title: An Integrative Approach to Assessing Effects of a Short-term Western Diet on Gene Expression in Rat Liver

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: Consumption of a diet rich in saturated fatty acids and carbohydrates contributes to the accumulation of fat in the liver and development of non-alcoholic steatohepatitis (NASH).  Herein we investigated the hypothesis that short-term consumption of a high fat/sucrose Western diet (WD) alters the genomic and translatomic profile of the liver in association with changes in signaling through the protein kinase mTORC1, and that such alterations contribute to development of NAFLD.  The results identify a plethora of mRNAs that exhibit altered expression and/or translation in the liver of rats consuming a WD compared to a CD.  In particular, consumption of a WD altered the abundance and ribosome association of mRNAs involved in lipid and fatty acid metabolism, as well as those involved in glucose metabolism and insulin signaling.  Hepatic mTORC1 signaling was enhanced when rats were fasted overnight and then refed in the morning; however, this effect was blunted in rats fed a WD as compared to a CD.  Despite similar plasma insulin concentrations, fatty acid content was elevated in the liver of rats fed a WD as compared to a CD.  We found that feeding had a significant positive effect on ribosome occupancy of 49 mRNAs associated with hepatic steatosis (e.g., LIPE, LPL), but this effect was blunted in the liver of rats fed a WD.  In many cases, changes in ribosome association were independent of alterations in mRNA abundance, suggesting a critical role for diet-induced changes in mRNA translation in the expression of proteins encoded by those mRNAs.  Overall, the findings demonstrate that short-term consumption of a WD impacts hepatic gene expression by altering the abundance of many mRNAs, but also causes wide-spread variation in mRNA translation that potentially contribute to development of hepatic steatosis.

overall_design: Obesity-prone Sprague Dawley rats (op-SD), initial body weight 160–190 g, were fed either a control diet (CD; TD 08485), or a Western diet (WD; TD 88137) ad libitum for 2 wks.  Rats were anesthetized and a sample (~1 g) of the left lobe of the liver was removed and homogenized.  Total RNA was extracted from the homogenates using Trizol, and equal amounts of RNA from 3 rats/condition were pooled.  Another aliquot of homogenate was subjected to sucrose density gradient centrifugation, and two fractions were collected from each gradient. The first fraction corresponded to the portion of the gradient containing mRNAs associated with three or fewer ribosomes (referred to hereafter as the light fraction), and the second fraction corresponded to the portion of the gradient containing mRNAs associated with four or more ribosomes (referred to as the heavy fraction). RNA was extracted from each fraction using Trizol.  20 µg of RNA from the livers of three rats/condition, i.e., rats fed either the CD or WD, or the light and heavy fractions from sucrose density gradients from three rats/condition, were combined prior RNAseq analysis.  RNA quality was assessed using an Agilent 2100 Bioanalyzer.Library preparation from each RNA fraction was performed using a KAPA RNA HyperPrep Kit with RiboErase (Roche Molecular Systems; no. KK8560) according to the manufacturer’s instructions.  The resulting libraries were amplified, and the quality was assessed by electrophoresis followed by RNAseq analysis using an Illumina Novaseq.

first: Jaclyn

last: Welles

first: Holly

last: Lacko

first: Michael

last: Dennis

first: Leonard

middle: S

last: Jefferson

first: Scot

last: Kimball


title: Essential role of MESP1-RING1A complex in cardiac differentiation

status: Public on Oct 17 2022

city: Philadelphia

first: Siqing

last: Wang

state: PENNSYLVANIA

address: 3401 Civic Center Blvd

department: Department of Pediatrics, Division of Hematology

country: USA

institute: Children’s Hospital of Philadelphia

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: Heart development is controlled by a complex transcriptional network composed of transcription factors and epigenetic regulators. Mutations in key developmental transcription factor MESP1, and chromatin factors such as PRC1 and cohesin components have been found in human congenital heart diseases (CHDs), although, their functional mechanism during heart development remains elusive. Here we find MESP1 interacts with RING1A/RING1, the core component of PRC1. RING1A depletion impairs human cardiomyocyte differentiation, and similar cardiac abnormalities were observed in Ring1A knockout mice as in patients with MESP1 mutations. Mechanistically, MESP1 associates with RING1A to activate cardiogenic genes through promoter-enhancer interactions mediated by cohesin and CTCF, and histone acetylation mediated by p300. Importantly, CHD mutations of MESP1 significantly affect such mechanisms and impair target gene activation. Together, our results demonstrate the importance of MESP1-RING1A complex in heart development and provide insights into pathogenic mechanisms of CHDs caused by mutations in MESP1, PRC1 and cohesin components.

overall_design: We performed ChIP-seq of MESP1 in human cardiac progenitor stage cells (CPCs, day 4 post differentiation from hESCs) overexpressing Dox-induced FLAG-MESP1 using anti-FLAG tag antibody. We performed ChIP-seq of RING1/RING1A and RING2/RING1B in hESCs and CPCs, ChIP-seq of H3K4me3 and H3K27ac in CPCs, ChIP-seq of RING1/RING1A and H3K27ac in MESP1 KO CPCs, Input of ChIP-seq in hESCs and CPCs, Hi-C of WT and RING1A KO CPCs (day 4 post differentiation from hESCs), mRNA-seq of WT, MESP1 KO, and RING1A KO CPCs (day 4 and day 6 post differentiation from hESCs).

first: Fei

last: Lan

first: Ning

last: Sun

first: Qianqian

last: Liang


title: SYK coordinates neuroprotective microglial responses in neurodegenerative disease [Bulk RNA-seq]

status: Public on Oct 15 2022

city: Charlottesville

first: Daniel

last: Shapiro

state: VA

address: 1340 Jefferson Park Ave

department: Neuroscience

institute: University of Virginia School of Medicine

summary: Many neurodegenerative diseases are thought to be caused by impaired containment and/or disposal of neurotoxic material such as amyloid beta (Ab) and myelin debris. Indeed, recent human genome-wide association studies (GWAS) and animal model studies have begun to reveal critical roles for the brain’s professional phagocytes, microglia, as well as various innate immune receptors expressed by microglia in the control of neurotoxic material and subsequent neurodegenerative disease pathogenesis. Yet, the critical intracellular molecules that orchestrate the neuroprotective functions of microglia in degenerative disorders remain poorly understood. In our studies, we have identified the innate immune signaling molecule spleen tyrosine kinase (SYK) as a key regulator of microglial phagocytosis in neurodegenerative disease. We find that targeted deletion of SYK in microglia leads to exacerbated Ab deposition, aggravated neuropathology, and cognitive defects in the 5xFAD mouse model of Alzheimer’s disease (AD). Furthermore, disruption of SYK signaling in this AD model was also shown to impede the development of disease-associated microglia (DAMs), alter AKT/GSK3b-signaling in microglia, and to cause severe deficits in the ability of microglia to phagocytose Ab. Importantly, these critical neuroprotective functions of SYK in microglia were not only restricted to Ab-driven models of neurodegeneration, as we found that SYK is also a critical regulator of microglial phagocytosis and DAM phenotype acquisition in demyelinating disease. Collectively, these results help to break new ground in our understanding of the key innate immune signaling molecules that instruct beneficial microglial functions in response to neurotoxic material. Moreover, these findings suggest that targeting SYK may offer a therapeutic strategy to treat a spectrum of neurodegenerative disorders.

overall_design: Comparison of 5xFAD severity and microglial response with or without SYK function. 4 replicates per group of non disase (control), SYK-deficient, 5xFAD, and 5xFAD Syk deficient

first: Hannah

last: Ennerfelt

first: Elizabeth

middle: L

last: Frost

middle: A

first: Coco

last: Holliday

first: Kristine

middle: E

last: Zengeler

first: Gabrielle

last: Voithofer

first: Ashley

middle: C

last: Bolte

first: Catherine

middle: R

last: Lammert

first: Joshua

last: Kulas

first: Tyler

middle: K

last: Ulland

first: John

last: Lukens


title: Kinetic comparative analysis of gene expression in whole adrenal glands from Znrf3 cKO and control mice

city: Aubiere

first: Pierre

last: Val

address: 24 avenue des Landais

country: France

institute: CNRS

summary: Unlike most cancers, adrenocortical carcinomas (ACC) are more frequent in women than men, but the underlying mechanisms of this sexual dimorphism remain elusive. Here, we show that inactivation of Znrf3 in steroidogenic cells of the mouse adrenal cortex is associated with sexually dimorphic tumour progression. Although female knockouts develop metastatic carcinomas at 18 months, adrenal hyperplasia regresses in male knockouts. This male-specific phenotype is associated with androgen-dependent induction of senescence, recruitment and differentiation of highly phagocytic macrophages that clear-out senescent cells. In contrast, in females, macrophage recruitment is delayed and dampened, which allows for aggressive tumour progression. Consistently, analysis of TCGA-ACC data shows that phagocytic macrophages are more prominent in men and associated with better prognosis. Altogether, these data show that phagocytic macrophages are key players in the sexual dimorphism of ACC and establish them as novel therapeutic targets for this devastating cancer.

overall_design: These data analyse gene expression in whole adrenals from  wild-type control mice and mice with conditionnal ablation of Znrf3 (Znrf3 cKO = Sf1-Cre;Znrf3F/F) in steroidogenic cells of the adrenal cortex. Adrenals were collected at different timepoints to evaluate kinetic evolution of the phenotype and in both males and females to evaluate sexual dimorphism. Wild-type and Znrf3 cKO mice were littermates.

last: VAL


title: Transgenerational tolerance to abiotic stresses induced by plant virus infection

status: Public on Oct 14 2022

city: Madrid

first: Francisco

last: Tenllado

address: Ramiro de Maeztu, 9

country: Spain

institute: CSIC

summary: Following pathogen infection, plants have developed diverse mechanisms of defense that enhance their immune system for more robust induction of defense responses against recurrent environmental stresses. This induced resistance can be heritable to the progeny, rendering them more tolerant to stressful events. Although within-generational induction of tolerance to abiotic stress is a well-documented phenomenon in virus-infected plants, the transgenerational inheritance of tolerance to abiotic stresses in their progenies has not been explored. Here, we show that infection of Nicotiana benthamiana plants by Potato virus X (PVX) and by a chimeric Plum pox virus (PPV) expressing the P25 protein of PVX (PPV-P25), but not by PPV, conferred tolerance to both salt and osmotic stresses to the progeny, which correlated with the level of virulence of the pathogen. This transgenerational tolerance to abiotic stresses in the progeny was partially sustained even if the plants experience a virus-free generation. Moreover, progenies from a Dicer-like3 mutant, irrespective whether their parents were infected or not, mimicked the enhanced tolerance to abiotic stress observed in progenies of PVX-infected wild-type plants, suggesting the involvement of 24-nt small interfering RNAs in the transgenerational tolerance to abiotic stress induced by virus infection. RNAseq analysis supported the upregulation of genes related to protein folding and response to stress in the progeny of PVX-infected plants. From an environmental point of view, the significance of virus-induced transgenerational tolerance to abiotic stress could be questionable, as its induction was offset by major reproductive costs arising from a detrimental effect on seed production

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Nicotiana bentamina seeds derived from plants of two different genotypes (Wt and Dcl3) that were either infected with Potato virus X (WtPVX and Dcl3PVX) or mock-inoculated (Dcl3Ctr and WtCtr). Three biological replicates were analyzed for each treatment.

middle: J

last: Hernández-Walias

first: Marina

last: García

last: Moreno

first: Ioannis

last: Giannoukos

first: Natalia

last: González

first: Eugenio

last: Sanz-García

first: Khouloud

last: Necira

first: Tomás

last: Canto


title: Transcriptome profiling of the aorta from NPR1 knockout heterozygous mice

city: Nanchang

first: Hongfei

last: Liu

state: Jiangxi

address: Nanchang university, 999 Xuefu Avenue, Xinjian District

country: China

institute: Nanchang University

summary:
To investigate the mechanism of NPR1 regulating vascular function, we established NPR1 knockout heterozygous mice by CRISPR-Cas9.
We performed high-throughput RNA sequencing to analyse the transcriptom of the aorta of NPR1 knocout heterogeneous mice.

overall_design: RNA-seq performed in mouse whole aorats from wild type and NPR1 knockout heterozygous mice, n=3 per experimental group, using  the BGISEQ-500 platform.

first: Changkun

last: Long

first: Wenxin

last: Zhan

first: Liping

last: Chen

first: Shenghan


title: Transcriptome analysis reveals the effect of Atractylodes macrocephala Koidz. on DSS-induced colitis in mice

city: Nanjing

first: Lixin

last: Sun

address: 24 Tong Jia Xiang

institute: China Pharmaceutical University

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

summary: Ulcerative colitis (UC), a subtype of inflammatory bowel disease (IBD), is characterized by chronic and relapsing mucosal inflammation initiating in the rectum and extending upward through part or the entire colon in a continuous fashion. Currently, 5-aminosalicylic acid agents, corticosteroids, immunomodulators, and surgery are the main treatments for UC, which are limited in clinical practice due to common nonadherence, serious adverse effects and heavy financial burden. Atractylodes macrocephala Koidz. (Baizhu) has been used for improving gastrointestinal function and treating digestive disorders for thousands of years, and is currently one of the most frequently used traditional Chinese medicines for the treatment of UC. The purpose of this study was to evaluate the effect and underlying mechanism of polysaccharide from Atractylodes macrocephala Koidz. (PAMK) on UC based on a mouse model of dextran sodium sulfate (DSS)-induced colitis. To investigate the mechanism of therapeutic effect of PAMK on colitis, we performed the microarray analysis of colonic tissues in Control, DSS and DSS+PAMK groups. The results indicated that the beneficial effect of PAMK on DSS-induced colitis may rely on the regulation of the immune response.

overall_design: Microarray analysis was performed on colonic tissues from the Control, DSS and DSS+PAMK (200 mg/kg PAMK, i.g.) groups (n=3)

first: Qianwen

last: Zhang

first: Mengjiao

last: Yang


title: Intestinal type 2 inflammation reprograms mesenteric adipose tissue and permanently alters its resident immune cell niche [2022_RNA_2]

status: Public on Oct 13 2022

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: In addition to adipocytes, adipose tissue (AT) is populated by mesenchymal stem cells (MSC) in stages of commitment to the adipocyte lineage, and immune cells which support homeostatic tissue function. How MSC and immune cells interact during infection is poorly understood. We found that during intestinal nematode infection, MSC in gut-associated AT (mFAT) exhibit a bias away from commitment to the adipocyte lineage towards a pluripotent progenitor state. During this time, MSC became metabolically active, and began secreting the alarmins IL-33 and TSLP, and extracellular matrix collagens. In parallel, mFAT became irreversibly populated by Th2 resident memory (Th2RM) cells, which make the tissue modulatory cytokines amphiregulin and TGFβ1. Secretion of these cytokines, and Th2RM activation and maintenance, was driven by IL-33 and TSLP and in turn MSC activation was induced by amphiregulin and TGFβ1. Our findings link Th2RM cells to reversible mFAT remodeling during intestinal infection and underscore the reciprocal dependence of stroma and resident immune cells for lasting tissue immunity.

overall_design: RNASeq on small intestine biopsies (healthy, granuloma, non-granuloma) from mice infected with H. poly.

first: Agniezka

middle: M

last: Kabat

first: David

last: Sanin

first: Edward

last: Pearce


title: Transcriptomic dynamics associate with constitutively active and dominant negative states of Rho GTPase MoRho3 in rice blast fungus Magnaporthe oryzae

city: Hangzhou

first: lianyu

last: lin

state: Zhejiang

address: Zijingang Campus of Zhejiang University,Yuhangtang Road No.866

institute: Zhejiang University

summary: RNA-seq of 9 M. oryzae isolates

overall_design: Total RNAs of 9 M. oryzae rice isolates in hyphal stage were extracted for sequencing

first: Qian

last: Li

first: Xi

first: Lianyu

last: Lin

first: Dongmei


title: Phosphate limitation intensifies negative effects of ocean acidification on globally important nitrogen fixing cyanobacterium

city: Eilat

first: Futing

address: Interuniversity Institute for Marine Sciences, Eilat, P.O.B 469

country: Israel

summary: The filamentous diazotrophic cyanobacteria Trichodesmium spp. supply fixed nitrogen (N) to the N-depleted oligotrophic oceans where their growth is often limited by the low availability of phosphorus(P) and/or iron. Previous studies have mostly been focused on the effects of ocean acidification on Trichodesmium under nutrient sufficient or iron-limited conditions. Only a few studies have examined the impacts of ocean acidification on Trichodesmium grown at low P concentrations using non-steady-state batch cultures. Here we cultured Trichodesmium using P-limited continuous cultures (chemostat) to mimic steady-state oceanic low P condition, and used comparative NGS-derived Trichodesmium transcriptome profiling (RNA-seq) analysis to find differentially expressed genes and cellular pathways in response to acidification.

overall_design: mRNA profiles of phosphorus limited Trichodesmium cultured at 400 µatm pCO2 (LP_400) and 750 µatm pCO2 (LP_800)

first: Zuozhu

last: Wen

first: Shanlin

last: Wang

first: Weiyi

last: Tang

first: Ya-Wei

last: Luo

first: Sven A.

last: Kranz

first: Haizheng

last: Hong

first: Dalin

last: Shi


title: Discovery of a Trans-Omics Biomarker Signature that Predisposes High Risk Diabetic Patients to Diabetic Kidney Disease

status: Public on Oct 12 2022

city: Miaoli County

first: Paul

middle: Wei-Che

last: Hsu

state: Taiwan

address: Zhunan: 35, Keyan Road, Zhunan Town

department: National Health Research Institutes

country: Taiwan

institute: National Health Research Institutes

type:
Genome variation profiling by array
SNP genotyping by SNP array

summary: Diabetic kidney disease is the leading cause of end-stage kidney disease worldwide; however, the integration of high-dimensional trans-omics data to predict this diabetic complication is rare. We develop artificial intelligence (AI)-assisted models using machine learning algorithms to identify a biomarker signature that predisposes high risk patients with diabetes mellitus (DM) to diabetic kidney disease based on clinical information, untargeted metabolomics, targeted lipidomics and genome-wide single nucleotide polymorphism (SNP) datasets. This involves 618 individuals who are split into training and testing cohorts of 557 and 61 subjects, respectively. Three models are developed. In model 1, the top 20 features selected by AI give an accuracy rate of 0.83 and an area under curve (AUC) of 0.89 when differentiating DM and non-DM individuals. In model 2, among DM patients, a biomarker signature of 10 AI-selected features give an accuracy rate of 0.70 and an AUC of 0.76 when identifying subjects at high risk of renal impairment. In model 3, among non-DM patients, a biomarker signature of 25 AI-selected features give an accuracy rate of 0.82 and an AUC of 0.76 when pinpointing subjects at high risk of chronic kidney disease. In addition, the performance of the three models is rigorously verified using an independent validation cohort. Intriguingly, analysis of the protein-protein interaction network of the genes containing the identified SNPs (RPTOR, CLPTM1L, ALDH1L1, LY6D, PCDH9, B3GNTL1, CDS1, ADCYAP and FAM53A) reveals that, at the molecular level, there seems to be interconnected factors that have an effect on the progression of renal impairment among DM patients. In conclusion, our findings reveal the potential of employing machine learning algorithms to augment traditional methods and our findings suggest what molecular mechanisms may underlie the complex interaction between DM and chronic kidney disease. Moreover, the development of our AI-assisted models will improve precision when diagnosing renal impairment in predisposed patients, both DM and non-DM. Finally, a large prospective cohort study is needed to validate the clinical utility and mechanistic implications of these biomarker signatures.

overall_design: The genomic DNA was collected from peripheral white blood cells using the phenol/chloroform DNA extraction method after lysis of red blood cells. Each subject was genotyped using Axiom Genome-Wide TWB 2.0 array plates. SNPs were excluding with a minor allele frequency rate of 0 or SNPs with a missing rate of more than 10%.

first: Huey-Kang

last: Sytwu

first: Ting-Fen

last: Tsai

first: Chi-Chun

last: Lai


title: HIV specific CD8+ Trm-like cells in tonsils express exhaustive signatures in the absence of natural HIV control

city: Cambridge

first: Alex

last: Shalek

state: MA

address: 45 Carleton Street

department: Chemistry

institute: MIT

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

overall_design: Refer to individual Series


title: Intestinal type 2 inflammation reprograms mesenteric adipose tissue and permanently alters its resident immune cell niche [2022_RNA_1]

first: Immunometabolism

last: Department

overall_design: RNASeq on stromal cells from EGFR flox male mice isolated on day 9 of primary H.poly infection.

first: Agniezka

last: Kabat

first: David

last: Sanin

first: Edward


title: HIV specific CD8+ Trm-like cells in tonsils express exhaustive signatures in the absence of natural HIV control [smart-seq 2]

summary: Lymphoid tissues are an important HIV reservoir site that persists in the face of antiretroviral therapy and natural immunity. Targeting these reservoirs by harnessing the antiviral activity of local tissue-resident memory (TRM) CD8+ T-cells is of great interest, but limited data exist on TRM-like cells within lymph nodes of people living with HIV (PLWH). Here, we studied tonsil CD8+ T-cells obtained from PLWH and uninfected controls from South Africa. We show that these cells are preferentially located outside the germinal centers (GCs), the main reservoir site for HIV, and display a low cytolytic and transcriptionally TRMlike profile distinct from blood CD8+ T-cells. In PLWH, CD8+ TRM-like cells are highly expanded and adopt a more cytolytic, activated, and exhausted phenotype not reversed by antiretroviral therapy (ART). This phenotype was enhanced in HIV-specific CD8+ T-cells from tonsils compared to matched blood suggesting a higher antigen burden in tonsils. Single-cell transcriptional and clonotype resolution showed that these HIV-specific CD8+ T-cells in the tonsils express heterogeneous signatures of T-cell activation, clonal expansion, and exhaustion ex-vivo. Interestingly, this signature was absent in a natural HIV controller, who expressed lower PD-1 and CXCR5 levels and reduced transcriptional evidence of T-cell activation, exhaustion, and cytolytic activity. These data provide important insights into lymphoid tissue-derived HIVspecific CD8+ TRM-like phenotypes in settings of HIV remission and highlight their potential for immunotherapy and targeting of the HIV reservoirs.

overall_design:
Tonsils from three HIV-positive individuals were dissociated and sorted with FACS for scRNA-Seq of T CD8+ cells. Fluorescence for a variety of important proteins as well as HIV-specificity. Single-cell TCR sequencing was run on these cells to identify expanded clones.

>>>Submitter states that raw data are not available due to patient privacy concerns<<<

first: Rabiah

last: Fardoos

first: Sarah

last: Nyquist

first: Osaretin

last: Asowata

first: Samuel

middle: W

last: Kazer

first: Alveera

last: Singh

first: Abigail

last: Ngoepe

first: Jennifer

last: Giandhari

first: Ntombifuthi

last: Mthabela

first: Dirhona

last: Ramjit

first: Samita

first: Farina

last: Karim

first: Søren

last: Buus

first: Frank

last: Anderson

first: James

middle: Z

last: Porterfield

first: Andile

last: Sibiya

first: Rishan

last: Bipath

first: Kumeshan

last: Moodley

first: Warren

last: Kuhn

first: Bonnie

last: Berger

first: Son

last: Nguyen

first: Tulio

last: de Oliveira

first: Thumbi

last: Ndung'u

first: Philip

last: Goulder

first: Alasdair

last: Leslie

first: Henrik

middle: N

last: Kløverpris


title: Expression data from testicular germ cell tumor cells

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

country: Japan

institute: Saitama Medical University

summary: To clarify the  mechanism of cisplatin resistance in testicular germ cell tumor (TGCT), cisplatin-resistant TGCT cells (N8R and G9R) were generated from parental NEC8 cells (N8P) and TGCT patient-derived cells (TGCT-PDC)(G9P), respectively, by culture in medium containing cisplatin. We used microarrays to detail the global programme of gene expression underlying cisplatin resistance and identified up- and down-regulated genes during this process.

overall_design: Total RNA was extracted from parental NEC8 (N8P) and TGCT-PDC (G9P) cells and from cisplatin-resistant NEC8 (N8R) and TGCT-PGC (G9R) cells. These RNAs were then used for Affymetrix microarrays analysis.

first: Sachi

last: Kitayama

first: Kuniko

last: Horie

first: Satoshi

last: Inoue


title: HIV specific CD8+ Trm-like cells in tonsils express exhaustive signatures in the absence of natural HIV control [Seqwell]

first: Alex

last: Shalek

overall_design:
This dataset is comprised of seven scRNA-Seq samples. Tissue samples from tonsils of healthy individuals were sequenced using scRNA-Seq with CD3 enrichment and without. PBMCs from three different donors were included to compare immune cells between blood and tonsil tissues.

>>>Submitter states that raw data are not available due to patient privacy concerns<<<

first: Rabiah

last: Fardoos

first: Sarah

last: Nyquist

first: Osaretin

last: Asowata

first: Samuel

last: Kazer

first: Alveera

last: Singh

first: Abigail

last: Ngoepe

first: Jennifer

last: Giandhari

first: Ntombifuthi

last: Mthabela

first: Dirhona

last: Ramjit

first: Samita

first: Farina

last: Karim

first: Søren

last: Buus

first: Frank

last: Anderson


title: mRNA sequencing of wildtype versus CEP83 knockout hiPSCs at diffirent time points of differentiation to kidney organoids

city: Hannover

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

department: Department of Nephrology and Hypertension

country: Germany

institute: Hannover Medical School


title: Identification of Tcf21 downstream genes in the epicardial cells and cardiomyocytes by transcriptomic analysis

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary:
Purpose: Studying the epicardium-myocardium crosstalk in the zebrafish larval heart. To do so, we aimed to identify, with RNA-seq, the genes dysregulated following the loss of the epicardial marker gene tcf21 in sorted epicardial cells and cardiomyocytes.
Results: We first analyzed the transcriptome of epicardial and myocardial WT cells and identified cell-type specific/enriched genes. Then, we identified several differential expressed genes in tcf21 mutants, including several ligand-receptor couples known to mediate the epicardium-myocardium crosstalk.

overall_design: Hearts were manually extracted from 96 hpf Tg(myl7:mcherry), TgBAC(tcf21:nls-EGFP) tcf21+/+ and tcf21-/- zebrafish larvae. Hearts were dissociated into single-cell suspensions and FACS was performed to sort epicardial and myocardial cells based on the fluorescence signal.

first: Giulia

last: Boezio

last: Guenther


title: RNA sequencing of HeLa cells

status: Public on Oct 11 2022

city: Newcastle upon Tyne

first: Thomas

middle: Joseph

last: Nicholls

address: Framlington Place

department: Wellcome Centre for Mitochondrial Research

country: United Kingdom

institute: Newcastle University

summary: DNA topoisomerase 3A (TOP3A) and mitochondrial DNA topoisomerase 1 (TOP1MT) play an important role in the maintenance and topological control of the mitochondrial DNA. In this study TOP3A, TOP1MT or both TOP3A and TOP1MT have been knocked down using siRNAs to determine the effect of the topoisomerases on mitochondrial transcription. RNA was isolated from ctrl siRNA, TOP3A siRNA, TOP1MT siRNA and TOP3A + TOP1MT siRNA transfected cells after 6 days of transfection.

overall_design: 3 replicates of each of  ctrl siRNA, TOP3A siRNA, TOP1MT siRNA and TOP3A + TOP1MT siRNA treated

first: Katja

last: Menger


title: Loss of the repressor REST affects progesterone receptor function and promotes uterine leiomyoma pathogenesis

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

institute: University of kansas medical center


title: mRNA sequencing of wildtype versus CEP83 knockout hiPSCs at diffirent time points of differentiation to kidney organoids [bulk RNA-seq]

summary: Centrosomal protein 83 (CEP83) is a component of the distal appendages proteins of centrioles, which is necessary for the assembly of primary cilia. Previous studies have implicated primary cilia in normal development and tissue homeostasis, including kidney development. The kidney develops from human induced pluripotent stem cell (hiPSCs) in a stepwise process involving induction of specialized Nephron progenitors (NPs) in the intermediate mesoderm (IM), followed by their differentiation into kidney epithelia. Here, we used CRISPR-cas9 technology to knockout CEP83 in hiPSCs that were differentiated versus the wildtype hiPSCs into IM followed by kidney epithelial differentiation to analyze the role of CEP83 in human kidney epithelial differentiation. We used morphological analyses, gene expression studies and immunostaining to analyze IM and nephron differentiation. Bulk RNA and single cell sequencing showed that CEP83-/- IM cells abnormally upregulate regulatory transcription factors of lateral plate mesoderm (LPM) including OSR1, FOXF1, FOXF2, HAND2 and FEDRR., and downregulate marker genes in specific NPs ncluding; PAX8, HOXB7 and EYA1.  Further, wildtype hiPSCs successfully differentiated into kidney organoids that upregulate key nephron markers, including NPHS1, CUBN and GATA3. In contrast, CEP83-/- hiPSCs failed to differentiate into nephron epithelia and didn’t express nephron marker genes. In a human system modeling kidney epithelial differentiation from hiPSCs, our data provide a new insight to the essential role of CEP83 in NPs differentiation and may help to better understand the pathogenesis of CEP83-associated renal developmental defects.

overall_design: The provided data comprise bulk RNA-sequencing data from wildtype and CEP83 knockout cells at different time point of differentiation: day 0 (hiPSCs stage), day 7 (intermediate mesoderm stage), and day 25 (organoid stage).

first: Fatma

last: Mansour

first: Narasimha

last: Telugu

first: Jelena

last: Kresoja

first: Iman

last: Shaheed

last: Mosimann

first: Sebastian

last: Diecke

first: Kai

last: Schmidt-Ott


title: Loss of the repressor REST affects progesterone receptor function and promotes uterine leiomyoma pathogenesis [RNA-seq]

summary: Uterine Leiomyomas (UL) are benign tumors that arise in the myometrium of the uterus. The standard treatment option for UL is hysterectomy but hormonal treatment options are emerging in the field. However, since the pathogenesis of UL is poorly understood, hallmarks that predict long-term efficacy and safety of these treatment options remain largely undefined. We have reported previously that REST/NRSF target genes are aberrantly expressed due to the near ubiquitous loss of this epigenetic repressor in UL tumors. We show that ablation of Rest in the mouse uterus leads to UL phenotype and altered response to steroid hormones estrogen and progesterone. Additionally, we demonstrate that a large number of REST target genes dysregulated in UL as well as in Rest cKO mice, are also targets of progesterone receptor (PR). Importantly, we identify a direct interaction between REST and PR in the healthy myometrium. Rest cKO mouse model phenocopies human UL, including gene expression profiles of UL as well as tumor formation in the myometrium. Our findings emphasize the critical role loss of REST plays in disease pathogenesis and the altered response to steroid hormones seen in UL.

overall_design: Whole uteri of Restf/f Amhr2+/cre cKO (n=3) and restf/f mice (n=3) aged 4 months were collected.

first: Ashley

last: Cloud

first: Michelle

last: McWilliams

first: Faezeh

last: Koohestani

first: Sornakala

last: Ganeshkumar

first: Amanda

last: Graham

first: Warren

middle: B

last: Nothnick

first: Vargheese

last: Chennathukuzhi


title: Loss of the repressor REST affects progesterone receptor function and promotes uterine leiomyoma pathogenesis [scRNA-seq]

overall_design: Whole uteri of Restf/f PR+/Cre cKO and control mice aged 5 months were isolated. Control samples (n=2) were pooled and cKO samples (n=2) were pooled.


title: mRNA sequencing of wildtype versus CEP83 knockout hiPSCs at diffirent time points of differentiation to kidney organoids [scRNA-seq]

first: Christian

last: Hinze

overall_design: The provided data comprise single cell sequencing data from wildtype and CEP83 knockout cells at  day 7 (intermediate mesoderm stage) of differentiation of hiPSCs toward kidney organoids.


title: Spatial transcriptomics of ovarian cancer tumors

status: Public on Oct 10 2022

city: Aurora

first: Kristen

last: Wells

state: CO

address: 1775 Aurora Ct,

department: Barbara Davis Center

institute: University of Colorado Anschutz

summary:
Several ovarian cancer tumors from different anatomical sites and therapy statuses.
A GUI to explore the data can be found at: https://visium-shiny-9hzfl.ondigitalocean.app/
Code to run the shiny app (same output as the GUI): https://github.com/kwells4/visium_public_shiny
Code to replicate the analysis can be found: https://github.com/kwells4/visium_ovarian_cancer

overall_design: Visium 10x spatial RNA-seq on 8 ovarian tumor samples.

first: Benjamin

last: Bitler


title: A novel signature of twelve-gene to evaluate neoadjuvant chemotherapy response and predict prognosis in breast cancer

city: Chongqing

first: Jin

last: Wu

state: 重庆

address: Gaotanyan Street

institute: Army Medical University

summary: In this study, we have analyzed the transcriptional patterns of breast cancer cell lines and tumors of NAC resistant patients evaluated by GGI, and screened potential genes associated with chemoresistance. Furthermore, we have constructed a neoadjuvant chemotherapy response risk model and examined the evaluation accuracy of the risk score for NAC response. We conducted molecular bioinformatics analysis of the genes that constitute the chemotherapy resistance risk score, and explored potential drugs to reverse breast cancer chemotherapy resistance. Finally, we have examined the the risk score for predicting prognosis in breast cancer. In all, we have reported a novel signature to evaluate neoadjuvant chemotherapy response and predicts prognosis in breast cancer, and screened out potential drugs to reverse chemotherapy resistance in breast cancer.

overall_design: we compared the expression profile of epirubicin-resistant cells with wild type cells.

first: Peng

last: Tang


title: Gene expression in human corneal epithelial cells (hCECs), human corneal fibroblasts (hCFs) or human corneal endothelial cells (hCEnCs) with or without exosomes derived from hCECs, hCFs or hCEnCs

city: Québec

first: Gaëtan

last: Le-Bel

state: Quebec

address: Local H2-00, Hôpital du Saint-Sacrement,1050 Chemin Sainte-Foy

country: Canada

institute: CUO-Recherche

summary: In this study, we evaluated the effects of the corneal exosomes on the gene profiling expression in hCECs, hCFS and hCEnCs

overall_design: One population of each cell type (hCECs, hCFS, hCEnCs) with exosomes derived from the three corneal cell types in monoculutre were analyzed by gene profiling

first: Pascale

last: Desjardins

first: Rébecca

last: Berthiaume

first: Camille

last: Couture

first: Vincent

last: Roy

first: François

last: Gros-Louis

first: Véronique

last: Moulin

first: Stéphanie

last: Proulx

first: Sylvaian

last: Chemtob

first: Lucie

last: Germain

first: Sylvain

last: Guérin


title: Divergent outcomes of anti-PD-L1 treatment coupled with host-intrinsic differences in TCR repertoire and distinct T cell activation states in responding versus non-responding tumors

city: Pittsburgh

first: Jing

middle: Hong

last: Wang

email: jhw51@pitt.edu, wangj28@upmc.edu

address: 5117 Centre Avenue, Suite 2.35

department: Department of Medicine

institute: University of Pittsburgh

summary: Differential responses to immune checkpoint inhibitors (ICI) may be attributed to tumor-intrinsic factors or environmental cues; however, these mechanisms cannot fully explain the variable ICI responses in different individuals. Here, we investigate the potential contribution of immunological heterogeneity with a focus on differences in T-cell receptor (TCR) repertoire to ICI responses, which has not been defined previously.

overall_design: To reveal additional factors underlying heterogeneous responses to ICI, we employed a squamous cell carcinoma (SCC) mouse model in which tumor-bearing recipients unambiguously diverged into responders (R) or non-responders (NR) upon anti-PD-L1 treatment. We employed single-cell T-cell receptor (TCR) sequencing coupled with single-cell RNA sequencing to identify the difference in TCR repertoire of CD8 tumor infiltrating lymphocytes (TILs) in responders versus non-responders. Tumors and spleens were harvested from responders (n=4) and non-responders (n=4) and CD8 T cells were isolated and subjected for coupled scRNA-seq and single-cell TCR V(D)J sequencing (both CD8 TIL and splenic CD8 T cells) using 10× Genomics platform.

first: Jessy

last: John

middle: H


title: Perinuclear force regulates SUN2 dynamics and distribution on the nuclear envelope for proper nuclear mechanotransduction

city: Beijing

first: Wenxue

last: Zhao

address: Yiheyuan Road

institute: Peking University

summary: The trans-luminal LINC (Linker of Nucleoskeleton and Cytoskeleton) complex plays a central role in nuclear mechanotransduction by coupling the nucleus with cytoskeleton. High spatial density and active dynamics of LINC complex have hindered its precise characterization for the understanding of underlying mechanisms how the linkages sense and respond to mechanical stimuli. In this study, we focus on SUN2, a core component of LINC complex interconnecting the nuclear lamina and actin cytoskeleton and apply single molecule super-resolution imaging to reveal how SUN2 responds to actomyosin contractility. Using stochastic optical reconstruction microscopy (STORM), we quantitated the distribution pattern and density of SUN2 on the basal nuclear membrane. We found that SUN2 undergoes bidirectional translocation between ER and nuclear membrane in response to actomyosin contractility, suggesting that dynamic constrained force on SUN2 is required for its proper distribution. Furthermore, single molecule imaging unveils interesting dynamics of SUN2 molecules that are regulated by both actomyosin contractility and laminA/C network, whereas SUN2 oligomeric states are not affected by actomyosin contractility. Lastly, the mechanical response of SUN2 to actomyosin contractility was found to regulate expression of mechano-sensitive genes located in lamina-associated domains (LADs) and perinuclear heterochromatin. Taken together, our results reveal how SUN2 responds to mechanical cues at the single-molecule level, providing new insights into the mechanism of nuclear mechanotransduction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wildtype MDA-MB-231 cells and SUN2-KO samples. We also designed two truncations of SUN2 to block different external forces, ΔKashlid (569-585aa) to cut off the connections between SUN2 and Nesprin-2G and ΔLBD (Lamin binding domain, 1-139aa) to cut off the connections between SUN2 and lamin networks (LBD and Kashlid samples).

first: Jiahao

last: Niu


title: Human papillomavirus 42 is an oncogenic driver in Digital Papillary Adenocarcinoma [transductions]

city: Vienna

first: Anna

last: Obenauf

state: Vienna

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

summary: The skin serves as a barrier to the environment and is constantly exposed to viral pathogens. However, whether and how viral pathogens contribute to oncogenesis of rare skin cancers has not been explored. We analyzed 18 skin cancers by exploiting sparse off-target reads from commonly available next-generation sequencing data and identify human papillomavirus 42 (HPV42) reads in digital papillary adenocarcinoma (DPA). We show that HPV42 recapitulates the molecular hallmarks of oncogenic HPVs and shares a conserved transcriptomic fingerprint of HPV-transformation. Finally, we show that HPV42 relies on established cellular targets of oncogenic HPVs for its transforming activity. The discovery of HPV42 as a novel oncogenic driver highlights the utility of next-generation sequencing data for the discovery of novel pathogen-disease associations and suggests expansion of current HPV vaccination programs to reduce the cancer burden in humans.

overall_design: Cells were transduced with empty vector (EV), HPV16-E7 or HPV42-E7.

first: Lukas

last: Leiendecker

first: Tobias

last: Neumann

first: Thomas

last: Wiesner


title: Human papillomavirus 42 is an oncogenic driver in Digital Papillary Adenocarcinoma.

overall_design: Refer to individual Series


title: Light-Seq: Light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing

city: Boston

first: Emma

last: West

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: We present a new approach, Light-Seq, for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding in fixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially-targeted, rapid photocrosslinking of DNA barcodes onto cDNAs in situ with a novel one-step DNA stitching reaction to create pooled, spatially-indexed sequencing libraries. This light-directed barcoding enables in situ selection of multiple cell populations in intact fixed tissue samples for full transcriptome sequencing based on location, morphology, or protein stains, without cellular dissociation. Applying Light-Seq to mouse retinal sections, we recovered thousands of differentially enriched transcripts from three adjacent cellular layers and discovered new biomarkers for a very rare neuronal subtype, dopaminergic amacrine cells, from only 4-8 individual cells per section. Light-Seq provides an accessible workflow to combine in situ imaging and protein staining with next-generation sequencing of the same cells, leaving the sample intact sample for further analysis post-sequencing.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Whole transcriptome sequencing of HEK and 3T3 cells in mixed culture and retinal neurons within fixed tissue samples using Light-Seq.

first: Jocelyn

middle: Y

last: Kishi

first: Ninning

last: Liu

first: Sinem

last: Saka

first: Peng

last: Yin

first: Connie

last: Cepko


title: SOX9 and SOX10 control fluid homeostasis in the inner ear for hearing through independent and cooperative mechanisms

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

summary: The embryonic endolymphatic sac mediates fluid resorption for which anion exchangers such as SLC26A4, and its transcriptional activator FOXI1, are required. Apart from FOXI1, little is known about transcriptional regulators of this fluid balance. Altered fluid homeostasis in the inner ear is the leading cause of congenital hearing loss. Some patients with campomelic dysplasia (CD) caused by heterozygous mutations in SOX9, in addition to skeletal malformation, are deaf, with an unknown etiology. In a mouse model of CD caused by the SOX9Y440X mutation, which results in a truncated protein lacking the transactivation domain, we show severe endolymphatic dysfunction leading to deafness and vestibular problems. Adult heterozygous Sox9Y440X mice that express the mutation in the developing inner ear display sensorineural deafness combined with endolymphatic hydrops and lack of endocochlear potential. The mutant inner ear is enlarged from E15 and fewer Slc26a4-expressing cells are present in the endolymphatic epithelium. By single cell RNA sequencing of mutant and wild-type endolymphatic sacs we find marked reduction in genes important for ion transport such as Slc24a4 and Ttyh1 and gap-junctions such as Gjb2 and up-regulation of Wnt signaling and Igfbp2 that promotes progenitor proliferation. The cochlea overexpresses Aqp3, which encodes a water channel. We find by biochemical and cell-based transactivation assays and genetic interaction tests that SOX9 and SOX10 normally work co-operatively to repress Aqp3 transcription: SOX9Y440X blocks this repression by dominant interference. Our study reveals the key roles of SOXE transcription factors in the development of endolymphatic sac function, and highlight a molecular mechanism whereby the CD mutation exerts both a dominant negative and haploinsufficient mechanisms in different compartments of the inner ear to maintain fluid homeostasis. In the cochlea, SOX9 and SOX10 together repress aquaporin expression whereas in the endolymphatic sac, SOX9 controls SOX10 expression and genes for ion transport and gap-junctions. We postulate that in addition to loss of control of cell proliferation results in the exhaustion of progenitors which in turn leads to a deficit in mitochondria-rich cells. These results highlight a multifaceted mechanism for maintaining the proper fluid balance for hearing.

overall_design: We sequenced 120 cells from mouse wild-type and Sox9Y440X/+ endolymphatic sacs by Smart-seq2 protocol

first: Irene

last: Szeto

first: Kathryn

middle: S

last: Cheah


title: SOX9 and SOX10 control fluid homeostasis in the inner ear for hearing through independent and cooperative mechanisms (scRNA-seq: batch2)

overall_design: We sequenced 126 cells from mouse wild-type and Sox9Y440X/+ endolymphatic sacs by Smart-seq2 protocol


title: Human papillomavirus 42 is an oncogenic driver in Digital Papillary Adenocarcinoma [full_genomes]

overall_design: Cells were transfected with re-circularized HPV genomes and pSV2-neo plasmid.


title: Propyzamide and a pre-clinical model of IBD

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus


title: Human papillomavirus 42 is an oncogenic driver in Digital Papillary Adenocarcinoma [tumors]

overall_design: Gene expression profiling of DPA tumor samples by 3'-mRNA sequencing.


title: TMEM100, a Lung-Specific Endothelium Gene

status: Public on Oct 08 2022

city: St. Louis

first: Zhiyu

last: Dai

state: MO

address: 4960 Childrens Place

institute: Washington University in St. Louis

summary: Total RNA was isolated from human pulmonary microvascular endothelial cells (HPMVEC) overexpressed with GFP or TMEM100


title: Death and birth of transposable elements underlie subgenome convergent and divergent transcription in common wheat

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

summary: Common wheat (T. aestivum) converged three subgenomes adapted to different environments. The combinatorial interaction between transcription factors (TFs) and regulatory elements (REs) defines a regulatory circuit that underlies subgenome convergence and divergence. Compared to the relatively conserved gene composition across subgenomes, the intergenic regions with abundant REs is drastically diversified by almost complete TE turnovers, raising major questions regarding how subgenome convergent and divergent regulation is encoded in the highly diversified intergenic regions, and the impact of TE evolution on regulatory conservation and innovation. In the present study, we created genome-wide TF binding catalog to assemble an extensive wheat regulatory network comprising connections among 182 TFs. The different effects of ancient and recent TE insertions on regulatory specificity were observed. Subgenome asymmetric TE expansion is an important source of subgenome divergent TFBS, which help explain the vast occupancy difference across subgenomes. Interestingly, the ancient expansion of RLC_famc1.4-derived TFBS occurred in more than 25% triads promoters. A significant fraction of these TE-derived TFBS subjected to region-specific evolutionary selections, resulting in subgenome-balanced TF binding but unbalanced degeneration of flanking TE sequences. These TE-derived subgenome convergent and divergent regulation linked to subgenome conserved and diversified pathways, suggesting that TEs are an important regulatory driving force contributed to polyploid evolution. Overall, this study demonstrated the impact of TEs on shaping the plasticity and adaptation of common wheat, enriched the theories of TE-promoted transcriptional innovation from the evolutionary aspects of polyploid regulation since first reported by McClintock.

overall_design: To elucidate the subgenome convergent and divergent regulation in common wheat, we performed DAP-seq to obtain a genome-wide binding profile of 182 TFs from a large spectrum of families.

first: Yijing

last: Zhang


title: Viral and Host Small RNA Response to SARS-CoV-2 Infection

city: Duarte

first: Guihua

last: Sun

state: CA

address: 1500 East Duarte Rd.

department: Department of Neurodegenerative Diseases

institute: City of hope

type: Non-coding RNA profiling by high throughput sequencing

summary: HEK293T cells overexpressing hACE2 were infected by SARS-CoV-2 (WA1) and small RNA-seq was performed to profile small RNAs in response to SARS-COV-2 infection

overall_design: HEK293T-hACE2 cell line, both mock and infection samples were duplicated, infected at MOI=1 for three days

first: Yanhong

last: Shi

first: Vaithilingaraja

last: Arumugaswami

first: Arthur

last: Riggs


title: Identification of Cytoprotective Small Molecule Inducers of Heme Oxygenase-1

status: Public on Oct 07 2022

city: Birmingham

first: Anupam

last: Agarwal

state: AL

address: 703 19th St S

institute: University of Alabama at Birmingham

summary: Acute kidney injury (AKI) is a major public health concern with significant attributable morbidity and mortality with no current FDA approved treatments other than supportive care through dialysis. Several pre-clinical studies have suggested that heme-oxygenase-1 (HO-1), an enzyme that catalyzes the breakdown of heme, has promise as a potential therapeutic target for AKI. Clinical trials involving HO-1 products (biliverdin, carbon monoxide, and iron), however, have not progressed beyond the Phase 1/2 level. We have identified small molecule inducers of HO-1 that enable us to exploit the full therapeutic potential of HO-1, the combination of its products, and as-yet-undefined effects of the enzyme system. Through cell-based, high throughput screens for induction of HO-1 through the human HO-1 promoter/enhancer, we identified two novel small molecules and broxaldine, an FDA approved antiprotozoal, for further consideration as candidate compounds exhibiting Emax ≥ 70% of 5 µM hemin and EC50<10 µM. RNA sequencing identified shared binding motifs to NRF-2, a transcription factor known to regulate antioxidant genes, including HO-1. siRNA knockdown of NRF-2 confirmed the role of NRF-2 in induction of HO-1. In vitro, cytoprotective function of the candidates was assessed against cisplatin-induced cytotoxicity and apoptosis. In vivo, delivery of candidate compounds induced HO-1 expression in the kidneys of mice. This study serves as the basis for further development of small molecule HO-1 inducers as preventative or therapeutic interventions for a variety of pathologies, including AKI.

overall_design: Bulk RNA sequencing of HEK293 cells treated with small molecules SRI-37618, SRI-40109,  broxaldine, hemin, or DMSO (vehicle) for 4 or 8 hours. N=2 per timepoint and condition.

first: Gelare

last: Ghajar-Rahimi

first: Amie

last: Traylor

first: Bini

last: Mathew

first: James

last: Bostwick

first: Ntsang

last: Nebane-Ngwa

first: Anna

last: Zmijewska

first: Stephanie

last: Esman

first: Ling

last: Zhai

first: Vijya

last: Sambandam

first: Rita

last: Cowell

first: Mark

last: Suto

middle: F

last: George

first: Corinne

last: Augelli-Szafran


title: Large scale functional screen identifies genetic variants with splicing effects in modern and archaic humans

city: Providence

first: William

last: Fairbrother

state: RI

address: 70 Ship St.

department: Molecular Biology, Cell Biology, and Biochemistry

institute: Brown University

summary: Humans co-existed and interbred with other hominins which later became extinct. These archaic hominins are known to us only through fossil records and for two cases, genome sequences. Here we engineer Neanderthal and Denisovan sequences into thousands of artificial genes to reconstruct the pre-mRNA processing patterns of these extinct populations. Of the 5,224 alleles tested in this massively parallel splicing reporter assay (MaPSy), we report 969 exonic splicing mutations (ESMs) that correspond to differences in exon recognition between extant and extinct hominins. Using MaPSy splicing variants, predicted splicing variants, and splicing quantitative trait loci, we show that splice-disrupting variants experienced greater purifying selection in anatomically modern humans than in Neanderthals. Adaptively introgressed variants were enriched for moderate effect splicing variants, consistent with positive selection for alternative spliced alleles following introgression. As particularly compelling examples, we characterized a novel tissue-specific alternative splicing variant at the adaptively introgressed innate immunity gene TLR1, as well as a novel Neanderthal introgressed alternative splicing variant in the gene HSPG2 that encodes perlecan. We further identified potentially pathogenic splicing variants found only in Neanderthals and Denisovans in genes related to sperm maturation and immunity. Finally, we found splicing variants that may contribute to variation among modern humans in total bilirubin, balding, hemoglobin levels, and lung capacity. Our findings provide novel insights into natural selection acting on splicing in human evolution and demonstrate how functional assays can be used to identify candidate causal variants underlying differences in gene regulation and phenotype.

overall_design: Illumina 2x150 paired-end sequencing data for massively parallel splicing assay (MaPSy) experiment with two separately transfected minigene pools (labeled N2A, N2B) each with three input replicates and three output library replicates (labeled a,b,c).

first: Stephen

last: Rong

first: Christopher

last: Neil

first: Samantha

last: Maguire

first: Ijeoma

last: Meremikwu

first: Malcolm

last: Meyerson

first: Ben

last: Evans

middle: G


title: Prostate cancer resistance leads to a global deregulation of translation factors and unconventional translation

city: Quebec City

first: Samer

last: Hussein

address: 9 rue Mcmahon

department: Departement of medecine

institute: CHU de Québec - Université Laval

summary: Using a newly generated enzalutamide-resistant prostate cancer model, we characterized alterations in the translatome during prostate cancer enzalutamide resistance acquisition. We show a discordance between the translatome and transcriptome of drug-resistant cells, a deregulation of proteins involved in translation and an overall decrease in translational efficiency upon resistance acquisition. Interestingly, long non-coding RNAs show higher translation efficiency in enzalutamide-resistant cells, and a strong correlation with poor patient prognosis. Taken together, this suggests that aberrant translation of coding and non-coding genes are strong indicators of PCa enzalutamide-resistance.

overall_design: RNA sequencing of Poly(A) RNA from enzalutamide sensitive VCaP and VCaP-CRPC (Castration Resistant Prostate Cancer) and of enzalutamide resistant VCaP-ER (Enzalutamide Resistant), and RNA sequencing of heavy polysome-bound RNA from VCaP-CRPC and VCaP-ER (as duplicates).

first: Emeline

last: Lelong

first: Gabriel

last: Khelifi

middle: I


title: miRNA profile at diagnosis predicts treatment outcome in patients with B-chronic lymphocytic leukemia: A filo study.

city: Montpellier

first: Jerome

last: Moreaux

address: 141 rue de la Cardonille

department: Institute of Human Genetics

institute: CNRS-UM

summary: During many years, chemo-immunotherapy fludarabine-cyclophosphamide-rituximab (FCR) was considered as the gold standard for the first line treatment of medically fit patients with symptomatic B-chronic lymphocytic leukemia (CLL). Over the last decade, targeted biotherapies have revolutionized the management of B-CLL patients' treatment and almost entirely supplanted FCR. However, no biomarker still exists to predict the complete remission (CR) with undetectable minimal residual disease (uMRD), which remains so far the best predictive factor for survival. Circulating miRNAs represent a class of molecular biomarkers which expression is altered in hematological disorders including B-CLL. Our present study aimed at identifying before treatment circulating miRNAs that predict the treatment outcome in previously untreated B-CLL patients (NCT 01370772, https://clinicaltrials.gov/ct2/show/NCT01370772). Using hierarchical clustering of miRNA expression profiles discriminating 8 patients who achieved CR with bone marrow (BM) uMRD, from 8 patients who do not achieved CR and displayed detectable BM MRD, we identified 25 miRNAs differentially expressed before treatment. The expression of 11 representative miRNAs was further validated on a larger cohort (n=123). Based on the dosage of 5 miRNAs at diagnosis, a decision tree was constructed to predict treatment outcome. Our results identified 6 groups of patients with a distinct probability of being CR with BM uMRD to FCR treatment, ranging from 72% (miR-125b, miR-15b and miR-181c high) to 4% (miR-125b and miR-193b low). Progression-free survival (PFS) was significantly different between the established groups (p=0.019). None of the patients displaying high expression levels of miR-125b, miR-15b and miR-181c (HHH group) relapsed during the follow-up of the study. In contrast, patients with miR-15b low and miR-412 high (HLH group), and patients with low expression levels of miR-125b and miR-193b (LL group) demonstrated a significant low PFS. By RNA sequencing blood at diagnosis, we compared mRNA expression profiles of these three groups, achieving or not CR with uMRD. We identified that patients relapsing after treatment are characterized by significant enrichment of gene signatures related to cell cycle, MYC target genes, metabolism and translation regulation at diagnosis. Conversely, patients achieving CR with uMRD displayed significant enrichment in genes related to communication between CLL cells and the microenvironment, immune system activation and upregulation of polycomb PRC2 complex target genes at diagnosis. Our results suggest that blood miRNAs are potent predictive biomarkers for treatment efficacy of FCR and might be implicated in the FCR efficacy in B-CLL patients. Further investigations could establish whether these miRNAs might also be used to stratify patients for new-generation treatments. Overall, our work provides insight into unmet need for the treatment of B-CLL patients and identified pathways potentially predictive of patients’ remission.

overall_design: Gene expression profiling of PBMC from treatment-naive patients (aged 18-65 years) diagnosed with confirmed chronic lymphocytic leukemia according to IWCLL 2008 criteria and Binet stage C or with active Binet stage A or B have been characterized by RNA-sequencing.

first: Isabelle

last: Duroux-Richard

first: Anne-Laure

last: Gagez

first: Elina

last: Alaterre

first: Rémi

last: Letestu

first: Olfa

last: Khalifa

first: Christian

last: Jorgensen

first: Stéphane

last: Leprêtre

first: Emmanuelle

last: Tchernonog

first: Jérôme

first: Guillaume

last: Cartron

first: Florence

last: Apparailly


title: Differentially expressed mRNA profiles between LPS and LPS + Tat (48-60) YVEEL induced FHC cells.

status: Public on Oct 06 2022

city: Nanjing

first: Xiangyun

last: Yan

address: 123rd Tian Fei Xiang, Mo Chou Road, Nanjing 210004

institute: Women’s Hospital of Nanjing Medical University,  Nanjing Maternity and Child Health Care Hospital

summary: To further explore the underlying mechanisms of the protection functions of Tat (48-60) YVEEL, high throughput sequencings were used to identify differentially expressed mRNA profiles between LPS and LPS + Tat (48-60) YVEEL induced FHC cells.

overall_design: Comparative gene expression profiling analysis of mRNA-seq data to further explore the underlying mechanisms of the protection functions of Tat (48-60) YVEEL

first: Yan

last: Cao


title: ATF6αis required for the inflammation and survival in rheumatoid arthritis fibroblast-like synoviocytes

city: Ji'nan

first: Wang

last: Lin

address: #6699,Qingdao Road

institute: Biomedical Sciences College & Shandong Medicinal Biotechnology Centre

summary: To characterize transcriptome changes upon ATF6α knockdown by the siRNA in rheumatoid arthritis fibroblast-like synoviocytes (RA FLSs)

overall_design: RA FLSs were isolated from the synovial tissue of RA patient who underwent knee joint replacement surgery. FLSs of passages 4 were used in this study. The RA FLSs seeded in six T75 culture flasks were classified into two groups (each group with triplicates): group 1 with negative control siRNA transfection (the siNC group), group 2 with ATF6α siRNA transfection (siATF6α group). RA FLSs transfected with either siNC or si ATF6α were trypsinized and collected 72 hours post transfection. Total RNA was extracted to conduct cDNA library construction for RNA transcriptome sequencing.

first: L

last: Ge

last: Wang

first: Y

last: Zhang


title: Vitamin C enhances NF-κB-driven DNA demethylation and immunogenic properties of dendritic cells [methylation II]

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute (IJC)

summary: Dendritic cells (DCs) are central in immune responses, bridging the adaptive and innate systems. The study of the in vitro differentiation of DCs from monocytes provides both an in-depth understanding of the analogous in vivo process and a potential source for cancer cell therapy. Active DNA demethylation has been previously reported to be crucial in DC differentiation. Vitamin C, an essential nutrient, is a known cofactor of ten-eleven translocation (TET) enzymes, which drive active demethylation. Currently, the effects of vitamin C treatment on human immune cells are poorly understood. In this study, we have analyzed the epigenomic and transcriptomic reprogramming orchestrated by vitamin C in monocyte-derived DC differentiation and maturation. We have detected extensive demethylation produced by vitamin C treatment, together with concordant gene expression changes during DC maturation. p65, a component of NF-kB, interacts with TET2 and produces both vitamin C-mediated gene upregulation and DNA demethylation during DC maturation, as demonstrated by chemical inhibition. Moreover, vitamin C increases TNFβ production in DCs through p65, in concordance with the upregulation of its coding gene and DNA demethylation of adjacent CpGs. Finally, vitamin C increases DC's ability to stimulate the proliferation of autologous antigen-specific T cells. This work provides a potential strategy for the improvement of cell therapies based on monocyte-derived DCs, as well as a feasible mechanism of action for intravenous high-dose vitamin C treatment in patients.

overall_design: Monocytes were differentiated to DCs in the presence/absence of vitamin C and maturated with LPS in presence or absence of NF-kB inhibitor (Bay 11-7082). Three biological replicates are included and four different conditions: mDC_DMSO, mDC_vitC_DMSO, mDC_Bay, mDC_vitC_Bay

first: Octavio

last: Morante-Palacios

first: Gerard

last: Godoy-Tena

first: Josep

last: Calafell-Segura

first: Laura

last: Ciudad

first: Eva

last: Martínez-Cáceres

first: Jose

middle: L

last: Sardina


title: Elucidating the mechanism underlying prostate turmorigenesis mediated by AR in Shh-responsive cells

first: Zijie

last: Sun

address: 1500 E. Duarte Rd.

department: Cancer Biology

institute: City of Hope

summary: The activation of the androgen receptor (AR) through binding of androgens is essential for prostate tumorigenesis. Although significant effort has been devoted to determining the intrinsic mechanism underlying AR action and designing therapies to directly target AR expressing tumor cells, these therapies failed in most prostate cancer patients. Here, we demonstrate that loss of AR in stromal sonic-hedgehog Gli1-lineage cells diminishes prostate epithelial oncogenesis and tumor development using both in vivo tissue recombination assays and mouse models. Single-cell RNA sequencing combined with other experimental analyses showed that AR loss in stromal Gli1-lineage niches resulted in robust increased expression of insulin-like growth factor binding protein 3 (IGFBP3) through attenuation of AR suppression on Sp1-regulated transcription. Aberrant increased IGFBP3 further inhibits IGF1 induced Wnt signaling activation in subsets of basal epithelial cells, impairing oncogenic cell growth and tumor development. IGFBP3 further showed to attenuate IGF1-induced oncogenic growth of prostatic organoids derived from mouse basal epithelia. Loss of human prostate tumor basal cell signatures was identified in basal cells with AR-deficient microenvironment. This study demonstrates the niche effect of stromal AR in Gli1-lineage cells in supporting prostate tumorigenesis, implicating co-targeting tumor epithelial and stromal AR signaling for treating advanced prostate cancer.

overall_design: Two sequencing datasets were analyzed containing HiMyc and HiMyc-ARKO mouse prostate tissues

first: WonKyung

last: Kim

first: Alex

last: Hiroto


title: Ribosome profiling (Ribo-Seq)  and mRNA sequencing (RNA-Seq) of Human leukemia monocytic cell line (THP-1) cells upon treatment with LPS and LPS+dexamethasone (Dex).

city: Neuherberg

first: Suhail

middle: A.

last: Ansari

address: Ingolstaedter Landstr.1

department: Institute for Diabetes and Endocrinology (IDE)

institute: Helmholtz Zentrum München

summary:
THP-1 cells were treated with vehicle control (0.1% ethanol/PBS), LPS and LPS+Dex for 3 hr.
We then performed combined analysis of ribosome footprints (RPF) and mRNA abundance using the data obtained by Ribo-Seq and RNA-seq in THP-1 cells.

overall_design: Integrative analysis of Ribo-Seq and RNA-Seq data from LPS and LPS+Dex treated THP-1 cells.

middle: A

first: Widad

last: Dantoft

first: Jorge

last: Ruiz-Orera

first: Sebastiaan

last: van Heesch

first: Norbert

last: Hübner

first: Nina

last: Uhlenhaut


title: CRAC of yeast RNA polymerase II  in WT and isw1Δ cells in standard conditions or upon ER stress.

first: Domenico

last: Libri

address: 1919 route de Mende

institute: IGMM - CNRS

summary: We obtained RNA polymerase II occupancy profile across the genome of WT and isw1Δ Saccharomyces cerevisiae strains grown under normal conditions or after ER stress induction for 2H with1 µg/mL tunicamycin (Tm).

overall_design: The nascent RNA was crosslinked to RNAPII (Rpb1) and sequenced after purification of Rpb1 under stringent and denaturing conditions. This reveals the position of the polymerase at the nucleotide resolution level.

last: Matabishi-Bibi

first: Drice

last: Challal

first: Mara

last: Barucco

first: Anna

last: Babour


title: Nutrient regulation of lipochitooligosaccharide recognition in plants via  NSP1 and NSP2

city: Cambridge

first: Darius

last: Zarrabian

address: 93 Lawrence Weaver Rd

department: Plant Sciences

institute: Crop Science Centre, University of Cambridge

summary: Many plants associate with arbuscular mycorrhizal fungi for nutrient acquisition, while  legumes also associate with nitrogen-fixing rhizobial bacteria. Both associations rely on  symbiosis signaling and here we show that cereals can perceive lipochitooligosaccharides  (LCOs) for activation of symbiosis signaling, surprisingly including Nod factors produced by  nitrogen-fixing bacteria. However, legumes show stringent perception of specifically decorated  LCOs, that is absent in cereals. LCO perception in plants is activated by nutrient starvation,  through transcriptional regulation of Nodulation Signaling Pathway (NSP)1 and NSP2. These  transcription factors induce expression of an LCO receptor and act through the control of  strigolactone biosynthesis and the karrikin-like receptor DWARF14-LIKE. We conclude that  LCO production and perception is coordinately regulated by nutrient starvation to promote  engagement with mycorrhizal fungi. Our work has implications for the use of both mycorrhizal  and rhizobial associations for sustainable productivity in cereals.

sample_organism:
Medicago truncatula
Hordeum vulgare

platform_organism:
Medicago truncatula
Hordeum vulgare

overall_design: RNA-seq of M. truncatula genes after various nutrient treatments (+P+N, +P-N, -P+N, -P-N) in wildtype (A17) and mutant (Mtnsp1-1, Mtnsp2-2) lines, with transgenic lines (MtNSP1ox, MtNSP2ox, miRR-MtNSP2ox) under +N+P treatment; RNA-seq of H. vulgare genes after various nutrient treatments (+P+N, +P-N, -P+N, -P-N) in wildtype (Golden Promise) and mutant (Hvnsp1-1, Hvnsp2-1) lines, with transgenic lines (MtNSP1ox, MtNSP2ox) under +N+P treatment

first: Xinran

last: Li


title: Vitamin C enhances NF-?B-driven DNA demethylation and immunogenic properties of dendritic cells [methylation I]

first: Esteban

last: Ballestar

overall_design: Monocytes were differentiated to Dcs in the presence/absence of vitamin C. DCs were maturated with LPS. Three biological replicates are included and three different conditions: monocytes, DC_d2, DC_d2vitC,  iDCs,  iDCvitC, mDCs, and, mDCvitC

first: Octavio

last: Morante-Palacios

first: Gerard

last: Godoy-Tena

first: Josep

last: Calafell-Segura

first: Laura

last: Ciudad

first: Eva

middle: M

last: Martínez-Cáceres

last: Sardina


title: Vitamin C enhances NF-κB-driven DNA demethylation and immunogenic properties of dendritic cells [RNA-Seq]

first: Jose


title: HMG20B stabilizes interaction of LSD1 with GFI1 on chromatin to confer transcription repression and leukemia cell differentiation block [RNA-seq]

city: Manchester

first: Tim

middle: C

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

institute: Cancer Research UK

summary: Pharmacologic inhibition of LSD1 induces molecular and morphologic differentiation of blast cells in acute myeloid leukaemia (AML) patients harboring MLL gene translocations. In addition to its demethylase activity, LSD1 has a critical scaffolding function at genomic sites occupied by the SNAG domain transcription repressor GFI1. Importantly, inhibitors block both enzymatic and scaffolding activities, in the latter case by disrupting the protein:protein interaction of GFI1 with LSD1. To explore the wider consequences of LSD1 inhibition on the LSD1 protein complex we made use of mass spectrometry approaches. We discovered that the interaction of the HMG-box protein HMG20B with LSD1 was also disrupted by LSD1 inhibition. Downstream investigations revealed that HMG20B is colocated on chromatin genome-wide with GFI1 and LSD1; the strongest HMG20B binding colocates with the strongest GFI1 and LSD1 binding. Functional assays demonstrated that HMG20B depletion induces leukaemia cell differentiation and further revealed that HMG20B is required for the transcription repressor activity of GFI1 through stabilizing the interaction on chromatin of LSD1 with GFI1. Interaction of HMG20B with LSD1 is through its coiled-coil domain. Thus, HMG20B is a critical component of the GFI1:LSD1 transcription repressor complex which contributes to leukaemia cell differentiation block.

overall_design: Human THP1 AML cells were infected with a lentivirus targeting HMG20B for KD or a non-targeting control (NTC) and selected using puromycin. Cells were subjected to RNA-sequencing four days upon KD. Three replicated were analysed.


title: Gene expression profiling in melanoma cell lines treated with THZ531 or DMSO

city: Montreal

first: Philippe

middle: P.

last: Roux

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cance

summary: RNA seq of BRAF-mutated melanoma cell lines (A375 and Colo829) treated with CDK12 inhibitor (THZ531, 500nM) for 6 hours

overall_design: We compared the transcriptomes of 2 melanoma Cell line, A375 and Colo829  treated with DMSO or THZ531 (500nM) during 6H (3 independents n for each cell lines and conditions)

first: Thibault

last: Houles

first: Genevieve

last: Lavoie

middle: P


title: Vitamin C enhances NF-κB-driven DNA demethylation and immunogenic properties of dendritic cells

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

overall_design: Refer to individual Series


title: HMG20B stabilizes interaction of LSD1 with GFI1 on chromatin to confer transcription repression and leukemia cell differentiation block


title: miRNA-150_R-1 mediates the HIF-1/ErbB signaling pathway to regulate the adhesion of endometrial epithelial cells in cows experiencing retained placenta

status: Public on Oct 05 2022

city: Lanzhou

first: Chen

last: Lv

address: No.1 Yingmen Village

institute: Gansu Agricultural University

summary: In this study, we performed RNA-sequencing to characterize gene expression profiles in caudal vein blood samples of postpartum Holstein cows whose fetal membranes were discharged normally or retained to identify retained placenta (RP)-related genes and evaluate their molecular mechanisms.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for caudal vein blood samples of postpartum Holstein cows whose fetal membranes were discharged normally (NC) or retained (n=3).


title: Targeted respiratory expression of B3GAT1 as a broadly acting, host-directed antiviral strategy

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

summary: Identification of influenza B virus host restriction factors

overall_design: A549-dCas9 VP64 cells were transduced with the Calabrese whole-genome sgRNA activation library. The overexpression cell library was then infected with multiple rounds of influenza B virus and sgRNA enrichment was determined in the surviving populations after each round of infection.

first: Joseph

middle: D

last: Trimarco

first: Sarah

last: Nelson

first: Ryan

middle: R

last: Chaparian

first: Alexandra

last: Wells

first: Carolyn

last: Coyne


title: HMG20B stabilizes interaction of LSD1 with GFI1 on chromatin to confer transcription repression and leukemia cell differentiation block [ChIP-seq II]

overall_design: Human THP1 AML cells were infected with a lentivirus targeting HMG20B for KD or a non-targeting control (NTC) and selected using puromycin. Cells were subjected to ChIP-sequencing for LSD1, GFI1, HMG20B and H3K27ac four days upon KD.


title: Identification of mechanism of monoallelic expression and allelic rheostat role of DNA methylation

city: Boston

first: Saumya

last: Gupta

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary: In mammalian cells, large groups of genes show epigenetically controlled unequal transcription of maternal and paternal alleles. Thousands of autosomal genes subject to monoallelic expression (MAE) comprise the largest such group. The initial random allelic choice in these loci is followed by mitotically stable transmission of the allele-specific state, leading to stable epigenetic and functional differences between clonal cell lineages. Molecular mechanisms underpinning MAE maintenance are not known. We devised and performed a drug screen for reactivation of epigenetically silenced alleles in mouse cells, using a new strategy based on deep targeted allele-specific RNA sequencing, which can read out multiple loci simultaneously. We found that, contrary to previous observations, DNA methylation plays a key role in mitotic memory of MAE in multiple autosomal loci. Having established that a specific perturbation can affect multiple loci, we assessed genome-wide impact of the drug exposure in several clonal cell lines, identifying over 600 genes with allele-specific expression changing with DNA methylation. We found that multiple distinct states of allele-specific expression correspond to the extent of DNA methylation and can be stably maintained, indicating allelic rheostat role of DNA methylation. Our findings reveal a previously unappreciated interplay of genetic and epigenetic control of allele-specific expression and reinforce the role of such regulation in maintaining differences between developmentally equivalent clonal cell lineages.

overall_design: RNA-seq was performed in immortalised B cell lines Abl.2, Abl.3 and Abl.4 clonal cell lines of 129xCastF1 background [1,2] in control condirions (dmso). Libraries (minimum 2 replicates per sample, were sequenced and data was analyzed. [1] Zwemer, L.M., Zak, A., Thompson, B.R., Kirby, A., Daly, M.J., Chess, A., and Gimelbrant, A.A. (2012). Autosomal monoallelic expression in the mouse. Genome Biol. 13, R10. [2] Nag, A., Savova, V., Fung, H.-L., Miron, A., Yuan, G.-C., Zhang, K., Gimelbrant, A.A., and Gingeras, T. (2013). Chromatin signature of widespread monoallelic expression. eLife 2, e01256.

first: Alexander

last: Gimelbrant


title: Epigenetic modifier, Brassica rapa CURLY LEAF (BrCLF) suppresses not only key developmental genes but also genes related to stress signaling and stress-responsive metabolism in Brassica rapa.

status: Public on Oct 04 2022

city: Anseong-Si

first: adji baskoro

last: dwi nugroho

state: Gyeonggi-do

address: Daedeok-myeon, Naeri, Chung-Ang University

country: South Korea

institute: Chung-Ang University

summary: Transcriptomic analysis provided that BrCLF play prominent roles in B. rapa developmental processes, stress signaling, and stress-responsive metabolisms.

overall_design: Experiment was performed using three biological replicates for both 2-week-old seedling of ‘brclf’ mutant and ‘R-o-18’ as a wild type.

first: Kim

last: Dong-Hwan


title: Profiling and characterization of constitutive chromatin enriched RNAs

city: Beijing

first: Yan

last: Zhang

state: Not Applicable

address: Dongdajie street

institute: Beijing institute of Biotechnology


title: Specialized germline P-bodies are required to specify germ cell fate in C. elegans embryos

city: Baltimore

first: Geraldine

last: Seydoux

state: MD

address: 725 N. Wolfe St. PCTB 706

department: Molecular Biology and Genetics

institute: Johns Hopkins School of Medicine

summary: In animals with germ plasm, specification of the germline involves “germ granules”, cytoplasmic condensates that enrich maternal transcripts in the germline founder cells. In C. elegans embryos, P granules enrich maternal transcripts, but surprisingly P granules are not essential for germ cell fate specification. Here we describe a second condensate in the C. elegans germ plasm. Like canonical P-bodies found in somatic cells, “germline P-bodies” contain regulators of mRNA decapping and deadenylation and, in addition, the intrinsically-disordered proteins MEG-1 and MEG-2 and the TIS11-family RNA-binding protein POS-1. Embryos lacking meg-1 and meg-2 do not stabilize P-body components, miss-regulate POS-1 targets, miss-specify the germline founder cell, and do not develop a germline. Our findings suggest that specification of the germ line involves at least two distinct condensates that independently enrich and regulate maternal mRNAs in the germline founder cells.

overall_design: Gene expression profiling comparing meg-1/2 mutants to wild-type

first: Madeline

last: Cassani


title: Antitumor immunity induced by antibody-based natural killer cell engager therapeutics armed with not-alpha IL-2 variant

city: Marseille

first: Eric

last: Vivier

address: 117 Avenue de Luminy BP 30191

institute: Innate Pharma

summary: We report here the design of new antibody-based natural killer cell engager therapeutics (ANKET), single tetraspecific molecules engaging the NK cell activating receptors NKp46 and CD16, the β chain of the interleukin-2 receptor (IL-2R) and a tumor-associated antigen (TAA).

overall_design: We performed transcriptome analysis on NK cells purified from blood and activated with tetraspecific ANKET, trispecific aNKp46/Fc/aCD20, the Fc-enhanced anti-CD20 mAb obinutuzumab or an IL-2v polypeptide (IL2v/IC/Fc null/IC) in the presence of CD20+ tumor target cells

first: Olivier

last: Demaria

first: Sabrina

last: Carpentier

first: Constance

last: Vagne

first: Luciana

last: Batista

first: Nicolas

last: Jarmuzynski


title: Single-cell RNA-sequencing of peripheral neuroblastic tumors reveals an aggressive transitional cell state at the junction of an adrenergic-mesenchymal transdifferentiation trajectory

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

summary: Peripheral neuroblastic tumors (PNTs) are the most common extracranial solid tumors in early childhood. They represent a spectrum of neural crest derived tumors including neuroblastoma, ganglioneuroblastoma and ganglioneuroma. PNTs exhibit heterogeneity due to interconverting malignant cell states described as adrenergic/nor-adrenergic or mesenchymal/neural crest cell in origin. The factors determining individual patient levels of tumor heterogeneity, their impact on the malignant phenotype, and the presence of other cell states are unknown. Here, single-cell RNA-sequencing analysis of cells from 10 PNTs demonstrated extensive transcriptomic heterogeneity. Examination of PNT microenvironments showed that neuroblastomas contained low immune cell infiltration, high levels of non-inflammatory macrophages, and low cytotoxic T lymphocyte levels compared with more benign PNT subtypes. Trajectory modelling showed that malignant neuroblasts move between adrenergic and mesenchymal cell states via a novel state that we termed a “transitional” phenotype. Transitional cells are characterized by gene expression programs linked to a sympathoadrenal development, and aggressive tumor phenotypes such as rapid proliferation and tumor dissemination.

overall_design: Examination of single cell transcriptomes from 10 peripheral neuroblastic tumors.

first: Ying

last: Xu

first: Daniel

last: Carter

first: Chao


title: ATAC-seq essays in A549 and HeLaS3 during cell cycle

summary: To investigate the dynamic chromatin accessibility during cell cycle, we performed ATAC-seq both in interphase and mitosis in A549 and HeLaS3 cells. We compared ATAC signals around TSS regions of cheRNAs and their target genes with background controls, and found these cheRNAs were associated with open chromatin state and active transcription.

first: Wenlong

last: Shen

first: Man

last: Yin

first: Bingyu

last: Ye

first: Zhihu

last: Zhao


title: Nuclear fractionation to identify chromatin associated RNA in interphase and M-phase cells [RNA-seq]

first: Yan

summary: The composition and dynamics of tightly bound chromatin associated RNAs during mitosis remains elusive. Here we report identification of chromatin enriched (cheRNAs) by biochemical nuclear fractionation coupled with RNA-seq in both interphase and mitotic phase of A549 and HeLaS3 cell lines. We show that highly abundant cheRNAs, mostly small noncoding RNAs, are largely maintained in mitotic chromatin, and constitute a substantial part of chromatin throughout cell cycle. We also show that the mitotic retained cheRNAs tend to be cell type nonspecific. We speculate that these cell type nonspecific cheRNAs might play roles in chromatin state and gene expression control. We anticipate the panoramic landscape of RNA composition of chromatin both in interphase and M-phase would shed light on understanding the structure and function of chromatin in M phase and would also help the understanding of some fundamental biological functions.

overall_design: In this case, for each of A549 cells as well as HeLa-S3 cells, we performed RNA-seq on samples from two independent biological replicates of soluble nuclear extract (S) and chromatin pellet extract (P) both in asynchronized (with interphase accounting for ~95% of cells, we called these cells as “inter-phase cells” afterwards) and M-phase

first: Minglei

last: Shi

first: Ping

last: Li

first: Zhuang

last: Ma

first: Yang

last: Chen


title: Single-cell sequencing deconvolutes cellular responses to exercise in human skeletal muscle

status: Public on Oct 03 2022

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

summary: Regular physical activity is a key concept associated with a variety of health-related outcomes and successful ageing. While many of the beneficial effects of physical activity are undisputed, much of the adaptive mechanisms that lead to these benefits are not yet known. The skeletal muscle is a key contributor to physical performance and is also the target organ for many of the adaptive processes associated with exercise. Skeletal muscle is highly plastic, and changes in physical activity lead to a plethora of adaptive processes that, when repeated over time, result in structural and functional adaptations. Here we use single cell sequencing in humans to outline the effects of physical activity on cellular composition and cell type-specific processes in skeletal muscle. We show that myogenic cells in human skeletal muscle can be divided into three groups characterized by different degrees of cell maturation, and that exercise stimulates subpopulation of undifferentiated stem/progenitor myogenic cells to mature toward slow- or fast-twitch fibers. The cell type-specific adaptive mechanisms induced by exercise presented here contribute to the understanding of the skeletal muscle adaptations triggered by physical activity and may ultimately have implications for physiological and pathological processes affecting skeletal muscle, such as sarcopenia, cachexia, and glucose homeostasis.

overall_design: The mononuclear cells were isolated from skeletal muscle before and after exercise from three healthy individuals and subjected to single-cell sequencing.

first: Alen

last: Lovrić

first: Ali

last: Rassolie

first: Seher

last: Alam

first: Mirko

last: Mandić

first: Amarjit

last: Saini

first: Mikael

last: Altun

first: Rodrigo

last: Fernandez-Gonzalo

first: Thomas

last: Gustafsson


title: MicroRNA-874 targets phosphomevalonate kinase and inhibits cancer cell growth via the mevalonate pathway

first: Masanori

last: Fujimoto

state: MA

address: Center for Life Sciences 3 Blackfan Circle, Room CLS730

department: Division of Endocrinology

institute: Beth Israel Deaconess Medical Center, Harvard Medical School


title: MicroRNA-874 targets phosphomevalonate kinase and inhibits cancer cell growth via the mevalonate pathway [scRNA-seq]

summary: The microRNA (miR) miR-874, a potential tumour suppressor, causes cell death via target gene suppression in various cancer types. Mevalonate pathway inhibition also causes cell death in breast cancer. However, the relationship between the mevalonate pathway and miR-874-induced apoptosis or its association with the tumour suppressor p53 has not been elucidated. We identified phosphomevalonate kinase (PMVK), a key mevalonate pathway enzyme, and sterol regulatory element-binding factor 2 (SREBF2), the master cholesterol biosynthesis regulator, as direct miR‑874 targets. Next-generation sequencing analysis revealed a significant miR-874–mediated downregulation of PMVK and SREBF2 gene expression and p53 pathway enrichment. Luciferase reporter assays showed that miR-874 directly regulated PMVK and SREBF2. miR-874–induced apoptosis was p53 dependent, and single-cell RNA sequencing analysis demonstrated that miR-874 transfection resulted in apoptosis and p53 pathway activation. Downregulation of PMVK expression also caused cell cycle arrest and p53 pathway activation, which was rescued by geranylgeranyl pyrophosphate (GGPP) supplementation. Analysis of The Cancer Genome Atlas (TCGA) database indicated a negative correlation between miR-874 and PMVK expression and between miR-874 and SREBF2 expression. These findings suggest that miR-874 suppresses the mevalonate pathway by targeting SREBF2 and PMVK, resulting in GGPP depletion, which activates the p53 pathway and promotes cycle arrest or apoptosis.

overall_design: Gene expression levels of MCF-7 cells from control, miR-874 or siPMVK transfection were evaluted using single cell RNA-seq.

first: Kazuyuki

last: Yamagata

first: Tomoaki

last: Tanaka


title: MicroRNA-874 targets phosphomevalonate kinase and inhibits cancer cell growth via the mevalonate pathway [bulkRNA-seq]

overall_design: MCF-7 cells of each genotype were transfected with control or miR-874 for 48 h. Then RNA of each sample was extracted and subjected to RNA-seq.

first: Bahityar

last: Nawai

first: Atsushi

last: Kaneda


title: speedingCARs: accelerating the engineering of CAR T cells by signaling domain shuffling and single-cell sequencing

city: Basel

first: Rocio

last: Castellanos Rueda

state: --None--

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH

summary: Due to the low-throughput process of systematically designing and functionally testing chimeric antigen receptors (CARs), only a small set of immune signaling domains have been thoroughly explored, despite their major role in T cell activation, effector function and persistence. SpeedingCARs presents an integrated method for engineering CAR T cells by signaling domain shuffling and functional screening by single-cell sequencing. Leveraging the inherent modularity of natural signaling domains, we generated a diverse library of 180 unique CAR variants, which were genomically integrated into primary human T cells by CRISPR-Cas9. Functional and pooled screening of the CAR T cell library was performed by co-culture with tumor cells, followed by single-cell RNA sequencing (scRNA-seq) and single-cell CAR sequencing (scCAR-seq), thus enabling high-throughput profiling of multi-dimensional cellular responses.

overall_design: A library of 180 unique CAR variants was genomically integrated into primary human T cells by CRISPR-Cas9 genome editing. Single-cell RNA sequencing data of pooled library CAR T cells from 3 different healthy donors was generated following 36h of co-culture with HER2 expressing breast cancer cell line SKBR3. As negative controls TCR negative T cells and CD28-CD3Z unstimulated CAR T cells were also sequenced.

first: Rocío

last: Castellanos-Rueda

first: Raphaël

middle: B

last: Di Roberto

first: Sai

middle: T

last: Reddy


title: Unravelling the impact of aging on the human endothelial lncRNA transcriptome [Young_vs_Aged RNA-seq]

status: Public on Oct 02 2022

city: Bad Nauheim

first: Sweta

last: Talyan

address: Ludwigstraße 43

institute: MPI

summary: Bulk RNA sequncing from human native young and aged endothelial cells

overall_design: Gene expression profiling analysis was performed using the RNA-Seq data obtained from young and aged endothelial cells isolated from human vessels

first: Sofia-Iris

last: Bibli


title: Transcriptional programing of helper T cell metabolism by the IL-2-STAT5 axis

city: Bethesda

first: Hong-wei

last: Sun

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary: Activated lymphocytes adapt their metabolism to meet the energetic and biosynthetic demands imposed by rapid growth and proliferation. Common gamma chain (c𝛾) family cytokines are central to this process but the role of downstream STAT5 signaling, a cardinal feature of all members, remains loosely defined. Using genome-, transcriptome- and metabolome-wide analyses, we demonstrate that STAT5 is a master regulator of energy and amino acid metabolism in CD4+ ‘helper’ T cells. Mechanistically, we find that STAT5 localizes to a suite of enhancers and promoters for genes encoding essential, often rate-limiting enzymes and transporters, where it instructs transcription through p300 recruitment and epigenetic remodeling. We also find that STAT5 licenses the activity of other metabolic agents downstream of IL-2, namely the mTOR signaling pathway and the transcription factor, MYC, and present evidence for genome-wide cooperation between STAT5 and MYC in both normal and transformed T cells. Taken together, our data provide a molecular framework for transcriptional programing of T cell metabolism downstream of c𝛾 cytokines and emphasize the Jak-STAT pathway in powering cellular growth and proliferation.

overall_design: ChIP-seq and mRNA-seq analyses for STAT5 gain- and loss-of-funtion experiments in mouse CD4+ effector T cells

first: Alejandro

middle: V

last: Villarino

first: Stephen

last: Brooks

first: Hong-Wei

first: Yuka

last: Kanno

first: John

middle: J

last: O'Shea


title: Unravelling the impact of aging on the human endothelial lncRNA transcriptome


title: Unravelling the impact of aging on the human endothelial lncRNA transcriptome [HUVEC CTL_vs_PCAT14 RNA-seq]

summary: Gene expression profiling analysis was performed using the RNA-Seq data obtained from endothelial cells expressing or knockdown for PCAT14

overall_design: Human umbilical vein endothelial cells were transfected with 50nmol/L GapmeR targerting PCAT14 or the respective negative control (CTL). After 48h of incubation RNA was harvested with RNeasy mini plus kit (Qiagen) and whole transcriptome RNA sequencing analysis was performed.


title: AOS10-FMT could rescure the adverse effects of high fat diet & STZ on the liver [liver_RNA-seq]

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: We report the side-effects of High fat diet & STZ on the liver, and foud that the AOS could rescure the side-effect of High fat diet & STZ in many factors,such as lipid metabolism and oxidative stress

overall_design: Exploration of the FMT effects on the damaged liver induced by High fat diet & STZ

first: Yanan

last: Hao


title: A three-dimensional chromatin contact map of Puccinia graminis f.sp. tritici

status: Public on Oct 01 2022

city: Manhattan

first: Eduard

last: Akhunov

state: Kansas

address: 1712 Claflin Road

department: Plant Pathology

institute: Kansas State University

summary: Puccinia graminis f.sp. tritici (Pgt), the causal agent of stem rust disease in wheat, is one of the most destructive pathogens and can cause severe yield losses. Here, we utilize Hi-C sequencing technology to scaffold and phase the haplotypes for the genome assembly of a US Pgt isolate 99KS76A-1.

overall_design: Hi-C data for Puccinia graminis f.sp. tritici, isolate 99KS76A-1.