title: Clinical study of the effect of combined treatment of aspirin and zileuton on biomarkers of tobacco-related carcinogenesis in current smokers

city: Boston

first: Adam

last: Gower

state: MA

address: 72 East Concord Street, E632

department: Department of Medicine

institute: Boston University School of Medicine

summary:
A chemopreventive effect of aspirin (ASA) on lung cancer risk is supported by epidemiologic and preclinical studies. Zileuton, a 5-LOX inhibitor has single agent activity and adds to the activity of NSAIDs in preclinical models of tobacco carcinogenesis   We hypothesized that COX inhibitor + 5-LOX inhibitor may be more effective than placebo in modulating nasal epithelium gene signatures of tobacco exposure and lung cancer. We conducted a randomized, double-blinded study of low dose ASA plus zileuton vs. double placebo in current smokers to compare modulating effects on nasal epithelium gene expression and arachidonic acid (AA) metabolism. Sixty-three participants were randomized to combined treatment of ASA (81 mg QD) and zileuton (Zyflo CR) two 600 mg extended release tablets BID or placebo pills for 12 weeks. Combined ASA plus zileuton had minimal effects on nasal gene expression of nasal or bronchial gene expression signatures associated with smoking, lung cancer and chronic obstructive pulmonary disease but did favorably modulate a bronchial gene signature of squamous dysplasia. Combined ASA plus zileuton suppressed urinary leukotriene (LTE4) (change of 89.867±68.35 from baseline to 32.25±23.25, p <0.001), a surrogate of 5-LOX mediated AA metabolism but did not suppress urinary prostaglandin E2 metabolite (PGEM), a surrogate of cyclooxygenase-mediated AA metabolism.
In conclusion, combined COX and 5-LOX inhibition by combined low dose ASA with zileuton in smokers favorably modulated a bronchial squamous dysplasia gene expression signature in the nasal epithelium of current smokers but had minimal effects on other carcinogenesis gene signatures. This combination decreased 5-LOX but not COX-2 mediated AA metabolism. Nasal gene expression signature determination is a novel approach to biomarker analysis, giving an approximation of the pulmonary milieu without having to perform invasive tissue sampling.

overall_design: The study was a single center randomized, double-blinded, placebo controlled trial to determine the modulatory effects of combined treatment of ASA and zileuton on nasal epithelium gene expression and arachidonic acid metabolism in current smokers

first: Christopher

last: Husted

first: Jennifer

last: Beane


title: Ethanol-treated Lytechinus variegatus (sea urchin) embryos

status: Public on Jun 28 2022

first: Cynthia

last: Bradham

state: Massachusetts

address: 24 Cummington Mall

department: Biology

country: USA

institute: Boston University

type: Expression profiling by high throughput sequencing

summary: The effects of ethanol on developmental gene expression in sea urchins is compared to controls at three time points during gastrulation.

overall_design: Control and ethanol-treated sea urchin embryos at 15, 18, and 21 hpf.

first: Nahomie

last: Rodriguez-Sastre

first: Dakota

middle: Y

last: Hawkins

middle: A


title: Transcriptomic profile of reactive astrocytes induced by activation of the JAK2-STAT3 pathway in mouse striatal astrocytes

status: Public on Jun 29 2022

city: EVRY

first: céline

last: DERBOIS

state: essonne

address: 2 rue Gaston crémieux

country: France

institute: CEA/CNRGH

summary:
We analyzed the transcriptional profile of normal astrocytes and astrocytes made reactive by AAV gene transfer of a contitutive form of JAK2 (JAK2ca).
We show that activation of the JAK2-STAT3 pathway by JAK2ca induces significant transcriptional changes in astrocytes, recapitulating several molecular hallmarks of reactivity

overall_design: Total RNA was extracted from GFP+ astrocytes isolated by FACS from C57bl6 mice injected with an AAV targeting astrocytes and encoding GFP alone (controls, N=4) or JAK2ca and GFP (N=4, same total viral load). Non GFP+ cells (including microglia, neurons, oligodendrocytes, non infected astrocytes, called OTHER) were analyzed as  well, in 2 samples of the control group.

first: Lucile

last: Ben Haim

first: Céline

last: Derbois

first: Jean-François

last: Deleuze

first: Robert

last: Olaso

first: Carole

last: Escartin


title: Integrative Transcriptomics and Cell Systems Analyses Reveal Protective Pathways Controlled by Igfbp-3 in Anthracycline-Induced Cardiomyocyte Injury

city: Los Angeles

first: Junjie

last: Chen

state: California

address: 650 Charles E Young Dr

department: medicine

institute: UCLA

summary: Anthracyclines such as doxorubicin (Dox) are effective chemotherapeutic agents, however their use is hampered by subsequent cardiotoxicity risk. Our understanding of cardiomyocyte protective pathways activated following anthracycline-induced cardiotoxicity (AIC) remains incomplete. Insulin-like growth factor binding protein (IGFBP) 3 (Igfbp-3), the most abundant IGFBP family member in the circulation, is associated with effects on the metabolism, proliferation, and survival of various cells. Whereas Igfbp-3 is induced by Dox in the heart, its role in AIC is ill-defined. We investigated molecular mechanisms as well as systems-level transcriptomic consequences of manipulating Igfbp-3 in AIC using neonatal rat ventricular myocytes and human induced pluripotent stem cell-derived cardiomyocytes.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Igfbp-3 was overexpressed or silenced in neonatal rat ventricular myocytes (NRVM) and human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CM) by adenovirus or siRNA. In Dox treated conditions, cells were subject to 1uM Dox treatment for 24 hours. 2x150 bp sequencing strategy was adopted and an average of 55.5 million reads for each sample acquired. Raw reads were aligned to the rat (mRatBN7.2) or human (grch38) transcriptome by Salmon using default parameters.

first: René

middle: R

last: Sevag Packard


title: Consticted migration is associated with stable 3D genome structure differences in cancer cells (RNA-Seq)

city: Knoxville

first: Rosela

last: Golloshi

state: TN

address: 1311 Cumberland Avenue

department: Department of Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee Knoxville

summary: We investigated the effect of constricted migration (using transwell assays with 5-μm or 12-μm in diameter) on the organization of the 3D genome in melanoma cells.

overall_design: RNA-Seq was performed to investigate gene expression changes after constricted migration. This experiment was performed on all A375-sub-populations of cells and two biological replicates were performed for each condition.

last: Playter

first: Trevor

middle: F

last: Freeman

first: Priyojit

last: Das

first: Thomas

middle: I

last: Raines

first: Joshua

middle: H

last: Garretson

first: Delaney

last: Thurston

first: Rachel

middle: P

last: McCord


title: STING activation promotes robust immune response and NK cell- mediated tumor regression in glioblastoma models

first: Sean

last: Lawler

address: 75 Francis St

institute: Brigham and Women's Hospital

summary: Immunotherapy has had a tremendous impact on cancer treatment in the past decade, with hitherto unseen responses at advanced and metastatic stages of the disease. However, the aggressive brain tumor glioblastoma (GBM) is highly immunosuppressive and remains largely refractory to current immunotherapeutic approaches. The cGAS-STING cytoplasmic double stranded DNA (dsDNA) sensing pathway has emerged as a next-generation immunotherapy target with potent local immune stimulatory properties.   Here, we investigated the status of the STING pathway in GBM and the modulation of the brain tumor microenvironment (TME) with the STING agonist ADU-S100. Our data reveal the presence of STING in human GBM specimens, where it stains strongly in the tumor vasculature. We show that human GBM explants can respond to STING agonist treatment by secretion of inflammatory cytokines. In murine GBM models, we show a profound shift in the tumor immune landscape after STING agonist treatment, with massive infiltration of the tumor-bearing hemisphere with innate immune cells including inflammatory macrophages, neutrophils and NK populations. Treatment of established murine intracranial GL261 and CT-2A tumors by biodegradable ADU-S100-loaded intracranial implants demonstrated a significant increase in survival in both models and long-term survival with immune memory in GL261. Responses to treatment were abolished by NK cell depletion. This study reveals therapeutic potential and deep remodeling of the TME by STING activation in GBM and warrants the further examination of STING agonists alone or in combination with other immunotherapies such as cancer vaccines, CAR T cells, NK therapies or immune checkpoint blockade.

overall_design: Comparative gene expression with/without STING agonist treatment and isolation of the brain infiltrating leukocytes from GL261 implanted mice (tumor-bearing hemisphere at 72 h)

first: Gilles

last: Berger

first: Kwasi

last: Adu-Berchie

middle: E


title: The role of Dppa3 in mESC through RNA-seq

city: tianjin

first: wen

last: hang

address: tianjing city

country: China

institute: nankai university

summary: Distinct cell types emerge from embryonic stem cells through a precise and coordinated execution of gene expression programs during lineage commitment. This is established by the action of lineage specific transcription factors along with chromatin complexes. Numerous studies focused on epigenetic factors that affect ESC self-renewal and pluripotency. Through our laboratory's previous studies on ESCs pluripotency, we found that Dppa3, as a Naive state marker gene, is of great significance to the transformation of mESCs pluripotency. However, the influence of overexpression of Dppa3 in ESCs on mESCs status has not been determined. Our results show that overexpression of Dppa3 induces global DNA demethylation, which is beneficial to the maintenance of pluripotency, but its differentiation ability is significantly impaired. In mESCs, Dppa3 regulates mESCs pluripotency by inhibiting de novo methylation pathway, maintaining methylation pathway, promoting demethylation pathway Tet2, up-regulating active histone modification and down-regulating heterogeneous histone modification. The 2C-like state of ESCs recapitulates key aspects of the two-cell stage mouse embryo both phenotypically and molecular, which providing a cellular model to investigate the progress of ZGA. Our results found Dppa3 promote facilitate 2C-state conversion.

overall_design: Detection of Dppa3 function in embryonic stem cells

first: Chuanyu

last: Zhang

first: Hang

last: Wen

first: Siying

last: Liu

first: Lu

last: Yu


title: Mitochondrial protease Lonp1 localizes to the nucleus in response to heat shock

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

country: Italy

institute: University of Padova

summary: We analyzed the effects of Lonp1 silencing on the response to heat shock by analyzing the transriptomic profile of SW620 colon cancer cells undergoing heat shock. Briefly, Lonp1 has been silenced by using a specific siRNA, then cells have been kept at 42°C for 1 hour, and left at 37°C for one hour.

overall_design: RNAseq of SW620 cells undergoing heat shock after Lonp1 silencing.

first: Marcello

last: Pinti

first: Lara

last: Gibellini

first: Rebecca

last: Borella

first: Giada

last: Zanini


title: The DREAM complex antagonizes WDR5a and represses the productive elongation of transcription in Arabidopsis [GRO-seq]

city: Beijing

first: Yangyang

last: Fan

address: No.5 Yiheyuan Road Haidian District,

institute: Peking University

summary: The master transcriptional repressor DREAM (dimerization partner, RB-like, E2F and multi-vulval class B) complex regulates cell cycle in eukaryotes, but much remains unknown about how it transmits repressive signals on chromatin to the primary transcriptional machinery (e.g., Pol II). Through a genetic screen, we identified BTE1 (barrier of transcription elongation 1), a key component in the plant DREAM complex. The subsequent characterization demonstrated that the DREAM complex represses Pol II elongation. The core DREAM subunits E2F transcription factors recruit BTE1 to accumulate at the promoter-proximal regions of target genes. DREAM target genes exhibit characteristic enrichment of H2A.Z and H3K4me2 modification on chromatin. The DREAM complex BTE1 subunit interacts with WDR5a, repressing WDR5a chromatin binding and the productive elongation of transcription on BTE1-targeted genomic loci. Thus, we demonstrate a major role of DREAM complex in the control of transition from transcription initiation to productive elongation around TSSs on the open chromatin via inhibiting WDR5a function.

overall_design: Three biological replicates of each genotype were used for high-throughput sequencing analysis. All experiments wer conducted using  9-day-old seedlings grown in continuous white light.

first: Yuqiu

last: Wang

first: De

first: Xing

middle: W

last: Deng

first: Danmeng

last: Zhu


title: Identification of genes differentially expressed between breast cancer cell lines MCF7-TWIST1 and MCF7-Ctrl

city: Houston

first: Xiaobin

state: TX

address: One Baylor Plaza

department: MCB

institute: Baylor College of Medicine

summary: In this study, we aimed to characterize the stimulatory role of TWIST1 in breast cancer cell proliferation, EMT and metastasis, uncover the underlying molecular mechanism, and identify potential therapeutic targets for treating BLBC. RNA-Seq analysis were performed to identify differentially expressed genes influenced by TWIST1 overexpression in breast cancer cell MCF7. Pathway enrichment analysis and gene set enrichment analysis were performed to identify TWIST1-regulated signaling pathways, particually the cancer-associated pathways. ChIP-Seq analysis was further performed to identify TWIST1-associated genomic regions in MCF7-TWIST1 cells. The potential direct target genes of TWIST1 were identified by combined analysis of the gene expression profiling data and ChIP-Seq data.

overall_design: Gene expression profiles in breast cancer cell lines MCF7-TWIST1 and MCF7-Ctrl.

first: Jianming

last: Xu


title: Effect of formoterol and tumor necrosis factor (TNFα) alone and in combination on gene expression changes in human primary bronchial epithelial cells: a comparison with forskolin treatment

city: Calgary

first: Omar

last: Hamed

state: AB

address: 2500 University DR NW

department: Physiology and Pharmacology

country: Canada

institute: University of Calgary

summary: RNA sequencing was performed to study the genomic effects of formoterol, a long acting β2-adrenoceptor agonist, alone and in combination with the pro-inflammatory cytokine, TNFα in human primary bronchial epithelial cells, and to compare its effect to forskolin. Our results show that formoterol promoted a profound genomic response alone and on background of an inflammatory stimulus. Moreover, formoterol and forskolin regulated transcriptomes were highly rank order correlated which suggests that formoterol-mediated gene expression changes are cAMP dependent

overall_design: Human primary bronchial epithelial cells obtained by proteinase digestion of non-transplanted, normal airways of five lung donors obtained from a tissue retrieval service at the International Institute for the Advancement of Medicine (Edison, NJ, USA), were grown as monolayers in submersion culture. Confluent cells were cultured for 1, 2, 6 and 18 h with vehicle, TNFα (10 ng ml-1), formoterol (1 nM), TNFα and formoterol in combination or forskolin (10 µM). Total RNA was extracted, quantified, processed into mRNA libraries, and sequenced across five high-throughput sequencing kits on a NextSeq 500 instrument (Illumina).

first: Mark

last: Giembycz


title: The DREAM complex antagonizes WDR5a and represses the productive elongation of transcription in Arabidopsis [RNA-seq]


title: In vivo profiling of individual multi-ciliated cells during acute influenza A virus infection

status: Public on Jun 27 2022

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

summary: The breadth of responses to influenza infection in epithelial cells in vivo is understudied. We isolated ciliated cells, a target of influenza virus, at multiple timepoints following infection for scRNAseq analysis

overall_design: Mock, bystander, or infected ciliated cells were isolated from mice using FACs based on tdTomato and GFP expression

first: Cait

last: Hamele

first: Alistair

middle: B

last: Russell

middle: S


title: Nuclear Myosin 1 depletion leads to a metabolic reprogramming of cells and tumorigenesis in mice

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: Metabolic reprograming is one of the hallmarks of tumorigenesis. Using a combination of multi-omics, here we show that nuclear myosin 1 (NM1) serves a key regulator of cellular metabolism. As part of nutrient-sensing PI3K/Akt/mTOR pathway, NM1 forms a positive feedback loop with mTOR, and directly affects mitochondrial oxidative phosphorylation via transcriptional regulation of mitochondrial transcription factors TFAM and PGC1α. NM1 depletion leads to a suppression of PI3K/Akt/mTOR pathway, underdevelopment of mitochondria inner cristae and redistribution of mitochondria within a cell,  which is associated with reduced expression of oxidative phosphorylation genes, decreased mitochondrial DNA copy number, and deregulated mitochondrial dynamics. This leads to a metabolic reprogramming of NM1 KO cells from oxidative phosphorylation to aerobic glycolysis and with that associated metabolomic profile typical for cancer cells, namely, increased amino acid-, fatty acid-, and sugar metabolism, and increase in glucose uptake, lactate production and intracellular acidity. We show that NM1 KO cells are able to form solid tumors in a nude mouse model even though they have supressed PI3K/Akt/mTOR signalling pathway suggesting that the metabolic switch towards aerobic glycolysis provide a sufficient signal for carcinogenesis. We suggest that NM1 plays a key role as tumor suppressor and that NM1 depletion may be partly responsible for the Warburg effect at the early onset of tumorigenesis.

overall_design: RNA seq of NM1 KO mouse embryonic fibroblasts and slow- and fast-growing tumors derived from these cells

first: Tomas

last: Venit

first: Nizar

last: Drou


title: Overlapping transcriptional programs promote survival and axonal regeneration of injured retinal ganglion cells [1]

city: Cambridge

first: Wenjun

last: Yan

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

summary: Neurons of the central nervous system (CNS) display only a limited ability to survive and regenerate their axons after an injury. In mice, 85% of retinal ganglion cells (RGCs) die within 2 weeks of axotomy by optic nerve crush (ONC) and only few survivors regenerate axons. In the past years, a multitude of interventions have been identified to improve RGC survival and regeneration after an injury, however, each only protects a subset of neurons and stimulates axon regrowth in an even smaller set.. Here, we sought out to elucidate the molecular mechanisms underlying this selective responsiveness and investigated genes regulated by three well established survival and regeneration-promoting interventions – activation of the MTOR pathway via deletion of its inhibitor Pten, activation of the Jak/Stat-pathway by deletion of its endogenous inhibitor Socs3, and overexpression of the neurotrophic cytokine CNTF. Analysis of the transcriptomes from >125,000 single RGCs at various time points after ONC showed that while broad survival of all RGC types could be induced with each intervention, type-independent axon regeneration was only overcome with the manipulation of multiple pathways. Those RGCs were able to mitigate the injury response and simultaneously upregulated survival and regeneration associated programs (prior and after injury). Four independent ways of analysis identified these programs to be differentially regulated among RGCs, with distinct signatures for degenerating, surviving and regenerating cells. Finally, testing some genes associated with the regeneration-program in vivo identified potential future therapeutic targets to promote neuroprotection and axonal regeneration.

overall_design: In these experiments, we FACS sorted for retinal ganglion cells using a combination of a transgenic reporter (Thy1-YFP17) crossed with Pten fl/fl or Pten/Socs3 fl/fl mice and a surface protein (CD90) from dissociated retinas of adult (6-8 wk old) mice, including uninjured controls, and at 3 time points following optic nerve crush (2d, 7d, 21d).

first: Anne

last: Jacobi

middle: M

last: Tran

first: Inbal

last: Benhar

first: Feng

last: Tian

first: Rebecca

last: Schaffer

first: Zhigang

last: He

first: Joshua

last: Sanes


title: Assessing Radiation Therapy induced changes in Androgen Receptor Pathway activity using hK2-targeted PET imaging

city: New York

first: Benjamin

last: Glicksberg

state: NY

address: 1 Gustave Levy Place

department: Genetics and Genomics

institute: Icahn School of Medicine at Mt Sinai

summary: To investigate the effects of external beam radiation therapy on androgen receptor pathway transcriptomic expression in prostate cancer, we performed RNAseq on EBRT-treated LNCAP xenograft tumors.

overall_design: Gene expression was compared between untreated LNCAP tumors and EBRT-treated tumors using data from RNAsequencing.

first: Mesude

last: Bicak

first: Claire

last: Storey

first: David

last: Ulmert


title: Fate specification of GFAP-negative primitive neural stem cells and their progeny at clonal resolution

city: Toronto

first: Gary

last: Bader

state: Ontario

address: 160 College St

department: Molecular Genetics

institute: University of Toronto

summary: The mature brain contains an incredible number and diversity of cells that are produced and maintained by heterogeneous pools of neural stem cells. Two distinct types of neural stem cells (NSCs) exist in the developing and adult mouse brain: GFAP (Glial Fibrillary Acid Protein)-negative primitive (p)NSCs and downstream GFAP-positive definitive (d)NSCs. To better understand the embryonic functions of NSCs, we performed clonal lineage tracing within neurospheres grown from either pNSCs or dNSCs to enrich for their most immediate downstream neural progenitor cells (NPCs). These clonal progenitor lineage tracing data allowed us to construct a hierarchy of progenitor subtypes downstream of pNSCs and dNSCs that were then validated using single cell transcriptomics. Further, we identify Nexn as required for neuronal specification from neuron/astrocyte progenitor cells downstream of rare pNSCs. Combined, these data provide single cell resolution of NPC lineages downstream of rare pNSCs that likely would be missed from population level analyses in vivo.

overall_design: Primary neurospheres derived from forebrain lateral ventricles were grown in Leukemia Inhibitory Factor (LIF) to generate primitive Neural Stem Cells.  Neurospheres were dissociated and analysed by DropSeq snRNAseq.

first: Samantha

middle: Z

last: Yammine

first: Ian

last: Burns

first: Jessica

last: Gosio

first: Andrew

last: Peluso

first: Daniel

last: Merritt

first: Brendan

middle: T

last: Innes

middle: D

first: Cindi

last: Morshead

first: Derek

last: van der Kooy


title: The cross-talk between DNA damage, oxidative stress and epidermal barrier in keratinocytes after exposure to particulate matters and carbon black

city: Chengdu

first: Jie

last: Tang

state: Sichuan

address: No. 5, Gong Xing Road

institute: West China Hospital of Sichuan University

summary: To determine the main similarities and differences on health skin between the adverse effects of S1650b (PM2.5 simulant) and CB (nanoparticle) on DNA damage, oxidative stress and epidermal barrier in keratinocytes. RNA sequencing is used to study the DEGs, GO enrichment and KEGG pathway of keratinocytes exposed to S1650b and CB.

overall_design: Briefly, total RNA of HaCaT cells treated by CB (25 μg/mL) and S1650b (50 μg/mL) for 24 hours were extracted. Then, RNA sequence assay was performed.

first: Lidan

last: Xiong

first: Ping

last: Diao


title: Real-time quantitative PCR analysis of Clade A PP2C genes in Brassica juncea var. tumida of different tissues and under multiple stresses

city: Chongqing

first: Zhaoming

last: Cai

state: Fuling

address: Juxian Road NO. 16 Fuling

institute: Yangtze Normal University

summary: Clade A PP2C genes in different organs and responding to stresses were screened using qPCR. The BjuACTINs were regarded as house keeping gene.To analyze the gene expression patterns of clade A BjuPP2Cs genes under biotic stress, 14-day-old seedlings were treated with P. brassicae liquid (OD600=0.07) for 0, 0.25, 0.5, 1, 3, 5, 7, and 9 days; to analyze the gene expression patterns of clade A BjuPP2Cs genes under abiotic stresses, 5-day-old seedlings were treated with 50 μM ABA, 100 mM NaCl and 4℃ treatment for 3 h. To analysis the gene expression level in different growth stages of stem swelling, the samples D1 (the stems of 1-month-old seedlings, six leaf stage), D2 (the stems of 2-month-old seedlings, primary stage of stem swelling), D3 (the stems of 3-month-old seedlings, early stage of stem swelling), D4 (the stems of 4.5-month-old seedlings, fast-growing stage of stem swelling) and D5 (the stems of 5-month-old seedlings, last stage of stem swelling) of B. juncea var. tumida which were grown in the field were collected.

overall_design: The experiment was designed to gain insight into the temporal and spatial transcription patterns of 20 Clade A PP2C genes in tuber mustard.The experiment was designed to examine the transcription patterns of 20 Clade A PP2C genes in different organs and different stages of stem swollen, as well as response to 50 μM ABA, 100 mM NaCl and 4℃ treatment for 3 h, and response to the pathogen Plasmodiophora brassicae in different time points.

first: C

last: Cheng

first: Z


title: Chronic responses to direct Ras-targetted therapies

city: Liverpool

last: Prior

address: Crown Street

department: Molecular Physiology and Cell Signalling

country: United Kingdom

institute: University of Liverpool

summary: To investigate the response of H358 lung cancer cells to long term treatment with a panel of direct Ras and Ras pathway inhibitors. H358 cells harbour a heterozygous G12C mutation of KRAS.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for H358 cells + IC90 concentrations of each inhibitor or vehicle controls. 1 replicate of each.

first: Hannah

last: Warren


title: Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence [Cell line ChIP-Seq]

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

summary: In prostate cancer, androgen receptor (AR)-targeting agents are very effective in various stages of the disease. However, therapy resistance inevitably occurs and little is known about how tumor cells adapt to bypass AR suppression. Here, we performed integrative multi-omics analyses on tissues isolated before and after 3 months of AR-targeting enzalutamide monotherapy from high-risk prostate cancer patients enrolled in a neoadjuvant clinical trial. Transcriptomic analyses demonstrated that AR inhibition drove tumors towards a neuroendocrine-like disease state. In addition, epigenomic profiling revealed massive enzalutamide-induced reprogramming of pioneer factor FOXA1 – from inactive chromatin binding sites towards active cis-regulatory elements that dictate pro-survival signals. Notably, treatment-induced FOXA1 sites were enriched for the circadian rhythm core component ARNTL. Post-treatment ARNTL levels associated with poor outcome, and ARNTL suppression decreased cell growth in vitro. Our data highlight a remarkable cistromic plasticity of FOXA1 following AR-targeted therapy, and revealed an acquired dependency on circadian regulator ARNTL, a novel candidate therapeutic target.

overall_design: FOXA1 and ARNTL ChIP-seq data for prostate cancer cell line models.

first: Simon

last: Linder

first: Marlous

last: Hoogstraat

first: Andre

last: Bergman


title: Hyperactivation of Necdin, a new biomarker for Cockayne syndrome neurological disease

city: Guangzhou

first: Yuming

last: Wang

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

summary: To investigate the cooperative roles of CSB and NDN interaction in the regulation of neural function in vivo, we generated AAV constructs for the expression of shRNA-CSB or shRNA-NDN. We then delivered these viruses into the bilateral V1 region of mice cortex in which each target gene has been knocked down.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of mouse cortex V1 region, two female mice per genotype were used.

first: Fangkeng

last: Liang

first: Bijuan

last: Li

first: Yingying

last: Xu

first: Junwei

last: Gong

first: Shaohui

last: Zheng

first: Yunlong

last: Zhang


title: Potato psyllids mount distinct gut responses upon infection with each of the two ‘Candidatus Liberibacter solanacearum’ haplotypes

city: Hangzhou

first: Xiaotian

last: Tang

state: Zhejiang

address: Agro-Bio-Environ Building, Zhejiang University

department: Entomology

institute: Zhejiang University

summary: The global transcriptional responses of the adult potato psyllid gut upon infection of the two Candidatus Liberibacter solanacearum (Lso) haplotypes using Illumina sequencing

overall_design: Examination of the responses of the adult potato psyllid gut upon infection of the two Lso haplotypes, using RNA-seq

first: Cecilia

last: Tamborindeguy


title: Transcriptomic analysis of undifferentiated hESC, hESC -derived cell populations and human Embryonic Liver (EL) cell populations.

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

summary: RNA microarrays technology  was used to compare hESC-derived cell populations to undifferentiated hESC and to human EL cell populations. Microarrays confirmed the hematoendothelial, endothelial and hematopoietic identity of hPSC-derived CD144+-EBs, BCs and ECs, respectively, and the similarities between hESC-derived cell populations and human EL equivalent populations.

overall_design: hPSC-EC, hPSC-CD144+EB, hPSC-BC and hPSC CD144+CD45+BC were derived from undifferentiated hESC (H1). Endo 144+45-34+, Endo-Hemato 144+45low34+, Hemato 144-45low34+, Hemato 144-45high34- cell populations were freshly isolated from human EL. Undifferentiated hESC (H1), hESC-derived cell populations and EL cell populations were lysed and RNA was extracted of each sample. RNA was quantified and qualified after purification and same quantity of RNA was used for each sample for microarray analyses.

first: Estelle

last: Oberlin

first: Sebastien

last: Jacques

first: Morgane

last: Legall


title: Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence [Tissue RNA-Seq]

first: Wilbert

last: Zwart

overall_design:
RNA-seq data for primary prostate carcinomas before and after neoadjuvant enzalutamide therapy. The raw sequencing data cannot be stored with GEO due to patient privacy and was uploaded to the European Genome/Phenome Archive (EGAS00001006016).
For tissue ChIP-seq and RNA-seq, the raw sequencing data cannot be stored with GEO due to patient privacy and had to be uploaded to the European Genome/Phenome Archive (ChIP-seq: EGAS00001006017, RNA-seq: EGAS00001006016).


title: The functional roles of ANG,  RNASE1, and AGO2 in the biogenesis and stablization regualtion of cellular and extracellular tDRs

city: Boston

first: Guoping

address: Cardiovascular Research Center, 185 Cambridge St, Simches 3.5000

department: CVRC

institute: Massachusetts General Hospital

summary: The cellular response to stress is an important determinant of disease pathogenesis. Uncovering the molecular fingerprints of distinct stress responses may identify novel biomarkers and key signaling pathways for different diseases. Emerging evidence shows that tRNA-derived small RNAs (tDRs) play pivotal roles in stress responses. However, the RNA modifications on tDRs have been obstacles for accurately identifying tDRs with conventional RNA sequencing.  Here, we use AlkB-facilitated methylation sequencing (ARM-seq) to uncover a comprehensive landscape of cellular and extracellular tDR expression in various cells during different stress responses. We find that extracellular tDRs have a distinct fragmentation signature from intracellular tDRs and these tDR signatures are better discriminators of different stress responses than miRNAs. The distinct extracellular tDR fragmentation pattern and signatures are also noted in plasma from patients on cardiopulmonary bypass. Most importantly, we demonstrate that ANG and RNASE1 critically contribute to the stress-modulated cellular and extracellular tDR signatures and we identify a sub population of extracellular tDRs that are either transported or stabilized by AGO2. Together, our findings further the knowledge about tDR biogenesis in both cells and extracellular environments in response to different stressors and position extracellular tDRs as reliable candidates for novel biomarkers in human diseases.

overall_design: Cellular and extracellular tDRs expression profiles of ANG knockout, RNASE1 knockout, and AGO2 knockout HEK cells with different stress treatments (3 independent replicates for each condition)

first: Aidan

last: Manning

first: Alex

last: Bagi

first: Xinyu

last: Yang

first: Jonathan

last: Howard

first: Patricia

last: Chan

first: Thadryan

last: Sweeney

first: Brice

last: Laurent

first: Haobo

first: Maria

last: Kontaridis

first: Louise

middle: C

first: Kendall

last: Van Keuren-Jensen

first: Jochen

last: Muehlschlegel

first: Robert

last: Kitchen

first: Todd

last: Lowe

first: Saumya

last: Das


title: Effect of anti-osteoporotic treatments on circulating and bone microRNA patterns in osteopenic ZDF ratsEffect of anti-osteoporotic treatments on circulating and bone microRNA patterns in osteopenic ZDF rats

city: Wien

first: Andreas

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

type: Non-coding RNA profiling by high throughput sequencing

summary: We studied microRNA expression levels from serum and ulna bone in an in vivo model of type II diabetes (ZDF rats) by investigating different anti-osteoporotic treatments (anti-sclerostin, PTH and insulin). Serum and ulna bone RNA were extracted and subject to small RNA sequencing on an Illumina NextSeq550 SR75 High using 75bp, single end reads. After mapping against Rnor.6.0 provided by Ensembl and miRBase v22.1 differential expression analysis was undertaken with edgeRv3.32 using a quasi-likelihood negative binomial generalized log-linear model. We identified a panel of altered small non-coding RNAs.

overall_design: Examination of small non-coding RNAs in serum and ulna bone samples of ZDF rats under different anti-osteoporostic treatments using pairwise comparisons.

first: David

last: Vázquez

first: Matthias

last: Hackl

first: Martina

last: Rauner

first: Marianne

last: Pultar


title: Single-cell and bulk RNA-seq of human tumor-benign prostate adenocarinoma samples

city: Innsbruck

first: Georgios

last: Fotakis

state: Tyrol

address: Innrain 80-82

department: Bioinformatics

institute: Medical University Innsbruck

summary: Here we performed a detailed characterization of prostate cancer (PCa) tumor endothelial cells (TEC) in order to delineate intercellular crosstalk between TEC and the TME.

overall_design: TEC from PCa patients were studied by multi-omic ex vivo characterization and orthogonal validation of TEC functions and key markers by immunohistochemistry (IHC) and immunofluorescence (IF). In order to identify targetable cell-cell interactions in TEC, we used single cell RNA sequencing (scRNAseq) to catalogue cell types in the TME. Targtes were cross validated either by publicly available dataset or by a xenograft mouse model.

first: Isabel

last: Heidegger

last: Pircher

first: Asma

last: Noureen

first: Anne

last: Krogsdam

first: Jermaine

last: Goveia

first: Christina

last: Plattner


title: Changes of miRNA expression profile after avian reovirus infection

city: Beijing

first: Linyi

last: Zhou

address: No. 2, Yuanmingyuan West Road, Haidian District, Beijing, China

institute: China Agricultural University

summary: We infected DF-1 cells with avian reovirus, and then used high-throughput sequencing to detect changes in miRNA expression profiles. This research provides a more comprehensive understanding of the interaction between viruses and host cells

overall_design: Examination of the expression changes of miRNA before and after virus infection.


title: Gene expression in Day-8 equine embryos from young nulliparous mares

city: PALAISEAU

first: Emilie

last: Derisoud

state: Essonne

address: 26 Rue des Prés,

institute: INRAE

summary: The aim of the global study was to compare the effects of maternal age and parity on gene expression of equine embryos. For that, 17 embryos were collected at 8 days post ovulation (expanded blastocyst stage) from 3 groups of young or old nulliparous or multiparous mares: 6 from young nulliparous mares (5 or 6 year-old, never foaled before), 5 from young multiparous mares (6 year-old and foaled at least once) and 6 from old multiparous (10-16 year-old and foaled at least once).  Embryos collected were cut in 2 parts: one hemi-embryo containing pure trophoblast and the other one containing trophoblast + inner cell mass. ARN extractions were performed for all samples using PicoPure RNA isolation kit (Applied Biosystem). Five nanograms of both parts of each embryo were sequenced in paired-end with a length of 30-50bp separately using Illumina NextSeq 500 High. Data were trimmed using Cutadapt. Sequences with less than 10bp were removed.   Data for young and old multiparous mares had been already published in [accession: GSE162893; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE162893]. Only data for embryos collected from young nulliparous mares are deposited here

overall_design: 6 embryos cut in ICM and TE parts analyzed according to maternal parity (Nulliparous or multiparous mares)

first: Luc

last: Jouneau

first: Cédric

last: Dubois

first: Catherine

last: Archilla

first: Yann

last: Jaszczyszyn

first: Rachel

last: Legendre

first: Nathalie

last: Daniel

last: Peynot

first: Michele

last: Dahirel

first: Laurence

last: Wimel

first: Véronique

last: Duranthon

first: Pascale

last: Chavatte-Palmer


title: Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence

first: Wilbert

last: Zwart

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: Cellular and extracellular tRNA-derived fragments demonstrate distinct signatures in cellular stress

first: Guoping

last: Li

state: MA

summary: The cellular response to stress is an important determinant of disease pathogenesis. Uncovering the molecular fingerprints of distinct stress responses may yield novel biomarkers for different diseases, and potentially identify key signaling pathways important for disease progression . tRNA and tRNA-derived small RNAs (tDRs) comprise one of the most abundant RNA species in cells and have been associated with cellular stress responses. However, systematic characterization of tDRs have been challenged by the technical difficulties in accurately profiling tDRs with normal small RNA sequencing techniques due to the presence of RNA modifications.  Here we use AlkB-facilitated methylation sequencing (ARM-seq) to uncover a comprehensive landscape of cellular and extracellular tDRs expression in a variety of human and rat cells during common stress responses, including nutrition deprivation, hypoxia, and oxidative stress. We found that extracellular tDRs have a distinct fragmentation signature with a predominant length of 31-33 nts and a highly specific termination position when compared with intracellular tDRs, and comprise signatures that improve discrimination of different cellular stress responses compared to extracellular miRNAs. Distinct extracellular tDR signatures for each profiled stressor are elucidated in 4 different types of cells. This distinct extracellular tDR fragmentation pattern is also noted in plasma extracellular RNA from patients on cardiopulmonary bypass with significant overlap with the signatures of  nutrition depravation and oxidative stress in our cellular models, providing preliminary in vivo correlation of our findings. Future application of our findings to human disease models may have promise in yielding novel biomarkers.

overall_design: Cellular and extracellular tDRs expression profiles of 4 cell types under 4 different treatments (3 independent replicates for each condition)

first: Aidan

last: Manning

first: Alex

last: Bagi

first: Xinyu

last: Yang

first: Jonathan

last: Howard

first: Patricia

last: Chan

first: Thadryan

last: Sweeney

first: Brice

last: Laurent

first: Haobo

first: Maria

last: Kontaridis

first: Louise

first: Kendall

last: Van Keuren-Jensen

first: Jochen

last: Muehlschlegel

first: Robert

last: Kitchen

first: Todd

last: Lowe

first: Saumya

last: Das


title: Genome binding/occuoancy profiling by high throughout sequencing in Wild Type and ID1/3 double knockout hESCs

first: Haibin

last: Jiang

address: Dongdan Santiao 5#

institute: Peking Union Medical College

summary: TCF3 belongs to E protein family and has the function of transcription factor. TCF3 can directly interact with HLH family proteins ID1 and ID3 to play biological functions. ID1 and ID3 do not have the ability to directly bind to DNA and need to be regulated by TCF3. We found changes in pluripotency in ID1 and ID3 double knockout lines of human ESC, so we suspected that ID1 / 3 played a regulatory role through TCF3. Therefore, TCF3 ChIP-seq was done in WT and KO lines, hoping to find the downstream genes regulated by ID1 / 3 through TCF3, and then regulate hESC pluripotency through these genes.

overall_design: TCF3 ChIP-seq in Wild Type and ID1/3 KO hESCs

first: Jia

last: Lei

first: Jun


title: Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence [Tissue ChIP-Seq]

first: Wilbert

last: Zwart

overall_design:
AR, FOXA1 and H3K27ac ChIP-seq data on primary prostate carcinomas before and after neoadjuvant enzalutamide therapy. The raw sequencing data cannot be stored with GEO due to patient privacy and was uploaded to the European Genome/Phenome Archive (EGAS00001006017).
For tissue ChIP-seq and RNA-seq, the raw sequencing data cannot be stored with GEO due to patient privacy and had to be uploaded to the European Genome/Phenome Archive (ChIP-seq: EGAS00001006017, RNA-seq: EGAS00001006016).

first: Simon

last: Linder

first: Marlous

last: Hoogstraat

first: Andre

last: Bergman


title: Profiling of Gata2 binding in primary erythroid cells by CUT&RUN

city: Oxford

last: Beagrie

address: Headley Way

department: Molecular Haematology Unit

institute: MRC Weatherall Institute of Molecular Medicine

summary: The chromatin landscape of developing erythroblasts changes dramatically during differentiation. We have profiled the change in Gata2 binding in primary erythroid cells entering terminal differentiation using CUT&RUN.

overall_design: This series contains CUT&RUN datasets for Gata2 binding in FACS sorted primary erythroid cells. There are multiple biological replicates for each progenitor population, plus IgG control datasets.

first: Douglas

last: Higgs


title: Profiling of Gata1 binding in primary erythroid cells by CUT&RUN

summary: The chromatin landscape of developing erythroblasts changes dramatically during differentiation. We have profiled the change in Gata1 binding in primary erythroid cells entering terminal differentiation using CUT&RUN.

overall_design: This series contains CUT&RUN datasets for Gata1 binding in FACS sorted primary erythroid cells. There are multiple biological replicates for each progenitor population, plus IgG control datasets.


title: DNA damage-induced transcription stress triggers the genome-wide degradation of promoter-paused Pol II

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: The precise regulation of RNA Polymerase II (Pol II) transcription after genotoxic stress is crucial for proper execution of the DNA damage-induced stress response. While stalling of Pol II on transcription-blocking lesions (TBLs) blocks transcript elongation and initiates DNA repair in cis, TBLs additionally elicit a response in trans that regulates transcription genome-wide. Here we uncover that after an initial elongation block in cis, TBLs trigger the genome-wide VCP-mediated proteasomal degradation of promoter-paused Pol II in trans. This degradation is mechanistically distinct from processing of TBL-stalled Pol II, is signaled via GSK3, and contributes to the TBL-induced transcription block, even in transcription-coupled repair-deficient cells. Thus, our data reveal the targeted degradation of promoter-bound Pol II as an important new component of the transcription stress response that enables the genome-wide adaptation of transcription to genotoxic stress.

overall_design: Pol2 ChIP-seq upon different treatments

last: Steurer

first: Ritwick

last: Sawarkar

first: Jurgen

last: Marteijn


title: Genome-wide measurement of LPS-induced Poly(A) tail length changes in macrophage cells

city: Ithaca

first: Andrew

last: Grimson

state: New York

address: Biotechnology building, 526 campus road,  room 445

department: Molecular biology and genetics

institute: Cornell University

summary: We applied  Tail-end-displacement sequencing (TED-seq) for high-throughput profiling of poly(A) tail length dynamics induced by LPS stimulation in macrophage cells. We generate a time-course poly(A) tail length profiles in PMA-differentated THP-1 cells upon LPS stimulation (unstimulated, and post-stimulation 1, 2, and 4 h). This approach enabled us to profile induced poly(A) tail length dynamics with high accuracy and with 3´isoform resolution, generating  a comprehensive view of poly(A) tail length dynamics induced upon an environmental signal in post-embryonic systems, and its biological implications.

overall_design: Examination of nascent RNA synthesis, poly(A) tail lengths and mRNA levels with 3´UTR isoform resolution in PMA-differentiated THP-1 cells before and after LPS stimulation time-course. This study consists of 24 libraries generated from 2 bioreplicates per condition (0, 1, 2, and 4 hours upon LPS) for PRO-seq, TED-seq, and 3′-seq, respectively.

first: Yeonui

last: Kwak

first: Hojoong


title: iTag labelling of Liver, Plasma and VsWAT RNA

city: Munich

first: Raffaele

last: Teperino

address: Ingolstaedter Landstrasse 1

department: IEG

institute: Helmoltz Munich

summary:
Using a novel method for metabolic labelling of RNA called iTag RNA we
isolate hepatocytes' and kidney proximal epithelial cells'
transcriptional response to a dietary challenge and identify
multiple hepatocyte-secreted small ccfRNAs in plasma,
and transfer of these hepatic derived ccfRNAs to VsWAT

overall_design: mRNA /small RNA sequencing from liver plasma and kidney of male 12 week old mice following 2w of high fat diet feeding or low fat diet control

first: Teperino

last: Raffaele


title: H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination [RNA-seq]

first: Falong

last: Lu

address: 1 West Beichen Road Chaoyang District

institute: Institute of Genetics and Developmental Biology

summary: DNA methylation and histone lysine tri-methylation at H3K27 (H3K27me3) are the two primary epigenetic marks for transcriptional silencing essential for cell fate determination and cell lineage commitment during development1, 2. These two marks are mutually exclusive and target distinct sets of genes in the mammalian genome3. However, whether and how H3K27me3 shapes the DNA methylome remains unknown. Here, we report that the loss of H3K27me3 modification leads to increased DNA methylation at previously marked H3K27me3 sites, revealing that H3K27me3 negatively regulates DNA methylation. Genome-wide analysis of H3 ubiquitination, essential for recruitment and activation of DNA methyltransferase DNMT14, reveals the absence of H3 ubiquitination at H3K27me3 marked nucleosomes. Moreover, loss of H3K27me3 modification induces an increase in H3K18 ubiquitination at the corresponding hypermethylated loci. Importantly, we show that H3K27me3 directly inhibits UHRF1-mediated H3 ubiquitination toward nucleosomes in a defined biochemical assay. Furthermore, UHRF1 is required for the increase in DNA methylation at previously marked H3K27me3 sites in cells with abolished H3K27me3 modification. Taken together, our findings reveal a general mechanism for H3K27me3-mediated shaping of the mammalian DNA methylome via modulation of H3 ubiquitination.

overall_design: We performed WGBS (whole genome bisulfite sequencing) in WT HeLa cell, SUZ12 KO HeLa cell (two replications), WT E14 cell, Suz12 KO E14 cell, Uhrf1 KO E14 cell, Suz12/Uhrf1 double KO E14 cell. We mapped H3K27me3 ChIP-seq and H3K27me3 ChIP-BS-seq(chromatin immunoprecipitation bisulfite sequencing) in WT HeLa cell. We did RNA-seq in WT and SUZ12 KO HeLa cell (two replications). H3K18ub ChIP-seq in WT HeLa cell, SUZ12 KO HeLa cell, WT E14 cell and Uhrf1 KO E14 cell were also performed.

first: H

last: Zhang

first: Y

last: Liu

last: Zhu

last: Xie

first: J

first: F


title: Piperlongumine (PL) conjugates induce targeted protein degradation

status: Public on Jun 26 2022

city: Gainesville

first: Dongwen

last: Lyu

state: FL

address: Basic Science Building, BG-003F, 1345 Center Drive

institute: UF

summary: PROteolysis Targeting Chimeras (PROTACs) are bifunctional molecules that degrade target proteins through recruiting E3 ligases. However, their application is limited in part because few E3 ligases can be recruited by known E3 ligase ligands. In this study, we identified piperlongumine (PL), a natural product, as a covalent E3 ligase recruiter, which induces CDK9 degradation when it is conjugated with SNS032, a CDK9 inhibitor. The lead conjugate 955 can potently degrade CDK9 in a ubiquitin-proteasome-dependent manner and is much more potent than SNS-032 against various tumor cells in vitro. Mechanistically, we identified KEAP1 as the E3 ligase recruited by 955 to degrade CDK9 through a TurboID-based proteomics study, which was further confirmed by KEAP1 knockout and the nanoBRET ternary complex formation assay. In addition, PL-Ceritinib conjugate can degrade EML4-ALK fusion oncoprotein, suggesting that PL may have a broader application as a covalent E3 ligase ligand in targeted protein degradation.

overall_design: To evaluate the anti-cancer efficacy and the specificity of 955, RNA-seq was performed to compare 955 with its warhead SNS-032 in MOLT4 cells.

last: Lv


title: Expression profile of shMCT-1 in 4T1 metastatic murine triple-negative breast cancer (TNBC) cell lines

status: Public on Jun 25 2022

city: Zhunan

first: Hsin-Ling

last: Hsu

state: Miaoli

address: 35 Keyan Road

department: Institute of Molecular and Genomic Medicine

country: Taiwan

institute: National Health Research Institutes

summary:
MCT-1 (malignant T cell amplified sequence) is an oncoprotein encoded by Mcts1 gene that regulates translation re-initiation, ribosomal recycling, and tumorigenicity. We have characterized the metastasis cascade, immune evasion,and inflammatory responses which are suppressed by silencing of MCT-1 (shMCT-1) through transcriptional profiling of the 4T1 metastatic TNBC cell line.
shMCT-1-altered gene lists are related to the IFNα-response, IFNγ-response, IL-6/JAK/STAT pathway, inflammatory response. shMCT-1 also suppresses expression of upstream regulators of PD-L1  and epidermal growth factor receptor (EGFR) ligands as compared to scramble cells.

overall_design: Samples include two independent biological replicates of the scramble cells (negative control or NC) and MCT-1 silencing (shMCT-1) cells in 4T1 metastatic murine TNBC cells.

first: Aushia

last: Al-Haq


title: Detection of methylation of genomic DNA from lung cancer and correlated nornal tissue

first: Di

last: Wu

address: No. 268, Kaixuan Road

summary: To research the relationship between methylation of genomic DNA and lung cancer, lung cancer and correlated normal tissue were used to extract genomic DNA, followed with detection of methylation.

overall_design: One sample was used which provided both normal lung and tumor tissue.


title: Adamantinomatous craniopharyngioma   cyst fluid can trigger inflammatory activation   of microglia to damage the hypothalamic   neurons by inducing the production   of β-amyloid

first: Yilamujiang

last: Ainiwan

address: No. 1838, Guangzhou North Road

department: Neurosurgery

institute: Southern Medical University , Nanfang Hospital

summary: Introduction: The mechanism by which adamantinomatous craniopharyngioma (ACP) damages the hypothalamus   is still unclear. Cyst fuid rich in lipids and infammatory factors is a characteristic pathological manifestation of ACP   and may play a very important role in hypothalamic injury caused by tumors.  Objective: The objective of this study was to construct a reliable animal model of ACP cyst fuid-induced hypotha lamic injury and explore the specifc mechanism of hypothalamic injury caused by cyst fuid.  Methods: An animal model was established by injecting human ACP cyst fuid into the bilateral hypothalamus   of mice. ScRNA-seq was performed on the mice hypothalamus and on an ACP sample to obtain a complete gene   expression profle for analysis. Data verifcation was performed through pathological means.  Results: ACP cystic fuid caused growth retardation and an increased obesity index in mice, afected the expres sion of the Npy, Fgfr2, Rnpc3, Sst, and Pcsk1n genes that regulate growth and energy metabolism in hypothalamic   neurons, and enhanced the cellular interaction of Agrp–Mc3r. ACP cystic fuid signifcantly caused infammatory   activation of hypothalamic microglia. The cellular interaction of CD74–APP is signifcantly strengthened between   infammatory activated microglia and hypothalamic neurons. Beta-amyloid, a marker of neurodegenerative diseases,   was deposited in the ACP tumor tissues and in the hypothalamus of mice injected with ACP cyst fuid.  Conclusion: In this study, a novel animal model of ACP cystic fuid-hypothalamic injury was established. For the frst   time, it was found that ACP cystic fuid can trigger infammatory activation of microglia to damage the hypothalamus,   which may be related to the upregulation of the CD74–APP interaction and deposition of β-amyloid, implying that   there may be a similar mechanism between ACP cystic fuid damage to the hypothalamus and neurodegenerative   diseases.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 1 case of mouse hypothalamus injected with human ACP cystic fluid,1 case of mouse hypothalamus injected with PBS,1 case of human ACP tumor tissue were used for scRNA-seq

first: Yiguang

last: Chen

first: Chaofu

last: Mao

first: Jun

last: Pan


title: Simultaneous multifunctional transcriptome engineering by CRISPR RNA scaffold

city: Farmington

first: Paul

last: Robson

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory For Genomic Medicine

summary: RNA processing and metabolism are subjected to precise regulation in the cell to ensure integrity and functions of RNA. Though targeted RNA engineering has become feasible with the discovery and engineering of the CRISPR-Cas13 system, simultaneous modulation of different RNA processing steps remains unavailable. In addition, the off-target events resulting from the effectors fused with dCas13 limit its application. Here we developed a novel platform, Combinatorial RNA Engineering via Scaffold Tagged gRNA (CREST), which can simultaneously execute multiple RNA modulation functions on different RNA targets. In CREST, RNA scaffolds are appended to the 3’ end of Cas13 gRNA and their cognate RNA binding proteins are fused with enzymatic domains for manipulation. We show that CREST is capable of simultaneously manipulating RNA alternative splicing and A-to-G or C-to-U base editing. Furthermore, by fusing two split fragments of the deaminase domain of ADAR2 to dCas13 and PUFc respectively, we reconstituted its enzyme activity at target sites. This split design can reduce more than 90% of off-target events otherwise induced by a full-length effector. The flexibility of the CREST framework will enrich the transcriptome engineering toolbox for the study of RNA biology and the development of RNA-focused therapeutics

overall_design: RNA deep sequencing from plain HEK293T cell and HEK293T cell transfected with different components for RNA AtoG editing as indicated in the metadata to quantify the RNA editing off-target events at the transcriptome wide.

first: Zukai

first: Albert

last: Cheng


title: A role for phase separation to prevent RNA:DNA hybrids

city: Tucson

first: Jacob

middle: C.

last: Schwartz

state: AZ

address: 1501 N Campbell Ave, LSN649

department: Pharmacology

institute: University of Arizona

summary: The function of phase separation for many RNA-binding proteins is poorly understood, including FUS (FUSed in sarcoma). FUS binds RNA Pol II and controls phosphorylation of serine-2 (Ser2P). We uncovered a FUS activity involving no interactions with the polymerase. FUS could activate transcription of a non-eukaryote polymerase by preventing RNA invasion of DNA to form R-loops. This activity required binding to the nascent transcript and phase separation. We confirmed the activity in human cells using DRIP-seq, where R-loop sites formed were consistent with characteristic features of FUS activity, including transcription start sites where Ser2P signals accumulate after FUS knockdown. R-loop sites were enriched for sequences favored by the degenerate binding specificity of FUS. FUS also regulated R-loops near active retrotransposons and regions associated with DNA repeat expansion disorders. These findings offer a unified model that incorporates RNA-binding and phase separation to guard against instability from disruptive nucleic acid structures.

overall_design: Comparison of R-loops using DRIP-seq with and without knockdown of FUS by siRNA

first: Valery

last: Thompson


title: Recombinant irisin enhances the differentiation, remodeling potential, and the mechanical properties of 3D-cultured human periodontal ligament cells

city: Oslo

first: Yang

last: Yang

address: Geitmyrsveien 71

department: Faculty of dentistry

country: Norway

institute: University of Oslo

summary:
Irisin is recognized as a myokine produced by muscles, regulating metabolism and energy homeostasis, however, it may play a role in many other biological functions. Little is known about its effect on periodontal ligament cells.
We employed Affymetrix to profile mRNA expression patterns between 3D human periodontal ligament cell spheroids treated with and without irisin. The mRNA expression profiling identified approximately 1000 mRNAs to be differentially expressed between the two groups, which suggests that irisin is involved in gene regulation in human periodontal ligament cells.

overall_design: The 3D cultured human periodontal ligament cells were treated with 10 ng/ml irisin or miliQ water (control) for 14 days, total RNA was extracted from 3 replications from each group and sent for Affymetrix.

first: Ole

middle: K

last: Olstad

first: Jianying

last: He

first: Anne

last: Agger

first: Bjørn

last: Skallerud

first: Maria

last: Landin

first: Catherine

last: Heyward

first: Tianxiang

last: Geng

first: Helen

last: Pullisaar

first: Janne

last: Reseland


title: ERK1/2 signaling and cortical interneuron development

city: Tempe

first: Jason

middle: Marshall

last: Newbern

state: Arizona

address: ISTB1 320

department: School of Life Sciences

institute: Arizona State University

summary: We used RNA sequencing to profile the translatome of GABAergic neurons in P7.5 cortices in wildtype and Cre-directed ERK1/2 mutated animals. Using a Cre-dependent RiboTag approach, we enriched IP samples for cortical GABAergic neuron transcripts.

overall_design: RNA sequencing of P7.5 mouse cortical INPUT samples and RNA immunoprecipitated samples enriched in GABAergic neurons with or without genetic modification of ERK1/2.

first: Sara

middle: J

last: Knowles

first: George

last: Bjorklund


title: Targetting interleukins and chemokine mediated signalling pathway in DCM caused by LMNA 289A>G

city: Kolkata

first: Kaushik

last: Sengupta

state: West Bengal

address: 1/AF Bidhannagar

department: Biophysics and Structural Genomics

country: India

institute: Saha Institute of Nuclear Physics

summary: Lamins are type V intermediate filament proteins underlying the inner nuclear membrane which provide structural rigidity to the nucleus, tether the chromosomes and maintain nuclear homeostasis. Studies have identified developmentally regulated regions of the genome that are dynamically associated with the nuclear lamina. A large number of mutations in LMNA gene encoding lamin A/C results in a wide array of human diseases, collectively termed as laminopathies. Dilated Cardiomyopathy (DCM) is one such cardiovascular disease which is associated with systolic dysfunction of left or both ventricles leading to cardiac arrhythmia culminating into myocardial infarction.  In this work, we have unravelled the gene expression by RNA Sequencing analysis in mouse myoblast cell line in the context of the missense mutation LMNA 289A>G (Lys97Glu) that is found in DCM afflicted patients with severe symptoms.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of wild type lamin A and K97E lamin A (DCM mutant) transfected C2C12- mouse myoblast cells. All the samples were studied in duplicates.

first: Duhita


title: Maggot extracts overcome cisplatin resistance of ovarian cancer cells by targeting HSP90AB1/IGF1R signaling

city: Nanjing

first: Daojuan

last: Wang

state: Jiangsu

address: Hankou Road, Gulou District

institute: Nanjing University

summary: To investigate the main mechanism underlying cisplatin resistance in ovarian cancer, A2780/CDDP and SKOV3/CDDP cell lines were treated with both maggot extracts and cisplatin. We then performed gene expression profiling analysis using data obtained from RNA-seq of A2780 and A2780/CDDP cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for A2780  and A2780/CDDP cell lines.

first: Xun

last: Tang

first: Zhengquan

last: Zhu

first: Rong

first: Yajing

last: Weng

first: Tingyu

first: Ying

last: Huang

first: Hongwei

first: Zhenzi

last: Su

first: Gaojian

last: Tao

first: Yong


title: PKN2 deficiency leads both to prenatal ‘congenital’ cardiomyopathy and defective angiotensin II stress responses

status: Public on Jun 24 2022

city: Reading

first: Angela

last: Clerk

state: Berkshire

address: Whiteknights Campus

department: School of Biological Sciences

institute: University of Reading

summary: Background: The protein kinase PKN2 is required for embryonic development, and PKN2 knockout mice die as a result of failure in expansion of mesoderm tissues, cardiac development and neural tube closure. In the adult, cardiomyocyte PKN2 and PKN1 (in combination) are required for cardiac adaptation to pressure-overload. The role of PKN2 in contractile cardiomyocytes during development and its role in the adult heart remain to be fully established.  Methods: We used mice with cardiomyocyte-directed knockout of PKN2 or global PKN2 haploinsufficiency. Cardiac function and dimensions were assessed with high resolution episcopic microscopy, MRI, micro-CT and echocardiography. Biochemical and histological changes were assessed. Results: Cardiomyocyte-directed PKN2 knockout embryos displayed striking abnormalities in the compact myocardium, with frequent myocardial clefts and diverticula, ventricular septal defects and abnormal heart shape. The sub-Mendelian homozygous knockout survivors developed cardiac failure. RNASeq data showed upregulation of PKN2 in patients with dilated cardiomyopathy, suggesting an involvement in adult heart disease. Given the rarity of homozygous survivors with cardiomyocyte-specific deletion of PKN2, this was explored using mice with constitutive heterozygous PKN2 knockout. Cardiac hypertrophy resulting from hypertension induced by angiotensin II was reduced in haploinsufficient PKN2 mice relative to wild-type littermates, with suppression of cardiomyocyte hypertrophy and cardiac fibrosis.  Conclusions: Cardiomyocyte PKN2 is essential for heart development and formation of compact myocardium, and is also required for cardiac hypertrophy in hypertension. Thus, PKN signalling may offer therapeutic options for managing congenital and adult heart diseases.

overall_design: This experiment was carried out using RNA derived from 4 groups, with 5 mice in each. Male mice with constitutive heterozygous PKN2 knockout, and wild-type male littermates, were treated with Angiotensin II or vehicle for 7 days. RNA was extracted from the apex of hearts.

first: Christopher

last: Barrington

first: Jacqueline

last: Marshall

first: Peter

last: Parker

first: Joshua

last: Cull

first: Hajed

middle: O

last: Alharbi

first: Susanna

last: Cooper

first: Daniel

middle: N

last: Meijles


title: RNA sequencing of Rictor-deficient epidermis

city: Cologne

first: Sabine

last: Eming

state: NRW

address: Kerpener Str. 62

department: Department of Dermatology

institute: Uniklinik Koeln

summary: We sequenced mRNA from control and Rictor -/- epidermis at E19.5, 3 biological replicates each.

overall_design: Examination of mRNA levels in control and Rictor -/- epidermis.

first: Xiaolei

last: Ding

middle: A


title: The RNA binding protein Swm is critical for Drosophila melanogaster intestinal progenitor cell maintenance

city: Bloomington

first: Nick

last: Sokol

state: IN

address: 1001 E 3rd Street, Biology Building

institute: Indiana University

summary: The regulation of stem cell survival, self-renewal, and differentiation is critical for the maintenance of tissue homeostasis. Although the involvement of signaling pathways and transcriptional control mechanisms in stem cell regulation have been extensively investigated, the role of post-transcriptional control is still poorly understood. Here we show that the nuclear activity of the RNA-binding protein Second Mitotic Wave Missing (Swm) is critical for Drosophila melanogaster intestinal stem cells (ISCs) and their daughter cells, enteroblasts (EBs), to maintain their progenitor cell properties and function. Loss of swm causes ISCs and EBs to stop dividing and instead detach from the basement membrane, resulting in severe progenitor cell loss. swm loss is furthermore characterized by nuclear accumulation of poly(A)+ RNA in progenitor cells. Swm associates with transcripts involved in epithelial cell maintenance and adhesion, and the loss of swm, while not generally affecting the levels of these Swm-bound mRNAs, leads to elevated expression of proteins encoded by some of them, including the fly ortholog of Filamin. Taken together, this study indicates a nuclear role for Swm in adult stem cell maintenance, raising the possibility that nuclear post-transcriptional gene regulation plays vital roles in controlling adult stem cell maintenance and function.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Drosophila intestinal progenitor cells and its KD derivatives (swm RNAi) and CLIP-seq analysis of SWM immunoprecipitates and total inputs derived from diessected Drosophila intestines.

first: Ishara

last: Ariyapala

first: Kasun

last: Buddika

first: Nicholas


title: Multiple Histone modifications ChIP-seq in MCF7 cells corresponding to Ctr9 KD (paper title: Ctr9, the scaffold subunit of PAFc, govens PRC2-mediated H3K27me3 domains in breast cancer cells)

city: Madison

first: Wei

last: Xu

state: WI

address: 1111 Highland Ave

institute: University of Wisconsin-Madison

summary: We want to examine the alternation of histone modification spectrum on chormatin in corresponding to Ctr9 loss either in an inducible KD or stable KD fashion in MCF7 breast cancer cells.

overall_design: We applied 5 samples by indiviaually pulling down Histone H3K4me3/H3K27me3/H3K36me3 enriched DNA followed by deep sequencing. Two samples are MCF7-tet-on-shCtr9 cells either treated with Vehicle (control) or Doxycycline(+ Dox: inducible Ctr9 KD) for 7 days. The other three samples are MCF7 cells stablying expressing scarmbolled shRNA or two distinct lentiviral shRNAs target to Ctr9 transcript. (shCtr9#3/shCtr9#5)

first: Ngai

last: Chan

first: Peng

last: Liu

first: Irene

last: Ong


title: Influence of a ketogenic diet on glial metabolism in vivo - Astrocytes

first: Moritz

last: Rossner

address: Nussbaumstr. 7

department: Psychiatry

summary: To maintain homeostasis, the body including the brain reprograms its metabolism in response to altered nutrition or disease. However, the consequences of these challenges for the energy metabolism of the different brain cell types remain unknown. Here, we generated a proteome atlas of the major CNS cell types from young and adult mice, after feeding the therapeutically relevant low-carbohydrate, high-fat ketogenic diet (KD) and during neuroinflammation. Under steady-state conditions, CNS cell types prefer distinct modes of energy metabolism. Surprisingly, the comparison with KD revealed distinct cell type-specific strategies to manage the altered availability of energy metabolites. Astrocytes and neurons but not oligodendrocytes demonstrated metabolic plasticity. Unexpectedly, inflammatory demyelinating disease changed the neuronal metabolic signature in a similar direction as KD. Together, these findings highlight the importance of the metabolic crosstalk between CNS cells and between the periphery and the brain to manage altered nutrition and neurological disease.

overall_design: Mice are reared on ketogenic diet (KD) until P42, morphological and metabolic changes are investigated globally with transcriptomic analysis. Astrocytes were purified by MACS.

first: Tim

last: Düking

first: Gesine

last: Saher

first: Nirmal

last: Kannaiyan


title: Single cell RNA-sequencing of vehicle- and UK5099-treated mouse prostate organoids

city: Los Angeles

first: Xia

last: Yang

state: California

address: 610 Charles E. Young Drive East

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

summary: The goal of this study was to determine how modulation of mitochondrial pyruvate metabolism regulates gene expression in a three-dimensional organoid model of mouse prostate epithelium. Organoids were treated with the small molecule UK5099, which impairs mitochondrial pyruvate uptake, and subjected to single-cell RNA-sequencing. Our analysis revealed considerable heterogeneity within prostate organoids characterized by distinct cell clusters expressing markers associated with basal, luminal and mesenchymal-like cells. UK5099 treatment led to a reduction in epithelial populations and an enrichment in mesenchymal-like cells. These findings indicate that pyruvate metabolism can modulate features of cell fate in prostate epithelium.

overall_design: Single cell RNA-sequencing of mouse prostate organoids treated with vehicle or UK5099

first: Andrew

last: Goldstein

first: Jenna

last: Giafaglione


title: Gene expression changes in femur tissues of ovariectomy-induced osteoporosis rats

city: Dalian

first: Hao

last: Li

email: lihao0362@sina.com, lih@dmu.edu.cn, lh1362230894@outlook.com, lihao7y6@foxmail.com

state: Liaoning Province

address: lunshun nanlu

department: Department of pharmacy

institute: Dalian Medical University, Dalian, China

summary:
To study the differentially expressed genes in postmenopausal osteoporosis , a  postmenopausal osteoporosis rat model  were constructed by bilateral ovariectomy.
We then performed gene expression profiling analysis using data obtained from RNA-seq of the rat femur tissues.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the femurs of ovariectomy-induced osteoporosis rats  and sham operation group rats.

first: Huijun

last: Sun

first: Yukun

last: Zhang


title: Tissue-resident CXCR4+ macrophage as a poor prognosis signature promotes pancreatic ductal adenocarcinoma progression

city: Shanghai

first: Zhenyu

last: Liao

address: No.270 Dongan Road

institute: Fudan University Shanghai Cancer Centre

summary: In this study, we explored the CXCR4+ macrophages subset on its prognosis value, immune profile and distinct function in pancreatic cancer progression. RNA-seq analysis is performed to find the distinct characters of mouse tumor-derived Cxcr4+ macrophages.

overall_design: RNA-seq analysis is performed to find the distinct characters of mouse tumor-derived Cxcr4+ macrophages (three Cxcr4+ macrophage samples and three Cxcr4- macrophage samples).

first: Longyun

last: Ye

first: Tianjiao


title: Real-time quantitative PCR analysis of NF-kB, TNFR1, BRAF, MEK and NRF2 genes in human D24, MM418-C1 melanoma and HaCaT cells

city: Bundoora

first: Dao

last: Nguyen

state: Victoria

address: 289 McKimmies Rd

department: School of Science and Health and Biomedical Science

country: Australia

institute: Royal Melbourne Institute of Technology

summary: D24, MM418-C1 melanoma and HaCaT cells were treated with 100 µg/mL of the different M. cochinchinensis seed extracts for 48 h prior to RNA collection. Results were presented as the fold change compared to untreated controls ± SEM (n=3), different letters indicated statistical significance at p≤0.05 between different treatments (Analysis by One-way ANOVA with Turkey’s LSD test).

overall_design: RNA was extracted using TRIzol™ Reagent (Life Technologies, Melbourne, Australia) as per the manufacturer’s protocol. RNA was quantified spectrophotometrically at 260 nm (Nanodrop ND1000), and its purity checked using the ratios of absorbance at 260/280 nm and 260/230 nm. cDNA was synthesized from 1 μg total RNA using SuperScript III reverse transcriptase (Thermo Fisher Scientific) with oligo (dT) primers according to the manufacturer’s instructions. Each transcript quantification was carried out in triplicate. Subsequently, 4 µL (10 ng/µL) cDNA was added to 10 µL SYBR mix, 0.8 µL of each (10 µM) forward and reverse primer, and 4.4 µL DEPC H2O. The qPCR was performed on a Qiagen Rotor-Gene Q (Qiagen, Germany) and analysed with inbuilt software (version 2.3.1.49). The thermal cycling conditions were as follows: initial activation at 95°C for 2 min, 39 cycles of 95°C 5 s, 60°C for 10 s, 72°C for 15 s, and melting curve from 65°C to 95°C. Relative quantitative analysis of TNFR1, NF-kB, BRAFWT, BRAFV600E and Nrf2 mRNAs were performed using the 2−ΔΔCq method which was normalized to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA. The expression was calculated as n-fold induction of the gene of interest in treated cells relative to that of untreated control cells

first: Tien

last: Huynh


title: Genome-wide identification of long noncoding RNA and their potential interactors in ISWI mutants

city: Beijing

first: Lin

address: Xinjiekouwai Street

institute: Beijing Normal University

summary: Long non-coding RNA (lncRNA) refers to non-coding RNA transcripts with a length of more than 200 nt. They regulate the expression level of target genes. However, the role of lncRNA in chromatin remodeling needs to be further explored. In this study, we used ISWI mutants (ISWI is a chromatin remodeling factor in Drosophila) to explore the function of lncRNA. Based on the transcriptome of ISWI mutant Drosophila, we analyzed the transcripts and conducted differential expression analysis. In ISWI mutants, the expression changes of lncRNAs were more significant. Our results provide a new perspective for understand the possible regulatory role of lncRNA in chromatin remodeling and identify possible lncRNA target genes in ISWI mutants.

overall_design: Compare the global expression of ISWI mutant and wildtype Drosophila.

first: Shuai

first: Ludan


title: Influence of a ketogenic diet on glial metabolism in vivo

city: Munich

first: Moritz

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

overall_design: Refer to individual Series


title: Influence of a ketogenic diet on glial metabolism in vivo - Oligodendrocytes

overall_design: Mice are reared on ketogenic diet (KD) until P42, morphological and metabolic changes are investigated globally with transcriptomic analysis. Oligodendrocytes were purified by MACS.

first: Tim

first: Gesine


title: Long-term exposure to PM2.5 aggravates pulmonary fibrosis and acute lung injury by disrupting Nrf2-mediated antioxidant function

first: Chen

last: Zhao

address: 22nd Hankou Road

summary: To investigate the difference damage patterns bewteen short-term and long-term exposure to PM2.5 particulate matter

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mice exposed to PM2.5 particulate matter

first: Wenyuan

last: Pu

first: Hongwei

last: Wang


title: Characterization of postnatal mouse adrenal chromaffin cells

city: Paris

first: Isabelle

last: Janoueix-Lerosey

address: 26 rue d'Ulm

institute: Institut Curie

summary: Chromaffin cells were selected from dissociated postnatal mouse adrenals by immunopanning using L1CAM, expanded in sphere cultures and analyzed by RNA sequencing

overall_design: Dissociated mouse adrenal cells were sorted into L1CAM-positive chromaffin cells and L1CAM-negative cells using an immunopanning protocol. L1CAM-positive and L1CAM-negative cell populations were maintained in sphere cultures for 5-8 days. The spheres were collected for RNA extraction and sequencing by centrifugation through a 3%BSA step gradient to eliminate debris. The cell pellet was dissolved in RA1 + beta-mercaptoethanol.

first: Hermann

last: Rohrer


title: Flavobacterial exudates disrupt cell cycle progression and metabolism of the diatom Thalassiosira pseudonana

city: Seattle

first: E. Virginia

last: Armbrust

state: WA

address: 616 NE Northlake Place

department: Oceanography

institute: University of Washington

summary: Phytoplankton and bacteria form the base of marine ecosystems and their interactions drive global biogeochemical cycles. The effect of bacteria and bacteria-produced compounds on diatoms range from synergistic to pathogenic and can affect the physiology and transcriptional patterns of the interacting diatom. Here, we investigate physiological and transcriptional changes in the marine diatom Thalassiosira pseudonana induced by extracellular metabolites of a known antagonistic bacterium Croceibacter atlanticus. Mono-cultures of C. atlanticus released compounds that inhibited diatom cell division and elicited a distinctive phenotype of enlarged cells with multiple plastids and nuclei, similar to what was observed when the diatom was co-cultured with the live bacteria. The extracellular C. atlanticus metabolites induced transcriptional changes in diatom pathways that include recognition and signaling pathways, cell cycle regulation, carbohydrate and amino acid production, as well as cell wall stability. Phenotypic analysis showed a disruption in the diatom cell cycle progression and an increase in both intra- and extracellular carbohydrates in diatom cultures after bacterial exudate treatment. The transcriptional changes and corresponding phenotypes suggest that extracellular bacterial metabolites, produced independently of direct bacterial-diatom interaction, may modulate diatom metabolism in ways that support bacterial growth.

overall_design: mRNA profiles of Thalassiosira pseudonana under control conditions, bactetrial filtrate treated conditions, and oxidative stress conditions.

first: Zinka

last: Bartolek

first: Shiri

middle: G

last: van Creveld

first: Sacha

last: Coesel

first: Kelsy

last: Cain

first: Megan

last: Schatz

first: Rhonda

last: Morales

first: E

middle: V


title: RNA-Seq analysis for giant cell tumour of the bone

city: shanghai

first: Song

last: Li

address: No.415 Fengyang Road

institute: shanghai chagnzheng hospital

summary: CircRNA sequencing was performed on 5 pairs of giant cell tumors of bone and their adjacent tissues.

overall_design: In total, 5 pairs of giant cell tumors of bone and their adjacent tissues.

first: Jianru

last: Xiao

first: Zhenhua

last: Zhou

first: Guoxu


title: Direct conversion of rod to cone-like photoreceptors by NRL knockdown with cell-penetrating siRNA

city: Seoul

first: Hyungwoo

last: Lee

address: 120-1 Neungdong-ro, Gwangjin-gu

country: South Korea

institute: Konkuk University School of Medicine

summary: To investigate the retinal transcriptome in which Nrl gene is  knocked down by cp-asiRNA (cp-asiNRL) in wildtype C57BL/6J mouse and laser-induced CNV model.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wildtype C57BL/6J mouse and laser-induced CNV model mouse when PBS or cp-asiRNA targeting Nrl were treated.

first: Hyoik

last: Jang

first: Jae-Byoung

last: Chae

first: Dong Ki

first: Hyewon

last: Chung


title: Optocoder: computational decoding of spatially indexed bead arrays

city: Berlin

first: Nikos

last: Karaiskos

address: Hannoversche Str. 28

institute: Max Delbrück Center for Molecular Medicine

summary: Spatial transcriptomics technologies that can quantify gene expression in space are transforming contemporary biology research. Some of such methods use spatially barcoded bead arrays that are optically sequenced by a microscopy setup to detect bead barcodes in space which can be consecutively matched to cell barcodes from the respective single cell sequencing experiment. To have good quality barcodes and a high number of barcode matches in space, robust and efficient computational pipelines are needed to process raw microscopy images and call the bases of bead barcodes accurately. Here, we present Optocoder, a computational pipeline that takes raw optical sequencing microscopy images as input and outputs bead barcodes in space. Optocoder efficiently aligns images, detects beads, and corrects for confounding factors of the fluorescence signal such as crosstalk and phasing before base calling. Furthermore, we implement a machine learning pipeline that is trained using the signal from the beads that match to illumina barcodes in order to predict non-matching bead barcodes which can boost up the number of barcode matches. We benchmark Optocoder using data from an in-house spatial transcriptomics platform as well as data from the Slide-seq method and we show that it can efficiently process both datasets with minimal modification.

sample_organism:
Mus musculus
unidentified

platform_organism:
Mus musculus
unidentified

overall_design: 4 spatial transcriptomics datasets. One with randomly distributed ERCC RNA Spike-Ins and three brain sections of E12 mice.

first: Stefano

last: Abbiati

first: Jonathan

last: Alles

first: Salah

last: Ayoub

first: Anastasia

last: Boltengagen

first: Sebastian

last: Ehrig

first: Giuseppe

last: Macino

first: Nikolaus

last: Rajewsky

first: Marie

last: Schott

first: Enes

last: Senel

first: Tamas

middle: R

last: Sztanka-Toth

first: Andrew

last: Woehler


title: Enforced MAB21L4 expression enhances epidermal diferentiation

city: Stanford

first: Carolyn

state: CA

address: 269 Campus Drive

institute: Stanford University School of Medicine

summary: RNA-seq was used to define the role of MAB21L4 in epidermal differentiation by placing primary human keratinocytes transduced to overexpress MAB21L4 onto human dermis and grown for three days at the air-liquid interface to generate organotypic skin tissue.

overall_design: Total RNA was then isolated from human skin organoids using QIAshredder (Qiagen) and Trizol (ThermoFisher) followed by DNA removal with the TURBO DNA-free kit (Ambion) according to the manufacturer’s instructions. RNA integrity was verified using an Agilent 2100 Bioanalyzer. RNA-Seq libraries were prepared with the mRNA Seq Sample Prep Kit (Illumina, Inc.) as recommended by the manufacturer. 100 bp paired-end sequencing reads were obtained using the Illumina HiSeq platform.

first: Tomas

last: Bencomo

first: Dane

last: Sessions


title: Retinal Ganglion Cell Expression of Cytokine Enhances Occupancy of NG2 Cell-Derived Astrocytes at the Nerve Injury Site: Implication for Axon Regeneration

city: Miami

first: Kyung (Kevin)

last: Park

address: 1095 NW 14th Terrace, Miami Project to Cure Paralysis, LPLC room 4-20

department: Neurological Surgery

institute: University of Miami

summary: Following injuryin the central nervous system, a population of astrocytes occupy the lesion site, form glial bridges and facilitate axon regeneration. Theseastrocytes originate primarily from resident astrocytes orNG2+ oligodendrocyteprogenitor cells. However, theextentto which these cell types give rise to the lesion-filling astrocytes,andwhethertheastrocytes derived from differentcell typescontribute similarly to optic nerve regenerationremain unclear.Here we examine the distributionof astrocytes and NG2+ cellsin an optic nerve crush model.Weshow that optic nerve astrocytes partially fill the injury site over timeafter a crush injury.Viral mediated expression of a growth-promotingfactor,ciliary neurotrophic factor (CNTF),in retinal ganglion cells (RGCs) promotesaxon regeneration without altering the lesion size or the degreeof lesion-filling GFAP+ cells. Strikingly, using inducible NG2Cre driver mice, wefoundthat CNTF overexpression in RGCs increasesthe occupancy ofNG2+ cell-derived astrocytes in the optic nerve lesion. An EdU pulse-chase experiment showsthat the increase in NG2 cell-derived astrocytes is not due to an increase in cell proliferation.Lastly, we performedRNA-sequencing on the injured optic nerve and reveal that CNTF overexpression in RGCs results in significant changes in the expression of distinct genes,including those that encode chemokines, growth factor receptors,and immune cell modulators.Even though CNTF-induced axon regeneration has long been recognized, this is the first evidence of this procedure affecting glial cell fate at the optic nerve crush site.We discuss possible implication of theseresultsforaxon regeneration.

overall_design: Animals received intravitreal injection of AAV-CNTF or AAV-null, followed by optic nerve crush 2 weeks later. Seven days after optic nerve crush, we removed and processed the optic nerves for RNAseq. Totally, we prepared three animal groups; 1) sham injury (i.e., optic nerve exposed but not crushed) with AAV-null, 2) optic nerve crush with AAV-null and 3) optic nerve crush with AAV-CNTF (five biological replicates per group).

first: Marcio

last: Ribeiro

first: Ana

last: Ayupe

first: Felipe

last: Beckedorff

first: Konstantin

last: Levay

first: Benito

middle: E

last: Yon

first: Rodriguez

last: Sara

first: Lee

last: Jae

first: Tsoulfas

last: Pantelis

first: Nascimento-dos-Santos

last: Gabriel

first: Kevin


title: D- 2-hydroxyglutarate is an immunometabolite that accumulates in macrophages after TLR activation and inhibits inflammatory responses

city: Amsterdam

first: Jan

last: Van den Bossche

address: De Boelelaan 1108

department: Molecular Cell Biology and Immunology

institute: Amsterdam UMC, VUmc

summary: Macrophages undergo extensive metabolic rewiring upon activation and this serves many roles beyond the production of energy and anabolic building blocks. So-called immunometabolites that accumulate upon immune activation can serve as co-factors for enzymes and can mediate posttranslational modifications of histones, transcription factors, enzymes and other key proteins that modulate macrophage function. As such, the Krebs-cycle-associated metabolites succinate and itaconate emerged as key regulators of macrophages. 2-hydroxyglutarate (2HG) is structurally similar to Krebs-cycle metabolite alpha-ketoglutarate and exists as two enantiomers. D-2HG is well studied as an oncometabolite in cancer cells and more recently, L-2HG received some attention in the immunometabolism field. Here we describe that 2HG levels peak during later stages of LPS-induced inflammatory responses in mouse and human macrophages. Surprisingly, D-2HG was the most abundant enantiomer in macrophages and its LPS-induced accumulation may be explained by the inverse kinetics of D-2HG-degrading D-2HG dehydrogenase (D2HGDH) and the time-dependent induction of Hydroxyacid-Oxoacid Transhydrogenase (HOT), which makes D-2HG as a byproduct. D-2HG kinetics fit transcriptomics and functional data, together indicating that D-2HG suppresses inflammatory responses in macrophages in vitro. D-2HG also regulates local and systemic inflammatory responses in vivo. Finally, we show that D-2HG likely exerts in anti-inflammatory effects on NFkB target genes independently of aKG-dependent dioxygenases. Together, this study unexpectedly classifies D-2HG as an immunometabolite that can inhibit inflammatory macrophage responses.

overall_design: RNA-seq of bone marrow-derived macrophages from WT C57Bl/6 mice to assess effect of D2HG octyl ester on LPS responses.

first: Kyra

last: de Goede


title: CACYBP is required for epidermal homeostasis

last: Lee

summary: RNA-seq was used to define the role of CACYBP in epidermal differentiation by first employing CRISPR/Cas9 to disrupt CACYBP with two independent single guide RNAs (sgRNAs) to create pools of CACYBP-ablated primary human keratinocytes that were immortalized with HPV E6/E7 and then placed onto human dermis and grown for three days at the air-liquid interface to generate organotypic skin tissue.

overall_design: Total RNA was then isolated from human skin organoids using QIAshredder (Qiagen) and Trizol (ThermoFisher) followed by DNA removal with the TURBO DNA-free kit (Ambion) according to the manufacturer’s instructions. RNA integrity was verified using an Agilent 2100 Bioanalyzer. RNA-Seq libraries were prepared with the mRNA Seq Sample Prep Kit (Illumina, Inc.) as recommended by the manufacturer. 75 bp paired-end sequencing reads were obtained using the Illumina HiSeq platform.

middle: S

first: Cristina

last: Tommasi


title: RET activation controlled by MAB21L4-CacyBP interaction in squamous cell carcinoma

first: Carolyn


title: Hierarchical accumulation of histone variant H2A.Z regulates transcriptional states and histone modifications in early mammalian embryos [RNA-seq]

city: Wuhan

first: Jing-Jing

last: Zhang

state: Hubei

address: 1 Lion Rock Street

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction

institute: Huazhong Agricultural University

summary: Early embryos undergo extensive epigenetic reprogramming to achieve gamete-to-embryo transition, which involves the loading and removal of histone variant H2A.Z on chromatin. Although the H2A.Z landscapes in sperm have been investigated, its dynamics during early development remain unrevealed. Here, by using ultra-low-input native chromatin immunoprecipitation and sequencing (ULI-NChIP-seq), we map the genome-wide distribution of H2A.Z in mouse oocytes and early embryos. We find that paternal H2A.Z is removed upon fertilization, followed by unbiased accumulation on parental genomes during zygotic genome activation (ZGA). More importantly, H2A.Z exhibits hierarchical accumulation as different peak types at promoters. We identify that double H2A.Z peaks co-localizes with H3K4me3 and facilitates transcriptional activation, bivalent markers (H3K4me3+H3K27me3) prefer to occupy single H2A.Z peak and inhibits developmental gene expression, while promoters with no H2A.Z accumulation exhibit gene silencing in early embryos. Remarkably, H2A.Z depletion changes the enrichments of histone modifications and RNA polymerase II (Pol II) binding at promoters, resulting in abnormal gene expression and developmental arrest during lineage commitment. Hence, H2A.Z plays dual roles in regulating the epigenomes required for proper gene expression during preimplantation development.

overall_design: The RNA-Seq experiments of the control and H2A.Z KD embryos at the 2-cell, morula and blastocyst stage.

first: Xin

last: Liu

first: Jingjing

first: Yi

middle: L

last: Miao


title: MAB21L4 is required for epidermal homeostasis

summary: RNA-seq was used to define the role of MAB21L4 in epidermal differentiation by first employing CRISPR/Cas9 to disrupt MAB21L4 with two independent single guide RNAs (sgRNAs) to create pools of MAB21L4-ablated primary human keratinocytes that were  then placed onto human dermis and grown for three days at the air-liquid interface to generate organotypic skin tissue.

first: Tomas

last: Bencomo

first: Dane

last: Sessions


title: Comparison of gene expression in NEDD8-sufficient or -deficient neonatal liver

first: Jiyan

state: China

address: 27 Taiping Road, East Building, Rm0749

institute: Institute of Basic Medical Sciences

summary: The total RNA was prepared from the postnatal day 3 NEDD8-sufficient or -deficient liver and subjected to microarray.

overall_design: The liver isolated from a postnatal day 3 Nedd8(flox/flox) mouse was named as W10, whereas the liver from a littermate Nedd8(flox/flox; Alb-cre) mouse was named as K3. The total RNA was prepared and subjected to microarray.

first: Lu

last: Guo


title: Enrichment and single-cell sequencing of the ventricular cells from zebrafish telencephalon

city: New York

first: Caghan

last: Kizil

state: NY

institute: Columbia University Irving Medical Center

summary: Zebfrafish brains were injected with neutral cell tracking dye. Zebrafish telencephalon were dissociated and dye postive cells were sorted by FACS and single-cell sequencing performed from these cells.

overall_design: Zebrafish ventricular cells fom telencephalon were enriched by using cell tracking dye, single-cell sequencing of these cells was performed by  10X Genomics.

first: Mehmet

middle: I

last: Cosacak


title: Hierarchical accumulation of histone variant H2A.Z regulates transcriptional states and histone modifications in early mammalian embryos

sample_organism:
Sus scrofa
Mus musculus

platform_organism:
Sus scrofa
Mus musculus


title: Identification of RNAs containing TOP3B cleavage complexes

city: Bethesda

first: Lorinc

last: Pongor

state: MD

address: 37 Convent Dr,

department: DTB

institute: NIH

summary: Human TOP3B is unique as it can act as RNA topoisomerase. For identification of  RNAs with  TOP3B cleavage sites, we engineered a “self-trapping” mutant of TOP3B (R338W TOP3B) and performed performed native RNA Immunoprecipitation and sequencing without crosslinking (Native RIP seq). 2,856 RNAs (Supplementary Figure 7F) were enriched in R338W TOP3B immunoprecipitated samples and found that TOP3B regulates key cellular RNA-related pathways.

overall_design: Native RIP-seq in HEK293 cells transfected with FLAG tagged R338W TOP3B

first: Saha

last: Sourav

first: Pongor

last: Lorinc

first: Pommier

last: Yves


title: Compound-induced NR5A1 circular RNA and aberrant multiple exon-skipping attenuate aberrant steroidogenesis

city: Fukuoka

first: Kenji

last: Ohe

state: Fukuoka

address: 8-19-1, Jyonan-ku, nanakuma

department: Faculty of Pharmaceutical Sciences

country: Japan

institute: Fukuoka University

summary: Despite the intensive search for an effective drug to ameliorate excess steroid production, there are few pharmacological options, especially for diseases as steroid-producing adrenocortical cancers. While splice-modifying-compounds have pleiotropic effects including anticancer properties, none have been tested on abnormal steroidogenesis. Using H295R adrenocortical carcinoma cells, CX-4945 induced multiple exon skipping of the NR5A1 gene, the master regulator of steroidogenesis. The resulting exon-skipped NR5A1 proteins were non-functional when added-back to NR5A1 knocked down H295R cells. This eventually suppressed steroidogenesis and induced dysfunctional autophagy with progression to ER-stress-related apoptosis. Intriguingly, a circular RNA of NR5A1 exons (circNR5A1 ex2-4 RNA) not originating from the skipped exons, was induced. Transient expression of this circNR5A1 ex2-4 RNA induced the same multiple exon-skipped isoforms of the NR5A1 gene. This potential pharmacological control of NR5A1 aberrant multiple exon-skipping and interplay with its circNR5A1 RNA gives us a novel target for treating abnormal steroidogenesis in adrenocortical carcinomas.

overall_design: CX-4945-induced gene expression in H295R adrenocortical cancer cells was compared with solvent (DMSO) treated H295R cells.

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