title: Dissecting Super-enhancer driven Transcriptional Dependencies Reveals Novel Oncogenes and Therapeutic Strategies of Group 3 Subtype Medulloblastoma [ChIP-seq]

status: Public on Oct 04 2021

first: Yujie

last: Tang

address: 280 South Chongqing Road

department: Pathophysiology

institute: Shanghai Jiao Tong University School of Medicine

summary: Medulloblastoma (MB) is the most common malignant pediatric brain tumor and group 3 subtype (G3-MB) exhibits the worst prognosis. Dissecting super-enhancer (SE) driven transcriptional dependencies of cancer has been shown to facilitate identifying novel oncogenic mechanisms and therapeutic targets or strategies. In this study, our integrative SE analyses of primary tissues and patient-derived tumor cell lines of G3-MB revealed their partially conserved SE-associated transcripts were enriched of subtype-specific tumor-dependent genes and MB patients harboring enrichment of those transcripts exhibited worse prognosis. Fourteen such conserved SE-associated genes were identified to be members of SE-driven core transcriptional regulatory network of G3-MB, including three well-recognized master TFs and eleven newly identified effector oncogenes. ARL4D, one of the effector oncogenes, was further demonstrated to exert its oncogenic role via maintaining cell-cycle progression and stemness of G3-MB cells. Moreover, BET inhibition with CDK7 inhibition or proteasome inhibition, two combinatory strategies of targeting SE complex components (BRD4, CDK7) or SE-associated effector oncogene (PSMB5), were shown to exhibit synergistic therapeutic effects against G3-MB. Taken together, our study verifies the oncogenic role and therapeutic potential of SE-driven transcriptional dependencies of G3-MB, resulting in better understanding of its tumor biology and identification of novel SE-associated therapeutic targets or strategies.

overall_design: To identify the super-enhancer landscape of Medulloblastoma, we performed chromatin-immunoprecipitation with sequencing (ChIP-seq) of H3K27ac antibody and RNA-seq analyses in three human primary Group 3 subtype MB cell lines (MB002, D425, HD-MB03) and SHH subtype MB (UW228). ROSE (Rank Ordering of Super-Enhancers) algorithm was used for calling SE and SE-associated genes.

first: Meng

last: Li

first: Chaochen

last: Wang

first: Wenfeng

last: Kang


title: Computational Repurposing of Bumetanide for Preventing or Treating Alzheimer’s Disease [AT01_J20_apoEKI_Bumex_snRNA-seq]

status: Public on Oct 03 2021

city: San Francisco

first: Alice

last: Taubes

state: CA

address: 1650 Owens Street

department: Neurological Disease

country: USA

institute: Gladstone Institute of Neurological Disease

type: Expression profiling by high throughput sequencing

summary: The evident genetic, pathological, and clinical heterogeneity of Alzheimer’s disease (AD) poses challenges for traditional drug development. We conducted a computational drug repurposing screen for drugs to treat apolipoprotein (apo) E4-related AD. We first established apoE-genotype-dependent transcriptomic signatures of AD by analyzing publicly-available human brain database. We then queried these signatures against the Connectivity Map database containing transcriptomic perturbations of >1300 drugs to identify those that best reverse apoE-genotype-specific AD signatures. Bumetanide was identified as a top drug for apoE4 AD. Bumetanide treatment of apoE4 mice without or with Ab accumulation rescued electrophysiological, pathological, or cognitive deficits. Single-nucleus RNA-sequencing revealed transcriptomic reversal of AD signatures in specific cell types in these mice, a finding confirmed in apoE4-iPSC-derived neurons. In humans, bumetanide exposure was associated with a significantly lower AD prevalence in individuals over the age of 65 in two EHR databases, suggesting effectiveness of bumetanide in preventing AD.

overall_design: Single Nucleus Seq of the hippocampus of J20/apoE4-KI 10 month old mice treated with 0.2 mg/kg bumetanide or vehicle control

first: Phil

last: Nova

first: Kelly

middle: A

last: Zalocusky

first: Idit

last: Kosti

first: Mesude

last: Bicak

first: Misha

middle: Y

last: Zilberter

first: Yanxia

last: Hao

first: Seo

last: Yoon

first: Silvia

last: Pineda

first: Bin

last: Chen

first: Emily

last: Aery Jones

first: Krishna

last: Choudhary

first: Brian

last: Grone

first: Maureen

middle: E

last: Balestra

first: Fayzan

last: Chaudhry

first: Ishan

last: Paranjpe

first: Jessica

last: De Freitas

first: Nicole

last: Koutsodendris

first: Nuo

first: Celine

first: William

last: Chang

last: An

first: Benjamin

middle: S

last: Glicksberg

first: Marina

last: Sirota

first: Yadong

last: Huang


title: Computational Repurposing of Bumetanide for Preventing or Treating Alzheimer’s Disease [AT2123B_iPS_Bumex_RNA-seq]

first: Alice

last: Taubes

overall_design: RNA-Seq of human apoE4/4 iPSC-derived neurons treated with 10 uM of Bumetanide, vehicle, or untreated harvested at 6 hours after addition of treatment

first: Phil

last: Nova

first: Kelly

last: Zalocusky

first: Idit

last: Kosti

first: Mesude

last: Bicak

first: Misha

last: Zilberter

first: Yanxia

last: Hao

first: Seo

last: Wang


title: Computational Repurposing of Bumetanide for Preventing or Treating Alzheimer’s Disease [AT02_apoE4KI_Bumex_snRNA-seq]

last: Yoon

first: Silvia

last: Pineda

first: Bin

last: Chen

first: Emily

last: Aery Jones

first: Krishna

last: Choudhary

first: Brian

last: Grone

first: Maureen

last: Balestra

first: Fayzan

last: Chaudhry

first: Ishan


title: Dissecting Super-enhancer driven Transcriptional Dependencies Reveals Novel Oncogenes and Therapeutic Strategies of Group 3 Subtype Medulloblastoma

city: Shanghai

first: Yujie

last: Tang

country: China

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Baseline signatures associated with clinical, virologic, and immunologic outcomes in patients with mild to moderate COVID-19

status: Public on Oct 01 2021

first: Zicheng

last: Hu

address: 490 Illinois Street

institute: University of California San Francisco

summary: The vast majority of SARS-CoV-2 infections are uncomplicated and do not require hospitalization, but these infections contribute to ongoing transmission. There remains a critical need to identify host immune biomarkers predictive of virologic and clinical outcomes in planning future treatment studies of COVID-19.   We recently completed a randomized clinical trial of Pegylated PegIinterferon Lambda for treatment of SARS-CoV-2 infected patients conducted in the Stanford COVID-19 CTRU. Leveraging longitudinal samples and data from this trial, we define early immunebaseline and infection-induced signatures that predict the duration of viral shedding, resolution of symptoms, and immunologic memory.

overall_design: We recruited 108 subjects between age 18 to 75 who are PCR positive for SARS-CoV-2. The subjects were randomized to receive a single dose of Peginterferon Lambda or placebo at their first visit (day 0). In-person follow-up visits were conducted on Day 1, 3, 5, 7, 10, 14, 21, and 28, with the assessment of symptoms and vitals and collection of oropharyngeal swabs for SARS-CoV-2 testing. To profile the immune response in the COVID-19 patients, we conducted RNA-sequencing assays using blood samples collected at day 0 and day 5 after enrollment.

first: Prasanna

last: Jagannathan

first: Kattria

last: van der Ploeg

first: Diego

last: Martinez Mori


title: Computational Repurposing of Bumetanide for Preventing or Treating Alzheimer’s Disease

first: Alice

last: Taubes

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Gene expression profiling during  treatment of HT29 cells with selumetinib

status: Public on Sep 12 2021

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

summary: Here, we investigate gene expression response of the BRAFV600E mutant cell line COLO205  to the MEK inhibitor selumetinib / AZD6244 / ARRY-142886.   Although selumetinib causes long term G1 arrest, we observe cells stochastically entering the cell cycle without re-activation of ERK and initiation of a normal proliferative gene expression programme.   Genes encoding DNA replication and repair factors are downregulated during G1 arrest, but many of these are transiently induced when cells escaping arrest enter S and G2.   Nonetheless, mRNAs encoding key DNA replication factors including the MCM replicative helicase complex, PCNA and TIPIN remain at very low abundance.

overall_design: 1) HT29 cells either untreated or treated 24 hours with 1 µM selumetinib were glyoxal fixed and stained for CCNB1 then flow sorted into CCNB1 positive and CCNB1 negative fractions, RNA extracted and mRNA-seq performed.

last: Channathodiyil

first: Anne

last: Segonds-Pichon

first: Paul

middle: D

last: Smith

first: Simon

middle: J

last: Cook

first: Jonathan

last: Houseley


title: Dissecting Super-enhancer driven Transcriptional Dependencies Reveals Novel Oncogenes and Therapeutic Strategies of Group 3 Subtype Medulloblastoma [RNA-seq]

overall_design: Group 3 subtype MB (G3-MB) cells MB002 and D425 were treated with BET inhibitor JQ1 and CDK7 inhibitor THZ1 followed by RNA-seq analysis to identify the transcriptome changes compared with DMSO (control group). Next, to unveil the oncogeneic mechanism of ARL4D, we knocked down ARL4D with two separate shRNA in MB002, then processed RNA-seq to identify the downstream genes of ARL4D. Finally, we tested the SHH subtype MB (SHH-MB) cell UW228 basic gene expression level with RNA-seq

first: Meng

last: Li

first: Chaochen

last: Wang

first: Wenfeng

last: Kang


title: Gene expression in human corneal epithelial cells without or with Wnk inhibitor

status: Public on Sep 08 2021

city: Québec

first: Gaëtan

last: Le-Bel

state: Quebec

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

country: Canada

institute: CUO-Recherche

summary:
In the present study, we investigated the molecular mechanisms by which Wnk contributes to human corneal epithelial wound healing. To better understand the process, we cultivated human corneal epithelial cells without or with Wnk inhibitor.
Using gene profiling, we compared the mRNA profiles of passage 3 human corneal epithelial cells cultivated without Wnk inhibitor with passage 3 human corneal epithelial cells cultivated with Wnk inhibitor. Human corneal epithelial cells are isolated from eye bank donor corneas.

overall_design: Three human corneal epithelial cell populations cultivated with Wnk inhibitor and two human corneal epithelial cell populations cultivated without Wnk inhibitor

first: Pascale

last: Desjardins

first: Sergio

last: Cortez Ghio

first: Lucie

last: Germain

first: Sylvain

last: Guérin


title: Host methylation predicts SARS-CoV-2 infection and clinical outcome

status: Public on Sep 20 2021

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado - Anschutz Medical Campus

summary: Genome-wide DNA methylation profiling of peripheral blood from 164 SARS-CoV-2 positive, 296 SARS-CoV-2 negative, and 65 other respiratory infection patient samples. Samples were profiled on a custom Illumina Infinium HumanMethylation BeadChip array including all MethylationEPIC-B4 probes and additional custom content targeting immune genes. SARS-CoV-2 positivity is defined by a positive RT-PCR test. "Other infection" samples are SARS-CoV-2 negative and were tested with a panel of common human acute respiratory infection pathogens.

overall_design: Bisulfite converted DNA from 525 samples were hybridised to a custom Illumina Infinium HumanMethylation BeadChip with the EPIC-B4 backbone and 7831 additional custom probes

first: Iain

middle: R

last: Konigsberg

first: Bret

last: Barnes

first: Kathleen

middle: C


title: microRNA expression signature of colorectal cancer

status: Public on Sep 06 2021

city: Kagoshima

first: Yuto

last: Hozaka

address: 8-35-1 Sakuragaoka

department: Digestive Surgery, Breast and Thyroid Surgery

country: Japan

institute: Kagoshima University

type: Non-coding RNA profiling by high throughput sequencing

summary: To elucidate novel aspects of the molecular pathogenesis of colorectal cancer (CRC), we have created a new microRNA (miRNA) expression signature based on RNA-sequencing. Analysis of the signature showed that 84 miRNAs were upregulated and 70 were downregulated in CRC tissues. Interestingly, our signature indicated that both guide and passenger strands of some miRNAs were significantly dysregulated in CRC tissues. In this analysis, we obtained between 11,432,618 and 19,286,983 total sequence reads. After the trimming procedure, we mapped them to the human genome and deter-mined that 3,018,259 to 16,436,280 sequences were small human RNAs.

overall_design: A total of 10 samples (5 CRC tissues and 5 noncancerous tumor-adjacent tissues) were analyzed using RNA sequencing techniques to generate a CRC miRNA signature.

first: Naohiko

last: Seki


title: Early anteroposterior regionalisation of human neural crest is shaped by a pro-mesodermal factor

status: Public on Sep 23 2021

city: Napoli

first: Ilaria

last: Granata

address: Via Pietro Catellino, 111

department: Institute for high performance computing and networking (ICAR)

country: Italy

institute: National Research Council of Italy (CNR)

summary: Undifferentiated human embryonic stem cells (hESCs) were treated with WNT and FGF agonists for three days to generate NMP-like axial progenitors (NMPs).

overall_design:
Triplicate samples of undifferentiated hESCs (TBXT NEGATIVE) and NMPs (TBXT POSITIVE) were harvested, pooled and analysed by ChiP-seq

We employed ATAC-seq to interrogate the chromatin accessibility landscape in neuromesodermal progenitor (NMP)-like cells and their derivatives, trunk neural crest and pre-neural spinal cord progenitors following differentiation of a human embryonic stem cell (hESC) line engineered to exhibit shRNA-mediated, tetracycline (Tet)-inducible knockdown of TBXT expression. hESCs were first differentiated towards NMPs (Day 3) and subsequently either trunk neural crest (tNC; upon culture in BMP/WNT agonists for 5 days) or pre-neural spinal cord progenitors (PNE; upon culture in WNT/high FGF for 4 days) in the presence (Pos) or absence (Neg) of Tetracycline.

first: Anestis

last: Tsakiridis


title: Influence of epigenetic modifications in Flt3-ITD induced AML

status: Public on Sep 02 2021

city: INDIANAPOLIS

first: Xiaoyu

last: Lu

state: IN

address: 410W 10TH ST

department: school of medicine

institute: INDIANA UNIVERSITY

summary: Gene expression analysis of mutations of WT, Tet2/FLT3, Dnmt3a/FLT3, and Dnmt3a/Tet2/FLT3 from bone marrow cells of mice to study regulation of AML in humans.

overall_design: Examination of RNASeq from four different genotype

first: Reuben

last: Kapur


title: HIGH-THROUGHPUT IDENTIFICATION OF RNA LOCALIZATION ELEMENTS REVEALS A REGULATORY ROLE FOR A/G RICH SEQUENCES

status: Public on Sep 03 2021

first: Matthew

last: Taliaferro

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

summary: Hundreds of RNAs are enriched in the projections of neuronal cells. For the vast majority of them, though, the sequences within them that regulate their localization are unknown. To identify RNA elements capable of directing transcripts to neurites, we designed and deployed a massively parallel reporter assay that tested the localization regulatory ability of thousands of sequence fragments drawn from endogenous 3′ UTRs. We identified peaks of regulatory activity within several 3′ UTRs and found that sequences derived from these peaks were both necessary and sufficient for RNA localization to neurites. These active localization elements were rich in adenosine and guanosine residues. They were also required to be dozens of nucleotides long as subsequences showed significantly reduced activity. Using RNA affinity and mass spectrometry, we found that the RNA-binding protein Unk was associated with the active localization elements. Depletion of Unk in cells reduced the neurite-enrichment of the active localization, indicating a functional requirement for Unk in their trafficking. These results provide a framework for the unbiased, high-throughput identification of RNA elements and mechanisms that govern transcript localization.

overall_design: Massively parallel reporter assay designed to identify sequences that regulate RNA transport in neuronal cells


title: Decoding A Gene Regulatory Network Behind Bronchopulmonary Dysplasia

status: Public on Aug 31 2021

city: Los Angeles

first: Fremont

last: Gao

state: California

address: 2011 Zonal Ave, HMR 903

institute: USC

summary: To know the transcriptomic gene expression of alveolar epithelium type 2 cells (AT2) from mouse lung at postnatal 14.

overall_design: Profiling of gene expression in GFP+ cells sorted from PN14 lungs dissected from Sftpc-GFP mouse by deep sequecing using Illumina HiSeq2500.

first: Changgong

last: Li

first: Parviz

last: Minoo


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type animal fed normal and high glucose diets at different age

city: Singapore

first: Guillaume

last: Thibault

address: 60 Nanyang Dr

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary: Metabolic diseases are strongly associated with endoplasmic reticulum (ER) stress. Upon ER stress, the unfolded protein response (UPR) is activated to limit cellular damage. However, escalating cellular UPR response weakens with age. Here, we show that 5-day-old Caenorhabditis elegans fed a bacteria diet with 2% glucose (high glucose diet, HGD-5) extend their lifespan while shortening the lifespan of 1-day-old (HGD-1) animals. We observed a metabolic shift in HGD-1 as glucose and fertility synergistically prolonged the lifespan of HGD-5, independently of DAF-16. Notably, we identified that UPR stress sensors ATF-6 and PEK-1 extended the longevity of HGD-5 worms, while the ire-1 ablation drastically increased HGD-1 lifespan. Based on these observations, we postulate that HGD activates the otherwise quiescent UPR in aged worms to overcome ageing-related stress and restore ER homeostasis. In contrast, young animals subjected to HGD provokes unresolved ER stress, conversely leading to a detrimental stress response.

overall_design: Wild type (WT, N2) C. elegans mRNA profiles of day 8 adulthood fed normal OP50 diet (ND) or supplemented with 2% glucose at day 1 (HGD-1) or day 5 (HGD-5) of adulthood

first: Celik

last: Cenk

first: Beaudoin-Chabot

last: Caroline

first: Thibault

last: Guillaume


title: From carrier to responder - few commensals restore immunocompetence in adult germfree mice via maturation of the intestinal vascular system

status: Public on Sep 09 2021

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

country: Germany

institute: University Medical Center Mainz

summary: The intestinal microbiota fundamentally influences the development of a normal intestinal physiology and education and functioning of the mucosal immune system. Using the C. rodentium carrier model of germfree mice (GF), we found that colonization of adult GF with 14 selected commensals (OMM12+MC2) was sufficient to convert a carriers into responders through maturation of intestinal crypts, increasing intestinal angiogenesis and stimulation of the immune system. While the immature colon of C. rodentium infected GF did not allow sufficient extravasation of neutrophils into the gut lumen, colonization with these commensals triggered activation and proliferation of endothelial cells, enabling granulocytes to transmigrate into the gut lumen. Enhanced angiogenesis and morphological maturation development of the intestine was most likely due to sensing of commensals by Paneth cells and subsequent secretion of antimicrobial peptides and angiogenetic factors. This demonstrates the therapeutic value of few commensal bacteria to complete morphological and immunological maturation in of the adult intestinal mucosa enabling rendering this organ immunocompetent against infections and responsive to therapies.

overall_design: Endothelial cells from germ free and conventional mice were analyzed for mRNA profiles

first: Rossana

last: Romero

first: Ulrich

last: Steinhoff

first: Wilhelm

last: Bertrams


title: Chromatin organizer SATB1 controls the cell identity of CD4+ CD8+ double-positive thymocytes by compacting super-enhancers

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

summary: CD4+ and CD8+ double-positive (DP) thymocytes are at a critical stage during the T cell development in thymus. DP cells rearrange the T cell receptor gene Tcra to generate T cell receptors with TCR. Then DP cells differentiate into CD4 or CD8 single-positive (SP) thymocytes, Regulatory T cells, or invariant nature kill T cells (iNKT) according to the TCR signal. Chromatin organizer SATB1 is highly expressed in DP cells and plays an essential role in regulating Tcra rearrangement and differentiation of DP cells. Here we explored the mechanism of SATB1 orchestrating gene expression in DP cells. Single-cell RNA sequencing assay of SATB1-deficient thymocytes showed that the cell identity of DP thymocytes was changed, and the genes specifically highly expressed in DP cells were down-regulated. ChIP-seq and ATAC-seq data showed the similar tendency. The super-enhancers regulate the expressions of the DP-specific genes, and the SATB1 deficiency reduced the super-enhancer activity. Hi-C data showed that interactions in super-enhancers and between super-enhancers and promoters decreased in SATB1 deficient thymocytes. We further explored the regulation mechanism of two SATB1-regulating genes, ETS2 and Bcl6, in DP cells and found that the knockout of the super-enhancers of these two genes impaired the development of DP cells. Our research reveals that SATB1 globally regulates super-enhancers of DP cells and promotes the establishment of DP cell identity, which helps understand the role of SATB1 in thymocyte development.

overall_design: scRNA-seq analysis of Satb1+/+ and Satb1-/- thymus;Bulk RNA-seq analysis of Satb1+/+ and Satb1-/- DP thymocytes(triplicates);H3K4me3 and H3K27me3 ChIP-seq analysis of Satb1+/+ and Satb1-/- DP thymocytes(duplicates);ATAC-seq analysis of Satb1+/+ and Satb1-/- DP thymocytes(duplicates);Hi-C analysis of Satb1+/+ and Satb1-/- DP thymocytes(duplicates);3C-HTGTS analysis of Satb1+/+ and Satb1-/- DP thymocytes (duplicates)using different baites(promoters of Bcl6 or Ets2);3C-HTGTS analysis of Bcl6SE +/+ and Bcl6SE-/- thymus at the baits of promoters from Bcl6;4C-seq analysis of Ets2SE +/+ and Ets2SE-/- thymus at the baits of promoters from Ets2(duplicates);5'RACE analysis of TCRA repertoire in Bcl6SE +/+ and Bcl6SE-/- thymus;5'RACE analysis of TCRA repertoire in Ets2SE +/+ and Ets2SE-/- thymus (duplicates).

first: Delong

last: Feng

first: Yanhong

last: Chen

first: Ranran

last: Dai

first: Wei

last: Xue

first: Shasha

last: Bian

first: Yongchang

last: Zhu

first: Zhaoqiang

first: Yiting

last: Yang

first: Yan

last: Zhang

first: Jiarui

first: Jie

last: Bai

first: Litao

last: Qin


title: RNA seq analysis of murine whole colon using Takara SMART-Seq Stranded kit. Libraries were sequenced on an Illumina NovaSeq 6000 to an approximate sequencing depth of 60 million total reads

status: Public on Aug 09 2021

city: Marburg

state: Hessen

address: Hans Meerwein Str. 2D

department: Institute of medical microbiology

institute: Philipps University Marburg

summary: The intestinal microbiota fundamentally influences the development of a normal intestinal physiology and education and functioning of the mucosal immune system. The goal of this study is to analyze how the transcriptional profile of the murine colon can be influence by colonization of gnotobiotic mice with specific bacterial strains .

overall_design: Whole colon RNA profiles of GF (Germ free), OMM12 (Oligo mouse microbiota 12), OMM12 + MC2 (Oligo mouse microbiota 12 + minimal consortium 2) and SPF (specific pathogen free) mice

first: Krishnaraj

last: Rajalingam

first: Kushal

last: Suryamohan


title: Comparative transcriptomic profiles in U-BIOPRED and Australian Newcastle severe asthma cohorts [biopsy]

status: Public on Jul 31 2021

city: New Lambton Heights

first: Stephany

last: Sanchez

state: NSW

address: Lot 1 Kookaburra Circuit

department: Respiratory and Sleep Medicine

country: Australia

institute: University of Newcastle

summary:
Severe asthma is a heterogeneous disease. Transcriptomic analysis contributes to understanding the driver mechanisms necessary for developing new therapies.
The aim of this study was to identify mechanistic pathways of severe asthma across two independent cohorts.

overall_design: This cross-sectional study examined transcriptomic data from endobronchial biopsies (n=73) and induced sputum (n=44) in an Australian Newcastle severe asthma cohort and the U-BIOPRED cohort.

last: Sánchez-Ovando

first: Stelios

last: Pavlidis

first: Nazanin

last: Zounemat Kermani

first: Katherine

last: Baines

first: Daniel

last: Barker

first: Ian

middle: M

last: Adcock

first: Kian

middle: F

last: Chung

first: Jodie

middle: L

last: Simpson

first: Peter

last: Wark


title: Comparative transcriptomic profiles in U-BIOPRED and Australian Newcastle severe asthma cohorts


title: Neuro-immune organoid model reveals a role of microglia in cell stress response and emergence of neural activity

status: Public on Jul 30 2021

first: Chang

last: Kim

address: 505 Parnassus Ave

institute: UCSF

summary:
Purpose: Many fundamental questions about microglia diversity and function during development remain unanswered as we lack experimental strategies to interrogate their interactions with other cell types and responses to perturbations ex vivo.
Methods: By using 10X Genomics scRNAseq, we generated transcriptomic data across different microglia models. Additionally, we performed microglia engraftment into cortical brain organoids and analyzed molecular changes in different cell types occurring in response to the presence of microglia.
Results: We compared human microglia states across culture models, including cultured primary microglia and pluripotent stem cell-derived microglia and developed a ‘report card’ of gene expression signatures differentially recruited and attenuated across these distinct experimental models.

overall_design: Single-cell RNA sequencing profliling of microglia transcriptional states in response to different in vitro model conditions

first: Galina

last: Popova

first: Tomasz

last: Nowakowski


title: Sex-specific transcriptome of spinal microglia in neuropathic pain due to peripheral nerve injury

status: Public on Jul 27 2021

city: Sydney

first: Gila

last: Moalem-Taylor

address: Wallace Wurth Building, Level 3, Room 355B

department: School of Medical Sciences

institute: University of New South Wales

summary: Neuropathic pain is a prevalent and debilitating chronic disease that is characterized by activation in glial cells in various pain-related regions within the central nervous system. Recent studies have suggested a sexually dimorphic role of microglia in the maintenance of neuropathic pain in rodents. Here, we utilized RNA sequencing analysis of microglia to identify whether there is a common neuropathic microglial signature and characterize the sex differences in microglia in pain-related regions in nerve injury and chemotherapy-induced peripheral neuropathy mouse models. Whilst mechanical allodynia and behavioral changes were observed in all models, transcriptomic analysis of microglia revealed no common transcriptional changes in spinal and supraspinal regions and in different neuropathic models. However, there was a substantial change in microglial gene expression within the ipsilateral lumbar spinal cord 7-days after chronic constriction injury (CCI) of the sciatic nerve. Both sexes upregulated genes associated with inflammation, phagosome, and lysosome activation, though males revealed a prominent global transcriptional shift not observed in female mice. This study demonstrates a lack of a common neuropathic microglial signature and indicates distinct sex differences in spinal microglia, suggesting they contribute to the sex-specific pain processing following nerve injury.

overall_design: RNA-seq of isolated microglia after chronic constriction injury or sham surgery (day 7) from male and female mice. Four blocks of CNS were run following CCI or Sham surgery ; (1) the ipsilateral (left) lumbar spinal cord (L3-L5); (2) the medial prefrontal cortex, hippocampus and amygdala; (3) posterior thalamus and S1 cortex relating to the hindlimb; and (4) the periaqueductal gray and rostroventral medulla.

first: Nathan

middle: T

last: Fiore

first: Zhuoran

last: Yin

first: Dilansu

last: Geneykaya

first: Christian

last: Gauthier

first: Jessica

middle: P

last: Hayes

first: Aaron

last: D'Hary

first: Oleg

last: Butovsky


title: RSC mediated nucleosome positioning and GRFs form barriers in promoters to limit divergent noncoding transcription

city: London

first: Folkert

last: van Werven

address: 1 Midland Road

institute: Francis Crick Institute

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

overall_design: Refer to individual Series


title: Comparative transcriptomic profiles in U-BIOPRED and Australian Newcastle severe asthma cohorts [sputum]

first: Stephany

last: Sanchez

last: Sánchez-Ovando

first: Stelios

last: Pavlidis

first: Nazanin

last: Zounemat Kermani

first: Katherine

last: Baines

first: Daniel

last: Barker


title: Multipolar zygotic divisions are characterized by parental genome segregation errors

status: Public on Aug 21 2021

city: Leuven

first: Joris

middle: R.

last: Vermeesch

address: Herestraat 49 box 606

department: Department of Human Genetics

country: Belgium

institute: KU Leuven

type: Genome variation profiling by genome tiling array

summary: The first mitotic division causes both parental genomes present in the zygote to segregate into two biparental diploid daughter cells. This fundamental tenet was challenged by the observation that blastomeres with different genome ploidy and distinct parental genotypes can coexist within individual embryos. We hypothesized that whole parental genomes can segregate into distinct blastomere lines during the multipolar division of the zygote, a phenomenon referred to as “heterogoneic” cell division. Here, we provide evidence of genome-wide segregation errors in two human blastocysts and further pinpoint its origin in a bovine model by mapping the genomic landscape of 82 blastomeres from 25 embryos that underwent multipolar division at the zygote stage using genome-wide SNP arrays and sequencing. In most embryos, the coexistence of androgenetic and diploid or polyploid blastomeres with or without anuclear blastomeres, androgenetic and anuclear blastomeres, and androgenetic and gynogenetic blastomeres within the same embryo provided proof that multipolar zygotic division coincides with heterogoneic segregation of the parental genome. By mapping the segregational origin of the genomic content, we deduced distinct segregation mechanisms underlying heterogoneic cell division including segregation by a tripolar spindle, the pronuclear extrusion of a paternal genome and, the operation of an ectopic paternal or private parental spindles. Polyspermic embryos expel excessive paternal genomes resulting in an androgenetic or polyploid blastomere. Confirming the results in human blastocysts we found genome-wide segregation errors to persist in bovine blastocysts.

overall_design: The genome-wide haplotype and copy number of a total of 146 bovine samples (82 blastomeres and two fragments isolated immediately upon time-lapse observation of multipolar division and 62 single cells derived from six dissociated blastocysts developing after multipolar division) belonging to 17 bovine pedigrees was determined to understand the origin and further development of mixoploid and/or chimeric embryos. The semen from three bulls was used for embryo production. Ovarian tissue samples from the donor cows (mothers), semen from the bull (father) or father of the bull (paternal grandparent) and blood of the mother of the bull (maternal grandparent) were used to extract bulk DNA (DNeasy Blood and Tissue kit, Qiagen, Germany). Ovaries were collected separately and retrieval of the oocytes was followed by routine in vitro embryo production. Single blastomeres and fragments were isolated immediately upon identification of a multipolar division by digestion of the zona pellucida with pronase and mechanical dissociation. Single cells derived from embryos that developed to the blastocyst stage following multipolar division were isolated by a zona pellucida digestion and subsequent trypsinization and mehchanical dissociation. All samples and sibling embryos were whole-genome amplified (WGA) using commercial multiple displacement amplification kit (Repli-G Single Cell kit, Qiagen, Germany). WGA products and bulk (grand)parental and sibling DNA were then SNP genotyped on BovineHD BeadChip arrays using Infinium HD whole-genome genotyping assay (Illumina Inc., USA). Subsequently, the SNP logR and SNP B-allele frequency (BAF) values, as well as the discrete SNP genotype calls were obtained for each single cell and applied in further single-cell analysis to obtain genome-wide haplarithm profiles using a modified version of the siCHILD algorithm (Zamani Esteki et al. 2015).

first: Tine

last: De Coster

first: Heleen

last: Masset

first: Olga

last: Tšuiko

first: Maaike

last: Catteeuw

first: Nicolas

last: Dierckxsens

first: Katrien

last: Smits

first: Ann

last: Van Soom


title: Macrophage-derived cholesterol contributes to therapeutic resistance in prostate cancer

status: Public on Jul 23 2021

city: Tampa

first: Chia-Ho

last: Cheng

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: Impact of macrophage depletion and/or lupron (androgen deprivation therapy) on transcriptome of murine TMPRSS2-ERG+ expressing prostate tumors.

overall_design: C57BL/6J mice were orthopically injected with 100,000  PTE-82 prostate cancer cells in 40 ul 1:1 PBS/Matrigel on Dec 2nd 2019. Indicated mice were randomized and treated with 0.6 mg Lupron / mouse on December 6th 2019.  Indicated mice were treated with with α-CSF1 (anti-CSF1) on December 11th and December 16th 2019. On day 17 post-tumor injection, mice bearing orthotopic prostate tumors were cardiac perfused with PBS (without heparin), following by resection of tumors and immediate freezing in liquid nitrogen. RNA from prostate tumor tissue was extracted using RNeasy® Plus Mini kit (Qiagen) according to manufacturer’s protocol with on-column DNase digestion and screened for quality on an Agilent Tape-Station (Agilent Technologies, Inc., Wilmington DE).

first: Brian

last: Ruffell

first: Xiaoqing

last: Yu

first: Asmaa

last: El-Kenawi


title: RNA-binding Mex3a promotes epithelial stemness and represses Klf4-dependent differentiation upon intestinal homeostasis, regeneration and cancer

status: Public on Jul 09 2021

city: Beijing

first: Yang

last: Xu

address: Beijing HaiDian District, Mingyuanxilu No.2

institute: China Agricultural University

summary: The precise control of the self-renewal and differentiation of intestinal stem cells (ISCs) is essential for intestinal homeostasis, efficient regeneration and prevention of tumorigenesis. However, the underlying molecular mechanisms remain only partially understood, especially in regeneration and cancer. Here, it is demonstrated that RNA-binding protein Mex3a is specifically expressed in ISCs and promotes their stemness and proliferative status. Its depletion results in compromised ISCs, impaired intestinal regeneration and suppressed oncogenic transformation. Mechanistically, upregulation of Mex3a in ISCs at homeostasis, in postirradiation regenerative foci and in colorectal cancer model is regulated by the upstream transcription factor E2f3. In turn, Mex3a activates Wnt signaling by directly suppressing pro-differentiation transcription factor Klf4 at the mRNA level. Furthermore, expression of E2F3 and MEX3A significantly increases in human radiation enteritis and colorectal carcinoma (CRC), accompanied by KLF4 downregulation and Wnt signaling hyperactivation. These findings indicate that the E2f3-Mex3a-Klf4-Wnt as the critical molecular switch between ISC self-renewal and differentiation. It can represent a putative therapeutic target for CRC and regeneration-related gut diseases.

overall_design: Intestinal crypt mRNA profiles of 8-week-old wild type (WT) and Mex3a-/- mice

first: Xu

last: Yang

first: Zhengquan


title: Genome-wide maps of MbovP475-binding sits in BoMac cells.

status: Public on Jul 14 2021

city: Wuhan

first: Gang

last: Zhao

address: sizhisan street 1

institute: huazhong agriculture university

summary: We used Next-generation sequencing (NGS) to reveal MbovP475-binding sites in BoMac cells.  We extracted the genome of BoMac infected with mycoplasma bovis by sonication, then the sheared chromatin in the supernatant was incubated with purified rabbit polyclonal IgG against MbovP475 and protein A/G magnetic beads. The DNA was eluted from the beads and subject to making sequencing library.  We totally got 2648 potential MbovP475-binding sites by ChIP-seq. Among them, CRYAB and MCF2L2 gene were further verifed to be down-reguated by MbovP475 through binding to the promoter region of two genes.

overall_design: Examination of MbovP475-binding sites in BoMac cells.

first: Aizhen

last: Guo


title: Integration of molecular inflammatory interactome analyses reveal dynamics of circulating cytokines and extracellular vesicle long non-coding RNAs and mRNAs in heroin addicts during acute and protracted withdrawal

status: Public on Jul 03 2021

first: Juehua

address: 615 Charles E. Young South BSRB 457

institute: UCLA

summary: Heroin addiction and withdrawal influence multiple physiological functions including immune responses, but the mechanism remains largely elusive. The objective of this study was to investigate the immune system function and molecular inflammatory interactome particularly the cytokines and RNA regulatory network in heroin addicts undergoing withdrawal compared healthy controls.

overall_design: a cross-sectional study


title: Human smooth muscle cells.

status: Public on Jul 07 2021

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

institute: Kyushu University

type: Methylation profiling by high throughput sequencing


title: RSC mediated nucleosome positioning and GRFs form barriers in promoters to limit divergent noncoding transcription [nascent RNA-Seq]

first: Folkert

last: van Werven

summary: The directionality of gene promoters, the proportion of protein coding over divergent noncoding transcription, is highly variable and regulated. How promoter directionality is controlled remains poorly understood. We show that chromatin remodelling complex RSC, general regulatory factors (GRFs) including transcription factors (TFs) can facilitate promoter directionality by attenuating divergent noncoding transcription. Depletion of RSC increased divergent noncoding and decreased protein coding transcription of promoters with strong directionality. Consistent with RSC’s role in regulating chromatin, RSC depletion negatively impacts nucleosome positions upstream of the nucleosome depleted region where divergent transcription initiates, suggesting that nucleosome positioning upstream in promoters physically blocks the recruitment of transcription machinery. Likewise, divergent transcription can be suppressed by targeting GRFs and TFs or the bulky dCas9 protein to transcriptional initiation sites. We propose that RSC mediated nucleosome positioning, GRFs including TFs form the physical barriers in promoters for limiting of divergent transcription, thereby controlling promoter directionality.

overall_design: Nascent RNA-Seq analysis of Saccharomyces cerevisiae. Rap1, Sth1 or Sth1/Rap1 (co) depleted cells were used for RNA-Seq libraries, respectively.

first: A

last: Wu

first: C

last: Vivori

first: H

last: Patel

first: T

last: Sideri

first: F


title: Scottish Colorectal Cancer Vitamin D Intervention Study (SCoViDS)

status: Public on Jun 23 2021

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

institute: University of Edinburgh, The Institute of Genetics and Cancer


title: ATAC-seq of mouse melanoma cells with micro-domain sAC expression

status: Public on Oct 11 2021

city: New York

first: Ashley

middle: Stephen

last: Doane

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

summary: Transcriptome sequencing of mouse melanoma cell lines containing micro-domain localized sAC under control of doxycycline.

overall_design: Three dox-inducible nuclear-sac cell lines with matched dox vs control, and 2 cell lines with lacz (no sac).


title: INTS13 Mutations Causing a Developmental Ciliopathy Disrupt Integrator Complex Assembly

status: Public on Jul 11 2021

city: Galveston

first: Nathan

middle: David

last: Elrod

state: TX

address: 1005 Strand Street

department: BMB

institute: University of Texas Medical Branch at Galveston

summary: Oral-facial-digital syndromes (OFD) are a heterogeneous group of congenital disorders characterized by malformations of the face and oral cavity, and digit anomalies. To date, mutations in 12 ciliary-related genes have been identified to cause several OFD types suggesting OFDs constitute a subgroup of developmental ciliopathies. Through homozygosity mapping and exome sequencing performed on two families with variable OFD type 2, we identified distinct germline mutations in INTS13, a subunit of the Integrator Complex. This 14-component complex associates with RNAPII and can cleave nascent RNA to modulate gene expression. We determined that INTS13 utilizes a discrete domain within its C-terminus to bind the Integrator cleavage module, which is disrupted by the identified germline INTS13 mutations.  Depletion of INTS13 disrupts ciliogenesis in human cultured cells and causes dysregulation of a broad collection of ciliary genes. Accordingly, its knockdown in Xenopus embryos lead to motile cilia anomalies. Altogether, we show that mutations in INTS13 cause an autosomal recessive ciliopathy, which reveal key interactions within Integrator components.

overall_design: Examination of 9 samples (3 biological replicate sets of ARPE-19 cells: control knockdown; IntS13 body targeting knockdown;  IntS13 utr targeting knockdown)

first: Lauren

middle: G

last: Mascibroda

first: Mohammad

last: Shboul

first: Laurence

last: Colleaux

first: Hanan

last: Hamamy

first: Kai-Lieh

last: Huang

first: Natoya

last: Peart

first: Moirangthem

middle: K

last: Singh

first: Hane

last: Lee

first: Barry

last: Merriman

first: Jeanne

middle: N

last: Jodoin

first: Laura

first: Raja

last: Fathalla

first: Baeth

last: Al-Rawashdeh

first: Osama

last: Ababneh

last: El-Khateeb

first: Nathalie

last: Escande-Beillard

first: Stanley

last: Nelson

first: Yixuan

first: Liang

last: Tong

first: Linda

last: Kenney

first: William

last: Russell

last: Amiel

first: Bruno

last: Reversade

first: Eric

last: Wagner


title: Cross breed RNASEQ analysis of cervical tissues in sheep

status: Public on Jul 08 2021

city: Dunsany

first: Paul

last: Cormican

address: Grange

department: Bioscience

country: Ireland

institute: Teagasc

summary: Aim to characterize the cervical transcriptome of four European ewe breeds with known differences in pregnancy rates following cervical AI using frozen-thawed semen.

overall_design: 115 samples were analyzed across 4 breeds and 2 phases (follicular and Luteal) and 2 cycle types (induced and natural)

last: Abril-Parreño


title: The transcriptome of rat hippocampal subfields

status: Public on Jun 30 2021

city: Campinas

first: Andre

last: Schwambach Vieira

state: SP

address: Rua Monteiro Lobato, 255 - Bloco J - 1 piso - Sala 3

country: Brazil

institute: State University of Campinas

summary:
Purpose: In this study, we used LCM and RNA-Seq to characterize differences in the rat hippocampal expression profiles of CA1, CA2, CA3, and DG subfields
Methods: Each subfield was bilaterally laser microdissected, collected from the rat's hippocampus (n=4), and submitted to Illuminas for massively parallel sequencing.
Results: We found evident segregation of the transcriptomic profile from different regions of the hippocampus. Gene ontology enrichment analysis of CA1 subfield results in actin regulation genes and postsynaptic membrane AMPA receptors that are indispensable for long-term potentiation and learning and memory. CA2 and CA3 transcripts were found associated with the higher metabolic processes. DG expression was enriched for ribosome and spliceosome, both required for protein synthesis and maintenance of cell life.
Conclusion: The present findings contribute to a deeper understanding of the differences in the molecular machinery expressed by the rat hippocampal neuronal populations, further exploring underlying mechanisms responsible for each subflied specific functions.

overall_design: Hippocampal subfield mRNA profiles of Wistar Rat

first: JoãoPaulo

last: Machado

first: Maria

last: Athie

first: Alexandre

middle: H

last: de Matos

first: Iscia

last: Lopes-Cendes

first: André

middle: S

last: Vieira


title: Specialisation and plasticity in a primitive social insect (Bisulfite-Seq)

status: Public on Jun 16 2021

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

institute: Altos Labs

summary: Biological systems not only have the remarkable capacity to build and maintain complex spatio-temporal structures in noisy environments, they can also rapidly break up and rebuild such structures. How such systems can simultaneously achieve both robust specialisation and plasticity is poorly understood. Here we use primitive societies of Polistes wasps as a model system where we experimentally perturb the social structure by removing the queen and follow the re-establishment of the social steady state over time. We combine a unique experimental strategy correlating time-resolved measurements across vastly different scales with a theoretical approach. We show that Polistes integrates antagonistic processes on multiple scales to distinguish between extrinsic and intrinsic perturbations and thereby achieve both robust specialisation and rapid plasticity. The long-term stability of the social structure relies on dynamic DNA methylation which controls transcriptional noise. Such dynamics provide a general principle of how both specialization and plasticity can be achieved in biological systems.

overall_design: All individuals from Polistes canadensis nests were collected from the area of Puta Galeta, Colon (9°21’30.877’’N, 79°54’0.0053’’W). Characterisation of individual brain methylome was performed using Bisulfite-sequencing. Individuals were collected under two conditions: 1/ Control (unmanipulated nests) and 2/Queen removal (queen was removed from the nest and individuals were collected 4-5 days after the emergence of a new queen).

first: Solenn

last: Patalano

first: Seirian

last: Sumner

first: Wolf

last: Reik

first: Steffen

last: Rulands


title: Effects of five developmental neurotoxicants on neuronal differentiation of human embryonic stem cell derived neural progenitors

status: Public on Jun 01 2021

city: Bilthoven

first: Victoria

last: de Leeuw

address: PO box 1

country: Netherlands

institute: National Institute for Public Health and the Environment

summary: Neuronal differentiation of human embryonic stem cells (hESC) is a promising tool to assess developmental neurotoxicity (DNT) in an animal-free manner. We analysed the transcriptomic profiles of hESC-derived neural progenitors (NPCs) and neuron-astrocyte co-cultures differentiated for 10 days from these same NPCs to identify the most dominant biological processes during neuronal differentiation. In addition, we exposed the NPCs for 10 days to five known or suspected neurodevelopmental toxicants: acrylamide, chlorpyrifos, fluoxetine, methyl mercury or valproic acid at non-cytotoxic (IC20/100) and slightly cytotoxic (IC5) levels. Each compound and concentration revealed unique transcriptomic changes that showed some of the known in vivo mechanisms of these compounds. This study provides evidence that this assay, the human neural progenitor test (hNPT) can be pivotal, together with other animal-free methods, to assess chemical-induced DNT in vitro.

overall_design: mRNA profiles of human stem cell (H9)-derived neural progenitor cells and differentiated neuron-astrocyte co-cultures (day 10), and neuron-astrocyte co-cultures that were exposed to five compounds at two concentrations. N=1 and n=8 for all experimental conditions.

first: Conny

last: van Oostrom

last: Wackers

first: Jeroen

last: Pennings

first: Hennie

last: Hodermaekers

first: Aldert

last: Piersma

first: Ellen

middle: V

last: Hessel


title: Genome-wide methylation analysis of murine innate lymphoid cells

status: Public on May 31 2021

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

summary:
Purpose: Identification of differentially methylated regions (DMRs) in murine innate lymphoid cells (ILC)
Methods: Numerous preparations of lymph node cells from mice were independently sorted by flow cytometry to isolate Natural killer (NK) cells, ILC1, ILC2, ILC3 and lymphoid tissue inducer (LTi) cells. Genomic DNA from the sorted, fixed cells was extracted using the NucleoSpin Tissue kit (Macherey-Nagel), including a crosslink removal step that was described recently (Kyburz et al., J Allergy Clin Immunol 143, 1496-1512 e1411 (2019)). The resulting single-stranded DNA was converted with bisulfite using the EZ DNA Methylation-Direct Kit (Zymo Research) and fragmented by sonication (Covaris S220, 10% duty cycle, 175W peak incident power, intensity 5, 200 cycles per burst, 120 seconds). The fragmented DNA served as input for the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences) and resulted in libraries that were sequenced on an Illumina NovaSeq 6000 . After quality control, trimming and mapping by using BSMAP, we identified differentially methylated regions by pairwise comparison of the samples by using metilene.
Results: The sequencing depth of our libraries varies between 210 and 282 million paired end reads. More than 98% of the murine CpG motifs were covered one time and 76% of the motifs at least five times. The pairwise comparison of the methylomes identified most of the differential methylated regions around the transcriptional start sites. Less differences were found between NK and ILC1 as well as between ILC3 and LTi cells. Among the DMRs showing meaningful differences we identified known demethylated regions in Tbx21, Ifng, Gata3, Il5 and Ccr6 as well as so far uncharacterized regions in Gpr18, Ptgir, Il22 or Il23r.
Conclusions: Here we report for the first time a genome-wide methylation study on ILC subpopulations that will help to understand development and function of these cells.

overall_design: Examination of murine NK cells, ILC1, ILC2, ILC3 and LTi cells from lymph nodes.

first: Chia-Wen

last: Lu

first: Matthias

last: Lochner

first: Stefan

last: Floess


title: RNA surveillance and the periphery: a novel role for nuclear envelope protein Lem2

city: Planegg

first: Sigurd

middle: J

last: Braun

address: Großhaderner Str. 9

department: BMC

institute: LMU

summary: Transcriptionally silent chromatin often localizes at the nuclear periphery, but whether post-transcriptional gene repression also occurs at the nuclear envelope (NE) remains unknown. Here we demonstrate that the NE protein Lem2 cooperates with the nuclear exosome in RNA degradation. Loss of Lem2 causes the accumulation of non-coding RNAs and meiotic transcripts. We demonstrate that an engineered exosome RNA substrate preferentially localizes at the nuclear periphery dependent on Lem2. While Lem2 itself does not bind RNA, it physically interacts with the exosome-targeting MTREC complex and promotes the recruitment of RNAs. This Lem2-dependent pathway acts separately from nuclear bodies into which exosome factors assemble, revealing the existence of multiple degradation pathways. We propose that Lem2 recruits exosome co-factors to the nuclear periphery to coordinate RNA surveillance and fine-tunes the transcriptional program during the switch from mitotic to meiotic growth.

overall_design: RNA sequencing of logaritmically growing cells

first: Lucía

last: Martín Caballero

first: Thomas

last: van Emden


title: Quantifying Biopolymer Sequence Recognition using Biophysically Informed Machine Learning

status: Public on Jun 02 2021

city: Merced

first: Hans

middle: Tomas

last: Rube

address: 5200 North Lake Rd.

department: Bioengineering

institute: UC Merced

summary: Quantifying sequence-specific protein-ligand interactions is critical for understanding and exploiting numerous cellular processes, including gene expression regulation and signal transduction. Given their importance, next-generation sequencing (NGS) based assays that characterize such recognition with high-throughput are increasingly being used to profile a range of protein classes and interactions. However, these methods do not measure the biophysical parameters that have long been used to uncover the quantitative rules underlying sequence recognition. We developed a highly flexible machine learning framework, called ProBound, to quantify sequence recognition in terms of biophysical parameters based on NGS data. ProBound quantifies transcription factor (TF) behavior with models that accurately predict binding affinity over a range exceeding that of previous resources, captures the impact of DNA modifications and conformational flexibility of multi-TF complexes, and infers specificity directly from \textit{in vivo} data such as ChIP-seq without peak calling. When coupled with a new assay called Kd-seq, it quantifies the absolute affinity of protein-ligand interactions. Its applicability extends beyond thermodynamic equilibrium binding, to the kinetics of kinase-substrate interactions. Altogether, ProBound provides a versatile algorithmic framework for understanding sequence recognition in a wide variety of biological contexts.

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: SELEX-seq was performed using the three homeodomain transcription factor Homothorax, Extradenticle and Ultrabithorax (Slattery, Cell, 2011). EpiSELEX-seq, generalize to assay 6mA and 5hMC modified DNA in addition to normal and meCpG, was performed for CEBPg and CEBPg together with ATF4 (Kribelbauer, Cell reports, 2017). K_D-seq was performed for Distal-less. Kinase-substrate sequencing was performed for SRC.

first: Harmen

last: Bussemaker

first: Richard

last: Mann

first: Neel

last: Shah

first: H


title: Scottish Colorectal Cancer Vitamin D Intervention Study (SCoViDS) [RNA-seq]

status: Public on Jun 22 2021

first: Graeme

last: Grimes

summary: Controversy surrounds whether vitamin D reduces colorectal cancer (CRC) risk, and/or beneficially impacts on CRC survival. We sought to delineate the transcriptomic in vivo response of human colorectal epithelium to vitamin D supplementation, define inter-subject variability and develop a predictive biomarker of response consistent with anti-tumour effects.  Methodology  Blood and rectal normal mucosa (NM) were sampled (176 subjects) and correlation sought between circulating vitamin D (25-OHD) level and NM gene expression (HT12 microarray) in the observational study. Oral vitamin D (3200IU/day) supplements were administered to 50 participants in an intervention study. Blood and NM (sigmoidoscopic biopsy) were sampled after 12 weeks. Transcriptomic analysis (HT12 and RNAseq) of post-treatment biopsies assessed enrichment for candidate genes and GO processes prioritised in the observational study. We identified transcriptomic changes in rectum that are consistent with anti-tumour responses. We then sought blood biomarkers predicting this response using receiver-operator curves and calculation of C-statistic. An independent expression dataset (BEST-D trial) was then used to validate candidate blood biomarkers of vitamin D response.

overall_design: 98 rectal biopsy from 49 Patient's  taken pre and post (12 weeks) oral vitamin D supplementation

middle: R

first: Peter

last: Vaughan-Shaw


title: Transcriptome-wide regulation of host m6A mRNA methylation by malaria parasite infection

status: Public on May 24 2021

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: N6-Methyladenosine (m6A) modification has been found to play important roles in diverse pathogen infections and host responses, here we report host m6A mRNA transcriptome profiles regulated by the infections of two strains of malaria parasite Plasmodium yoelii (N67 and N67C). We showed that malaria infection can regulate host m6A mRNA modification and reprogram host m6A mRNA methylome by mediating corresponding m6A catalytic enzyme levels. Our data suggested m6A modification as a significant transcriptome-wide mark during host-malaria interactions.

overall_design: m6A mRNA modifications were profiled in mice infected with two strains of malaria parasite Plasmodium yoelii (N67 and N67C) compared to noninfection control

first: Tao

last: Pan


title: Next generation expression analysis of murine innate lymphoid cells

summary:
Purpose: Characterization of murine innate lymphoid cells (ILC) by next generation expression analysis
Methods: Lymph node cells from Rorc(gt)-GFP reporter mice were independently sorted three times by flow cytometry to isolate ILC1, ILC2, ILC3 and lymphoid tissue inducer (LTi) cells. Subsequently RNA was prepared (Rneasy Micro Kit, Qiagen) and subjected to cDNA synthesis by using the SMART Seq v4 Ultra Low Input RNA Kit (Takara Bio) according to the manufacturer's protocol. Library preparation was performed with Nextera XT DNA Library Prep Kit (Illumina) and next generation sequencing was carried out on an Illumina HiSeq2500 using 50 bp single reads.  Adapter contamination were removed by trim_galore and cutadapt from the sequence reads that passed quality filters (Phred score > 30). Resulting libraries were aligned to the mouse reference genome (GRCm38) using the RNA-seq aligner STAR with default parametrization. Reads aligned to annotated genes were quantified with the HTseq-count program using gene annotations from Ensembl release 81. The determined read counts served as input to DESeq2 for pairwise detection and quantification of differential gene expression. For DESeq2 parametrization we used a beta prior and disabled the Cook distance cutoff filtering.
Results: The sequencing depth of our libraries varies between 25.5 and 39.2 million reads. The mapping rates for the libraries were found in the range between 93.9 and 98.0 %. Unsupervised hierarchical clustering of the top 50 differentially expressed genes show a close relationship of the samples within a group and higher similarity between ILC3 and LTi cells whereas ILC1 and ILC2 appear as separated populations. Among the differentially expressed genes we identified already described transcripts like Gzma (ILC1), Klrg1 (ILC2) and Il22 (ILC3, LTi) as well as uncharacterized genes that may play a role for the ILC lineage and function in lymphoid organs.
Conclusions: We report a detailed next generation transcriptome analysis of ILC populations from murine lymph nodes. Our analysis helps to define the developmental status of ILC in secondary lymphoid organs, which might represent a precursor state that can be further modulated in tissues.

overall_design: Examination of murine ILC1, ILC2, ILC3 and LTi cells from lymph nodes.


title: Different expression of microRNAs in human sepsis

status: Public on May 17 2021

city: Hohhot, Inner Mongolia

first: Jingping

last: Yang

address: Jinshan Development Zone

institute: Inner Mongolia Medical University

summary: To obtain novel biomarkers that serve as prompt indicators of sepsis, we aimed to screen out the differentially expressed miRNAs (DEMs) contribute to sepsis susceptibility and analyze the correlation of DEMs with inflammatory response. This case-control study included 40 sepsis patients and 40 physical examination donors as a control group. RNA-seq technology and bioinformatics analysis were used to screen out the DEMs between sepsis patients and normal people. The expression of these DEMs were subsequently verified by qRT-PCR. There were 305 DEMs (p<0. 05, |Fold change| ≥2) between sepsis and normal people were identified and top eighteen upregulated or downregulated miRNAs were picked out for QRT-PCR verification. Among them, 11 DEMs were high expression while 7 DEMs were low expression. Collectively, miRNA-3663-3p may be a potentially powerful diagnostic and predictive biomarker for sepsis.

overall_design:
This case-control study included 40 sepsis patients and 40 physical examination donors as a control group. RNA-seq technology and bioinformatics analysis were used to screen out the DEMs between sepsis patients and normal people. The expression of these DEMs were subsequently verified by qRT-PCR. In addition, interleukin-6 (IL-6), IL-21, CXCL-8, monocyte chemotactic protein-1 (MCP-1), and molecular determination of the expression levels of TDAG8 and TLR4 mRNA were assessed. Finally, the relationship between miRNA-3663-3p and pro-inflammatory cytokines secretion or TDAG8/TLR4 mRNA expression were evaluated by linear correlation analysis.
This dataset includes samples from 12 sepsis patients and 6 control donors.


title: RNA seq analysis in human smooth muscle cells.

first: Hiromitsu

last: Araki

summary: Macrophage-like cells derived from vascular smooth muscle cells (SMCs) play critical roles in atherogenesis, and TET2-mediated DNA hydroxymethylation was implicated to regulate the transdifferentiation. We examined transcriptomes and (hydroxy)methylomes of human coronary artery SMCs during cholesterol-induced transdifferentiation. A unique approach of gene ontology (GO)-centric clustering of differentially expressed genes exhaustively identified through all possible pairwise comparisons (pan-DEGs) revealed dynamic and multifaceted modulations of genes involved in extracellular matrix organization, angiogenesis, cell migration, hypoxia response, and cholesterol biosynthesis. Intriguingly, transient activation was observed for an immuno-metabolic circuit consisting of type I interferon response and cholesterol metabolism. We found neither global nor DEG-proximal change in (hydroxy)methylation. These datasets would serve as a unique resource to address the mechanisms underlying cholesterol-induced transdifferentiation of SMCs. Moreover, GO-centric clustering of pan-DEGs may provide a useful approach to interpret multifaceted transcriptomic alterations.

overall_design: We conducted a series of genome and epigenome analysis, including RNA-sequencing and  DNA methylation and hydroxymethylation status in human smooth muscle cells.

first: Kentaro

last: Inoue

first: Fumihito

last: Miura

first: Takashi

last: Ito


title: Specialisation and plasticity in a primitive social insect (RNA-seq)

first: Felix

last: Krueger

department: Bioinformatics

overall_design: All individuals from Polistes canadensis nests were collected from the area of Puta Galeta, Colon (9°21’30.877’’N, 79°54’0.0053’’W). Characterisation of individual brain transcriptome was performed using RNA-sequencing. Individuals were collected under three conditions: 1/ Control (unmanipulated nests), 2/Queen removal (early commitment) (queen was removed from the nest and individuals were collected 4-5 days after the emergence of a new queen) and 3/ Queen removal (late commitment) (queen was removed from the nest and individuals were collected 2 weeks after the emergence of a new queen).

first: Solenn

last: Patalano

first: Irene

last: Hernando-Herraez

first: Seirian

last: Sumner

first: Wolf

last: Reik

first: Steffen

last: Rulands


title: LncRNA Airn alleviates liver fibrosis and maintains LSECs differentiation via the KLF2-eNOS-sGC pathway

status: Public on May 11 2021

city: Tianjin

first: chen

last: ting

state: Tianjin

address: 22 Meteorological Tai Road, Heping District, Tianjin, China

department: School of Basic Medical Sciences

institute: Tianjin Medical University

summary: Long noncoding RNAs (lncRNAs) have emerged as important regulators in a variety of human diseases. It has been suggested that dysregulation of liver sinusoidal endothelial cells (LSECs) phenotype is a critical early event in the fibrotic process. However, the biological function of lncRNAs in LSECs still remains unclear. Here, we identified that lncRNA-Airn was significantly up-regulated in liver tissues and LSECs of CCl4-induced liver fibrosis. Moreover, the expression of AIRN in human cirrhotic liver tissues and serums was remarkably increased as compared with healthy controls. In vivo studies showed that Airn deficiency aggravated CCl4- and BDL-induced liver fibrosis, while Airn overexpression by adeno-associated viral vector serotype 8 vector alleviated CCl4-induced liver fibrosis. Furthermore, we revealed that Airn maintained LSECs differentiation in vivo and in vitro. Additionally, Airn inhibited hepatic stellate cells (HSCs) activation indirectly by regulating LSECs differentiation and promoted hepatocytes (HCs) proliferation by the increased paracrine secretion of Wnt2a and HGF from LSECs. Mechanistically, our results demonstrated that Airn maintained LSECs differentiation through KLF2-endothelial nitric oxide synthase (eNOS)-soluble guanylate cyclase (sGC) pathway, thereby promoting HSCs quiescence and HCs proliferation. In conclusion, our work identified that Airn is beneficial to liver fibrosis by maintaining LSECs differentiation and might be a novel serum biomarker for liver fibrogenesis.

overall_design: mRNA profiles of Primary LSECs  infected with two separated siAirn

first: Wei

last: Hong

last: Han

first: Kun

last: Zhang

first: Ting

last: Chen


title: Single cell RNA-sequencing reveals placenta cellular heterogeneity in adverse pregnancy

status: Public on May 04 2021

city: Changzhou

first: Yu

last: Bin

address: 16 Dingxiang Road, Changzhou City, Jiangsu Province

institute: Changzhou Maternal And Child Health Care Hospital

summary: The placenta is a highly heterogeneous organ and is closely related to adverse pregnancy. The previous bulk sequencing of whole tissue  could not show the characteristics of individual cells and the interactions between cells. Here, we select the placental tissues of the gestational diabetes group(GDM), preeclampsia group(PE), advanced age group(GL) and normal control group for single-cell sequencing in order to explain the mechanism of related diseases in more depth.nated spatial and temporal regulation of gene expression in the murine hindlimb determines the identity of mesenchymal progenitors and the development of diversity of musculoskeletal tissues they form. Hindlimb development has historically been studied with lineage tracing of individual genes selected a priori, or at the bulk tissue level, which does not allow for the determination of single cell transcriptional programs yielding mature cell types and tissues. To identify the cellular trajectories of lineage specification during limb bud development, we used single cell mRNA sequencing (scRNA-seq) to profile the developing murine hindlimb.

overall_design: 2 placenta samples from PE, GDM, the elderly group and the control group respectively.

first: Bin

last: Yu

first: Yuqi

first: Wenbo

last: Zhou


title: WNT5A Drives IL-6-Dependent Epithelial-to-Mesenchymal Transition via the JAK/STAT Pathway in Keloid Pathogenesis

status: Public on May 06 2021

city: Seoul

first: Young In

last: Lee

address: 50-1 Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei College of Medicine

summary:
Purpose: We aimed to identify the molecular drivers that initiate or sustain keloid pathogenesis.
Method: Bulk tissue RNA sequencing of Asian keloid and normal tissues was performed to identify genes that contribute to keloid pathogenesis. We also established a preclinical model of inflammatory skin fibrosis by injecting C57BL/6 mice with bleomycin intradermally for 3 weeks to provide an alternative animal model of keloid scar.
Result: Gene set enrichment analysis revealed upregulation of WNT5A gene expression, along with significant enrichment of genes related to EMT in keloid tissues. These results correlate with those of histological analysis in which human keloid tissues and the bleomycin-induced fibrosis animal model showed increased WNT5A expression along with EMT markers. Our in vitro data showed increased expression of the IL-6/JAK/STAT pathway and subsequent elevation in EMT markers on keratinocytes when co-cultured with WNT5A-activated fibroblasts or keloid fibroblasts. Silencing of WNT5A reversed the hyperactivation of the STAT pathway and EMT.
Conclusion: IL-6 secreted from WNT5A-activated fibroblasts or keloid fibroblasts may induce adjacent keratinocytes to express EMT markers by activating the JAK/STAT signalling pathway. A better understanding of keloid pathogenesis and the role of WNT5A in EMT will promote the development of next-generation targeted treatments for keloid scars.

overall_design: Bulk RNA sequencing for Asian keloid tissues vs. normal tissues

first: Young-In

first: Jung-Eun

last: Shim

first: Won-Jai

first: Ju-Hee


title: Lizard feeding enhances Ixodes pacificus vector competence

status: Public on Apr 27 2021

city: San Francisco

first: Seemay

last: Chou

address: 499 Illinois St, 4th Floor

institute: Chan Zuckerberg Biohub

summary: Ixodes pacificus, the vector of Borrelia burgdorferi (Bb) on the west coast, feeds on a variety of hosts including rodents, birds, and lizards. While rodents are reservoirs for Bb and can infect juvenile ticks, lizards are Bb-refractory. Despite the range of bloodmeals for I. pacificus, it is undetermined how larval host bloodmeal identity may affect future nymphal vector competence. Here, we conducted a transcriptome analysis on I. pacificus to determine whether and through what mechanisms host bloodmeal history affects vector competency of I. pacificus for the Lyme disease pathogen.

overall_design: We experimentally evaluated the influence of larval host bloodmeal on nymphal I. pacificus Bb acquisition. Larval I. pacificus were fed on either lizards or mice and after molting, nymphs were fed on Bb infected mice. To investigate mechanisms by which host blood meal may alter vector competency, we compared gene expression profiles for I. pacificus ticks following mouse or lizard larval blood meals by conducting the first RNA-seq analysis on whole-bodied I. pacificus nymphs.

first: Kacie

last: Ring

first: Lisa

last: Couper

first: Anne

last: Sapiro

first: Fauna

last: Yarza

first: Frank

last: Yang

first: Keith

last: Clay

first: Andrea

last: Swei


title: RNA sequencing of control and TBXT-depleted human NMP-like axial progenitors

status: Public on Sep 23 2021

city: Napoli

first: Ilaria

last: Granata

address: Via Pietro Catellino, 111

department: Institute for high performance computing and networking (ICAR)

institute: National Research Council of Italy (CNR)

summary: A Tetracycline (Tet)-inducible TBXT shRNA human embryonic stem cell (hESC) line was treated with WNT and FGF agonists in the presence and absence of Tet for three days to generate NMP-like axial progenitors

overall_design: Gene expression profiling utilised total RNA extracted from +/-Tet hESC-derived NMPs

first: Ichcha

last: Manipur

first: Anestis

last: Tsakiridis


title: A massively parallel reporter assay for RNA localization in neurons

status: Public on Apr 23 2021

city: Haifa

first: Martin

last: Mikl

address: Abba Khoushy 199

department: Department of Human Biology

country: Israel

institute: University of Haifa

summary: We performed a massively parallel reporter assay for RNA localization in two mouse neuronal cell lines, CAD and Neuro-2a. We transfected a library of around 50,000 different 3'UTR reporters (cloned downstream of GFP) into cells grown on transwell plates and collected soma and neurite fractions separately. RNA was extracted and cDNA synthesized, followed by targeted amplification of the reporter mRNA and Illumina sequencing.

overall_design: Amplicon sequencing of a 3'UTR reporter library in CAD and Neuro-2a, in cell bodies and neurites.

first: Andreas

last: Moor


title: TGF-β modulation of cell-cell and cell-extracellular matrix interactions in post-confluent corneal endothelial cells

status: Public on Apr 22 2021

city: Québec

first: Stéphanie

last: Proulx

state: Qc

address: 1050 Chemin Ste-Foy

institute: Université Laval

summary: We isolated healthy human corneal endothelial cells from EyeBank research-grade corneas. Passage 3 cells were grown to confluency and exposed to TGF-b2 for 7 days.

overall_design: Four populations of corneal endothelial cells were exposed (or not) to TGF-b2 for 7 days.

first: Sergio

middle: C

last: Ghio

first: Mathieu

last: Thériault

first: Kim

last: Santerre


title: siRNA knockdown of hnRNP K in human SH-SY5Y cells

status: Public on Mar 30 2021

city: London

first: Pietro

last: Fratta

address: Queen Square House

institute: University College London

summary: The RNA-binding protein hnRNP K was knocked down using siRNA in human SH-SY5Y. As a control, cells were treated with an siRNA against firefly luciferase.

overall_design: Three replicates of hnRNP K knockdown, three controls

first: Emanuele

last: Buratti

first: Jack

last: Humphrey


title: Specialisation and plasticity in a primitive social insect

first: Felix

last: Krueger

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of human regulatory (Treg) and effector (Teff) CD4+ memory T cells in the presence of oral cancer secretome versus not malignant secretome

status: Public on Apr 08 2021

city: Concepcion

first: Estefania

last: Nova-Lamperti

email: enova@udec.cl, enovalamperti@gmail.com

state: BioBio-Concepcion

address: Victor Lamas

department: Clinical Biochemistry and Immunology

country: Chile

institute: Universidad de Concepción

summary: The immune system plays a key role in the protective response against oral cancer; however, the tumour microenvironment (TME) is able to impair this anti-cancer response by modulating T helper (Th) responses and promoting an anti-inflammatory environment. Regulatory T cells (Tregs) and Th2 effector cells (Teff) have been associated with bad prognosis in oral squamous cell carcinoma (OSCC), however, it is unknown the main immunomodulatory mechanisms associated with the enrichment of these subsets in OSCC. We characterized Th-like lineages in Tregs and Teff and evaluated the main immunomodulatory changes induced by the TME in OSCC. Our phenotypic data revealed a higher distribution of tumour-infiltrating CCR8+ and Th2-like Treg in OSCC in comparison with non-malignant samples, whereas the percentages of Th1 cells were reduced in cancer. We then analyzed the direct effect of the TME by exposing T cell subsets to cancer secretomes and we observed that the OSCC secretome induced CCR8 expression and reduced cytokine production on both subsets. Transcriptomic analysis showed that the co-culture with OSCC secretome induced several gene changes associated with the vitamin D (VitD) signaling pathway in T cells. In addition, a proteomic analysis identified the presence of several proteins associated with prostaglandin E2 (PGE2) production by rapid membrane VitD signaling and an reduce presence of the VitD binding protein. Thus, we analyzed the effect of VitD and PGE2 and we observed that VitD promote a regulatory Th2-like responses and CCR8 expression, whereas PGE2 also modulate CCR8 but inhibited cytokine production in combination with VitD. Finally, we evaluated the presence of CCR8 ligand in OSCC and we observed higher presence of chemokine CCL18, which was also able to up regulate CCR8 in activated Th cells. Overall, our data showed that the immunomodulatory changes induced by the TME regarding CCR8 expression and regulatory Th2 phenotypes are associated with PGE2 mediated VitD signaling pathway and CCL18 expression in OSCC.

overall_design: Pre-activated human regulatory and effetor CD4+ memory T cells from healthy donors were co-cultured with OSCC and control (non-malignant oral tissue) secretomes for 48h a 37ºC. Cell were then lysed on Trizol before transcriptomic analysis.

first: Guillermo

last: Nourdin

first: Francisco

last: Alvarez

first: Felipe

last: Zuñiga

first: Mabel

last: Vidal


title: Host Immune Response to Clinical Hypervirulent Klebsiella pneumoniae Pulmonary Infections via Transcriptome Analysis

city: Chongqing

first: Jintao

last: Zou

state: China

address: Gaotanyanstreet

institute: Army Medical University

summary: Klebsiella pneumoniae is an arising threat to human health. However, host immune responses in response to this bacterium remain to be elucidated. The goal of this study was to identify the dominant host immune responses associated with Klebsiella pneumoniae pulmonary infection. Pulmonary mRNA profiles of 6-8-weeks-old BALB/c mice infected with/without Klebsiella pneumoniae were generated by deep sequencing using Illumina Novaseq 6000. qRT–PCR validation was performed using SYBR Green assays. Using KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, we identified several immune associated pathways, including complement and coagulation cascades, Toll-like receptor signaling pathway, Rap1 signaling pathway, chemokine signaling pathway, TNF signaling pathway, phagosome and NOD-like receptor signaling pathway, were involved in Klebsiella pneumoniae pulmonary infection. Using ICEPOP (Immune CEll POPulation) analysis, we found that several cell types were involved in the host immune response to Klebsiella pneumoniae pulmonary infection, including dendritic cells, macrophages, monocytes, NK (natural killer) cells, stromal cells. Further, IL-17 chemokines were significantly increased during Klebsiella pneumoniae infection. This study provided evidence for further studying the pathogenic mechanism of Klebsiella pneumoniae pneumonia infection.

overall_design: Lung mRNA profiles of 6-8 weeks old BALB/c mice infected with/without Klebsiella pneumoniae clinical strain YBQ

first: Langhuan

last: Lei

first: Jinyong

last: Zhang

first: Xingyong

last: Wang


title: Activation of cGAS-STING signal to inhibit the proliferation of bladder cancer: the immune effect of cisplatin

status: Public on Mar 31 2021

city: Hangzhou

first: Baiye

last: Jin

state: Zhejiang

address: Qinchun Road No.17

department: Urology

institute: Zhejiang University

summary: our findings indicated a cisplatin dependent cGAS-STING signal in bladder cancer. This signal could be enhanced by accumulation of dsDNA and chromatin dissociated cGAS and would finally recruit infiltration DCs and CD8+ T cells in bladder cancer bladder cancer tumor microenvironment. However, the specific role and effect of this signal towards bladder cancer tumor microenvironment need to be further clarified.

overall_design: Objective to identify the expression difference between bladder cell line T24 with or without cisplatin treatment

first: Guanghou

last: Fu


title: Transcriptome-Wide 2’-O-Methylation Mapping at Single-base Resolution by Nm-REP-seq

status: Public on Mar 25 2021

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

summary: 2’-O-methylation (Nm) is one of the most abundant RNA epigenetic modification and plays vital roles in the post-transcriptional regulation of gene expression. Current Nm mapping approaches are normally limited to highly abundant RNAs and have significant technical hurdles in mRNAs or relatively rare non-coding RNAs (ncRNAs). Here, we developed a new method for enriching Nm sites by using RNA exoribonuclease (M. genitalium RNase R, MgR) and periodate oxidation reactivity to eliminate 2’-hydroxylated (2’-OH) nucleosides, coupled with sequencing (Nm-REP-seq). We revealed several novel classes of Nm-containing ncRNAs as well as mRNAs in humans, mice, and drosophila. We found that some novel Nm sites are present at fixed positions in different tRNAs and are potential substrates of fibrillarin (FBL) methyltransferase mediated by snoRNAs. Importantly, we discovered, for the first time, that Nm located at the 3’-end of various types of ncRNAs and fragments derived from them. Our approach precisely redefines the genome-wide distribution of Nm and provides new technologies for functional studies of Nm-mediated gene regulation.

overall_design: Total RNA or polyA RNA was extracted from HEK293T cells and subjected to Nm-REP-seq library construction protocol, in three biological repeats (rep1, rep2 and rep3).

first: Ping

first: Bin

last: Li

first: Wujian

last: Zheng

first: Lifan

last: Chen

first: Shurong

last: Liu

first: Xiaoqin

first: Anrui

first: Jie

last: Zhou

first: Zhirong

first: Qiaojuan

last: Huang

first: Lianghu

last: Qu

first: Jianhua


title: Gene copy number variation profiling by microarray

status: Public on Mar 23 2021

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

institute: The Babraham Institute

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

summary: Here, we investigate focal amplification patterns in and around the BRAF locus in BRAFV600Emutant COLO205 cells that acquire resistance to the MEK inhibitor Sleumetinib / AZD6244 / ARRY-142886. We find that BRAF amplifications occur frequently in COLO205 cells during acquisition of selumetinib resistance and that BRAFamplifications pre-exist selumetinib treatment but occurs predominantly via de novo mutations

overall_design: Genomic DNA extracted from parental COLO205 cells and their selumetinib-resistant dervatives were profiled for gene copy number variation using Infinium CytoSNP 850K beadchip microarrays (Illumina)

first: Prasanna

last: Channathodiyil

first: Anne

last: Segonds-Pichon

first: Paul

middle: D

last: Smith

first: Simon

last: Cook

first: Jonathan

last: Houseley


title: RSC mediated nucleosome positioning and GRFs form barriers in promoters to limit divergent noncoding transcription [RNA-Seq]

status: Public on Jul 27 2021

first: Folkert

last: van Werven

address: 1 Midland Road

institute: Francis Crick Institute

summary: The directionality of gene promoters, the proportion of protein coding over divergent noncoding transcription, is highly variable and regulated. How promoter directionality is controlled remains poorly understood. We show that chromatin remodelling complex RSC, general regulatory factors (GRFs) including transcription factors (TFs) can facilitate promoter directionality by attenuating divergent noncoding transcription. Depletion of RSC increased divergent noncoding and decreased protein coding transcription of promoters with strong directionality. Consistent with RSC’s role in regulating chromatin, RSC depletion negatively impacts nucleosome positions upstream of the nucleosome depleted region where divergent transcription initiates, suggesting that nucleosome positioning upstream in promoters physically blocks the recruitment of transcription machinery. Likewise, divergent transcription can be suppressed by targeting GRFs and TFs or the bulky dCas9 protein to transcriptional initiation sites. We propose that RSC mediated nucleosome positioning, GRFs including TFs form the physical barriers in promoters for limiting of divergent transcription, thereby controlling promoter directionality.

overall_design: RNA-Seq analysis of Saccharomyces cerevisiae with spiked in S. pombe cells. Rap1, Sth1 or Sth1/Rap1 (co) depleted cells were used for RNA-Seq libraries, respectively.

first: A

last: Wu

first: C

last: Vivori

first: H

last: Patel

first: T

last: Sideri

first: F


title: Epigenome analysis of normal and cervical cancer with human papilloma virus type 16 or 18 positive

status: Public on Mar 26 2021

city: jiang su

first: Jing

state: su zhou

address: Industrial park

institute: suzhou university

type: Methylation profiling by genome tiling array

summary: The Illumina 850k Human DNA methylation EPIC BeadChip was used to obtain DNA methylation profiles across  approximately 850,000 CpGs in the formalin-fixed and paraffin-embedded tissue sections(FFPE). Samples included 3 normal samples without HPV and 6 cervical cancer samples (three HPV 16 positive,three HPV 18 positive).

overall_design: Bisulphite converted DNA from the 9 samples were hybridised to The Illumina 850k Human DNA methylation EPIC BeadChip

first: Yanyun

last: Ma

first: Chunxia

last: Wang

first: Meie

last: Zhao

first: Xiaofeng

last: Tang

first: Donghai

last: Li

first: Hongfang

first: Tuanjie

last: Che


title: Regional identity of human neural stem cells determines oncogenic responses to histone H3.3 mutants

status: Public on Mar 24 2021

city: Edinburgh

first: Ben

last: Southgate

address: Little France Dr

institute: University of Edinburgh


title: Gene expression profiling during  treatment of COLO205 cells with selumetinib

first: Laura

last: Biggins

summary: Here, we investigate gene expression response of the BRAFV600E mutant cell line COLO205  to the MEK inhibitor selumetinib / AZD6244 / ARRY-142886.   Although selumetinib causes long term G1 arrest, we observe cells stochastically entering the cell cycle without re-activation of ERK and initiation of a normal proliferative gene expression programme.   Genes encoding DNA replication and repair factors are downregulated during G1 arrest, but many of these are transiently induced when cells escaping arrest enter S and G2.   Nonetheless, mRNAs encoding key DNA replication factors including the MCM replicative helicase complex, PCNA and TIPIN remain at very low abundance.

overall_design: 1) An mRNA-seq timecourse of COLO205 cells across 48 hours selumetinib treatment. 2) COLO205 cells either untreated or treated 24 hours with 1 µM selumetinib were glyoxal fixed and stained for CCNB1 then flow sorted into CCNB1 positive and CCNB1 negative fractions, RNA extracted and mRNA-seq performed. Equivalent cell populations were pulsed for 4 hours with EdU, stained and sorted into EdU negative and positive cohorts that were then used for mRNA-seq.

first: Prasanna

last: Channathodiyil

first: Anne

first: Paul

first: Simon


title: Regional identity of human neural stem cells determines oncogenic responses to histone H3.3 mutants [RNA-Seq]

summary: Point mutations within the histone H3.3 are frequent in aggressive childhood brain tumours known as paediatric high-grade gliomas (pHGGs). Intriguingly, different mutations arise in discrete anatomical regions: H3.3-G34R within the forebrain and H3.3-K27M preferentially within the hindbrain. The reasons for this contrasting aetiology are unknown. By engineering human foetal neural stem cell cultures from distinct regions, we demonstrate here that cell-intrinsic regional identity provides differential responsiveness to each mutant that mirrors the origins of pHGGs. Focusing on H3.3-G34R, we find that the oncohistone supports proliferation of forebrain cells, while inducing a cytostatic response in the hindbrain. Mechanistically, H3.3-G34R does not impose widespread transcriptional or epigenetic changes, but impairs recruitment of ZMYND11, a transcriptional repressor of highly expressed genes. We therefore propose that H3.3-G34R promotes tumorigenesis by stabilising the expression of key progenitor genes and, thus, locking initiating forebrain cells into their preexisting immature state.

overall_design: Fresh human foetal CNS tissue was obtained following elective termination of pregnancy at 13.5, 15.0 and 19.3 weeks of gestational age (WGA) (specimens GCGR-NS13, GCGR-NS15 and GCGR-NS19, respectively). The regions of interest were dissected under a stereoscope in ice-cold PBS and one half was directly lysed in Qiagen RLT plus buffer for RNA extraction. NSCs lines were established from the respective second halves as previously described (Conti et al., 2005 PloS Biology). Engineered WT or G34R lines overexpressed v5-tagged wild-type or G34R-mutant H3.3. PP5W and PP5G lines were engineered to overexpress wild-type and G34R-mutant H3.3 in combination with PDGFRa overexpression and knockout of endogenous TP53 gene.

first: Raul

middle: B

last: Bressan

first: Benjamin

first: Carla

last: Blin

first: Kirsty

middle: M

last: Ferguson

first: Vivien

last: Grant

first: Neza

last: Alfazema

first: Jimi

last: Wills

first: Maria

middle: A

last: Marques-Torrejon

first: Gillian

last: Morrison

first: James

last: Ashmore

first: Faye

last: Robertson

first: Charles

last: Williams

first: Leanne

last: Bradley

first: Alex

last: von Kriegsheim

first: Richard

last: Anderson

last: Tomlinson

first: Steven

last: Pollard


title: Selumetinib

first: Laura

last: Biggins


title: A histological and transcriptional characterization of the pancreatic acinar tissue in type 1 diabetes

status: Public on Feb 19 2021

city: Uppsala

first: Anders

middle: Roger

last: Hedin

state: Uppland

address: Dag Hammarskjölds väg 20.

department: Clinical immunology

country: Sweden

institute: Uppsala University

summary: Despite reduced function and volume of the exocrine pancreas in type 1 diabetes, literature describing the histology and the molecular biological profile in this area is limited. Here, the density of acinar cells was examined adjacent to and at varying distances from islets and the transcriptome was analyzed on laser capture microdissected (LCM) tissue from organ donors with and without type 1 diabetes. We demonstrate preserved acinar nuclei density in type 1 diabetes and find no support of acinar atrophy in pancreata devoid of insulin. The density of acinar nuclei was unaltered in type 1 diabetes. Principal component analysis of the transcriptomes of acinar tissue extracted from various areas of the pancreas showed no apparent clustering based on disease status, and few differentially expressed genes were discovered. However, when performing GSEA, transcriptional alterations were present in the acinar tissue independently of the distance from islets. Two gene sets were enriched in all exocrine regions; Myc Targets V2 and Estrogen Response Early. The alteration of these is a possible link to the increased incidence of pancreatic cancer in type 1 diabetes. Taken together, these new data shed light on the pathogenesis of type 1 diabetes and its involvement of the entire pancreas.

overall_design: Transcriptome analysis of  7 type 1 diabetic donors and 8 matched non-diabetic control donors.

first: Louise

last: Granlund

first: Miriam

last: Wahlhütter

first: Peter

last: Seiron

first: Olle

last: Korsgren

first: Oskar

last: Skog

first: Marcus

last: Lundberg


title: Transcriptomic profiling of human corona virus (HCoV)-229E -infected human cells

status: Public on Mar 03 2021

city: Shoham

first: jasmine

last: Jacob

state: -Select-

address: haChevel 33

institute: Sheba Medical Center at Tel HaShomer

summary: Human coronaviruses (HCoVs) cause mild to severe respiratory infection. Most of the common cold illnesses are caused by one of four HCoVs, namely HCoV-229E, HCoV-NL63, HCoV-HKU1 and HCoV-OC43. Several studies have applied global transcriptomic methods to understand host responses to HCoV infection, with most studies focusing on the pandemic severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome CoV (MERS-CoV) and the newly emerging SARS-CoV-2. In this study, Next Generation Sequencing was used to gain new insights into cellular transcriptomic changes elicited by alphacoronavirus HCoV-229E. HCoV-229E-infected MRC5 cells showed marked downregulation of superpathway of cholesterol biosynthesis and eIF2 signaling pathways. Moreover, upregulation of cyclins, cell cycle control of chromosomal replication, and role of BRCA1 in DNA damage response, alongside downregulation of the cell cycle G1/S checkpoint, suggest that HCoV-229E favors S phase for viral infection. Intriguingly, more than 80% of key factors of cell innate immunity, interferon-stimulated genes (ISGs) and other transcripts of early antiviral response genes were downregulated early in HCoV-229E infection. This study will enhance our understanding of commonly circulating HCoVs and hopefully provide critical information about still-emerging coronaviruses.

overall_design: a 24-hour culture to 80-90% confluency, cells were infected with 0.01 multiplicity of infection (MOI) of HCoV-229E  virus. Total RNA was extracted at 0, 6, 24, 48 and 72 post-HCoV-229E infection. At each time point, three biological repeats were tested.

first: Nehemya

last: Friedman

first: Jasmine

last: Jacob-Hirsch

first: Yaron

last: Drori

first: Eyal

last: Eran

first: Nitzan

last: Kol

first: Omri

last: Nayshool

first: Ella

last: Mendelson

first: Gideon

last: Rechavi

first: Michal

last: Mandelboim


title: Synthetic spike-in controls enable sensitive and reproducible cell-free methylome interrogation

status: Public on Feb 16 2021

city: Toronto

first: Michael

last: Hoffman

state: ON

address: 101 College St.

department: Research

institute: Princess Margaret Cancer Centre

summary: Background.The cell-free methylated DNA immunoprecipitation-sequencing (cfMeDIP-seq) method, is adapted to work with low input DNA and with circulating cell-free DNA (cfDNA). This method allowsfor epigenetic profiling from liquid biopsy samples, providing potential information about tissue of origin. Similar to classical immunoprecipitation based enrichment protocols, interpretation requires a referenceor control to draw inference against a composite experimental baseline and against designed standards allowing for cross-experiment comparisons.  Methods.To meet the need for a reference control in cfMeDIP-seqexperiments, we designed spike-in controlsand integrated the use of unique molecular index (UMI) to adjust for polymerase chain reaction (PCR)bias, and immunoprecipitation bias caused by the fragment length, G+C content, and CpG density ofthe DNA fragments. This enables for absolute quantification of methylated DNA in picomoles, while retaining epigenomic information that allows for sensitive, tissue-specific detection as well as comparableresults between different experiments. We designed 54 DNA fragments with combinations of methylationstatus (methylated and unmethylated), fragment length in base pair (bp) (80 bp,160 bp,320 bp), G+C content (35%,50%,65%), and fraction of CpGs within a fragment (1/80 bp,1/40 bp,1/20 bp). We checked spike-in control DNA sequence to ensure they had no cross alignment to the human genome and minimized formation of secondary structures to avoid issues with amplification. We carried outcfMeDIP-seq on either solely spike-in DNA fragments, spike-in DNA added to sheared HCT116 genomic DNA or spike-inDNA added tocfDNAfrom acute myeloid leukemia (AML) samples to assess technical and biological biases, determine optimal amount of spike-in DNA required for an experiment and to assess batch effects,respectively.  Results. We show thatcfMeDIP-seqenriches for highly methylated regions, with less than 0.01%non-specific binding and preference to high G+C content and CpG fraction DNA fragments. The use of 0.01 ngof spike-in control DNA results in sufficient sequencing reads to adjust for variance due to fragment length,G+C content and CpG fraction without negatively impacting the number of sequencing reads generatedfor each sample. With known amount of each spike-in control, we generated a generalized linear modelthat can absolutely quantify molar amount from read counts while adjusting for fragment length, G+C content, and CpG fraction. Using our spike-in controls, we show that we can greatly mitigate batch effects,reducing batch associated variance in the data to ≤5%of the total variance.  Conclusions.The incorporation of spike-in controls allows for easier interpretation of data generated from cfMeDIP-seq and MeDIP-seq experiments when compared to relative read count. Through the use of  a generalized linear model tailored to each experiment, molar amount for each genomic region can becalculated, greatly mitigating both biological and technical biases in the data. We have created an Rpackage, spiky, to convert read counts to DNA picomoles while adjusting for fragment length, G+C contentand CpG fraction.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design:
Evaluation of the use of synthetic spike-in control DNA in cfMeDIP-seq experiments.

>>>Submitter states that raw data for all AML patient samples have been deposited at EGA under study accession EGAS00001005069<<<

first: Samantha

middle: L

last: Wilson

first: Shu

middle: Y

last: Shen

first: Daniel

last: De Carvalho