

first: Alykhan

middle: F

last: Shamji

first: Nathanael

last: Gray

last: Decker

first: Vivian

last: Gersuk

first: David

middle: E

last: Levy

first: Isabelle

last: Marié

first: Ziaur

last: Rahman

first: Ye

last: Zheng

first: Peter

last: Linsley

first: Ramnik

last: Xavier

first: Bernard

last: Khor


title: Single cell RNA-sequencing reveal a murine gallbladder cell transcriptome atlas during the process of cholesterol gallstone formation

status: Public on Jul 08 2021

city: shanghai

first: wentao

last: shao

address: 150, jimo road

department: Shanghai East Hospital

institute: Tongji University School of Medicine

summary: Gallstone disease is a worldwide common disease. However, the knowledges concerning the gallbladder in the pathogenesis of cholesterol gallstone formation remains limited. In this study, using single-cell RNA sequencing (scRNA-seq), we showed cellular heterogeneity and transcriptomic dynamics in murine gallbladder cells during the process of lithogenesis. Our results indicated gallbladder wall were subjected to remodeling during the process of lithogenesis. The major molecular events happened included proliferation of epithelial cells, infiltration of immune-cells, activation of angionesis and extracellular matrix modulation. Furthermore, we observed partial reversal of gallbladder cell transcriptomes by ursodeoxycholic acid treatment. This work thus provides novel and integral knowledges on the cellular changes during lithogenesis, which is of great significance to the understanding of pathogenesis and treatment of cholesterol gallstone.

first: Zhaoyan

last: Jiang

first: Wentao

last: Shao


title: In-depth molecular characterization of neovascular membranes suggests a role for hyalocytes-to-myofibroblasts transdifferentiation in proliferative diabetic retinopathy

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

summary: Background: Proliferative diabetic retinopathy (PDR) is hallmarked by the formation of retinal neovascularization (RNV) membranes, which can lead to a tractional retinal detachment, the primary reason for severe vision loss in end-stage disease. The aim of this study was to characterize the molecular and cellular features of RNV in order to unravel potential novel drug treatments for PDR.  Methods: A total of 42 patients undergoing vitrectomy for PDR, macular pucker or macular hole (control patients) were included in this study. The surgically removed RNV and epiretinal membranes were analyzed by RNA sequencing, single-cell based Imaging Mass Cytometry and conventional immunohistochemistry. Since macrophages were found to be abundant in RNV tissue, vitreal macrophages, also known as hyalocytes, were isolated from the vitreous of patients with PDR by flow cytometry, cultivated and characterized by immunhistochemistry. A bioinformatical drug repurposing approach was applied, in order to identify novel drug options for end-stage diabetic retinopathy disease.  Results: The in-depth transcriptional and single-cell protein analysis of diabetic RNV tissue samples revealed an accumulation of endothelial cells, macrophages and myofibroblasts as well as an abundance of secreted ECM proteins such as SPARC, FN1 and several types of collagen in RNV tissue. The immunohistochemical staining of cultivated vitreal hyalocytes from patients with PDR showed that hyalocytes express α-SMA (alpha-smooth muscle actin), a classic myofibroblast marker. According to our drug repurposing analysis, imatinib emerged as a potential drug option for future treatment of PDR.  Conclusion: This study delivers the first in-depth transcriptional and single-cell proteomic characterization of RNV tissue samples. Our data suggest an important role of hyalocyte-to-myofibroblast transdifferentiation in the pathogenesis of diabetic vitreoretinal disease and suggests their modulation as a novel possible clinical approach.

overall_design: RNA sequencing of 7 human RNV membranes, 10 macular pucker and 7 macular hole samples

first: Stefaniya

last: Boneva

first: Julian

last: Wolf

first: Rozina

last: Hajdu

first: Gabriele

last: Prinz

first: Henrieke

last: Salié

first: Anja

last: Schlecht

first: Saskia

last: Killmer

first: Yannik

last: Laich

first: H

last: Faatz

first: A

last: Lommatzsch

first: Felicitas

last: Bucher

first: Andreas

last: Stahl

first: Daniel

last: Böhringer

first: Bertram

last: Bengsch

first: Günther

last: Schlunck

first: Hansjürgen

last: Agostini


title: Integrative tissue analysis of men with prostate cancer V

first: Adam

last: Sowalsky

summary: Prostate cancer is readily curable if detected early. The overall goal of this study is to conduct integrative profiling of tumor and blood genomics and transcriptomics.

overall_design:
To identify potential genomic drivers of tumor aggressivity, we conducted whole transcriptome sequencing.
*Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.*

first: Eytan

last: Ruppin

first: Kenneth

middle: D

last: Aldape


title: Gene expression of CTCL cell line MyLa transduced with Empty-GFP or miR-26a-GFP expressing vector

status: Public on Jul 21 2021

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

institute: Akita univ.

summary: By using a CTCL cell line MyLa transduced Empty-GFP or miR-26a-GFP, we conducted whole genome gene screening against the cells.

overall_design: We performed comprehensive gene expression analysis on the miR-26a transduced myLa cell line and extracted several genes that have decreased expression by miR-26a

first: Fumito

last: Abe

first: Hiroyuki

last: Tagawa


title: PKCl/i inhibition activates an ULK2-mediated interferon response to repress tumorigenesis [ATAC-Seq]

status: Public on Sep 23 2021

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

summary: The interferon (IFN) pathway is critical for cytotoxic T cell activation, which is central to tumor immunosurveillance and successful immunotherapy. We demonstrate here that PKCl/i inactivation results in the hyper-stimulation of the IFN cascade and the enhanced recruitment of CD8+ T cells that impaired the growth of intestinal tumors. PKCl/i directly phosphorylates and represses the activity of ULK2, promoting its degradation through an endosomal microautophagy-driven ubiquitin-dependent mechanism. Loss of PKCl/i results in increased levels of enzymatically active ULK2 that by direct phosphorylation activates TBK1 to foster the activation of the STING-mediated IFN response. PKCl/i inactivation also triggers autophagy that prevents STING degradation by chaperone-mediated autophagy. Thus, PKCl/i is a hub regulating the IFN pathway and three autophagic mechanisms that serve to maintain its homeostatic control. Importantly, single cell multiplex imaging and bioinformatics analysis demonstrated that low PKCl/i levels correlate with enhanced IFN signaling and good prognosis in colorectal cancer patients.

overall_design: ATACseq samples from small intestinal epithelial cells from WT and intestinal epithelial cell-specific atypical PKClambda mice.

first: Juan

last: Linares

first: Xiao

last: Zhang

first: Anxo

last: Martinez-Ordoñez

first: Angeles

last: Duran

first: Hiroto

last: Kinoshita

first: Hiroaki

last: Kasashima

first: Naoko

last: Nakanishi

first: Yuki

first: Ryan

last: Carelli

first: Luca

last: Cappelli

first: Esperanza

last: Arias

first: Masakazu

last: Yahiro

first: Masaichi

last: Ohira

first: Sanjay

last: Patel

first: Giorgio

last: Inghirami

first: Massimo

last: Loda

first: Ana

last: Cuervo

first: Maria

middle: T

last: Diaz-Meco


title: Integrative tissue analysis of men with prostate cancer IV

city: Bethesda

first: Adam

last: Sowalsky

type: Methylation profiling by genome tiling array

overall_design: To identify potential genomic drivers of tumor aggressivity, we conducted whole genome methylation analysis using Illumina EPIC microarrays.

first: Eytan

last: Ruppin

first: Kenneth

last: Aldape


title: Human subcutaneous preadipocytes RNAseq

status: Public on Aug 19 2021

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

summary: we performed RNA-seq and pathways analysis on human preadipocytes isolated from abdominal (A) and gluteofemoral (GF) fat of 10 apple-shaped women and 7 pear-shaped women . Out of the 23,511 annotated transcripts, 636 and 752 genes were differentially expressed in apple- compared to pear-shaped cells in A-FAT and GF-FAT respectively. Interestingly, one of the most significantly over-represented pathways from the apple-specific gene list was “Nucleotide Excision Repair pathway”.

overall_design: Culture preadipocytes isolated from Abdominal (A) and gluteofemoral (GF) adipose tissue obtained from premenopausal apple-shaped and pear-shaped women were used to perform transcriptome analysis by RNA-seq

first: S

last: Smith

first: T

last: Osborne


title: TMC4 is a novel chloride channel involved in high-concentration salt taste sensation

status: Public on Sep 14 2021

city: Bunkyo-ku

first: Yoichi

last: Kasahara

state: Tokyo

address: 1-1-1 Yayoi

department: Graduate school of Agricultural and life science

institute: Taste science

summary: Taste substances are received by taste receptors expressed in taste cells. “Salty taste” sensation is evoked when sodium and chloride ions are present together in the oral cavity. The presence of an epithelial cation channel that receives Na+ has previously been reported. However, no molecular entity involving Cl- receptors has been elucidated. We report the strong expression of transmembrane channel-like 4 (TMC4) in the circumvallate and foliate papillae projected to the glossopharyngeal nerve, mediating a high-concentration of NaCl. Electrophysiological analysis using HEK293T cells revealed that TMC4 was a voltage-dependent Cl- channel and the consequent currents were completely inhibited by NPPB, an anion channel blocker. This channel could be activated without an increase in intracellular calcium ion. TMC4 allowed permeation of organic anions including gluconate, but their current amplitudes at positive potentials were less than that of Cl-. Tmc4-deficient mice showed significantly weaker glossopharyngeal nerve response to high-concentration of NaCl than the wild-type littermates. These results indicated that TMC4 is a novel chloride channel that responds to high-concentration of NaCl.

overall_design: The number of RNA sequence trials was once per tissue. Total RNA was extracted from the circumvallate papillae or the epithelium without papillae of tongue using C57BL/6J mice (n = 20 or more) and pooled for each.

first: Masataka

last: Narukawa

first: Yoshiro

last: Ishimaru

first: Keiko

last: Abe

first: Tomiko

last: Asakura


title: PKCl/i inhibition activates an ULK2-mediated interferon response to repress tumorigenesis

first: Jorge

last: Moscat

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

overall_design: Refer to individual Series


title: Most primitive Human Hematopoietic Stem Cell Populations

status: Public on Jul 01 2021

city: Frankfurt

first: Florian

last: Buettner

state: Germany

address: Theodor-Stern-Kai 7

department: DKTK Frankfurt

institute: DKFZ

summary:
Transcriptomic profiling (RNA-seq) of the four most primitive human stem and progenitor populations.
Purpose: to compare the transcriptomic profile of the four most primitive human stem and progenitor populations (all are CD34+CD38-CD45RA-): CD90+CD49f+, CD90-CD49f+, CD90+CD49f-, CD90-CD49f-.
Conclusions: previouls study of gene expression analysis of these populations were performed using microarray hence, this study represents the first analysis of transcriptomes from these populations generated by RNA-seq technology.
The optimized data analysis workflows reported here should  provide a framework for comparative investigations of expression profiles of other human blood stem/progenitor populations.

overall_design:
Methods: cells were obtained from human cord-blood and flow-sorted using the surface antigens described. 3 biological replicates/ population were used to extract total RNA and quality was verified (RIN >8).
Libraries were prepared using with 20-25 ng/sample of starting RNA.

first: Fernando

last: Anjos-Afonso

first: Dominique

last: Bonnet


title: Newly defined Human Hematopoietic Stem Cell Populations

summary:
Purpose: to compare the transcriptomic profile of the two most primitive human EPCR+ stem and CD90+EPCR-  progenitor populations.
Methods: cells were obtained from human cord-blood and flow-sorted using the surface antigens described. 5 EPCR+ and 4 CD90+EPCR- biological replicates were used to extract total RNA and quality was verified (RIN >8).
Libraries were prepared using with 20-25 ng/sample of starting RNA. All samples were sequenced two independent times.
Conclusions: this study represents the first analysis of transcriptomes from the two most primitive human stem/progenitor populations, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should  provide a framework for comparative investigations of expression profiles of other human blood stem/progenitor populations.

overall_design: Transcriptomic profiling (RNA-seq) of the two most primitive human stem (CD34+CD38-CD45RA-EPCR+; hereafter EPCR+) and progenitor (CD34+CD38-CD45RA-CD90+EPCR-; hereafter CD90+EPCR-) populations.


title: The mitochondrial single-stranded DNA binding protein directs RNA primer formation for mtDNA replication [sRNA]

status: Public on Jul 06 2021

city: Perth

first: Stefan

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

summary: Single-stranded DNA (ssDNA) binding proteins protect regions of ssDNA formed during processes such as DNA replication and repair. We here devise a genetic screen and identify the mitochondrial ssDNA-binding protein (mtSSB) as a key regulator of mtDNA levels. In mitochondria, RNA synthesis from the light-strand promoter (LSP) is required for transcription as well as for generating the primers for initiation of mtDNA synthesis. We find that mtSSB is essential for mtDNA replication initiation, as transcription is strongly upregulated from the LSP in an mtSSB knockout mouse model, but cannot support the switch to replication. Using deep sequencing as well as biochemical reconstitution experiments, we find that mtSSB is also necessary to restrict transcription initiation and primer formation to specific promoters and origins of replication both in vitro and in vivo. Pathological mutations in human mtSSB cannot efficiently support primer maturation and origin specific initiation of mtDNA replication in vitro.

overall_design: Mitochondrial RNA coverage profiles for Ssbp-/- mouse heart tissue, relative to Ssbp+/+ mice, in triplicate

first: Min

last: Jiang

first: Xie

last: Xie

first: Xuefeng

last: Zhu

first: Shan

first: Dusanka

last: Milenkovic

first: Yonghong

last: Shi

first: Nirwan

last: Tandakur

first: Louise

last: Jenninger

first: Emily

last: Hoberg

first: Zsolt

last: Szilagyi

first: Bertil

last: Macao

first: Valerio

last: Carelli

first: Jack

last: Griffith

first: Claes

last: Gustafsson

first: Thomas

last: Nicholls

first: Alexandra

last: Filipovska

first: Nils-Göran

last: Larsson

last: Falkenberg


title: Chromatin accessibility and gene expression maps of Plasma Cells and Myeloma Plasma Cells [RNA-seq]

status: Public on Jun 29 2021

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

institute: University of Sheffield

summary: We report the application of paired Assay for Transposase-Accessible Chromatin (ATAC-seq) and RNA-seq data to profile the regulatory landscape and expression of 5 primary Plasma Cell (PC), 28 Multiple Myeloma (MM) PC as well as 5 cell lines samples. Findings discriminated MM and MM subgroup-specific changes such as the exclusive overexpression of CCND1 and CCND2 oncogenes. DNA accessibility changes were correlated to gene expression in a topologically constrained manner to elucidate novel enhancer - promoter interactions, genes and pathways critical for myeloma biology and developmentally activated or de novo formed enhancers. Additionally, the MM subgroup-specific TF network dependencies were studied to help identify prognostic markers. Finally, we discover and functionally validate the critical enhancer that regulates ectopic expression of CCND2 in MM.

overall_design: Examination of paired ATAC-seq and RNA-seq data of 5 primary Plasma Cell (PC), 28 Multiple Myeloma (MM) PC as well as 5 cell lines samples.

first: Jaime

last: Alvarez-Benayas

first: Alexia

last: Katsarou

first: Nikolaos

last: Trasanidis

first: Aristeidis

last: Chaidos

first: Kanagaraju

last: Ponnusamy

first: Xiaolin

last: Xiao

first: Marco

last: Bua

first: Maria

last: Atta

first: Irene

middle: A

last: Roberts

first: Holger

last: Auner

first: Evdoxia

last: Hatjiharissi

last: Papaioannou

first: Valentina

middle: S

last: Caputo

first: Anastasios

last: Karadimitris

first: Philippa

last: May


title: Genome wide methylation of cord blood from normal glucose tolerance pregnancies

status: Public on Jun 23 2021

city: Setagaya

first: Tomoko

last: Kawai

department: Department of Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

summary: Genome wide DNA methylation profiling of cord blood cells obtained from normal glucose tolerance (NGT) pregnancies. The Illumina EPIC methylation beadchip array was used to obtain DNA methylation profiles across approximately 850,000 CpG dinucleotide methylation loci in DNA isolated from cord blood. Samples include 61 NGT subjects.

overall_design: DNA methylation was assessed in cord blood of 61 normal glucose tolerance (NGT) pregnancies using the Illumina HumanMethylation EPIC array.

first: T

first: K

last: Miyakoshi

first: Y

last: Kasuga

first: M

last: Tanaka

last: Hata


title: The mitochondrial single-stranded DNA binding protein directs RNA primer formation for mtDNA replication [TruSeq]

first: Stefan

last: Siira

overall_design:
Total RNA differential gene expression and mitochondrial coverage profiles for Ssbp-/- mouse heart tissue, relative to Ssbp+/+ mice, in triplicate
Please note that the Ssbp_585H* and Ssbp_586H* processed data files were generated from both technical replicates and is linked to the corresponding *trep1  sample records.

first: Min

last: Jiang

first: Xie

last: Xie

first: Xuefeng

last: Zhu

first: Shan

first: Dusanka

last: Milenkovic

first: Yonghong

last: Shi

first: Nirwan

last: Tandakur

first: Louise

last: Jenninger

first: Emily

last: Hoberg

first: Zsolt

last: Szilagyi

first: Bertil

last: Macao

first: Valerio

last: Carelli

first: Jack

last: Griffith

first: Claes

last: Gustafsson

first: Thomas

last: Nicholls

first: Alexandra

last: Filipovska

first: Nils-Göran

last: Larsson

last: Falkenberg


title: Changes in the transcriptome of primary mouse mammary gland organoids in response to hyperactivation of the WNT/CTNNB1 pathway

status: Public on Jun 22 2021

city: Amsterdam

first: Renee

last: van Amerongen

address: Science Park 904

department: Swammerdam Institute for Life Sciences

institute: University of Amsterdam

summary: Purpose: WNT/CTNNB1 signaling promotes mammary tumor formation in mice, but the direct and immediate effects of elevated levels of WNT/CTNNB1 signaling on the mouse mammary epithelium remain unknown.  Using primary mouse mammary epithelial organoid cultures grown in minimal media we have studied the response of the mouse mammary epithelium to elevated levels of WNT/CTNNB1 signaling.

overall_design: Primary mouse mammary epithelial organoid cultures were established from 8-11 week old female FVB/N virgin mice.  Organoids were grown in the presence of either vehicle control (DMSO) or increasing concentrations of CHIR99021 (1 uM, 1.5 uM or 3 uM) for 7 days. RNA was harvested after 7 days of culture/treatment and used for bulk RNA sequncing.   n=3 independent organoid cultures (rep1, rep2, rep3) from n=3 individual animals were used for n=4 different treatments per experiment (DMSO, 1uM CHIR99021, 1.5 uM CHIR99021, 3 uM CHIR99021), resulting in 3 x 4 = 12 samples total.

first: Renée


title: Single Cell analysis of the two Human Hematopoietic Stem Cell Populations

first: Florian

last: Buettner

summary: Single cell transcriptomic profiling (sc RNA-seq) of the two Human Hematopoietic Stem Cell Populations: CD34+CD38-CD45RA-CD90+CD49f+ (hereafter CD90+CD49f+) and CD34+CD38-CD45RA-CD90-CD49f+ (hereafter CD90-CD49f+)

overall_design:
Purpose: to compare the single cells transcriptomic profiles of the two Human Hematopoietic Stem Cell Populations: CD90+CD49f+ and CD90-CD49f+ cells in order to find common marker genes.
Methods: single cells (from human cord-blood CD34+ cells) were flow-sorted directly into 6x96-well plates (wells A6-H7) of the two CD90+CD49f+ and CD90-CD49f+ cells; 3 independent sorts (S1, S2, S3); 3 plates per cell type.
Multiplexed Nextera XT was used to generate libraries. Each single cell was barcoded then all libraries were pooled per plated for sequencing.
Conclusions: this study led to the discovery of a group of cells expressing a common cell surface antigen.

first: Fernando

last: Anjos-Afonso

first: Dominique

last: Bonnet


title: FMRP-Mediated Gene Regulation in Human Brain Development

status: Public on Jun 19 2021

city: Houston

first: Ziyi

last: Li

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

summary: Fragile X syndrome (FXS) is the most common inherited form of intellectual disability and a leading genetic cause of autism. FXS is caused by the loss of functional fragile X mental retardation protein (FMRP). FMRP is an RNA-binding protein forming a messenger ribonucleoprotein complex with polyribosomes in the regulation of protein synthesis at synapses. Three-dimensional (3D) aggregate culture of human-induced pluripotent stem cells (iPSCs) has evolved from embryoid body cultures, quite faithfully following human organogenesis, and provides a new platform to investigate human brain development in a dish, otherwise inaccessible to experimentation. To determine whether the loss of FMRP could alter the development of human brain organoids, we have generated forebrain organoids from three FXS male patients and three healthy male controls. We observed reduced proliferation of neural progenitor cells and premature neural differentiation as well as perturbed cell cycle progression in FXS forebrain organoids. There is also a deficit in the production of GABAergic neurons as well as an altered balance between the number of excitatory and inhibitory neurons in FXS organoids. Interestingly these deficits were not observed with FXS mouse model. To compare the differential gene expression caused by the loss of FMRP between human and mouse, we then performed RNA-seq to identify the differentially expressed genes using both mouse embryonic brain cortex and human forebrain organoids at the comparable developmental stages. We detected very few genes differentially expressed in the absence of Fmrp in mouse. However, we identified 200 genes downregulated and 126 genes up-regulated in human FXS organoids, indicating human-specific impact caused by the loss of FMRP. Our bulk RNA-seq analyses revealed a more pervasive gene expression alteration in human organoids.  Thus, it is plausible to speculate that there could be important human-specific genes that might be related with FXS pathogenesis. To test this idea, we used human forebrain organoids and the mouse embryonic brains in parallel to perform enhanced crosslinking and FMRP immunoprecipitation followed by high-throughput sequencing and bioinformatics analysis (CLIP-seq). Our analyses identified more than 3,700 mRNA bound by FMRP in human organoids. Of the 3,700 mRNAs, ~1,600 overlapped with mouse mRNAs. Further, ~80% of the identified mouse mRNA species overlap with previously published results in mouse. To better understand the developmental, cellular and molecular changes and to gain insight beyond bulk gene expression analysis in forebrain organoids from FXS patients compared to control, we next performed single cell RNA-seq (scRNA-seq) to characterize distinct cell populations, specific cell types and cell states. We found that the population of specific neuron type were changed upon the loss of FMRP. Next, investigated if there were developmental differences in the transitioning from the early, primitive state to one of the more committed end states between control and FXS organoids, with many cells distributed along a “trajectory” between them. we found several bifurcation points of FXS cells from the general trajectory, and the cells of these subpopulations with altered neuronal states are strongly enriched for FXS. These results together suggest that the loss of FMRP could cause neurodevelopmental deficits specifically in human, and fragile X organoids could provide a unique platform to study the molecular pathogenesis of FXS and identify human-specific druggable targets for FXS and autism in general.

overall_design: RNA-seq of human organoids, human fetal brain and mouse fetal brain (control and FXS), eCLIP-seq of human organoids and mouse fetal brain (control and FXS), single-cell RNA-seq of human organoids (control and FXS).

first: Yunhee

last: Kang


title: Transcriptomic and epigenetic profiling of fibroblasts in Idiopathic Pulmonary Fibrosis (IPF) [RNA-seq]

status: Public on Jul 20 2021

first: Lisha

last: Zhu

address: 7000 fannin st

institute: UT Health Science Center at Houston

summary: RNA sequencing was used to identify differentially expressed genes (DEGs) which could reflect early disease in IPF.

overall_design: Primary human lung fibroblasts were isolated directly from the upper half of the upper lobe from human lungs, there are 4 healthy controls and 5 IPF patients to identify differentially expressed genes between IPF patients and healthy controls.

first: Harry

last: Karmouty-Quintana


title: Cross-species comparative analysis using single-cell RNA-sequencing data of Drosophila hemocytes, zebrafish, mouse and human immune cells

status: Public on Sep 26 2021

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

country: South Korea

institute: Hanyang University

summary: Drosophila hemocytes are the primary defense system required for the animals to thrive and overcome harmful threats and are often compared to the innate immune system of vertebrates.  However, their homology has been described using only a limited number of genes and a systematic analysis using transcriptomic data would provide novel insights about the evolution of immune systems. In this study, we performed cross-species comparative analysis using single-cell RNA-sequencing data of Drosophila hemocytes, zebrafish, mouse, and human immune cells in both supervised and unsupervised manner. A small subset of prohemocytes with hematopoietic potential displayed a homology to progenitor populations in vertebrates. Drosophila hemocytes appeared to be largely homologous to the myeloid cells of vertebrates, especially plasmatocytes to monocytes/macrophages and lamellocytes to neutrophils. CG14767 (LAPTM4A) which encodes a lysosomal protein is well conserved in various phagocytic cells suggesting its common role in degradation of foreign uptake. Our results provide deeper understanding in molecular conservation of the Drosophila immune system.

overall_design: Single-cell RNA-sequencing of circulating hemocytes from larvae of Drosophila melanogaster

first: Sang-Ho

last: Yoon

first: Bumsik

last: Cho

first: Hanji

last: Kim

first: Ji-Won

last: Shim


title: The mitochondrial single-stranded DNA binding protein directs RNA primer formation for mtDNA replication

first: Stefan

last: Siira


title: Deacetylation of HP1g enhances multiple myeloma drug resistance through DNA damage repair and liquid-liquid phase separation (RNA-Seq)

status: Public on Jun 11 2021

city: Tianjin

first: Liu

last: Zhiqiang

address: 22 Qxiangtai Rd

institute: Tianjin Medical University

summary: Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during drug resistance, but the underlying mechanisms are not fully understood. Here we demonstrate that HP1g  regulates chromatin dynamic and gene transcription during drug resistance in multiple myeloma. To study the cellular and molecular function of HP1g during bortezomib resistance, we used RNA sequencing (RNA-seq) to generate gene expression profiling under HP1g steady overexpression  in LP-1. We identified multiple genes whose expression is significantly affected by HP1g levels.

overall_design: For overexpression condition, LP-1 were infected with HP1g or vector 72h and screened steady the HP1g overexpressed cell lines. Cells were harvested for gene expression profiling including vector and HP1g overexpression cell line. Two replicates were performed per sample.

first: Xin

first: Sheng

last: Wang


title: ATAC-Seq of pDC Transcriptomes

status: Public on Jun 18 2021

city: Duesseldorf

first: Stefanie

last: Scheu

state: Nordrhein-Westfalen

address: Universitaetsstr. 1

department: Institute of Medical Microbiology and Hospital Hygiene

institute: University of Duesseldorf


title: Deacetylation of HP1g enhances multiple myeloma drug resistance through DNA damage repair and liquid-liquid phase separation


title: Genome wide methylation of cord blood from gestational diabetes mellitus

first: Tomoko

last: Kawai

summary: Genome wide DNA methylation profiling of cord blood cells obtained from gestational diabetes mellitus (GDM) pregnancies. The Illumina EPIC methylation beadchip array was used to obtain DNA methylation profiles across approximately 850,000 CpG dinucleotide methylation loci in DNA isolated from cord blood. Samples include 165 GDM subjects.

overall_design: DNA methylation was assessed in cord blood of 165 gestational diabetes mellitus (GDM) pregnancies using the Illumina HumanMethylation EPIC array.

first: Y

last: Kasuga

first: T

first: K

last: Miyakoshi

first: M

last: Tanaka

last: Hata


title: Single Cell analysis of the most primitive Human Hematopoietic Stem Cell Population.

status: Public on Jul 02 2021

first: Florian

last: Buettner

summary: Single cell transcriptomic profiling (sc RNA-seq) of the most primitive Human Hematopoietic Stem Cell Population described: CD34+CD38-CD45RA-CD49f+EPCR+ (hereafter EPCR+).

overall_design:
Purpose: to search for potential heterogeneity within EPCR+ HSCs at the single cell level.
Methods: single cells (from human cord-blood CD34+ cells) were flow-sorted fisrt then loaded into C1 Fludigm chips: 3 independent sorts; 4chips in total were used.
Multiplexed Nextera XT was used to generate libraries. Each single cell was barcoded.
Conclusions: this study supports that this population is highly homogeneous at the transcriptional level.

first: Fernando

last: Anjos-Afonso

first: Dominique

last: Bonnet


title: Deacetylation of HP1g enhances multiple myeloma drug resistance through DNA damage repair and liquid-liquid phase separation (ATAC-Seq)

summary: Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during drug resistance, but the underlying mechanisms are not fully understood. Here we demonstrate that HP1g coordinates histone H3 lysine 9 trimethylation (H3K9me3) to regulate chromatin dynamic and gene transcription during bortezomib resistance.Mechanistically, HP1g can interact with H3K9me3, its CD domain is responsible to read H3K9me3 to serve its function.

overall_design: ATAC-seq analysis from  WT or BR LP-1 cells and cells infected with overexpression HP1g plasmid or vector. Cells were harvested for chromatin accessibility profiling. Two replicates were performed per sample.

last: Li


title: Next Generation Sequencing  of Wild Type and Batf-knock out pDC Transcriptomes in a longitudinal activation study (CpG 0h, 2h, 6h, 12)

status: Public on Jun 08 2021


title: Longitudinal single-cell dynamics in chronic lymphocytic leukemia mirror disease history

status: Public on Jun 09 2021

city: Boston

first: Livius

last: Penter

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Longitudinally sampled peripheral blood samples of 9 CLL patients were subjected to single cell RNA sequencing before and at relapse after chemotherapy with fludarabine, cyclophosphamide and rituximab (FCR); allogeneic hematopoietic stem cell transplantation (RIC allo-HSCT); ibrutinib treatment, or before and after transformation to Richter's syndrome.

overall_design: Mononuclear cells from peripheral blood and bone marrow were obtained from nine human patients diagnosed with chronic lymphocytic leukemia and sequenced using scRNA-seq on the 10x platform

first: L

first: S

last: Gohil

first: C

last: Wu


title: Secondary Resistance to Anti-EGFR Therapy by Transcriptional Reprogramming in Patient-Derived Colorectal Cancer Models

status: Public on May 21 2021

city: Bochum

first: Stephan

last: Hahn

address: Universitaetsstrasse 150

department: MGO

institute: Ruhr-University Bochum

summary: Global mRNA expression profiling of patient derived colon cancer xenograft models (N=10)  showing disease control  under cetuximab treatment were collected using Agilent human whole genome array (G4845A AMADID  026652, cRNA 4x44k V2) .  All xenograft models were wildtype for KRAS, NRAS, BRAF and PIK3CA. All Mice were treated with cetuximab (Merck Serono) by intra peritoneal (i.p.) injection twice per week and dosed at 25mg/kg to establish response characteristics. Tumors were chronically treated to establish cetuximab secondary resistant tumors .

overall_design: Three conditions (untreated control (K) vs 5 days cetuximab treatment (5dC) while pdx tumors were responsive to cetuximab vs secondary resistant tumors (C) following chronic cetuximab treatment) were analyzed. Untreated control tumors are represented by two to four biological replicates, 5 days cetuximab treated tumors by 3-4 biological replicates. For cetuximab secondary resistant tumors, cases with only one secondary resistant tumor are represented by 3 technical replicates, cases with >1 secondary resistant tumors, each is (with the exception of one tumor) represented by two technical replicates or by biological replicates > 4.


title: RNA-seq analysis of dark-induced senescence of the leaves of Ran-GDP and Ran-GTP overexpression transgenic plants

status: Public on Apr 27 2021

city: Wonju-si

first: Soo-Hwan

last: Kim

state: Gangwon-do

address: 1, Yeonsedae-gil, Heungeop-myeon

department: DIVISION OF BIOLOGICAL SCIENCE AND TECHNOLOGY

institute: Yonsei University

summary: Comparing transcriptome of the leaves of Ran-GDP and Ran-GTP overexpression transgenic plants before and after dark incubation, we discovered 851 differentially expressed genes that designated as Ran-regulated genes. The RNA-seq result confirmed the early senescence phenotype of Ran-GTP overexpression plants and the up-regulation of several signaling pathways, implied their positive roles in Ran-regulated senescence and suggest potential downstream targets  of Ran. This study provided a mechanism that senescence process could be regulated by nuclear transportation machinery in Arabidopsis.

overall_design: The RNA expression profiles of the fifth and sixth leaves of 4 week-old RanT27N (Ran-GDP) and RanG22V (Ran-GTP) overexpression transgenic plants before and after 3 days in darkness were assessed.

first: Giang

last: Pham


title: Deciphering the principles of the RNA editing code via large-scale systematic probing

status: Public on May 05 2021

city: Rehovot

first: Anna

last: Uzonyi

address: 234 Herzl street

department: Department of Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: Here we utilized large-scale systematic probing and screening of ~2000 sequence and structural variants based on two long, perfect RNA hairpins to explore the structure and sequence context determining editability.

overall_design: 2 replicates of B2 or mNG first arm amplicon libraries from basal HEK293T, IFN-a stimulated HEK293T, siAdar treated HEK293T, MCF7, A549 and NIH3T3 cells. 2 replicates of B2 second arm amplicon libraries from basal HEK293T, IFN-a stimulated HEK293T and MCF7 cells. 1 sample each of poly-A selected library of HEK293T cells transfected with B2 or mNG positive control reporter constructs.

first: Schraga

last: Schwartz


title: StuA-Regulated Processes in the Dermatophyte T. rubrum: Transcription Profile, Cell-Cell Adhesion, and Immunomodulation

status: Public on May 14 2021

city: Ribeirão Preto

first: Pablo

middle: Rodrigo

last: Sanches

state: SP

address: Av. Bandeirantes, 3900

department: Genetics

country: Brazil

institute: University of São Paulo

summary:
Purpose: We aimed to gain more aspects about Stua-regulated processes in T. rubrum by assessing the global gene expression after its growth on keratin or glucose sources.
Methods: T. rubrum strain CBS118892 and the null mutant strain ΔstuA  were inoculated into 100 mL Sabouraud dextrose broth, and incubated under agitation at 28 °C for 96 h. Mycelia were aseptically transferred into 100 mL minimal medium (MM) at pH 5.0 containing 70 mM nitrate and 50 mM glucose (control) or 0.5% (w/v) bovine keratin (test condition) as an  alternative carbon source. The cultures were incubated under agitation at 28 °C for 24 h, 48 h, or 96 h. Equal amounts of RNA from three independent biological replicates of keratin or glucose cultures were sequenced with a NextSeq 500  sequencer. Paired-end reads of 150 bp in size were generated. Raw data obtained were processed for quality control by FastQC tool and trimmed with Trimmomatic to remove adapters and Illumina-specific sequences. Trimmed paired-end reads from each sample were aligned to the T. rubrum reference genome. Gene-level read counts were quantified with STAR’s ‘-quantModeGeneCounts’ parameter. Differential expression was analyzed with the DESeq2 bioconductor package. A Benjamini-Hochberg correction adjusted the P threshold and was applied to reveal statistically significant changes in gene expression levels. It was set to 0.05,  and a cut off threshold of ±1.5 log2-fold change was set to reveal statistically significant changes in expression levels, and referred  as differentially expressed genes (DEG). DEGs  were functionally categorized with the Gene Ontology (GO) terms assigned by the Blast2GO algorithm. Ultimately, the most representative categories for each experimental condition were identified by enrichment analysis using the BayGO algorithm .
Results: Our data showed the involvement of Stua in biological processes related to carbon central metabolism and glycerol catabolism, ROS metabolism, and cell wall construction. The deep changes in carbohydrate metabolism might be responsible for significant alteration in cell wall pattern and consequently in cell to cell interaction and adhesion as we also demonstrated in this study. The mutant strain presented an impairment in biofilm production and promoted an increase in pro-inflammatory cytokine secretion. Moreover, we displayed a StuA-dependent regulation on catalase genes.
Conclusions: In conclusion,  our data demonstrated the multitude of regulatory targets in TrStuA with a critical role in central metabolism that ultimately may be responsible to trigger a cascade of secondary effects with strong impacts on fungal physiology and virulence traits.

overall_design: We proceeded an RNA-Seq analysis of T. rubrum  stuA knock-out strain to consider changes in global gene expression promoted by the presence of keratin or glucose medium in comparison to wild type.

first: Tamires

last: Bitencourt

first: João

last: Neves-da-Rocha

first: Maira

last: Martins

first: Elza

last: Lang

first: Julio

middle: C

last: Bortolossi

first: Antonio

last: Rossi

first: Nilce

last: Martinez-Rossi


title: Essential role of ThPOK autoregulatory loop in maintenance of mature CD4 T cell identity and function

status: Public on Apr 05 2021

city: Philadelphia

first: Michael

last: Slifker

state: PA

address: 333 Cottman Ave.

institute: Fox Chase Cancer Center

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

overall_design: Refer to individual Series


title: Transcriptome sequencing (RNA-Seq) of HepG2 cells upon treatment of the 10μM Oridonin or DMSO(0.1%)for exploring the metabolic mechanism of Oridonin

status: Public on Apr 09 2021

city: Guangzhou

first: Lan

last: Tang

state: Guangdong

address: 1838  Guangzhou North Ave,

department: School of Pharmaceutical Science

institute: Southern Medical University

summary: Oridonin is a nature diterpenoid mainly isolated from Chinese herb Rabdosia rubescens and other Isodon species. Nowadays, most of studies focused on the pharmacological effects of oridonin, the metabolism of which remains unclear. In order to investigate the effect of oridonin on metabolism-related genes, we used the second-generation transcriptome sequencing(RNA-seq) to determine the expression changes of each gene in HepG2 cells treated with oridonin.

overall_design: mRNA profiles of  HepG2 cells upon treatment of the 10μM Oridonin or DMSO (0.1%) were generated by deep sequencing, using Illumina HiSeqTM 4000


title: Essential role of ThPOK autoregulatory loop in maintenance of mature CD4 T cell identity and function [ATAC-seq]

summary: The transcription factor ThPOK is critical for homeostasis and differentiation of mature T helper cells. Overall goal of this experiment is to show divergent Chromatin pattern of  ThPOK-dependent autoregulatory loop disrupted in CD4 T cells compared to WT.

overall_design: 5 × 10^4 flow sorted naïve CD4 cells from WT or CD4lo cells from OB11 mice were pelleted at 500 g for 5 min at 4 °C, and whole cell pellets resuspended in 50μL ATAC-RSB buffer (10 mM Tris-HCl pH 7.4 10 mM NaCl; 3 mM MgCl2 , 0.1% Igepal CA-630), 0.1% Tween 20 (Sigma),  and 0.01% Digitonin, and kept on ice for 3 min. 1ml of cold ATAC-RSB + 0.1% Tween20 was added, and samples centrifuged 500g for 10 min at 4°c (fixed angle rotor) to obtain nuclear pellet. Transposase reaction of open chromatin was achieved by resuspending free nuclei in tagmentation mix (22.5 μL Tagment DNA Buffer; 2.5 μL Tagment DNA enzyme; 25μL H2O) (Illumina, FC-121- 1030) and incubating at 37 °C for 30 min. Purification of DNA was performed with Diapure kit (Diagenode), according to the manufacturer’s protocol. Barcoding and amplification was performed using Nextera Index Kit (Illumina, FC-121-1011), as previously described56. Amplified ATAC-seq libraries were purified using Gene-Read Size Selection Kit (Qiagen, 180514) according to the manufacturer’s protocol. Quality and quantity of final ATAC-seq libraries were assessed with the High Sensitivity DNA kit (Agilent, 5067-4626) run on an Agilent 2100 Bioanalyzer. ATAC-seq libraries were sequenced using Illumina 125-bp paired-ends sequencing on a HiSeq2500 platform with, generating between 38 and 43 million reads per condition per biological replicate.

first: Jayati

last: Basu

first: Dietmar

last: Kappes


title: Glut1-dependent aging of tumor-associated neutrophils dictates tumor support and sensitivity to radiotherapy.

status: Public on Mar 18 2021

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics