title: JMJD4 regulates PKM2 degradation of cardiomyocytes and is critical in the development of dilated cardiomyopathy

status: Public on Aug 30 2022

city: Shanghai

first: yansong

last: Tang

address: 1239 Siping Road

institute: Tongji University

summary:
RNA-Seq results of adult mouse cardiomyocytes with Jmjd4 knockout and neonatal rat cardiomyocytes with Jmjd4 knockdown.
To investigate the role of Jmjd4 in dilated cardiomyopathy, we performed gene expression profiling with RNA-Seq results from heart samples of MCM+ Jmjd4f/f and control Jmjd4f/f mice, as well as neonatal rat ventricuar cardiomyocytes (NRVCs) treated with si-Jmjd4 and si-NC control.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: RNA-Seq analysis of Jmjd4 cKO mice heart tissue and Jmjd4 knock down NRVCs

first: Yansong

first: Hongjie

last: Zhang

first: Ke

last: Wei


title: RNA-seq for AML samples

status: Public on Jul 20 2022

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

country: China

institute: Children’s Hospital of Soochow University

type: Expression profiling by high throughput sequencing

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore RNA-seq results for AML samples.

overall_design: 9 AML samples


title: Longitudinal skeletal muscle transcriptomics in WT mice

status: Public on Oct 05 2022

city: Illkirch-Graffenstaden

first: Jocelyn

last: Laporte

address: 1 rue Laurent Fries

country: France

institute: IGBMC

summary: Paired-end 100bp RNA-sequencing from WT mice skeletal muscle at E18.5, 2 weeks and 7 weeks.

overall_design: mRNAs were extracted from tibialis anterior muscle of WT mice at 3 ages: E18.5, 2 weeks and 7 weeks (4 mice per age). Paired-end 100bp RNA-sequencing was performed to study splicing during post-natal development of muscle tissue in mice.


title: Small-molecule inhibition of the acyl-lysine reader ENL as a strategy against acute myeloid leukemia [ChIP-Seq]

city: Philadelphia

first: Liling

last: Wan

state: PA

address: 421 Curie Blvd

department: Cancer Biology

country: USA

institute: University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Acute myeloid leukemia (AML) is characterized by dysregulated transcriptional programs and these programs require support from chromatin regulators to maintain their hyperactive state. Recent studies have identified the histone acylation ‘reader’ ENL as being a critical dependency in AML, but the potential of therapeutic applications targeting this chromatin reader remains poorly understood. Here, we present a potent and orally bioavailable small-molecule inhibitor of ENL, TDI-055, which displaces ENL from chromatin by competitively blocking the interaction of its YEATS domain with acylated histones. We show that TDI-055 treatment preferentially inhibited the proliferation of human leukemia cells harboring MLL translocations or NPM1 mutations. Through a CRISPR/Cas9 saturated mutagenesis screen, we uncovered an ENL mutant that could confer cells resistance to TDI-055, thus providing compelling proof for the on-target activity of the compound. Rapid displacement of ENL from chromatin resulted in decreased recruitment of select ENL-associated complexes and impaired RNA polymerase II elongation which, in turn, led to the suppression of critical leukemogenic gene expression programs. Finally, pharmacological inhibition of ENL in vivo led to reduced AML growth and prolonged survival in cell line and patient-derived xenograft (PDX) models. Collectively, these results provide critical evidence and mechanistic insights to establish inhibition of ENL as a potential therapeutic strategy against molecularly defined AML, laying the foundation for rapid clinical translation of this approach.

overall_design: AFF4, Pol II, Pol II S2P, DOT1L, H3K79me2, PAF1 ChIP-seq for MV411 cells, Flag-ENL ChIP-seq for MOLM13 cells; AFF1, DOT1L, PolIIS2P ChIP-seq data of the MV4;11 cell treated with DMSO and TDI-055 for 0.5 or 2h.

first: Yiman

last: Liu

first: Hangpeng

last: Li

first: Qinglan


title: Topoisomerase 1 Nicking-dependent HP1gamma Engagement Mediates Acute Activation of Phase-separated Enhancers

status: Public on Aug 04 2022

city: La Jolla

first: Yuliang

last: Tan

state: California

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

institute: University of California, San Diego

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Depletion of Sun1/2 Induces Heterochromatin Accrual in MSCs

status: Public on Jul 13 2022

city: Boise

first: Matthew

last: Goelzer

state: Idaho

address: 1910 University Drive

department: Materials Science and Engineering

institute: Boise State University

summary: Mesenchyal Stem Cells (MSCs) differentiation into multiple lineages, such as osteocytes and adipocytes, has been shown to be regulated by mechanical signals. The Linker of the Nucleoskeleton and Cytoskeleton (LINC) complex has been shown to be required for mechanical signal transduction, regulation of MSCs differentiation, and nuclear integrity. The LINC complex is made of Nesprins and Sun proteins. Nesprin proteins associate with the cytoskeleton on the outer nuclear membrane and Sun proteins are bound to the inner nuclear membrane where they bind to inner nuclear proteins and chromatin. We investigated the role of the Sun1/2 in regulating the inner nuclear functions of chromatin organization and adipogenic differentiation independently of the LINC complex function.  We show that depletion of Sun1/2 increased nuclear area and perimeter, and decreased circularity. Expression of a dominant-negative KASH (dnKASH) domain targeting the SUN domain on Sun proteins inhibiting Nesprin-SUN association resulting a loss of Nesprin localization to the nuclear envelope decreased nuclear area and circularity. Adipogenesis was inhibited during Sun1/2 depletion while dnKASH expression accelerated adipgoenesis. RNA-seq data showed decreased adipogensis and increased immune response during Sun1/2 depletion. dnKASH responded oppositely with increased adipogenic gene expression and decreased immune response. We also observed increased H3K9me3 levels, increased H3K9me3 foci count, and enrichment on Adipoq during Sun1/2 depletion. No increase of H3K9me3 levels, foci count, or increased H3K9me3 enrichment on Adipoq was found during dnKASH expression. We conclude that physically decoupling of the LINC complex via dnKASH accelerates adipogenesis and that Sun1/2 regulates chromatin organization and adipogenesis independently of the LINC complex function.

overall_design: Investigation of the tole of Sun1/2 proteins in regulating adiogenic differentiation independent of LINC complex function. Sample groups are delineated via labeling of "M" followed by a number between 6-14. Such that samples labeled with "M6" are the first sample group and "M15" is the last. siSun depleted cells are labled  with “S” while siCntl treated cells are labeled with “C”. Dominant-negative KASH domain was induced by Doxycycline and is labeled with “D” no doxycycline control is labeled with “C”. Samples labeled with "Ap" are treated with only adiogeneic media. Samples labeled with "Na" have been grown in growth media. siSun and siCntl replication groups are M11-15. Dominant-negative KASH and control replication groups are M6-10.

first: Sean

last: Howard

first: Anamaria

last: Zavala

first: Andre

last: van Wijnen

first: Gunes

last: Uzer


title: Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion [bulkATAC-Seq]

status: Public on Jun 19 2022

city: Durham

first: Julie

last: Steinbrink

state: NC

address: 315 Trent Drive

department: Center for Applied Genomics and Precision Medicine

institute: Duke University

summary: SARS-CoV-2 infection triggers profound and variable immune responses in human hosts. Chromatin remodeling has been observed in individuals severely ill or convalescing with COVID-19, but chromatin remodeling early in disease prior to anti-spike protein IgG seroconversion has not been defined. We performed the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and RNA-seq on peripheral blood mononuclear cells (PBMCs) from outpatients with mild or moderate symptom severity at different stages of clinical illness. Early in the disease course prior to IgG seroconversion, modifications in chromatin accessibility associated with mild or moderate symptoms were already robust and included severity-associated changes in accessibility of genes in interleukin signaling, regulation of cell differentiation and cell morphology. Furthermore, single-cell analyses revealed evolution of the chromatin accessibility landscape and transcription factor motif accessibility for individual PBMC cell types over time. The most extensive remodeling occurred in CD14+ monocytes, where sub-populations with distinct chromatin accessibility profiles were observed prior to seroconversion. Mild symptom severity was marked by upregulation classical antiviral pathways, including those regulating IRF1 and IRF7, whereas in moderate disease, these classical antiviral signals diminished, suggesting dysregulated and less effective responses. Together, these observations offer novel insight into the epigenome of early mild SARS-CoV-2 infection and suggest that detection of chromatin remodeling in early disease may offer promise for a new class of diagnostic tools for COVID-19.

overall_design: To test whether chromatin accessibility can distinguish COVID-19 disease severity in individuals early in their disease course (prior to seroconversion) an Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was used to quantify differential chromatin accessibility in three groups: subjects with mild symptoms, subjects with moderate symptoms and pre-pandemic healthy controls

first: Christopher

middle: W

last: Woods


title: Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion [scATAC-Seq]

status: Public on Jun 23 2022

overall_design: Identify transcriptomic and epigenetic profiles of sub-populations of CD14+ monocytes that distinguished IgG- subjects with mild from moderate symptoms.


title: High grade serous ovarian cancer organoids as models of chromosomal instability

status: Public on Jul 17 2022

city: Cambridge

first: Lena

last: Morrill Gavarró

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute, University of Cambridge

summary: High-grade serous ovarian carcinoma (HGSOC) is the most genomically complex cancer, characterised by ubiquitous TP53 mutation, profound structural variation and heterogeneity. Multiple mutational processes driving chromosomal instability can be distinguished by specific copy number signatures. To develop clinically relevant models of these mutational processes we derived 15 continuous HGSOC patient-derived organoids (PDOs) and provide detailed transcriptomic and genomic profiles using shallow whole genome sequencing single cell and bulk analysis. We show that PDOs comprise communities of different clonal populations and represent models of CCNE1 amplification, chromothripsis, tandem-duplicator phenotype and whole genome duplication. PDOs can also be used as exploratory tools to study transcriptional effects of copy number alterations as well as compound-sensitivity tests. In summary, HGSOC PDO cultures provide a genomic tool for studies of specific mutational processes and precision therapeutics.

overall_design: Gene expression profiling analysis of bulk RNA-seq for organoid samples

first: Maria

last: Vias

middle: M

last: Gavarró

first: Carolin

last: Sauer

first: Debbie

last: Sanders

first: Anna

last: Piskorz

first: Dominique-Laurent

last: Couturier

first: Stéphane

last: Ballereau

first: Bárbara

last: Hernando

first: James

last: Hall

first: Filipe

last: Correia-Martins

first: Florian

last: Markowetz

first: Geoff

last: Macintyre

middle: D

last: Brenton


title: Gene expression data from human omental adipose tissue

status: Public on Jun 01 2022

city: Lille

first: Denis

middle: A

last: Mogilenko

address: 1 Rue du Professeur Calmette, BP245

institute: INSERM

summary: Among 226 morbidly obese patients who underwent gastric bypass surgery between 2013 and 2014 as part of the A Biological Atlas of Severe Obesity (ABOS) study (ClinicalTrials.gov; NCT01129297), 18 women who gave informed consent were recruited in this study for immunophenotyping and microarray analyses of omental adipose tissue (AT). We characterized T and NK cell populations in omental AT from morbidly obese women with varying levels of IR. AT IFN-gamma NK cells, but not CD4, CD8 or gamma delta T cells, were positively correlated with glucose levels, glycated hemoglobin (HbA1c), and IR. AT NK cells were linked to a pro-inflammatory gene expression profile in AT and developed an effector phenotype in response to IL-12 and IL-15. Moreover, integrated transcriptomic analysis revealed a potential implication of AT IFN-gamma NK cells in controlling adipose tissue inflammation, remodeling, and lipid metabolism, suggesting that NK cells are involved in metabolic homeostasis in visceral AT in humans.

overall_design: 18 morbidly obese women were recruited in this study for immunophenotyping and microarray analyses of omental AT. Omental AT samples were used for RNA isolation and flow cytometry. Glucose, insulin, glycated hemoglobin (HbA1c), and C-peptide were measured after overnight fasting and after a 75-g oral glucose tolerance test.

first: Francois

last: Pattou

first: Bart

last: Staels

first: David

last: Dombrowicz


title: Single-cell RNAseq of human pancreatic islets from control and type 2 diabetes donors

city: Stockholm

first: Jens

last: Hjerling-Leffler

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

summary: Perturbed secretion of insulin and other pancreatic hormones is the main cause of type 2 diabetes (T2D). The pancreatic islets harbor five cell types that are potentially altered differently by T2D. Whole-islet transcriptomics and single-cell RNA-sequencing (scRNAseq) studies have revealed differentially expressed genes but unfortunately without reaching consensus. We propose that, rather than analyzing expression of individual genes or structural changes in networks of genes, building and analyzing networks of differentially synchronized genes on single-cell level gives unprecedented insights to disease. To this end, we developed a differential gene synchronization network analysis (dGSNA) algorithm and used it to analyze a high-quality pancreatic islet scRNAseq dataset from T2D and non-T2D individuals. dGSNA on beta cells revealed T2D-induced changes in twelve networks of genes, representing both canonical and less studied biological processes in the context of T2D. Analysis of these networks suggested that in T2D, beta cell energy metabolism, cell growth, differentiation and proteolysis programs are perturbed, whereas exocytosis, insulin translation and the unfolded protein response programs instead are enhanced.  To validate our method, we showed that ten out of eleven selected node genes regulated insulin mRNA levels and/or secretion in INS-1 832/13 cells. Further, knockout mouse models for two of these genes (Tmem176a/b and Cebpg) exhibited reduced beta cell mass and perturbed insulin secretion. The dGSNA algorithm thus predicts central disease processes in T2D, which was replicated in an independent data set, revealing targetable cellular functions. We conclude that analysis of networks of differentially synchronized genes provides insight into the pathophysiology of T2D. This approach is likely generally applicable to other diseases where scRNAseq data can be obtained.

overall_design: The single-cell transcriptome data (6 control and 5 type 2 diabetes human donors) was generated at the Eukaryotic Single-cell Genomics facility at Science for Life Laboratory in Stockholm, Sweden.

first: Nils

last: Wierup


title: scRNA-seq of mouse lymph node stromal cells

status: Public on Jul 01 2022

city: BALTIMORE

first: yang

last: song

address: 670 W. Baltimore St.

institute: UNIVERSITY OF MARYLAND IN BALTIMORE

summary: C57BL/6 mouse lymph node stromal cells were isolated for scRNA-seq, more than 2x104 cells were run on the 10X Chromium Controller (10X Genomics) to partition single cells with uniquely barcoded beads and processed for sequencing library preparation using the Chromium Single Cell 3’ Reagent Kit. cDNA libraries were sequenced on a NovaSeq 6000 sequencing system. 4 x 103 cells per sample were captured on the 10X Chromium chip. 5-10 x 104 reads/cell were obtained with characterization of 2-3 x 103 transcripts/cell.

overall_design: After enzymatic digestion of the lymph nodes (LNs)from  C57BL/6 mice, CD45- cells were purified with the CD45 negative selection beads and were stained with anti-mouse CD45 before sorting for viable CD45- cells. For scRNA-seq, more than 2x104 CD45- LN stromal cells were run on the 10X Chromium Controller (10X Genomics) to partition single cells into nanoliter-scale droplets containing uniquely barcoded beads and processed for sequencing library preparation using the Chromium Single Cell 3’ Reagent Kit (v3 chemistry) (10x Genomics, Pleasanton, CA). Generated cDNA libraries were sequenced on a NovaSeq 6000 sequencing system. 4 x 103 cells per sample were captured on the 10X Chromium chip, 5-10 x 104 reads/cell were obtained with a characterization of 2-3 x 103 transcripts/cell.

first: Lushen

last: Li

first: Yang

last: Song

first: Jonathan

last: Bromberg


title: Glutamine deprivation enhances directed differentiation of renal organoids

city: CHICAGO

first: Manoj

last: Kandpal

state: Illinois

address: 1256 W NORTHSHORE AVE, 3R

institute: Northwestern University


title: Multi-scale chromatin footprinting reveals wide-spread alterations to the structure of DNA regulatory elements [SHARE-Seq]

status: Public on Mar 29 2023

first: Jason

last: Buenrostro

state: MA

address: 7 Divinity Ave

institute: Harvard University

summary: Cis-regulatory elements (CREs) are bound by diverse chromatin-associated proteins, cooperate to establish gene expression, and change in structure over time to alter cell fate and function1–3. Here, we develop a footprinting framework that uses deep learning to correct Tn5 sequence bias, improving accuracy and reducing false positives. This framework additionally identifies the interaction of DNA with objects of various sizes. Using these ‘multi-scale footprints’ we find that transcription factor (TF) binding occurs at well-defined distances from nucleosomes. Further, we demonstrate that multi-scale footprints, which include the positions of nucleosomes, enable more accurate inference of TF binding. Using multi-scale footprinting with single-cell multi-omics, we discover wide-spread structural and functional changes of CREs across hematopoiesis, wherein nucleosomes slide, expose DNA for TF binding, and promote gene expression. Finally, we apply this single-cell and footprint approach to characterize age-associated structural changes to CREs within hematopoietic stem cells and identify a spectrum of cells harboring age-associated changes to the epigenome. Interestingly, we find extensive changes to the structure of CREs upon aging, with many age-associated changes altering CRE structure while preserving overall accessibility. Collectively, we reveal the dynamics and functional importance of CRE structure, highlighting changes to gene regulation at single-cell and single-base-pair resolution.

overall_design: SHARE-Seq of HepG2 cells

first: Sai

last: Ma

first: Yan

last: Hu


title: targeted single-cell RNA sequencing data of residual TIM-3+ leukemic stem cells post-SCT_2

city: Fukuoka

first: Teppei

last: Sakoda

address: 3-1-1, Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

summary: Since AML is hierarchically organized by self-renewing LSCs with heterogeneous sub-populations, we employed single-cell RNA sequencing to evaluate the changes in AML heterogeneity in terms of gene expression profiling, throughout the clinical course.

overall_design: Purified CD34+ BM cells of the diagnostic, CR, and relapse phases, from identical patients, were subjected to BD Rhapsody Single-Cell Analysis System, and the expression of originally customized 435 target genes was quantified

first: Yuichiro

last: Semba


title: Streptococcus gordonii transcriptional response to salivary mucin

status: Public on May 05 2022

city: Minneapolis

first: Mark

middle: C

last: Herzberg

state: MN

address: 515 Delaware St., SE

institute: University of Minnesota

summary: All organisms throughout the tree of life sense and respond to their surface environments. To discriminate from among mucosal surface environmental cues, we grew Streptococcus gordonii biofilms over night at 37C on surfaces coated with the salivary mucin MUC5B, or a low density protein fraction derived from human saliva.

overall_design: Biofilms of Streptococcus gordonii were grown from an initial OD600nm = 0.1 in BHI broth for 16 to 18 h at 37°C and 5% CO2 on MUC5B- or LDP-coated plates. Sheer was applied by placing samples on a rocker during the overnight incubation period.

first: Bruno

last: Lima

first: Julia

last: Davies

first: Karen

last: Johnstone

first: Jeffrey

last: Hall

first: Gunnel

last: Svensater

first: Brittany

last: Nairn


title: Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion [bulkRNA-Seq]

first: Julie

last: Steinbrink

overall_design: Differential gene expression analysis of bulk RNA-seq data from mild IgG- COVID-19 subjects compared to healthy controls

first: Christopher

last: Woods


title: Directed differentiation to nephron progenitor cells [RNA Seq 1]

summary: Metabolic pathways driving differentiation into nephron progenitor cells (NPCs) and renal organoids from the pluripotency stage remain poorly understood. In this study, we systematically performed comprehensive metabolite and transcriptome profiling of human pluripotent stem cells (hPSCs) during differentiation into NPCs and further into multicellular organoids. We found activation of distinct metabolic pathways during early-stage progression from hPSCs to NPCs; however, later-stage differentiation from NPCs to organoids, and the intervening developmental stages between them, largely shared similar metabolic profiles. Among the pathways changing in early differentiation, the alanine-aspartate-glutamate and glutamine pathways were found to be significantly altered by both an enrichment and by pathway impact analysis. Moreover, hPSCs survived glutamine deprivation during in vitro differentiation, and NPCs were successfully generated both in the absence and presence of glutamine and glutamate. Surprisingly, glutamine deprivation resulted in enhanced maturation, by accelerating PAX8 expression, and enriching for podocytes as detected through single cell RNA-Seq analysis. Taken together, these findings highlight a critical regulatory role of glutamine metabolism in the derivation of nephron progenitor cells and renal organoids and identify a controlling metabolic pathway of early renal differentiation.

overall_design: Global gene profiling on days 0, 1, 3, 4, 6, 7 and 9 during directed differentiation to nephron progenitor cells

first: Iman

last: Sarami

last: Wertheim


title: A Single Intranasal Vaccination with a Rationally Attenuated SARS-CoV-2 Elicits Strong Humoral Immune Response and Is Protective in Syrian Hamsters

status: Public on Apr 04 2022

city: Gaithersburg

first: Prabha

last: Chandrasekaran

state: Maryland

address: 8348 Hawkins Creamery Rd

institute: ehealth&Informatics, LLC

summary: Very few live attenuated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines are currently in pre-clinical or clinical development. We rationally attenuated SARS-CoV-2 (isolate WA1/2020) by removing the polybasic cleavage site within the spike protein and the open reading frames (ORFs) 6-8, and by introducing a pair of mutations into the non-structural protein 1 (Nsp1). The derived virus (WA1-DPRRA-ORF6-8-Nsp1K164A/H165A) became severely attenuated in both the K18-human ACE2 (hACE2) transgenic mice and in Syrian hamsters. Transcriptomic profiling of nasal turbinates and lung tissues of infected Syrian hamsters confirmed that WA1-DPRRA-ORF6-8-Nsp1K164A/H165A attenuated the upregulation of proinflammatory pathways. A single intranasal immunization of just 100 PFU of the WA1-DPRRA-ORF6-8-Nsp1K164A/H165A elicited binding and neutralizing antibody responses in Syrian hamsters and completely protected against SARS-CoV-2-induced weight loss and pneumonia. These data demonstrate the feasibility of rational attenuation of SARS-CoV-2. WA1-DPRRA-ORF6-8-Nsp1K164A/H165A represents a promising live attenuated vaccine candidate.

overall_design: For challenge studies, adult (6-12 months old, male) Syrian hamsters were used. To test attenuation of recombinant SARS-CoV-2 viruses in vivo, adult K18-hACE2 transgenic mice were divided into five groupsand intranasally inoculated with 10^5 plaque forming unit (PFU) of WA1/2020 (n=3),  DPRRA (n=4), Nsp1-K164A/H165A(n=3), and Nsp1-N128S/K129E (n=4) or left uninfected (n=2). To assess changes at the molecular level, we isolated RNA from both nasal turbinates and lung homogenates at 4 dpi (days post infection) and performed RNAseq analyses.

first: Shufeng

last: Liu

first: Charles

middle: B

last: Stauft

first: Prabhuanand

last: Selvaraj

first: Chao-Kai

last: Chou

first: Wells

last: Wu

middle: Z

last: Lien

first: Clement

last: Meseda

first: Cyntia

middle: L

last: Pedro

first: Matthew

middle: F

last: Starost

first: Jerry

middle: P

last: Weir

first: Tony

middle: T

last: Wang


title: Analysis of fucoidan-induced global transcriptional changes in bone marrow-derived dendritic cells (BMDCs) using RNA-Seq technology

status: Public on Apr 21 2022

city: Daejeon

first: Suyoung

last: Choi

address: 266, Munhwa-ro, Jung-gu

department: Department of Medical Science

country: South Korea

institute: Chungnam National University

summary:
To investigate the fucoidan-induced global alteration of signalling pathways, we prepared bone marrow-derived dendritic cells (BMDCs) and treated them with fucoidan.
We then performed gene expression profiling analysis using RNA-seq data from 6 different cells at one time point.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for fucoidan-treated and vehicle (0.04% DMSO)-treated BMDC cells.


title: TAL1 cooperates with PI3K/AKT pathway activation in T-cell acute lymphoblastic leukemia

status: Public on Apr 02 2022

city: Leuven

first: Sofie

last: Demeyer

address: Herestraat 49 / bus 912

department: Center for Cancer Biology

country: Belgium

institute: KULeuven / VIB

summary: Ectopic TAL1 expression is frequently associated with PI3K-AKT pathway mutations in T-ALL. Here we developed inducible mouse models demonstrating cooperation between TAL1 and PI3K-AKT signaling and we used these models to study the effects of targeted inhibitors.

overall_design:
RNA sequencing of mice with AKT(E17K) or AKT(E17K)+TAL1, empty vector or TAL1 overexpression.
RNA sequencing of ProT cells with induced expression of TAL1 (with 4OH tamoxifen treatment).

first: Naomi

last: Thielemans

first: Jan

last: Cools


title: Nitrates increase abscisic acid levels to regulate haustoria formation in the parasitic plant Phtheirospermum japonicum

status: Public on May 17 2022

city: UPPSALA

first: Anna

last: Kokla

state: Select

address: Biocenter, Almas allé 5

department: Plant Biology

institute: SLU

summary: Transcriptomic changes during haustoria formation in the parasitic plant Phtheirospermum japonicum. We performed RNAseq on Phtheirospermum japonicum seedling infecting and not infecting over 5 time points during haustoria formation for the control treatment and over 3 time points for the ammonium nitrate and 6-Benzylaminipurine. We investigated the transcriptomic changes during haustoria formation and how this is affected in the transcritpome level by nitrate and cytokinin treatment.

sample_organism:
Arabidopsis thaliana
Phtheirospermum japonicum

overall_design: transcriptomic changes in the root of 7 days old Phtheirospermum japonicum (hasutorium formation site +/- 2mm) that has been infecting 7 days old Arabidopsis thaliana (Col-0). Samples taken at 0,12,24,48,72 hours post infection (hpi). Infecting plants were compared to not-infecting plants. For ammonium nitrate and 6-Benzylaminopurine  samples were collected for 0,12,24 hpi.

first: Martina

last: Leso

last: Melnyk


title: Directed differentiation to nephron progenitor cells in the presence and absence of glutamine [RNA Seq 2]

first: Manoj

last: Kandpal

overall_design: Global gene profiling on day 9 of directed differentiation to nephron progenitor cells derived in the presence and absence of glutamine

first: Iman

last: Sarami

first: Jason

last: Wertheim


title: Longitudinal dynamics of clonal haematopoiesis identifies gene-specific fitness effects

status: Public on May 03 2022

city: Glasgow

first: Neil

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

institute: University of Glasgow

summary: The prevalence of clonal haematopoiesis of indeterminate potential (CHIP) in healthy individuals increases rapidly from age 60 onwards and has been associated with increased risk for malignancy, heart disease and ischemic stroke. CHIP is driven by somatic mutations in stem cells that are also drivers of myeloid malignancies. Since mutations in stem cells often drive leukaemia, we hypothesised that stem cell fitness substantially contributes to transformation from CHIP to leukaemia. Stem cell fitness is defined as the proliferative advantage over cells carrying no or only neutral mutations. It is currently unknown whether mutations in different CHIP genes lead to distinct fitness advantages that could form the basis for patient stratification. We set out to quantify the fitness effects of CHIP drivers over a 12-year timespan in older age, using longitudinal error-corrected sequencing data. Two key results support the possibility for individualised clinical monitoring of CHIP: (i) We developed a new filtering method to extract fitness effects from longitudinal data using Bayesian inference, while taking into account individual mutational context and co-occurrence of mutations, and thus quantify the growth potential of variants within each individual. (ii) We show that gene-specific fitness differences can outweigh inter-individual variation and therefore could form the basis for personalised clinical management in the future.

overall_design: The Lothian Birth Cohort 1921 (LBC1921) contains a total of 550 participants at Wave 1 of their testing (done between 1999 and 2001) with a gender ratio of 234/316 (m/f) and a mean age at Wave 1 of 79.1 (SD=0.6) (Table 1) 17. The Lothian Birth Cohort 1936 (LBC1936), contains a total of 1091 participants at Wave1 of their testing (done between 2004 and 2007) with a gender ratio of 548/543 (m/f) and a mean age at Wave 1 of 69.5 (SD=0.8) (Table 1, (Taylor et al., 2018)). We previously identified 73 participants with CHIP at Wave 1 18. We sequenced DNA from those 73 LBC participants using a targeted gene panel (Table 2) and added 16 LBC participants with previously unidentified CHIP and 4-5 time-points. We have accepted 85 of 89 participants for inclusion in our study, removing 4 participants for failing to meet quality criteria (low library complexity), with a total of 248 samples together with 14 “Genome in a Bottle” (GIAB) controls - two per sequencing batch. In addition, two individuals carrying the JAK2V617F mutation received treatment for leukaemia after the first respective time point available - potentially driving the observed reductions in clone size. Those patients were omitted from further analysis after sequencing.

first: Eric

last: Latorre-Crespo

first: Maria

last: Terradas-Terradas

first: Linus

middle: J

last: Schumacher

first: Kristina

last: Kirschner

first: Tamir

last: Chandra


title: PHGDH heterogeneity potentiates cancer cell dissemination and metastasis

status: Public on Mar 30 2022

summary: Cancer metastasis requires the transient activation of cellular programs enabling dissemination and seeding in distant organs. Genetic, transcriptional and translational heterogeneity contributes to this dynamic process. Metabolic heterogeneity has also been observed, yet its role for cancer progression is less explored. Here, we discover that loss of phosphoglycerate dehydrogenase (PHGDH) potentiates metastatic dissemination. Specifically, we find that heterogeneous or low PHGDH expression in primary tumors of breast cancer patients is associated with decreased metastasis free survival time. In mice, circulating tumor cells and early metastatic lesions are enriched with PHGDH low cancer cells and silencing PHGDH in primary tumors increases metastasis formation. Mechanistically, PHGDH protein interacts with the glycolytic enzyme phosphofructokinase (PFK) and the loss of this interaction activates the hexosamine – sialic acid pathway, which provides precursors for protein glycosylation. Consequently, aberrant protein glycosylation including increased sialylation of integrin αvβ3 occurs, which potentiates cell migration and invasion. Inhibition of sialic acid metabolism counteracts the metastatic capacity of PHGDH low cancer cells. In conclusion, while the catalytic activity of PHGDH supports cancer cell proliferation, low PHGDH protein expression non-catalytically potentiates cancer dissemination and metastasis formation. Thus, the presence of PHDGH heterogeneity in primary tumors may be considered a sign of tumor aggressiveness.

overall_design: mRNA profiles of (i) 4T1 breast cancer cells transduced with pLKO scramble or PHGDH shRNA; (ii) 4T1 and EMT6.5 mono-cultured/co-cultured with Bend3; (iii) MDA-MB-231 control or transduced with pLHCX PHGDH cDNA to overexpress PHGDH.

first: Sarah

last: Fendt

first: Patricia

last: Altea-Manzano

first: Matteo

last: Rossi


title: miRNA and lncRNA expression networks modulate Cell Cycle and DNA repair inhibition in senescent prostate cells.

status: Public on Mar 03 2022

city: BELFAST

first: Gary

last: Hardiman

state: Antrim

address: 19 Chlorine Gardens,

institute: Queens University Belfast

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: miRNA and lncRNA expression networks modulate Cell Cycle and DNA repair inhibition in senescent prostate cells. [miRNA-Seq]

summary: Cellular senescence is a state of permanent growth arrest that arises once cells reach the limit of their proliferative capacity. It creates an inflammatory microenvironment favoring the initiation and progression of various age-related diseases, including the development and progression of prostate cancer. Non-coding RNAs have emerged as important regulators of cellular gene expression. Nonetheless, very little is known about the interplay of miRNAs and lncRNAs and how deregulation of ncRNA networks promotes cellular senescence. To investigate this, human prostate epithelial cells were cultured through different passages until senescent, and their RNA was extracted and sequenced using RNAseq. Differential Expression (DE) gene analysis was performed to compare senescent and proliferating cells.

overall_design: Biological Replicate Design, 4 samples, comparison of early passage (n=2) and late stage (n=2) senescent cell cultures of Primary prostate epithelial cells (PrECs)

first: Willian

last: da Silveira

first: Ludivine

last: Renaud

first: E

middle: S

last: Hazard


title: Subtle alterations in DNA methylation patterns in normal cells in response to dietary stilbenoids

status: Public on Jan 31 2022

city: Vancouver

first: Barbara

last: Stefanska

state: BC

address: 2205 East Mall

department: Land and Food Systems

country: Canada

institute: The University of British Columbia

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of human mammary epithelial MCF10A cell line treated with vehicle control (ethanol) and with RSV (resveratrol). The Illumina Infinium 450K Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in human cell lines exposed to described treatments. Samples included biological triplicate of MCF10A control (ethanol treated), biological triplicate of MCF10A treated with RSV.

overall_design: Bisulphite converted DNA from the 12 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2

first: Megan

last: Beetch

first: Katarzyna

last: Lubecka

first: Heather

last: Kristofzski

first: Matthew

last: Suderman


title: Histone turnover during DNA replication

status: Public on Feb 18 2022

city: Rehovot

first: Naama

last: Barkai

state: --- Select a state ---

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

summary: Using a recently established histone turnover sensor, we measured the genome-wide H3 turnover during S-phase in S.cerevisiae.

sample_organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

overall_design: Sensor-carrying cells are synchronized in G1 (alpha factor) and relased in to 200 mM HU-containing YPD medium. And sampled every 10-20 minutes for ChIPseq and DNA-seq.

first: Gilad

last: Yaakov

first: Felix

last: Jonas


title: The molecular profile and ability to promote axon regeneration after peripheral nerve injury by Repair Schwann cells is distinctly different from that for developing Schwann cells

status: Public on Jan 13 2022

city: Sapporo

first: Ken

last: Kadoya

state: Hokkaido

address: Kita-15, Nishi-7, Sapporo

institute: Hokkaido University

summary: Since Schwann cells (SCs) support axonal growth at development as well as after peripheral nerve injury (PNI), developing SCs might be able to promote axon regeneration after PNI. The purpose of the current study was to elucidate the capability of developing SCs to induce axon regeneration after PNI. SC precursors (SCPs), immature SCs (ISCs), repair SCs (RSCs) from injured nerves, and non-RSCs from intact nerves were tested by grafting into acellular region of rat sciatic nerve with crush injury. Both of developing SCs completely failed to support axon regeneration, whereas both of mature SCs, especially RSCs, induced axon regeneration. Further, RSCs but not SCPs promoted neurite outgrowth of adult dorsal root ganglion neurons. Transcriptome analysis revealed that the gene expression profiles were distinctly different between RSCs and SCPs. These findings indicate that developing SCs are markedly different from mature SCs in terms of functional and molecular aspects and that RSC is a viable candidate for regenerative cell therapy for PNI.

overall_design: mRNA profiles of Schwnn cell precursor from E14 and repair Schwann cell from adult rats  (N = 3 / group).

first: Takeshi

last: Endo

first: Tomoaki

last: Suzuki


title: Integrative transcriptomics reveals activation of innate immune responses and inhibition of inflammation during oral immunotherapy for egg allergy in children

status: Public on Jan 05 2022

city: Helsinki

first: Piia

last: Karisola

state: Southern Finland

address: Haartmaninkatu 3

department: Medical Faculty, Human Microbes Research Program Unit

country: Finland

institute: University of Helsinki

summary: The objective of the study was to investigate how oral immunotherapy (OIT) for food allergy modulates inflammation and immune cell responses. The blood cell transcriptome of 50 children receiving egg OIT was profiled using peripheral blood mononuclear cell (PBMC) samples obtained at baseline and after 3 and 8 months of OIT.

overall_design: Venous blood samples were collected from 50 egg allergic children at the baseline (L0), after 3 months (L2) or after 8 months (L3) of OIT with increasing consumption of egg, PBMCs were separated and totRNA extracted for microarray analyses.

first: Kati

last: Palosuo

first: Victoria

last: Hinkkanen

first: Lukas

last: Wisgrill

first: Terhi

last: Savinko

first: Nanna

last: Fyhrquist

first: Harri

last: Alenius

first: Mika

last: Mäkelä


title: miRNA and lncRNA expression networks modulate Cell Cycle and DNA repair inhibition in senescent prostate cells. [RNA-Seq]

first: Gary

last: Hardiman

first: Willian

last: da Silveira

first: Ludivine

last: Renaud

first: E

last: Hazard


title: The distinct function and control of regulatory T cell subsets during influenza infection

status: Public on Mar 31 2022

city: Charlestown

first: Jason

last: Griffith

address: 149 13th Street

department: Medicine

institute: Massachusetts General Hospital

summary: During influenza infection, Treg cells in the lung acquire at least 3 discernable phenotypes which can be characterized by the expression of the IL-33 receptor ST2, the Th1 associated chemokine receptor CXCR3 or neither receptor. It is known in the Treg field that Treg cell acquire different phenotypes to more specifically target related immune responses. For example, Th1 like CXCR3 expressing Treg cells are thought to traffic to and specifically suppress adaptive type 1 immune responses. We have found that during influenza infection, ST2+ Treg cells specifically target innate immune responses characterized by IL-1 mediated neutrophil and eosinophil recruitment and the activation of IL17 producing gamma delta T cells. In order to determine how ST2+ Treg cell perform their specific immunomodulatory function, we have performed RNAseq transcriptomic analysis to compare gene expression in ST2+ Tregs isolated from day 7 influenza infected lungs with CXCR3+ Treg cells and Treg cells expressing neither marker also from day 7 of influenza infected lungs as well as compared to total Treg cells from the spleen of uninfected mice.

overall_design: Distinct populations of ST2+, CXCR3+ and ST2-CXCR3- Treg cells (Viable, CD3+, CD4+, YFP+) were sorted from the lungs of day 7 influenza infected Foxp3YFPCre mice. In addition Treg cells (Viable, CD3+, CD4+, YFP+) from the spleens of naïve Foxp3YFPCre mice were also isolated. These cells were then subjected to RNAseq transcriptomic analysis.

first: Andrew

last: Luster


title: Intergenic DNA organization in the mammalian nervous system.

status: Public on Feb 07 2022

city: Mississauga

first: Ho Sung

last: Rhee

state: ON

address: 3359 Mississauga Rd

department: Cell and Systems Biology

institute: University of Toronto

summary: Eukaryotic genomes largely consist of non-coding DNA regions. Most non-coding DNA resides in intergenic DNA regions located between a gene and its nearest gene. Here, we demonstrate the relationship between intergenic DNA and gene regulation throughout the mammalian nervous system.

overall_design: Examination of ChIP-seq profiles of mouse ES cell-derived spinal motor neurons by deep sequencing.

first: Ssu-Yu

last: Yeh

first: Ravneet

last: Jaura

first: Zobia

last: Anwar

first: Ho


title: Expression data from TGFβ1(TGFbeta1) treated HCC cells

status: Public on Feb 23 2022

city: Beijing

first: Pengyuang

last: Yang

address: 15 Datun Road, Chaoyang District

department: Key Laboratory of Infection and Immunity of CAS

institute: Institute of Biophysics, Chinese Academy of Sciences

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

summary:
HCC cell lines with different metastatic potential (HepG2, Huh7, MHCC97 and PVTT cells) were treated with TGFbeta1 for 8 h
We used microarrays to discover the long non-coding RNAs (lncRNAs) expression underlying Hepatocellular carcinoma (HCC) TGFbeta1 treated and non-treated control cells to identify distinct lncRNAs during this process.

overall_design: We treated cells and RNAs were extracted and then hybridized on Aligent microarrays. We sought to identify distinct lncRNAs upon TGFbeta1 treatment.

first: Pengyuan


title: Whole-genome microarrays in the ischemic penumbra of mice and rats 2hrs and 6hrs after permanent middle cerebral artery occlusion (pMCAO)

status: Public on Dec 27 2021

city: Toronto

first: Michael

last: Tymianski

address: 60 Leonard Ave.

department: Fundamental Neurobiology

institute: Krembil Research Institute

summary:
Neuroprotection has not been successfully translated from animals to humans, and controversies persist about the suitability of animal models for the evaluation of putative stroke therapies. Of these, many appear to be less effective in mice as compared with rats. We hypothesized that this may be due to fundamental interspecies differences in stroke response.
Whole-genome microarrays were used to examine differential gene regulation in the ischemic penumbra of mice and rats 2hrs and 6hrs after permanent middle cerebral artery occlusion (pMCAO). The differentially expressed genes in the ischemic penumbra at each time point were compared between the two species.

overall_design: Tissue samples were obtained from the penumbras of rat and mouse brains at 2hrs or 6hrs after pMCAO. Control samples were obtained from similar ipsilateral regions of sham-operated brains of each species.  Total RNA was isolated from the tissue samples and analyzed by microarray analysis. For microarray analyses 24 animals were used [1 animal/microarray, n=3/group, 8 groups: Sham (SP) or MCAO (MP) in rats or mice at 2 hrs and 6 hrs, respectively].

first: Qiu

last: Wu

first: Xiujun

last: Sun

first: Lucy

last: Teves

first: Diana

last: Mayor


title: The isoxazole derivative of usnic acid induces ER stress response in breast cancer cells that leads to paraptosis-like cell death

status: Public on Dec 23 2021

city: Gdańsk

first: Marcin

last: Jakalski

address: Dębinki 7

department: 3P Medicine Laboratory

country: Poland

institute: Medical University of Gdańsk

summary: This work investigated the molecular mechanisms unterlying the previously reported anticancer activity of  the usnic acid isoxazole derivative, named 2b. Using RNA-seq technology transcriptoms of MCF-7 breast cancer cells treated with vehicle or 2b for two diffrent time periods were compared. Among differentially expressed genes, components of the protein processing in endoplasmic reticulum pathway were the most significantly upregulated by 2b.

overall_design: MCF-7 breast cancer cells were treated with DMSO or 2b at concentration 3 µg/ml for 6 or 24 h and RNA was isolated

first: Agnieszka

last: Pyrczak-Felczykowska

first: Tristan

last: Reekie

last: Jąkalski

first: Aleksandra

last: Hać

first: Marcelina

last: Malinowska

first: Anna

last: Pawlik

first: Kamil

last: Ryś

first: Beata

last: Guzow-Krzemińska

last: Herman-Antosiewicz


title: Transcriptome analysis of lung-derived MBP-specific T cells

status: Public on Dec 21 2021

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: Transcriptome analysis of MBP-reactive T cells isolated from the lungs of wild type LEW/Crl rats (Rattus norvegicus) pre-treated with PBS or NEO on day 0 and day 1 after intratracheal immunization with MBP.

overall_design: In order to investigate the effect of antibiotics on the expression profile of T cells, RNA-Seq analysis was performed on MBP-reactive T cells sorted from the lungs of LEW/Crl rats (Rattus norvegicus) intratracheally pre-treated for 7 days  with PBS or NEO. Analyis was performed on day 0 and day 1 after intratacheal immunization with MBP.

first: Shomroni

last: Orr

first: Leon

last: Hosang

first: Francesca

last: Odoardi


title: From nasal to basal: Single-cell sequence illustrates the winding infection route for IBDV and its influence on bursal cells

city: nanjing

first: Jian

last: Lin

state: jiangsu

address: tongwei road N0.1

department: Life Science

institute: nanjing agricultural university

summary: Nasal cavity is the main gateway for pathogen infection although it composed of many layers of defending barriers. Pathogens strongly willing to enter and infect from nasal cavity with the dominant form aerosol or respiratory droplets. However, the underlying mechanism of virus nasal infection and transmission are still unknown. Hence, a better understanding of this mechanism may provide insight into the pathogenesis of virus. In this study, IBDV was select as a model virus to study nasal infection and transmission for it could infect chicken from head (nasal) to tail (basal) and lead to massive destruction of bursal IgM+ B-lymphocytes. Initially, we found IBDV mostly entered and infected the interior of chicken’s nasal, where full of lymphoid tissue and easily for virus to transfer into blood. After passing nasal barriers, IBDV was subsequently transmit into blood and infected PBMCs. Following blood circulates, IBDV then infected bursal and hugely destroyed B-lymphocytes. However, the mechanism of how IBDV influenced the bursal cells, especially how virus destroyed B-lymphocytes were still unclear. With the help of single cells RNA sequence, we identified five vigorous clusters, including three immune cells types (B-cells: 64.70%, dendritic cells: 3.32% and T-cells: 6.33%) and two non-immune cell types (epithelial cells: 23.86% and fibroblast cells: 1.80% cells). Further analyses found that B-cells population were serious damaged, especially IgM+ B cells. However, the IgA+ B cells population hugely increased after IBDV infection. Interesting, we first demonstrated that basal cells and other non-immune cells in Bursa of Fabricius (BF) were the main target for IBDV infection and replication. Together, our study not only comprehensive elaborated the airborne IBDV and its transmission via intranasal route into the BF, but also explained its distribution in different immune and nonimmune cells and immunoglobulins rearrangement after immunosuppressive disorder on an age dependent infected organ.

overall_design: scRNA-seq of whole cells from four chicken’s bursal were performed to illustrate it. Chicken were grouped as:  S1. Control two weeks old chick, S2. IBDV infected two weeks old chick, S3. Control three weeks old chick and S4. IBDV infected three weeks old chick.

first: Abid

middle: U

last: Shah

first: Yucheng

last: Li

first: Qian

last: Yang


title: Short-term diet intervention alters the small non coding RNA (sncRNA) landscape of human sperm

status: Public on Oct 31 2021

city: Singapore

first: Neerja

last: Karnani

address: 30 Medical drive

country: Singapore

institute: Singapore Institute for Clinical Sciences, A*STAR

summary: Offspring health outcomes are often linked with epigenetic alterations triggered by maternal nutrition and intrauterine environment. Strong experimental data also link paternal preconception nutrition with pathophysiology in the offspring, but the mechanism(s) routing effects of paternal exposures remain elusive. Animal experimental models have highlighted small non-coding RNAs (sncRNAs) as potential regulators of these effects. This study characterised the baseline sncRNA landscape of human sperm and the effect of a 6 week dietary intervention on their expression profile. 5’tRFs, miRNA and piRNAs were the most abundant sncRNA subtypes identified; their expression was associated with age, BMI and sperm quality. Nutritional intervention with vitamin D and omega-3 fatty acids altered expression of 3 tRFs, 15 miRNAs and 112 piRNAs, targeting genes involved in fatty acid metabolism and transposable elements in the sperm genome.

overall_design: Sperm sncRNA profiling was performed on a subset (N=17) of participants enrolled in the PREconception dietary suPplements in Assisted REproductionin (PREPARE) study in the UK (N=111 recruited and 102 completed the study). Sperm samples were collected twice during the study, i.e. before and 6 weeks after the dietary intervention (visits MV1 and MV4). Of the 17 participants selected for sncRNA analysis, 9 were participants in the control arm, and 8 from the intervention arm of the trial. The intervention group received an olive oil based diet plus a supplemented drink enriched in vitamin D and omega-3 fatty acids for 6 weeks, while the control group received a sunflower oil based diet and a placebo drink for the same duration of time. Small RNA sequencing was performed on the total RNA extracted from the sperm samples.

first: Candida

last: Vaz

first: Keith

last: Godfrey

first: Karen

last: Lillycrop


title: Pancreas-specific miR-216a regulates proliferation and endocrine and exocrine cell function II

status: Public on Oct 22 2021

city: Edmonton

first: Patrick

middle: E

last: MacDonald

state: AB

address: 6-040 Li Ka Shing Centre

institute: University of Alberta

summary: Several miRNAs have tissue-specific patterns consistent with crucial functions in many biological processes and are candidate biomarkers of disease. Yet, there is limited knowledge about the role of pancreas-specific miRNAs in pancreatic pathologies. Here, we show that miR-216a is a conserved, pancreas-specific miRNA with important roles in pancreatic islet and acinar cells. By profiling miRNAs from human islets and subsequent systematic tissue analysis we found that miR-216a is highly enriched in endocrine and exocrine pancreas. Deletion of miR-216a in mice lead to a reduction in islet size, β-cell mass and insulin levels. RNA-sequencing indicated that cell cycle and proliferation were the most significantly regulated biological processes in miR-216 knockout pancreata. miR-216a was induced by TGF-β signalling and inhibition of miR-216a increased apoptosis and decreased cell proliferation in both β- and exocrine cells. Deletion of miR-216a in the pancreatic cancer prone mouse line Kras G12D ;Ptf1a CreER reduced the propensity of pancreatic cancer precursor lesions. Notably, circulating miR-216a levels were elevated in both mice and humans with pancreatic cancer. Collectively, our study gives insights into how β-cell mass and acinar cell growth are modulated by a pancreas-specific miRNA but also suggests miR-216a as a promising biomarker for diagnosis of pancreatic diseases.

overall_design: Six bulk RNA sequencing profiles from whole pancreas of 1 day old wild type (WT) and miR216a-/- mice

first: Suheda

last: Erener

first: Cara

last: Ellis

first: Timothy

last: Kieffer


title: Vision-dependent specification of cell types and function in the developing cortex

city: Berkeley

first: Salwan

last: Butrus

state: California

address: Stanley Hall Rm

department: Chemical and Biomolecular Engineering

institute: UC Berkeley

summary: The role of postnatal experience in sculpting cortical circuitry, while long appreciated, is poorly understood at the level of cell types. We explore this in the mouse primary visual cortex (V1) using single-nucleus RNA-sequencing, visual deprivation, genetics, and functional imaging.  We find that vision selectively drives the specification of glutamatergic cell types in upper layers (L) (L2/3/4), while deeper-layer glutamatergic, GABAergic, and non-neuronal cell types are established prior to eye opening. L2/3 cell types form an experience-dependent spatial continuum defined by the graded expression of ~200 genes, including regulators of cell adhesion and synapse formation. One of these, Igsf9b, a vision-dependent gene encoding an inhibitory synaptic cell adhesion molecule, is required for the normal development of binocular responses in L2/3. In summary, vision preferentially regulates the development of upper-layer glutamatergic cell types through the regulation of cell type-specific gene expression programs.

overall_design: Single-nucleus transcriptomics of P8, P14, P17, P21, P28, and P38 normally reared mice and P28 dark-reared, P38 dark-reared, and P28 dark-light reared mice. Each of the nine datasets was obtained from 30 mice.

first: Sarah

last: Cheng

first: Liming

last: Tan

first: Vincent

last: Xu

first: Srikant

last: Sagireddy

first: Joshua

last: Trachtenberg

first: Karthik

last: Shekhar

first: S

last: Zipursky


title: Pancreas-specific miR-216a regulates proliferation and endocrine and exocrine cell function

overall_design: Four single cell RNA sequencing profiles from isolated islets of 17 week old wild type (WT) and miR216a-/- mice following 9 weeks on a 60% high fat diet


title: Dietary curcumin ameliorates perturbed insulin homeostasis in the diet-induced obese aged mice

status: Public on Nov 04 2021

city: Gaithersburg

first: Prabha

last: Chandrasekaran

address: 8348 Hawkins Creamery Rd

institute: ehealth&Informatics, LLC

summary: Although aging is a physiological process to which all organisms are subject, the presence of obesity and type 2 diabetes accelerates biological aging. Recent studies have demonstrated the causal relationships between dietary interventions suppressing obesity and type 2 diabetes and delaying the onset of age-related endocrine changes. Curcumin, a natural antioxidant, has putative therapeutic properties such as reinstating insulin sensitivity in obese mice. However, how curcumin contributes to maintaining insulin homeostasis in aged organisms largely remains unclear. Thus, the objective of this study is to examine the pleiotropic effect of dietary curcumin on insulin homeostasis in a diet-induced obese (DIO) aged mouse model. Aged (18-20 months old) male mice given a high-fat high-sugar diet supplemented with curcumin displayed a different metabolic phenotype compared to mice given a high-fat high-sugar diet alone. Furthermore, curcumin supplementation altered hepatic gene expression profiling, especially insulin signaling and senescence pathways. We then mechanistically investigated how curcumin functions to fine-tune insulin sensitivity. We found that curcumin supplementation increased hepatic insulin degrading enzyme (IDE) expression levels and preserved islet integrity, both of which are beneficial during aging. Our findings suggest that the multifaceted therapeutic potential of curcumin can be used as a protective agent for age-induced metabolic diseases.

overall_design: Hepatic mRNA profiles of 83-91 weeks old NCD, NCD+CUR, HFHSD, HFHSD+CUR supplemented mice

first: Su

last: Lee

last: Chandrasekran

first: Caio

middle: H

last: Mazucanti

first: Jennifer

last: O’Connell

first: Josephine

last: Egan

first: Yoo

last: Kim


title: RNA-seq analysis for wild-type fibroblasts and patient fibroblasts bearing the m.3243A>G mutatioin

status: Public on Oct 09 2021

city: London

first: Michael

middle: R.

last: Duchen

address: Gower Street

department: Cell and Developmetal Biology

institute: University College London

summary: The goal of this study is to compare RNA-seq of wild-type fibroblasts and patient fibroblasts bearing the m.3243A>G mutatioin. When comparing patient fibroblasts to wild-type ones and using a significance level of false discovery rate (FDR) < 0.05, we identified 3394 transcripts of which 1849 were upregulated and 1545 were downregulated.

overall_design: Three replicates for each fibroblast line (passage 4). L1084, Control 1; L1028,Control 2; L1007, Patient 1; L1008, Patinet 2. Control fiborblasts sometimes refer to as wild-type or WT. Similarly Patient fiborblasts sometimes refer to as mutant or MT.

first: Chih-Yao

last: Chung

middle: R


title: Single-cell Definition of the full-term Developmental Program of Male Mouse Germline

status: Public on Oct 28 2021

first: Ping

last: Lu

address: 5 Yiheyuan Road

institute: Peking University

summary: Germ cells are essential for the genetic information transition to subsequent generations of the species relying on sexual reproduction. Full-term developmental trajectory of germ cells provides a paradigm for understanding mammalian germline and germline niches with pivotal knowledge from tremendous in vivo and in vitro studies on the critical role of master regulators in regulating the initiation and maintenance of germline.To characterise the dynamic process of transcriptional programme underlying male mouse germline development, we generated single-cell RNA sequencing profiles for 28 developmental time-points from dissected early embryos or male gonads that were collected between embryonic day (E) 6.5 and postnatal day (P) 8 at one-day intervals, P10-P14 at two-day intervals and at juvenile stage of P30 and P35 as well as adult (8-10 weeks).

overall_design: A full-term single cell transcriptome profile of mouse germline from PGCs in E6.5 to spermatid in 10w after birth were generated by next generation sequencing using Illumina HiSeq X-Ten.

first: Jiexiang

last: Zhao


title: Transcriptional profiling of Bordetella hinzii clinical isolates

status: Public on Sep 03 2021

city: Bethesda

first: Chao-Jung

last: Wu

state: MD

address: 9000 Rockville Pike

institute: NIH

summary: Transcriptome analysis of Bordetella hinzii isolates from chronic infection in a human host with interleukin-12 receptor deficiency

overall_design: Examination of RNA-Seq profiles of a series of Bordetella hinzii isolates from chronic infection grown in liquid culture without selection for 4 and 10 hours.

first: Chao

first: Adrien

last: Launay

first: Jung

last: Youn

first: Pavel

last: Khil

first: John

last: Dekker


title: Comparison of the expressed profiling between bulbs of virus-free and virus-accumulated garlic

status: Public on Oct 17 2021

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

summary: To explore the influence of virus-accumulation on garlic growth, we produced a virus-free garlic using the landrace “Chalingzipisuan” with great accumulation of viruses, based on the shoot-tip culture.  Then, using the viruses-accumulated garlic and corresponding virus-free garlic, we performed a transcriptomic investigation for the enlarging-growth bulbs, and identified 1,182 garlic genes with differential expression, suggesting these genes involved in the response to viruses-infection

overall_design: The viruses-accumulated garlic was used as the treatment, and virus-free garlic was used as the control. Three biological replicates were performed for each sample. The garlic were infected by four viruses, namely, garlic virus A, D, and X, and garlic latent virus


title: Transcriptome analysis of lung-derived MBP-specific T cells, spinal cord microglia and total spinal cord following antibiotic treatment of the lung

first: Gabriela

last: Salinas

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

overall_design: Refer to individual Series


title: Time dependence of volume overload on right ventricular remodeling during preadolescence

status: Public on Aug 16 2021

city: Shanghai

first: Sijuan

last: Sun

address: No.1678, Dongfang Road

institute: Shanghai Children’s Medical Center (SCMC) affiliated to Shanghai Jiaotong University School of Medicine

summary: We reported the RNAseq analyses of right ventricualr free wall myocardium in young volume overload (VO)  C57/BL6 mice.VO was induced by the fistula between abdominal aorta and inferior vena cava (AVF) on postnatal day 7(P7). RNAseq analyses of RV free wall at P14 and P21from VO and sham-operated mice revealed that there were 981 differentially expressed genes between VO and sham group at P14, this number increased to 1907 at P21, there were 3012 differentially expressed genes between P21 and P14 sham group, and the number increased to 3470 at the presence of VO. GO analysis showed that in the VO and sham comparison, the upregulated genes mainly mediated mitosis and cell division and the downregulated genes mainly mediated heart contraction at P14, and the upregulated genes mainly mediated immune response, and downregulated genes mainly mediated cellular respiration at P21. As expected, in the normal RV development during preadolescence (from P14 to P21), upregulated genes mainly mediated oxidative phosphorylation and cellular respiration and the downregulated genes mainly mediated vasculogenesis. VO changed the RV development, the upregulated genes mainly mediated heart contraction and the down regulated genes mainly mediated vasculogenesis and cell cycle. KEGG pathway analysis revealed that cell cycle pathway was upregulated and cardiac muscle contraction and thyroid hormone signaling pathway were downregulated between VO and sham group at P14, phagosome pathway was upregulated and citrate cycle (TCA) cycle and thermogenesis were downregulated at P21 between VO and sham group. In the normal RV development, TCA cycle and cardiac muscle contraction pathway were upregulated while VO changed that to the upregulations of cardiomyopathy pathways and thyroid hormone signaling pathway. All the above changes were further confirmed by the functional tests.

overall_design: RNAseq analyses of right ventricular free wall myocardium in young volume overload and sham-operated C57/BL6 mice

first: Shoubao

last: Wang

first: Lincai

last: Ye

first: Fen

last: Li


title: Switching of OAS1 splicing isoforms mitigates SARS-CoV-2 infection

status: Public on Aug 02 2021

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

institute: Kindai University

summary: We aimed to study impact of CDC-like kinase (CLK) inhibitor CaNDY on OAS1 splicing manipulation. Our data indicates CaNDY treatment induces switching of OAS1 splice isoforms to provide an increased resistance to SARS-CoV-2 infection.

overall_design: PolyA-tailed RNA profiles were obtained for Calu-3 cells, treated with 10 µM CaNDY (n=3) or 0.1% DMSO (n=3).

last: Iida

first: Masahiko

last: Ajiro

first: Masatoshi

last: Hagiwara


title: Gene expression in CD21low and CD21pos B cells from CVID patients

status: Public on Aug 05 2021

city: Freiburg

first: Baerbel

last: Keller

department: Department of Rheumatology and clinical immunology

institute: University Medical Center Freiburg

summary: A subgroup of CVID patients presents with a loss of switched memory B cells and an accumulation of CD21low B cells.RNAseq data from CVID derived CD21low and CD21pos B cells were compared to naive CD21pos B cells in Healthy controls. The data reveal a distinct gene expression profile in CD21low B cells compared to HD.

overall_design: CD21 low and CD21pos B cells were sorted from freshly isolated PBMCs of CVID patients and healthy controls. Sorting included gating on CD19pos, CD27neg, IgDpos naive B cells and CD21low and CD21pos B cells were differentiated by low expression of CD21 and CD38 or high expression of CD21 and intermediate  to low levels of CD38 respectively and cells were processed for RNA isolation.

first: B

first: K

last: Warnatz

first: J

last: Landry


title: Nucleosome exchange in budding yeast

status: Public on Jun 24 2021

city: Rehovot

first: Naama

last: Barkai

address: Herzl St 234

institute: Weizmann Institute

summary: Measuring nucleosome exchange of all four histone core subunits using novel sensors in budding yeast

overall_design: Yeast strains with subunit-specific nucleosome exchange markers were grown in various environmental conditions and nucleosome exchange was determined with ChIPseq

first: Gilad

last: Yaakov

first: Felix

last: Jonas


title: Tcf1 controls Treg functions that regulate inflammation, CD8 T-cell cytotoxicity, and severity of colon cancer

status: Public on Jun 01 2021

city: West Lafayette

first: Majid

last: Kazemian

state: Indiana

address: 610 Purdue Mall

institute: Purdue university

summary: Tcf1, the DNA-binding partner of β-catenin, is essential for the development and function of T regulatory cells (Tregs). However, how Tcf1 regulates Treg functional specification is less understood. Here, we ablated Tcf1 in Tregs to elucidate its role in Treg specification in healthy mice and mice with colon cancer. RNAseq and single-cell RNAseq revealed that Tcf1 deficient Tregs maintain their core transcriptional signature and diversity, but promote T-cell receptor, Tgfβ receptor, TH17, and Wnt/β-catenin signaling pathways. Central-memory-Tregs with low Klf2 and effector-Tregs with high Mif expression gain TH17 characteristics and mature into effector Treg subpopulations that strongly express cMaf. Tcf1 deficient Tregs exhibit enhanced suppression of T-cell proliferation and cytotoxicity but are compromised in controlling CD4+ T-cell polarization and inflammation. In mice with polyposis, Tcf1 deficient Tregs promote inflammation and tumor growth. Thus, Tcf1 determines Treg functions that regulate TH17 inflammation and the course and outcome of colorectal cancer.

overall_design: CD25+YFP+ Tregs were FACS sorted from MACS-pre-purified CD4+ T cells (mouse CD4+ T Cell Isolation Kit, Miltenyi) isolated from MLN of Foxp3Cre and Foxp3CreTcf7fl/fl mice. Total RNA was isolated using the PicoPure RNA Isolation Kit (Arcturus) following the manufacturer’s instructions. Libraries were generated and sequenced by the University of Chicago Genomics Facility. Samples from Foxp3Cre and Foxp3CreTcf7fl/fl mice are prepared and sequenced in triplicates. Whole live cells were washed twice in 1x PBS + 0.04% BSA and immediately submitted to the Core for Single Cell sorting. For single-cell RNAseq, the cells were first counted and measured for viability using the Vi-Cell XR Cell Viability Analyzer (Beckman-Coulter), as well as a basic hemocytometer with light microscopy. The barcoded Gel Beads were thawed from -80C and the reverse transcription master mix was prepared according to the manufacture’s instruction for Chromium Single Cell 3’ v2 library kit (10x Genomics). Tregs from the mesenteric lymph nodes (MLN) from four different genotypes of mice (n=2 replicates) aged to 5.5 month: Foxp3CreTcf7fl/fl and its control Foxp3Cre mice, the polyposis prone APC<delta>468 mice and control WT C57BL/6J (B6) mice are sequenced. Each sample was uniquely indexed.

first: Khashayarsha

last: Khazaie

first: Fotini

last: Gounari

first: Abu

last: Osman

first: Bingyu

last: Yan

first: Ying


title: Single cell transcriptomes of developing chicken hind limbs at stages HH21, HH24 and HH27

status: Public on May 18 2021

city: Berlin

first: Christian

middle: A.

last: Feregrino

address: Ihnestraße 63

institute: MPI - Molecular Genetics

summary: We sequenced single cells coming from three developmental stages of chicken forelimb. We identified different cell populations with distinct transcriptional profiles. The supplementary file contains processed UMI count matrices, which also include meta data of each cell, e.g. cluster.

overall_design: 10x single cell RNA-seq of dissociated developing forelimbs limbs of chicken at stages HH21, HH24 and HH27. Samples HH21 and HH24 were sequenced in two runs, of the same library.

first: Patrick

last: Tschopp


status: Public on Oct 06 2021

city: Birmingham

first: Thanh

middle: Minh

last: Nguyen

state: AL

address: 1670 University Blvd, Volker Hall G094

department: Department of Biomedical Engineering

institute: University of Alabama at Birmingham

summary: Background: In this study, we have extended the myocardial regenerative window to postnatal day 28 (P28) by a double injury pig model (ARP1MIP28) of apical resection at P1 (ARP1) and LAD ligation at P28 (MIP28). However, the molecular mechanism of regenerative window extension is not known. Results: Gene-expression profiles revealed that regenerating ARP1MIP28 hearts contained different subpopulations of cardiomyocytes early after 2nd injury. The six cardiomyocyte clusters were identified (CM1-CM6) by Louvain clustering. The CM6, CM3, and CM2 clusters have mainly consisted of fetal (92.4%), CTL-P1 (95.7%), and CTL-P56 (96.2%) cardiomyocytes. In contrast, the CM1 cluster has consisted of heterogeneous cardiomyocyte groups from all other animal groups, including less than 1% of fetal and CTL-P1 cardiomyocytes. The CM5 and CM4 clusters have mainly consisted of ARP1MIP28-P35 cardiomyocytes, 97.8%, and 68.6%, respectively. Sparse modeling analysis revealed that AR and MI injury, both alone and in combination, appeared to promote the proliferative capacity of cardiomyocytes and perturb cardiomyocyte maturation. Publication: This dataseries is associated to manuscript titled 'Single nucleus transcriptomics: Apical resection in newborn pigs extends the time-window of cardiomyocyte proliferation and myocardial regeneration', published in Circulation, 2021.

overall_design: The ARP1-MIP28 pig hearts demonstrated no visible myocardial structural or functional damage 4 weeks after LAD ligation. Here, ARP1 means that the pig heart received apical resection on postnatal day 1, and MIP28 means that the pig heart received LAD ligation on postnatal day 28. The nuclear RNA contents were isolated from pig hearts that received regenerative or non-regenerative types of cardiac surgery and performed snRNA-seq to characterize gene-expression profile of the ARP1MIP28 in cardiomyocytes. The study includes the following groups: FH, CTL-P1, CTL-P28, CTL-P56, ARP1-P28, ARP1-P56, MIP28-P56, ARP1-MIP28-P30, ARP1-MIP28-P35, ARP1-MIP28-P42, and ARP1-MIP28-P56. Here, FH means fetal heart, CTL means naïve postnatal heart (no injury), P1/P28/P30/P35/P42/P56 means the postnatal day (1/28/30/35/42/56, correspondingly) when the pig heart tissue was harvested and sent to single-nuclei sequencing.

first: Jianyi

last: Zhang

first: Yang

last: Zhou

first: Wuming

last: Gong

first: Eric

first: Erik

last: Skie

first: Yuhua

last: Wei

first: Meng

last: Zhao

first: Wangping

last: Chen

first: Jake

first: Gregory

last: Walcott

first: Daniel

last: Garry

first: Jiacheng

last: Sun

first: Syed

last: Raza


title: Gene expression data from patients with pancreatic ductal adenocarcinoma

status: Public on Sep 23 2021

city: New York

first: Masataka

last: Amisaki

state: NY

address: 1275 York Ave

department: Human oncology & pathogenesis program(HOPP)

institute: Memorial Sloan Kettering Cancer Center

summary:
Pancreatic ductal adenocarcinoma (PDAC) is one of the most treatment-resistant malignancies in human. To perform transcriptomic profiling on PDAC, we collected primary PDAC tissues from surgically resected PDAC patients at the Memorial-Sloan Kettering Cancer Center (NY, USA).  Morphogenesis of epithelial tissues relies on the precise developmental control of cell polarity and architecture. In the early Drosophila embryo, the primary epithelium forms during cellularisation, following a tightly controlled genetic programme where specific sets of genes are up-regulated. Some of them, for instance, control membrane invagination between the nuclei anchored at the apical surface of the syncytium.
We used microarrays to detail transcritomic profiling of PDACs.

overall_design: Total RNA was extracted from fresh frozen OCT-embedded human PDAC tumor tissues using TRIxol RNA Isolation Reagent (Life Technologies). RNA was processed with the WT Pico Reagent Kit (Affymetrix) and T7 in vitro transcription thechnology into the cRNA, then hybridiezd to GeneChip Human Transcriptome Array 2.0 (Affymetrix), and scanned using the GeneChip Scanner 3000.

first: Vinod

last: Balachandran

first: Alec

last: Moral

first: Julia


title: To identify novel targets of a zinc finger transcription factor, Mxr1p in Pichia pastoris cultured in medium containing ethanol

status: Public on Sep 22 2021

city: Bangalore

first: Aditi

last: Gupta

state: Karnataka

address: FE-15, Biological Sciences Building, Indian Institute of Science

department: Biochemistry

country: India

institute: Indian Institute of Science

summary: The role of transcription factor Mxr1p has so far been studied in methanol, amino acid and acetate metabolism. We have demonstrated a key role of Mxr1p in regulation of ethanol metabolism when cells are cultured in medium containing ethanol as sole carbon source. We employed RNA Seq to identify new targets of Mxr1p in medium containing ethanol.

overall_design: Wild type and knockout cells were cultured in minimal medium with ethanol as a carbon source. Cells were harvested after 14 hours followed by RNA preparation using QIAGEN RNEASY Mini Kit which was then subjected to RNA-SEQ.

first: PN

last: Rangarajan


title: Recurrent Integration of Human Papillomavirus Genomes at Transcriptional Regulatory Hubs

status: Public on Sep 01 2021

first: Alison

middle: Anne

last: McBride

address: 33 North Drive

department: DIR

institute: NIAID

summary: Oncogenic human papillomavirus (HPV) genomes are often integrated into host chromosomes in HPV-associated cancers. HPV genomes are integrated either as a single copy, or as tandem repeats of viral DNA interspersed with, or without, host DNA. Integration occurs frequently in common fragile sites susceptible to tandem repeat formation, and the flanking or interspersed host DNA often contains transcriptional enhancer elements. When co-amplified with the viral genome, these enhancers can form super-enhancer-like elements that drive high viral oncogene expression. Here, we compiled highly curated datasets of HPV integration sites in cervical (CESC) and head and neck squamous cell carcinoma (HNSCC) cancers and assessed the number of breakpoints, viral transcriptional activity, and host genome copy number at each insertion site. Tumors frequently contained multiple distinct HPV integration sites, but often only one “driver” site that expressed viral RNA. Since common fragile sites and active enhancer elements are cell-type specific, we mapped these regions in cervical cell lines using FANCD2 and Brd4/H3K27ac ChIP-seq, respectively. Large enhancer clusters, or super-enhancers, were also defined using the Brd4/H3K27ac ChIP-seq dataset. HPV integration breakpoints were enriched at both FANCD2-associated fragile sites, and enhancer-rich regions, and frequently showed adjacent focal DNA amplification in CESC samples. We identified recurrent integration “hotspots” that were enriched for super-enhancers, some of which function as regulatory hubs for cell-identity genes. We propose that during persistent infection, extrachromosomal HPV minichromosomes associate with these transcriptional epicenters, and accidental integration could promote viral oncogene expression and carcinogenesis.

overall_design: ChIP-seq analysis of FANCD2 binding in cervical carcinoma cell lines (C33-A and HeLa) following 0.2 µM aphidicholin treatment to induce mild replication stress. ChIP-seq analysis of Brd4 and H3K27ac in HPV16-positive W12 cervical keratinocytes (20831, 20861, 20862 and 20863)

first: Alix

last: Warburton

first: Tovah

last: Markowitz

middle: A


title: Gene expression in anti-IgM IFNg treated B cells

status: Public on Aug 11 2021

first: Baerbel

last: Keller

summary: RNAseq data of human naive B cells untreated or stimulated with anti-IgM and IFNg

overall_design: Isolated naive B cells of healthy human individuals were eiter left untreated or stimulated with anti-IgM and IFNg for 2 days

first: Bärbel

first: Geoffroy

last: Andrieux


title: mRNAs and LncRNA microarray of HBE cell exposed to Al2O3 NPs, PM2.5, DEP

status: Public on Sep 15 2021

city: Beijing

first: Rui

address: No.10 Xitoutiao, You An Men

institute: Capital medical university

summary:
mRNAs and LncRNAs have been implicated in the regulation of a board range of biological processes including development, immunity and inflammation
We used mRNA and LncRNA microarray to explore the detailed biological processes and mechanisms underlying matter-induced pulmonary toxicity

overall_design: Microarray expression screening was performed using HBE cells exposed to PBS, Al2O3 NPs, PM2.5, DEP.

first: Xiaobo

last: Li


title: FBXO11-Mediated Proteolysis of BAHD1 Relieves PRC2-dependent Transcriptional Repression in Erythropoiesis

status: Public on Dec 31 2020

city: Memphis

first: Mitch

last: Weiss

state: Tennessee

address: 262 Danny Thomas Place

department: Hematology

institute: st jude children's research hospital

summary: The histone mark H3K27me3 and its reader/writer Polycomb repressive complex 2 (PRC2) mediate widespread transcriptional repression in stem and progenitor cells. Mechanisms that regulate this activity are critical for tissue development but poorly understood. Here we show that the E3 ubiquitin ligase FBXO11 relieves PRC2-mediated repression during erythroid maturation by targeting its newly identified substrate BAHD1, an H3K27me3 reader that recruits transcriptional co-repressors. Erythroblasts lacking FBXO11 are developmentally delayed, with reduced expression of maturation-associated genes, most of which harbor bivalent histone marks (activating H3K4me3 and repressive H3K27me3), bind BAHD1, and fail to recruit the erythroid transcription factor GATA1. The BAHD1 complex interacts physically with PRC2 and depletion of either component restores FBXO11-deficient erythroid gene expression. Previous studies showed that FBXO11 promotes B-cell development and inhibits lymphomagenesis by degrading the transcriptional repressor BCL6. We show that in aggressive B-cell lymphoma lines, depletion of FBXO11 causes the accumulation of both BCL6 and BAHD1, and that suppression of BAHD1 slows cell expansion. Our studies identify BAHD1 as a novel effector of PRC2-mediated repression and reveal how a single E3 ubiquitin ligase eliminates PRC2 repression at developmentally poised bivalent genes during erythropoiesis. The FBXO11-BAHD1 regulatory axis may function in other developmental pathways, including B-lymphopoiesis and lymphomagenesis.

overall_design: The goals of this study are to compare the transcriptomes in wild type HUDEP-2 and FBXO11 -/- HUDEP-2 erythroblast.  We further compare the transcriptomes in BAHD1shRNA or shLuciferase treated FBXO11 KO HUDEP-2 cells. Finally we intergrate the RNA-seq data with CHIP-Seq data (BAHD1, H3K27me3, H4me3, GATA1) to support our hypothesis.

first: Peng

last: Xu

first: Beisi

first: Xing

last: Tang


title: Rigosertib, a potential RAS-targeted agent, induces CD40 expression on melanoma cells to enhance response to immune checkpoint inhibitors

status: Public on Jun 15 2021

city: Nashville

first: Chi

last: Yan

address: 432A Preston Res Building, 2220 Pierce Ave

institute: Vanderbilt University

summary:
Immune checkpoint blockade (ICB) is the current first-line treatment for metastatic melanoma. However, ICB fails in many patients and has dangerous side effects. Rigosertib (RGS), a non-ATP-competitive small molecule RAS mimetic, has the potential to block oncogenic RAS-RAF-MEK-ERK and/or PI3K-AKT-mTOR signaling pathways. RGS treatment (300mg/kg) of melanoma tumor-bearing mice is well tolerated and results in ~50% inhibition of tumor growth as monotherapy and ~70% inhibition in combination with ICB.  RGS-induced tumor inhibition depends on the induction of CD40 expression on melanoma cells, followed by immunogenic cell death, leading to an inflamed tumor microenvironment with enrichment of dendritic cells and activated CD8+ T cells.
Highlights  • RGS impairs melanoma tumor growth via direct killing and immunogenic cell death that promotes an inflamed tumor microenvironment.  • RGS-induced tumor inhibition depends on the induction of CD40 expression on melanoma cells.  • Combining RGS with αPD1+αCTLA4 improves tumor response.  • Tumor CD40 levels are prognostic for therapeutic response to RGS and BRAF inhibitor.
Significance:  A high CD40 expression level correlates with CD80, ICOS-L, beneficial type I T cell responses, and better survival in melanoma patients (cBioPortal database). Tumor CD40 levels are prognostic for therapeutic response to RGS and BRAF inhibitor (DepMap and Oncomine databases), and RGS induces CD40 expression in melanoma tumor cells. Our preclinical data support the therapeutic use of RGS plus αPD1+αCTLA4 in RAS/RAF/MEK and/or PI3K pathway-activated melanoma tumors and point to the need for clinical trials to determine the clinical benefit of RGS plus ICB for metastatic melanoma patients who do not respond to ICB alone.

overall_design:
The goal of this study is to identify Rigosertib-induced gene expression in YUMM3.3 melanoma tumors by RNA-Seq.
Tumors were collected into RNAlater. RNA was extracted using Qiagen RNAeasy plus mini Kit for three replicates from H20 and Rigosertib treated groups. Samples were submitted to Vanderbilt Technologies for Advanced Genomics (VANTAGE) for RNA QC, library prep and sequencing with a mean of ~30M reads/sample. Samples were sequenced on the Illumina NovaSeq 6000 using 150bp paired-end reads. Reads were then aligned to the STAR aligner for reads.

first: Ann

last: Richmond


title: Single-cell RNA sequencing of human airway epithelia infected with measles virus (MeV)

status: Public on Aug 06 2021

city: Iowa City

first: Alejandro

last: Pezzulo

state: Iowa

address: 6316 Pappajohn Biomedical Discovery Building

department: Department of Internal Medicine

institute: Universty of Iowa

summary: The goal of this study was to compare cell composition, gene expression, and infectivity of different cell types in human airway epithelia following exposure to measles virus. Samples included control epithelia exposed to a mock infection and measles-virus-exposed epithelia that were sorted according to detection of green fluorescent protein (GFP) prior to library preparation and sequencing.

overall_design: Primary basal cells were collected from lung donors, infected with Measles Virus, prepared for single-cell sequencing via 10X Genomics Chromium controller, and sequenced on Illumina NovaSeq6000.

first: Camilla

last: Hippee

first: Andrew

last: Thurman

first: Ashley

last: Cooney

first: Brajesh

middle: K

last: Singh

first: Paul

middle: B

last: McCray Jr.

first: Patrick

last: Sinn


title: Betaine is involved in regulation of translation through alteration of N6-methyladenosine RNA methylation in liver

status: Public on May 20 2021

city: Nanning

first: Yixing

address: Daxuedong Road, Xixiangtang District

department: Guangxi University

institute: Guangxi University

type: Methylation profiling by high throughput sequencing

summary: In order to explore the effect of betaine on NAFLD and its mechanism, we divided mice into  high-fat diet (HF) and high-fat diet with betaine (HB) groups, and used N6-methyladenosine sequence (m6A-seq), RNA-seq and mRNAs bound to ribosome-nascent chain complex sequencing (RNC-seq) to evaluate the gene expression levels in the liver of each group.

overall_design: Examination of anti-m6A antibody in liver tissue. Total RNA and ribosome-bound RNA were extracted from the livers of high-fat diet- (HF) and High-fat diet plus Betaine (HB)-fed mice, and the polyA+ mRNA was sequenced using Illumina HiSeq X Ten sequencer. The reads were mapped to RefSeq RNA reference sequences and the expression level were quantified by rpkM calculation.

first: Jingsu

last: Yu

first: Tengda

last: Huang

first: Zupeng

last: Luo

first: Lin

first: Siqi

last: Liu

first: Zeqiang

last: Ma

first: Liang

first: Mingming

first: Lei

last: Zhou


title: Blood DNA methylation profiles from schizophrenia cases, first episode psychosis patients and controls II

status: Public on Apr 07 2021

city: Exeter

first: Jonathan

last: Mill

address: RILD Building, RD&E Hospital

department: Medical School

institute: University of Exeter

summary: Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium HumanMethylation450K BeadChip (“450K array”) in DNA samples isolated from blood for schizophrenia cases, first episode psychosis patients and controls. These samples were profiled as part of a wider study where they were meta-analysed with other cohorts.

overall_design: This data includes 800 adult samples profiled as part of a psychosis case control study design. Specifically it includes data for 290 schizophrenia cases, 307 first episode psychosis patients and 203 controls. All samples were recruited as part of IoPPN studies.

first: E

last: Hannon

first: J


title: Transcription factor TCF1 is indispensable for the epigenetic priming of EILPs toward distinct cell fates

city: Bethesda

first: Keji

last: Zhao

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

summary: Differentiation of Innate lymphoid cells (ILCs) from hematopoietic stem cells needs go through several progenitor stages defined by various cell surface markers. The progenitor populations at specific developmental stages may have multiple lineage potentials. However, it is not clear whether the multipotency of the progenitors are induced in situ by differentiation signals or are already predefined by epigenetic states. Here we report the profiling of genome-wide nucleosome position and chromatin accessibility simultaneously in ILC progenitors EILPs and ILCPs by single-cell MNase-Seq. We find that EILPs contain distinct sub-populations epigenetically primed toward either myeloid or ILC lineages, while ILCPs contain cells mainly primed for the ILC lineage at epigenetic level. We further demonstrate that the transcription factor TCF1 is indispensable for the epigenetic priming of lineage-defining sites (LDSs) for both myeloid lineages and ILC lineages at the EILP stage, and deletion of TCF1 results in the epigenetic priming that favors the myeloid lineages. Our results suggest that the multipotency of progenitor cells is defined by the existence of heterogeneous population of cells epigenetically primed for distinct downstream lineages, which are regulated by key transcription factors.

overall_design: We performed scMNase-seq for wild-type EILPs, ILCPs, and Tcf7-deficient EILPs to profile nucleosome positions and chromatin accessibility in single cells for each cell type. We performed DNase-seq and ChIC-seq of H3K4me3, H3K27ac, and H3K27me3 for ALPs, EILPs, ILCPs and Tcf7-deficient EILPs to profile chromatin accessibility and histone modifications in bulk cells for each cell condition. We performed ChIC-seq of TCF1 for EILPs and ILCPs to profile TCF1 binding in bulk cells for each cell type.

first: Gang

last: Ren

first: Binbin

last: Lai

first: Christelle

last: Harly

first: Kairong

last: Cui

first: Avinash

last: Bhandoola


title: Expression of E. coli RNase toxins

status: Public on Jun 11 2020

city: Boston

first: Peter

last: Culviner

state: MA

address: 677 Huntington Ave

department: IID

institute: Harvard School of Public Health

summary: The purpose of this experiment was to identify cleavage sites of E. coli RNase toxins within the E. coli genome.

overall_design: Toxins were expressed either in a titratable strain (BW27783) or in MG1655 E. coli for 10 minutes. Cleavage sites were identified by loss of signal at toxin cleavage sites compared to empty vector controls under the same conditions.

first: Michael

last: Laub

first: Michele

last: LeRoux


title: Stress-induced RNA–chromatin interactions promote endothelial dysfunction (scRNA-seq human vascular)

status: Public on Aug 17 2020

city: La Jolla

first: Sheng

last: Zhong

state: CA

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California San Diego

summary: Chromatin-associated RNA (caRNA) has been proposed as a type of epigenomic modifier. Here, we test whether environmental stress can induce cellular dysfunction through modulating RNA-chromatin interactions. We induce endothelial cell (EC) dysfunction with high glucose and TNFα (H + T), that mimic the common stress in diabetes mellitus. We characterize the H + T-induced changes in gene expression by single cell (sc)RNA-seq, DNA interactions by Hi-C, and RNA-chromatin interactions by iMARGI. H + T induce inter-chromosomal RNA-chromatin interactions, particularly among the super enhancers. To test the causal relationship between H + T-induced RNA-chromatin interactions and the expression of EC dysfunction-related genes, we suppress the LINC00607 RNA. This suppression attenuates the expression of SERPINE1, a critical pro-inflammatory and pro-fibrotic gene. Furthermore, the changes of the co-expression gene network between diabetic and healthy donor-derived ECs corroborate the H + T-induced RNA-chromatin interactions. Taken together, caRNA-mediated dysregulation of gene expression modulates EC dysfunction, a crucial mechanism underlying numerous diseases.

overall_design: Performing single-cell RNA-seq in human mesenteric arterial endothelial cells in two healthy and two Type 2 Diabetes donors.

first: Riccardo

last: Calandrelli

first: Lixia

last: Xu

first: Yingjun

first: Weixin

last: Wu

first: Xiaochen

last: Fan

first: Tri

last: Nguyen

first: Chien-Ju

last: Chen

first: Kiran

last: Sriram

first: Rama

last: Natarajan

first: Zhen

last: Bouman-Chen


title: Transcriptional response of NGN3 J2 enteroids

status: Public on Nov 04 2020

city: Houston

first: Sara

middle: Chloe

last: Di Rienzi

state: TX

address: 1 Baylor Plaza Room 743E

department: Molecular Virology and Microbiology

institute: Baylor College of Medicine

summary: Enteroendocrine cells are hormonal secreting cells in the gut. However, as they comprise <1% of the total epithelial cell population, studies on their response to stimuli have been limited. Chang-Graham, Danhof, Engevik, and Tomaro-Duchesneau et al (PMID 31029854) developed a model enteroid system to overcome this limitation. By driving expression of NGN3 in human jejunal enteroids, their system allows for analysis of hormonal secretion and transcriptional analysis in response to a stimulus. To further characterize these NGN3 enteroids, we performed RNASeq on these enteroids in the induced or uninduced state.

overall_design: A total of 12 samples were sequenced. In the uninduced state (NGN3 not induced, low number of enteroendocrine cells), 2 batches of enteroids, triplicate enteroids for each treatment: media alone (LDM4) = 6 samples. In the induced state (NGN3 induced, high number of enteroendocrine cells), 2 batches of enteroids, triplicate enteroids for each treatment: media alone (LDM4)  = 6 samples.

middle: C

first: Heather

last: Danhof

first: Robert

last: Britton


title: Blood DNA methylation profiles from first episode psychosis patients and controls I

first: Jonathan

last: Mill

summary: Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium HumanMethylationEPIC BeadChip (“EPIC array”) in DNA samples isolated from blood for schizophrenia cases, first episode psychosis patients and controls. These samples were profiled as part of a wider study where they were meta-analysed with other cohorts.

overall_design: This data includes 934 adult samples profiled as part of a psychosis case control study design. Specifically it includes data for 458 first-episode psychosis (FEP) cases and 558 controls recruited as part of the EU-GEI study.

first: E

last: Hannon

first: J


title: Partial inhibition of mitochondrial complex I attenuates neurodegeneration and restores energy homeostasis and synaptic function in a symptomatic Alzheimer’s mouse model

status: Public on Oct 31 2020

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

summary: We performed next-generation RNA sequencing (RNA-seq) using brain tissue from 23 months old non-transgenic (NTG), non-treated and CP2 (mitochondrial complex I  inhibitor)-treated APP/PS1 (mouse model of Alzheimer`s disease). By comparing transcriptomic data of NTG and vehicle-treated APP/PS1 mice, we found processes affected by the disease in APP/PS1 such as impaired ATP metabolism, ion transport, nervous system development, synaptic transmission, and inflammation.  CP2-treatment in APP/PS1 positively affected genes related to immune system, axonogenesis, dendritic spine morphology, synaptic function, among the others. These data demonstrate that pathways improved by CP2 treatment in APP/PS1 mice comprise major pathways essential for therapeutic efficacy in Alzheimer`s disease.

overall_design: mRNA profiles of 23 months old non-transgenic (NTG) and non-treated and CP2 (mitochondrial complex I  inhibitor)-treated APP/PS1 mice were generated by deep sequencing, using Illumina HiSeq 4000 with paired end 101-bp read length.

first: Eugenia

last: Trushina


title: Differential Gene Expression in Cdh13 KO x Maternally separated mice

status: Public on Jan 30 2021

city: Würzburg

first: Richa

last: Bharti

state: Bavaria

address: Josef-Schneider-Straße 2 / Bau D15

department: IMIB,Core Unit Systemmedizin

institute: University of Wuerzburg

summary: We report the data of a GxE experiment. Cdh13 ko vs Cdh13 wt, who were either maternally separated or controls who were handled. Two age groups were created but analysed separatly.

overall_design: Examination of 1 brain region (hippocampus) over 2 age x 2 genotypes x 2 environmental groups. Analysis was done for each age group indepentently in a 2x2 design for GxE. G (Cdh13 knockout and Cdh13 wildtype), E (maternal separation and control).

first: Dominik

last: Kiser

first: Olga

last: Rivero

first: Klaus-Peter

last: Lesch


title: Single-cell analyses reveal increasing intratumoral heterogeneity as an essential component of treatment resistance in small cell lung cancer

status: Public on Feb 12 2020

first: Yuanxin

last: Xi

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

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

overall_design: Refer to individual Series


title: Single Cell and Spatial Analysis of Human Squamous Cell Carcinoma [single-cell RNA-seq]

status: Public on Jun 22 2020

first: Andrew

last: Ji

address: 1428 Madison Ave.

institute: Icahn School of Medicine at Mount Sinai

summary: To define the cellular composition and spatial architecture of the tumor micoenvironment, we combined single-cell RNA-sequencing, spatial transcriptomics, and multiplexed ion-beam imaging from 10 patient cutaneous squamous cell carcinoma tumors and  site-matched normal skin

overall_design: Patient tumors, normal skin, and tumor xenografts of human SCC cell lines in immunocompromised mice were dissociated into single-cell suspensions and scRNA-seq was performed with the 10X Chromium 3' v2 platform. A prior patient metadata file (patient_metadata.txt.gz) contained scrambled barcode names. An updated file (patient_metadata_new.txt.gz) is now corrected to match the counts matrix barcode names.

middle: L

first: Adam

last: Rubin