title: ATF3 is a converging node for AR signaling and fatty acid oxidation in castration-resistant prostate cancer

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

summary: Prostate cancer (PCa) is the second most prevalent cancer and leading causes of death among men worldwide. Androgen deprivation is the first line of treatment for locally advanced and metastatic PCa. For men who develop metastatic castration-resistant PCa (mCRPC), survival is limited. Thus, there is a need to identify synergistic pathways to either prevent or re-sensitize the castration-resistant phenotype. PCa has a long natural history of development and there is a significant correlation between age, diet, metabolism and progress of PCa. We have previously reported that treating PCa cells with fatty acid oxidation inhibitors (FAOi) sensitizes them to androgen blockade. Here we set out to evaluate how the two disparate pathways: AR signaling and FAO, influence one another hoping to identify new therapeutic vulnerabilities. We used CRPC cell models (LNCaP-MDV-resistant, and LNCaP-C4-2), as well as the FAOi (etomoxir and ranolazine) and the antiandrogen enzalutamide (MDV3100). Cells were treated for 48 hours, followed by gene expression, androgen signaling and growth analysis. Both FAOi strongly suppressed the androgen response hallmark in MDV-res cells, and this was associated with a significant upregulation of the ATF3 gene. Interestingly, knockdown (KD) of ATF3 with shRNAs resulted in differential responses to FAOi in these genetically-related cells. In the MDV-resistant cells, ATF3 KD resulted in increased PSA expression with FAOi treatment. On the other hand, in the C4-2 cells, ATF3 KD resulted in decreased PSA expression with FAOi treatment. These results suggested that ATF3 is a convergent point for AR and FAO pathways and that is cell-context dependent, and its expression status could be exploited to sensitize PCa cells to MDV3100 and/or the FAOi. Cell growth and apoptosis assays confirmed that the LNCaP-derived ATF3 KD were more sensitive to MDV3100 and FAOi compared to control cells. Examination of patient databases revealed an inverse correlation between AR and ATF3, a low expression of ATF3 in advanced cancers and better disease-free survival in patients with high ATF3 expression. These data support the role for FAOi to re-sensitize CRPC to endocrine therapies. In conclusion, we have identified ATF3 as a modulator of FAO and AR signaling that has predictive value for clinical outcomes using FAOi in CRPC.

overall_design: microarray of RNA isolated from control, Etomoxir, MDV3100, and Ranolazine treatments on CRPC cell model: LNCaP-MDV-resistant cells.

first: Molishree

last: Joshi

first: Maren

last: Salzmann-Sullivan

first: Gergana

middle: E

last: Stoykova

first: Jihey

first: Kristen

last: Boyle

first: Thomas

last: Flaig

first: Isabel

middle: R

last: Schlaepfer


title: Gene expression profiling of MM cells treated with FGF-trap molecule NSC12

status: Public on Apr 01 2022

city: Brescia

first: Roberto

last: Ronca

address: viale Europa 11

department: Molecular and Translational medicine

country: Italy

institute: University of Brescia

summary: Multiple myeloma (MM), the second most common hematological malignancy, frequently relapses because of chemotherapeutic resistance. Fibroblast growth factors (FGFs) act as pro-angiogenic and mitogenic cytokines in MM. Here, we demonstrate that the FGF system is essential for MM cell survival by protecting MM cells from oxidative stress-induced apoptosis. Accordingly, extracellular FGF blockade by an FGF trapping approach causes proteasomal degradation of the c-Myc oncoprotein. This triggers mitochondrial oxidative stress, DNA damage and apoptosis in MM cell lines and MM cells from both naïve and relapsed/refractory patients. Our data highlight the mechanism by which the FGF system contributes to MM cell survival and disease progression, representing a therapeutic target for MM patients with poor prognosis and advanced disease stage.

overall_design: KMS11 cells were treated with NSC12 for 6 and 12 hours

first: Arianna

last: Giacomini


title: Identification of candidate genes associated with temperature-dependent sex determination of Reeves' Turtle (Mauremys reevesii) by genome-wide transcriptome analysis

city: Zhengzhou

first: Liushuai

last: Hua

state: Henan

address: No.22 Huayuan Road

department: Institute of Animal Husbandry and Veterinary Science

country: China

institute: Henan Academy of Agricultural Sciences

type: Expression profiling by high throughput sequencing

summary: In the present study, the eggs of Chinese pond turtles (Mauremys reevesii) were incubated at three temperatures (26℃, 29℃ and 32℃). During the thermosensitive period (TSP) of incubation, the adrenal-kidney-gonad (AKG) complexes were sampled, and the transcriptome differences of the AKG samples were investigated using next-generation sequencing, then candidate genes associated with temperature-dependent sex determination of Reeves' Turtle were identified.

overall_design: The eggs were incubated at three different temperatures (the 26℃ is the male-biased temperature, 32℃ is the female-biased temperature, and 29℃ is sex mixed temperature), and three repetiton from each temperature were sampled. Then the candidate genes associated with temperature-dependent sex determination of Reeves' Turtle (Mauremys reevesii) were identified by genome-wide transcriptome analysis.

first: Wenxiu

last: Ru


title: SAFA in chromatin accessibility regulation

status: Public on Mar 31 2022

city: Beijing

first: Lili

last: Cao

address: datun Road

institute: Chinese Academy of Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Wild-type or SAFA-/- THP-1 cells were infected with VSV for 6 hours or 24 hours, samples were collected and send for ATAC-seq.

overall_design: Wile-type or SAFA-/- THP-1 cells were infected with 0.1MOI VSV for 6 hours or 24 hours. Then cells were collected and send for ATAC-seq.

first: Shengde

last: Liu


title: SAFA RGG domain in chromatin accessibility regulation

summary: Flag-SAFA or Flag-Del-RGG mutant stablely expressed THP-1 cells were infected with VSV for 6 hours, samples were collected and send for ATAC-seq.

overall_design: SAFA-/- THP-1 cells were stable expressed with Flag-tagged SAFA or Flag-tagged Del-RGG plasmids. Then cells were infected with 0.1MOI VSV for 6 hours. Then cells were collected and send for ATAC-seq.


title: wild-type and SAFA-/- cells

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

overall_design: Refer to individual Series


title: High grade neuroendocrine lung cancer expression profile

city: Tokyo

first: Shogo

last: Yamamoto

address: 4-6-1 Komaba, Megro-ku

department: Research Center for Advanced Science and Technology

country: Japan

institute: The University of Tokyo

summary:
Genomic gains and losses, particularly amplification of oncogenes and deletion of tumor suppressor genes, are critical molecular events involved in tumorigenesis and cancer progression. These genomic structural abnormalities trigger pathway alterations which activate/inactivate transcription factors along protein network, and then affect gene transcription profiles. Therefore, trace-back analysis of the pathway alteration by integrating genomic copy number, transcription profile, and known protein network data is expected to provide key information to interpret tumorigenesis and cancer progression processes. However, there are a number of pathway alteration candidates, so that it is difficult to understand overall picture. Primitive approaches such as filtering by arbitrary selection of thresholds involve a risk of overlooking important pathway alterations and their triggers. We proposed a visualization method for the trace-back analysis of pathway alterations, called a Cluster Overlap Distribution Map (CODM). We applied the CODM to trace-back analysis of pathway alterations related to subtype classifications of high grade neuroendocrine carcinoma samples; 1) small cell lung carcinoma (SCLC) vs. large cell neuroendocrine carcinoma (LCNEC), and 2) group1 vs. group2 (this is the classification based on transcription profiles and group2 has a higher survival rate than group1). By effective use of 3D and color spaces, the CODM allowed us to understand the overall picture of pathway alteration without arbitrary selection of thresholds and to extract 6 pathway alterations related to only group1 vs. groups2, 2 pathway alterations related to only SCLC vs. LCNEC, and 2 pathway alterations related to both group1 vs. group2 and SCLC vs. LCNEC.
Keywords: lung cancer profile

overall_design: High-grade neuroendocrine tumors of the lung were obtained from 29 patients undergoing pneumoresection at the Cancer Institute Hospital of Japanese Foundation of Cancer Research. All subjects gave their informed consent to participation in the study. Among the 29 patients, 20 were small cell lung carcinoma (SCLC) and 9 were large cell neuroendocrine carcinoma (LCNEC). About three-fourths of samples are common to the previous report (Jones MH, 2004). In the previous report, the samples were classified into group1 and group2 based on transcription profiles and statistical analysis indicated that group2 has a higher survival rate than group1. We also classified 29 samples into group1 and group2 based on transcription profiles and confirmed that group2 has a higher survival rate than group1.

first: Makoto

last: Kano

first: Shumpei

last: Ishikawa

first: Yukiko

last: Tanaka

first: Yuichi

first: Hiroyuki

last: Aburatani


title: Cellular microenvironment in inflammatory periapical tissue

city: Guangzhou

first: XInwei

last: Lin

address: No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China

department: Stomatology

institute: Sun Yat-sen University

summary: Chronic apical periodontitis, typified by inflammatory granulation tissue formation and alveolar bone destruction, is the immune response around the apical root caused by long-term infection and pathogenic stimulation in the root canal. Through the recruitment and infiltration of immune cells and inflammatory mediators, wound healing begins accompanied by the starting of infection. Hence, a comprehensive understanding of biological processes and disease development from the cellular microenvironment in inflammatory periapical areas has important implications.

overall_design: Two samples from extracted residual molars with chronic apical periodontitis

first: Zhongchun

last: Tong

first: Xinwei

first: Qimei

last: Gong

first: Xiaomin

last: Lv

first: Qingzhen

last: Meng

first: Hongbin

last: Lai


title: Temporal and functional determinants of intra-hepatic vascular homeostatic specialization [mouse liver]

city: NEW YORK

first: Jesus

middle: Maria

last: Gomez Salinero

state: NY

address: 1300 York Avenue

country: USA

institute: Weill Cornell Medicine

summary: Comparison of isolated mouse liver endothelial cells from Control and c-Maf endothelial deficient mice at 8 weeks of age.

overall_design: RNA sequencing of WT and c-Maf KO liver endothelial cells.

middle: M

first: Sean

last: Houghton

first: Shahin

last: Rafii


title: H3K27Ac ChIP-seq in wild-type and SAFA-/- cells

first: Lili

summary: wild-type or SAFA-/- THP-1 cells were infected with VSV for 8 hours or 24 hours, ChIP-seq was did with H3K27Ac antibody.

overall_design: wild-type or SAFA-/- THP-1 cells were infected with 0.1MOI VSV for 6 hours or 24 hours. Then cells were collected, and ChIP-seq was did with H3K27Ac antibody.

first: Yunfei

last: Li


title: Yin Yang 1 sets up the stage for cerebellar astrocyte maturation

city: Richmond

first: Tomasz

last: Kordula

state: VA

address: 1101 E Marshall ST

department: Biochemistry and Molecular Biology

institute: Virginia Commonwealth University

summary: Diverse subpopulations of astrocytes tile different brain regions to accommodate local requirements of neurons and associated neuronal circuits. Nevertheless, molecular mechanisms governing astrocyte diversity remain mostly unknown. We explored the role of a zinc finger transcription factor Yin Yang 1 (YY1) that is expressed in astrocytes. We found that specific deletion of YY1 from astrocytes causes severe motor deficits in mice, induces Bergmann gliosis, and results in simultaneous loss of GFAP expression in velate and fibrous cerebellar astrocytes. Single cell RNA-seq analysis showed that YY1 exerts specific effects on gene expression in subpopulations of cerebellar astrocytes. We found that although YY1 is dispensable for the initial stages of astrocyte development, it regulates subtype-specific gene expression during astrocyte maturation. Moreover, YY1 is continuously needed to maintain astrocyte identity in the adult cerebellum. Our findings suggest that YY1 plays critical roles regulating cerebellar astrocyte maturation during development and maintaining a mature phenotype of astrocytes in the adult cerebellum.

overall_design: 10X single-cell sequencing was done on two replicates of wildtype and YY1cKO cerebellum at P10 and P17.

first: Karli

last: Mockenhaupt

first: Katarzyna

last: Tyc


title: Combine single-cell transcriptome and CellTagging to identify the differentiation trajectory of human adipose-derived stromal cells

first: kai

last: lin

address: Dongdan three Dongcheng District No. 5

institute: Institute of Basic Medical Sciences Chinese Academy of Medical Sciences

summary: We combine single cell transcriptome sequencing with ‘CellTagging’ to track the differentiation process of the same MSC over time.

overall_design: Single RNA profiles of P0, P10 and P15 MSCs.

first: Kai

first: Yanlei

last: Yang

first: Yinghao

last: Cao

first: Junbo

last: Liang


title: Effects of Ultra-short Pulsed Electric Fields exposure on Glioblastoma Cells

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

summary:
Glioblastoma multiforme (GBM), is the most common form of adult malignant brain tumor, highly heterogeneous and relatively resistant to therapy with a poor prognosis. As other cancers, GBM starts from a relatively small fraction of poorly differentiated and particularly aggressive cancer stem cells (CSCs), responsible for aberrant proliferation and invasion, rapidly spreading the tumor growth in the other parts of the central nervous system. Due to the extreme tumor heterogeneity, standard therapies (i.e., surgery, chemotherapy and radiotherapy) provide poor positive outcomes and cancers usually recur. Therefore, alternative approaches, possibly targeting CSCs, are necessary for searching effective therapeutic strategies against GBM. Among many emerging new therapeutic strategies, ultra-short pulsed electric fields (PEF) are considered extremely promising in cancer therapy and our previous results demonstrated the capability of a specific electric pulse protocol, characterized by a high pulse amplitude and a short duration, to selectively affect medulloblastoma CSCs preserving normal cells.
Here, we tested the same exposure protocol to investigate the response of U87 GBM cells, and of U87-derived neurospheres. By analyzing different in vitro biological endpoints and taking advantage of transcriptomic and bioinformatics analyses, we found that, independently of CSCs content, PEF exposure affected cell proliferation and differentially regulated hypoxia, inflammation and P53/cell cycle checkpoints. PEF exposure also significantly reduced the clonogenic potential, reducing the ability to form new neurospheres, and inhibited the invasion potential. Importantly, exclusively in U87 neurospheres, PEF exposure changed the expression of stemness/differentiation genes. Our results, confirm this physical stimulus as a promising treatment to destabilize the extreme intra-tumoral GBM heterogeneity opening up the possibility to develop future therapeutic strategies mediated by PEF exposure.

overall_design: U87MG glioblastoma cell line cultured as monolayer or neuroshpere exposed to ultra short pulsed electric fields (four indipendent replicates for control and treated samples)

first: Silvia

last: Bresolin

first: Luca

last: Persano


title: DNA methylation-based age acceleration observed in IDH wild-type glioblastoma is associated with better outcome - including in elderly patients

city: Lausanne

first: Pierre

last: Bady

address: Quartier UNIL-Sorge

department: Swiss Institute of Bioinformatics

country: Switzerland

institute: CHUV / BCF / SIB

type: Methylation profiling by genome tiling array

summary: GBM samples (FFPE tissue) obtained from patients treated in clinical trials according to pre-specified clinical criteria (EORTC 26981/NCIC CE.3 pooled with the Lausanne Pilot trial, n=156).

overall_design: Bisulphite converted genomic DNA from the 156 samples were hybridised to the Illumina Infinium 450 Human Methylation Beadchip

first: Christine

last: Marosi

first: Michael

last: Weller

first: Bjørn

middle: H

last: Grønberg

first: Henrik

last: Schultz

first: Martin

middle: J

last: Taphoorn

first: Johanna

last: Gijtenbeek

last: van den Bent

first: Andreas

last: von Deimling

first: Roger

last: Stupp

first: Annika

last: Malmström

first: Monika

last: Hegi


title: Identification and characterization of Locusta migratoria microRNAs response to Metarhizium robertsii infection through high-throughput sequencing

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

institute: Anhui Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: a high-throughput Illumina/Solexa sequencing was conducted, 478262, 702593, 835394 and 894277 unique sRNAs was discovered from four periods of M. robertsii infection, uninfected (0h), infected for 12h, 24h and 36h. Then, 7, 7, 6 and 7 known pre-miRNAs were obtained, and 33, 58, 54 and 52 candidate novel miRNAs was detected in four periods. Further analysis showed that 24 of those candidate novel miRNAs were matched to other known insect miRNAs, while 36 of those miRNAs lacked sequence homologues of insect organisms.

overall_design: Locusts were randomly selected as 3rd instar and injected 5μl of 2ｘ107 spores/ml conidia suspensions into pronotum for each individual. Abdomens from uninfected locusts (0h) and infected 12h、24h and 36h locusts were collected respectively, flash frozen in liquid nitrogen, and stored at -80℃ until RNA extraction. Each sample contained three replications.

first: Bo

last: Huang


title: Gene expression signatures for apigenin treatment in human AML cell lines

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

summary: To investigate the effect of apigenin on gene expression, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to suppress the cell proliferation of human acute myeloid leukemia (AML) cell lines.  HL-60 amn NB4 cells were treated with apigenin for 24 h in vitro.

overall_design: HL-60 and NB4 cells were treated with apigenin for 24 h in vitro.

first: Sivasundaram

last: Karnan


title: Estrogen Modulation of the Pronociceptive Effects of Serotonin on Female Rat Trigeminal Sensory Neurons is Timing- and Dosage-Dependent and Requires Estrogen Receptor Alpha

city: Denton

first: Dayna

middle: Loyd

last: Averitt

state: Texas

address: 1000 Old Main Circle

department: Biology

institute: Texas Woman's University

summary: Since estrogen is a major hormone involved in multiple gene expression pathways in the cell, we wanted to determine the corresponding changes in trigeminal ganglia transcriptome of the E2-treated rats. Adult ovariectomized female rats were subcutaneneously implanted with either 5% (physiological level comparable to diestrus; 15-20 pg/ml; one capsule), 20% (physiological level comparable to proestrus; 40-60 pg/ml; 2 capsules of 10%), 40% (supraphysiological level; 2 capsules of 20%) E2, or control (2 capsules of 100% cholesterol) capsules. One week after implantation, nocifensive behaviors were recorded and trigeminal ganglia tissue was extracted.

overall_design: Total RNA was extracted from the right trigeminal ganglia (TG) tissue (n=3 per hormone treatment group) and sequenced [Novogene; sequencing lab at The University of California at Davis campus]

first: Sukhbir

last: Kaur

first: Taylor

last: Hickman

first: Angela

last: Lopez-Ramirez

first: Hanna

last: McDonald

first: Lauren

last: Lockhart

first: Omar

last: Darwish

middle: L


title: Expression data from human platelets after purification

city: Montpellier

first: Said

last: Assou

address: 80, av. Augustin Fliche

department: Institute for Regenerative Medecine and Biotherapy

country: France

institute: University Hospital of Montpellier, Inserm

summary:
Platelets are small anucleate cells derived from the fragmentation of megakaryocytes and are involved in different biological processes especially hemostasis, thrombosis and immune response. Platelet purification is a crucial step in transcriptomic analysis, and researchers usually encounter the problem of platelet contamination by leukocytes and erythrocytes. Leukocytes contain much more RNA than platelets, thus the presence of few contaminants in platelet preparation can strongly alter transcriptome results.
Using microarray technique, we compared transcriptome of platelets from the same donor, purified by common centrifugation method or using magnetic microbeads to eliminate contaminating cells.

overall_design: Platelets were isolated from blood of the same donor. Human Clariom D Human chips were performed to analyze the transcriptome. The GeneChip WT Pico Amplification Kitwas used to performed sample preparation. The gene expression data were extracted using Affymetrix Expression Console Software 1.4.1.

first: Mohamad

last: Chebbo

first: Véronique

last: Pantesco

first: Catherine

last: Duez

first: Marie

last: Alessi

first: Pascal

last: Chanez

first: Delphine

last: Gras


title: Toxicogenomics studies reveal common and specific pathways in pulmonary, hepatic, and neuronal cell models. [A549]

city: Milan

first: Chiara

last: Urani

address: Piazza della Scienza, 1

department: Dep. Earth and Environmental Sciences

institute: University of Milano-Bicocca

summary: To unravel possible mechanisms of Cd tissue-specificity, and to further deepen the understanding of cadmium mechanisms, we have compared transcriptomics data from cell models representative of three major Cd targets: pulmonary (A549), hepatic (HepG2), and neuronal (SH-SY-5Y) cells. Results from KEGG analysis show that only one specific pathway is dysregulated in a significant way in all cell models: the mineral absorption pathway.

overall_design: Human lung carcinoma cell line (A549) was exposed to non-cytotoxic cadmium concentrations (CdCl2) 10 or 20 µM for 24h. Two biological replicates of controls (cells grown in complete culture medium) were performd and 3 biologial replicates for each cadmium concentration.

first: Matilde

last: Forcella

first: Pierre

last: Lau

first: Marco

last: Fabbri

first: Paola

last: Fusi

first: Monica

last: Oldani

first: Pasquale

last: Melchioretto

first: Laura

last: Gribaldo


title: RNA biotype-associated molecular classification  in hepatitis B-related hepatocellular carcinoma

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

summary: Recent advance of RNA-seq technology enabled us to profile the diverse variations of RNA transcripts precisely, including the variants from alternative splicing as well as non-coding transcripts. Here, by performing transcriptome profiling including coding and noncoding transcripts, we identify four molecular subtypes of hepatitis B-related hepatocellular carcinoma (HCC) patients that are characterized by enriched expression of the RNA biotypes of noncoding (NC) and immune-related transcripts (IM) (i.e., IM+NC+, IM-NC+, IM+NC-, IM-NC-). The subtype IM+NC+ shows better prognostic outcome, while the subtype IM+NC- shows the worst prognostic outcome, respectively. Further interrogation of the subtypes identifies long noncoding transcripts (i.e., LINC00844, C3P1, and TRPG1-AS1) as well as an alternatively spliced event of USO1 that play pivotal roles in HCC progression. In addition, we report an oncogenic fusion transcript SLC39A14-PIWIL2 that promotes an aggressive phenotype of HCC. Our comprehensive and systematic analysis of HCC transcriptome identify RNA biotype-based molecular classification, revealing novel driver transcriptome variants that can be potential biomarkers and/or therapeutic targets for precision medicine.

overall_design:
Transcriptome profiling from 68 cases of HCC tissues and 10 adjacent non-tumoral tissues were performed.  Four subtypes:
S1: IM+NC+
S2: IM-NC+
S3: IM+NC-
S4: IM-NC-

first: Hyun

middle: G


title: CUT&Tag recovers up to half of ENCODE ChIP-seq peaks

city: London

first: Monika

last: Moissidis

address: New Hunt's House, Newcomen St

department: Centre for Developmental Neurobiology

country: United Kingdom

institute: King's College London

summary: We comprehensively benchmarked CUT&Tag for H3K27ac and H3K27me3 against published ChIP-seq profiles from ENCODE in K562 cells. Across a total of 30 new and 6 published CUT&Tag datasets we found that no experiment recovers more than 50% of known ENCODE peaks, regardless of the histone mark. We tested peak callers MACS2 and SEACR, identifying optimal peak calling parameters. Balancing both precision and recall of known ENCODE peaks, SEACR without retention of duplicates showed the best performance. We found that reducing PCR cycles during library preparation lowered duplication rates at the expense of ENCODE peak recovery. Despite the moderate ENCODE peak recovery, peaks identified by CUT&Tag represent the strongest ENCODE peaks and show the same functional and biological enrichments as ChIP-seq peaks identified by ENCODE. Our workflow systematically evaluates the merits of methodological adjustments and will facilitate future efforts to apply CUT&Tag in human tissues and single cells.

overall_design: 30 CUT&Tag experiments testing H3K27ac and H3K27me3 antibodies at different concentrations, with and without addition of HDAC inhibitor (TSA), performing SDS- or column-based DNA extraction, and using different numbers of PCR cycles for sequencing library amplification.

first: Di

last: Hu

first: Leyla

last: Abbasova

first: Brian

last: Schilder

first: Alexi

last: Nott

first: Nathan

last: Skene

first: Sarah

last: Marzi


title: Toxicogenomics studies reveal common and specific pathways in pulmonary, hepatic, and neuronal cell models. [SH-SY5H]

first: Chiara

overall_design: Human neuroblastoma cells (SH-SY5Y)  were exposed to non-cytotoxic cadmium concentrations (CdCl2) 10 or 20 µM for 24h. Two biological replicates of controls (cells grown in complete culture medium) were performd and 3 biologial replicates for each cadmium concentration used.


title: 14-3-3 protein constrains insulin secretion in pancreatic beta-cells by regulating mitochondrial function

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

country: Sweden

institute: Karolinska institute

summary: Members of the 14-3-3 protein family are often assumed to have redundant, over-lapping roles due to their high sequence homology and ubiquitous expression. To better understand the role of 14-3-3 in beta-cells, we generated beta-cell-specific 14-3-3 knockout (14-3-3KO) mice, 14-3-3KO mice displayed potentiated insulin secretion due to enhanced mitochondrial function and ATP synthesis.

overall_design: Islets isolated from WT and beta14-3-3 KO mice at 12-14 weeks were dispersed after an overnight recovery. Dead cells were removed by using a dead cell removal kit and MS columns (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). Single-cell RNA-seq libraries were made with the 10x Genomics Chromium Next GEM Single Cell 3' Library Kit (v3.1) and sequenced using an Illumina NovaSeq6000 (100bp x2, 50k reads/cell). Approximately 9600 cells were loaded per sample with an anticipated recovery of 6000 cells.

first: Yves

last: Mugabo

first: Ju

last: Tan

first: Anindya

last: Ghosh

first: Scott

middle: A

last: Campbell

first: Evgenia

last: Fadzeyeva

first: Frédéric

last: Paré

first: Siew

middle: S

last: Pan

first: Maria

last: Galipeau

first: Julia

last: Ast

first: Johannes

last: Broichhagen

first: David

last: Hodson

first: Erin

last: Mulvihill

first: Sophie

last: Petropoulos

first: Gareth

last: Lim


title: Streptococcus mutans suppresses filamentous growth of Candida albicans through secreting mutanocyclin, an unacylated tetramic acid

city: Shanghai

first: LI

last: TAO

state: Shanghai

address: Yangpu district Songhu Road

institute: Fudan University

summary: In this study, we discovered that S. mutans represses filamentous development and virulence in C. albicans through secreting a secondary metabolite, mutanocyclin (a tetramic acid).

overall_design: total RNA profiles of C. albicans cells treated with mutanocyclin

first: Guanghua

last: Huang

first: Li

last: Tao


title: Single cell RNA-seq of brain cells in mice lacking Notch3

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

summary: In this single cell RNAseq analysis, we compared brain transcriptomes from Notch3 knock out and control.

overall_design: Brain single cells from Notch3 knockout and control were sorted into 384-well-plates and RNA-sequenced using the SmartSeq2 method

first: Francesca

last: Del Gaudio

first: Urban

last: Lendahl


title: Effects of Autophagy Modulators Tamoxifen and Chloroquine on the Expression Profiles of Long Non-Coding RNAs in MIAMI Cells Exposed to IFNg

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

summary: Mesenchymal stromal cells (MSCs) can be utilized clinically for treatment of conditions that result from excessive inflammation. In a pro-inflammatory environment, MSCs adopt an anti-inflammatory phenotype resulting in immunomodulation. A sub-type of MSCs referred to as “marrow-isolated adult multilineage inducible” (MIAMI) cells, which were isolated from bone marrow, were utilized to show that the addition of autophagy modulators, tamoxifen (TX) or chloroquine (CQ), can alter how MIAMI cells respond to IFNg exposure in vitro resulting in an increased immunoregulatory capacity of the MIAMI cells. Molecularly, it was also shown that TX and CQ each alter both the levels of immunomodulatory genes and microRNAs which target such genes. However, the role of other non-coding RNAs (ncRNAs) such as long non-coding RNAs (lncRNAs) in regulating the response of MSCs to inflammation has been poorly studied. Here, we utilized transcriptomics and data mining to analyze the putative roles of various differentially regulated lncRNAs in MIAMI cells exposed to IFNg with (or without) TX or CQ. The aim of this study was to investigate how the addition of TX and CQ alters lncRNA levels and evaluate how such changes could alter previously observed TX- and CQ-driven changes to the immunomodulatory properties of MIAMI cells. Data analysis revealed 693 long intergenic non-coding RNAS (lincRNAs), 480 pseudogenes, and 642 antisense RNAs that were differentially regulated with IFNg, IFNg+TX and IFNg+CQ treatments. Further analysis of these RNA species based on the existing literature data revealed 6 antisense RNAs, 2 pseudogenes, and 5 lincRNAs that have the potential to modulate MIAMI cell’s response to IFNg treatment. Functional analysis of these genomic species based on current literature linking inflammatory response and ncRNAs indicated their potential for regulation of several key pro- and anti-inflammatory responses, including NFkB signaling, cytokine secretion and auto-immune responses. Overall, this work found potential involvement of multiple pro-and anti-inflammatory pathways and molecules in modulating MIAMI cells’ response to inflammation.

overall_design: Examination of changes in ncRNA expression due to treatments

first: Rajkaran

last: Banga

first: Veerkaran

first: Amr

last: Eltalla

first: Lauren

last: Shahin

first: Sonam

last: Parag

first: Maha

last: Naim

first: Easha

last: Iyer

first: Neha

last: Kumrah

first: Brian

last: Zacharias

first: Vladimir

last: Beljanski


title: A rapid assessment model for liver toxicity of macrolides and an integrative evaluation for azithromycin impurities

city: Beijing

first: Miaoqing

last: Zhang

state: Please Select

address: No. 1, TianTan XiLi, Dong-cheng district

institute: Institute of Medicinal Biotechnology

summary: we report an assessment of macrolides related liver toxicity by using ADMET prediction, molecular docking, structure-toxicity relationship and experimental verification via detecting the c-fos gene expression in liver cells.We employed the model to virtual screening of azithromycin impurities with high hepatotoxicity, and then experimental confirmed by liver toxicity in zebrafish, and c-fos gene expression.

overall_design: Integrative evaluation for liver toxicology of azithromycin impurities in zebrafish larvae.

first: Jingpu

first: Changqin

last: Hu


title: Transcriptome sequencing analysis of CSF-1Rhigh TAMs and CSF-1Rlow TAMs in colon adenocarcinoma.

city: 南通

first: xingchao

last: wang

state: Jiangsu

address: Xinchengqiao

institute: Affiliated Hospital of Nantong University

summary: Tumor-associated macrophages (TAMs) are a major component of the leukocyte and a heterogenous population in tumors. Recent reports have increasingly suggested that manipulating the function of TAMs may serve as a promising therapeutic strategy against advanced tumors. Our present work indicates that CSF-1R+ TAMs are abundantly found in a significant proportion of COAD specimens. Therefore，to determine the role of the CSF-1Rhigh TAMs in COAD, we sorted the CSF-1Rhigh TAMs and the CSF-1R low TAMs from the colon adenocarcinomas for Smart-seq2. We found that CSF-1Rhigh TAM infiltration involved in multiple tumor immune signaling pathways. CSF-1Rhigh TAMs mostly exhibited a immunosuppressive phenotypes, and were associated with enhanced levels of Treg cells. CSF-1R high TAMs promotes COAD progression by modulating tumor immunity environment

overall_design: RNA samples from CSF-1Rlow TAMs and CSF1Rhigh TAMs in colon adenocarcinomas

first: Fei

last: Qian

first: Baoying

first: Xingchao

last: Wang


title: Transcriptional profiling of cadmium effect in human adipocytes

first: Federica

last: Gilardi

address: chemin de la Vulliette 4

department: University Center of Legal Medicine

institute: University of Lausanne

summary: Adipose tissue is a potential site of accumulation of toxicants, including trace elements, which can have an impact on tissue functionality. To investigate the molecular perturbations induced by Cd in mature adipocytes, we treated Adipose Tissue-derived human mesenchymal stem cells (AD-hMSCs) with 1microM cadmium for 48h and we used microarrays to detail the global program of gene expression.

overall_design: We examined 2 experimental groups: control cells (C) and cadmium treated cells (Cd). For each experimental group we analysed the transcriptional profile of 3 biological replicates.

first: Marie

last: Gasser

first: Sebastien

last: Lenglet

first: Aurelien

last: Thomas


title: DNA methylation-based age acceleration observed in IDH wild-type glioblastoma is associated with better outcome - including in elderly patients [GBMnordic]

first: Pierre

last: Bady

summary: GBM samples (FFPE tissue) obtained from patients treated in clinical trials according to pre-specified clinical criteria (Nordic, n=116).

overall_design: Bisulphite converted genomic DNA from the 116 samples were hybridized to the Illumina Infinium 450 Human Methylation Beadchip

first: Christine

last: Marosi

first: Michael

last: Weller

first: Bjørn

last: Grønberg

first: Henrik

last: Schultz

first: Martin

last: Taphoorn

first: Johanna

last: Gijtenbeek

last: van den Bent

first: Andreas

last: von Deimling

first: Roger

last: Stupp

first: Annika

last: Malmström

first: Monika

last: Hegi


title: Lymphatic vessels drain monosodium urate and activate immunity in gouty arthritis

status: Public on Apr 02 2022

city: shanghai

first: Junli

last: Chang

address: Wanping South Road 725

institute: Long hua Hospital

summary:
Gouty Arthritis (GA) is caused by urate deposition in the joint capsule, cartilage, bone, and surrounding tissues to trigger recurrent attacks of acute joint inflammation. However, the clearance mechanism of urate deposition is still not clear. We aimed to investigate whether lymphatics vessels can drain monosodium and involve in the immune process of GA.
Methods: Inguinal lymph nodes (LNs) in 4 normal volunteers and 4 patients with acute flare of GA were examined by ultrasound. Acute and chronic GA flare mouse models were established by intra-footpad administrations of monosodium urate (MSU) for 1 week or 1 month. Mice were treated with VEGFR-3 inhibitor or undergone popliteal lymph node (PLN) excision or PLN macrophage depletion. The severity of foot inflammation, lymphatic draining function, concentration of uric acid (UA), and macrophage population were examined. Macrophages were co-cultured with MSU-treated lymphatic endothelial cells (LECs) and differential gene expression of LECs was assessed by Agilent gene expression microarray.
Results: 1) Draining LNs were enlarged in patients with GA flare and GA mouse models. 2) The lymphatic function and structure were abnormal in GA mouse models. 3) Acute GA mice had elevated UA levels in draining LNs, but not in the serum, while chronic GA mice had elevated UA levels in both LNs and serum. 4) Blockade of VEGFR-3 reduced foot inflammation in chronic GA mice. 5) MSU induces pro-inflammatory polarization of macrophages by inducing LEC inflammation. 6) PLN local depletion of macrophages or removal of PLNs alleviated foot inflammation in GA.
Conclusions: Lymphatics drain MSU to the draining LNs to clear deposited urate in the distal extremity and induce LECs to stimulate macrophage pro-inflammatory response during GA. We have identified a novel mechanism about MSU clearance and pro-inflammatory macrophage activation, and provided possible therapeutic approach for GA.

overall_design: Lymphatic endothelial cells (LECs) were seeded in 6-well for 24 h at 37°C. Then the cells were treated with PBS and 300μg/ml monosodium urate (MSU) for 24h, respectively. PBS treatment group was the control group, the other group was the MSU group. Every group had three samples.

first: Qianqian

last: Liang


title: Activation of AhR promotes phosphorylation of ARNT isoform 1 as a switch for optimal AhR activity in human T cell malignancies.

city: GALVESTON

first: Kamil

last: Khanipov

state: TX

address: 301 University Blvd

institute: University of Texas Medical Branch

summary: The aryl hydrocarbon receptor nuclear translocator (ARNT) is a transcription factor present in immune cells as a long and short isoform, referred to as isoform 1 and 3, respectively. However, investigation into potential ARNT isoform-specific immune functions is lacking despite the well-established heterodimerization requirement of ARNT with, and for the activity of, the aryl hydrocarbon receptor (AhR), a critical mediator of immune homeostasis. Here, using global and targeted transcriptomics analyses we show that the relative ARNT isoform 1:3 ratio in human T cell lymphoma cells dictates the amplitude and direction of AhR target gene regulation. Specifically, shifting the ARNT isoform 1:3 ratio lower by suppressing isoform 1 enhances, or higher by suppressing isoform 3 abrogates AhR responsiveness to ligand activation through preprograming a cellular genetic background that directs explicit gene expression patterns. Moreover, the fluctuations in gene expression patterns that accompany a decrease or increase in the ARNT isoform 1:3 ratio are associated with inflammation or immunosuppression, respectively. Molecular studies identified the unique casein kinase 2 (CK2) phosphorylation site within isoform 1 as an essential parameter to the mechanism of ARNT isoform-specific regulation of AhR signaling. Notably, CK2-mediated phosphorylation of ARNT isoform 1 is dependent on ligand-induced AhR nuclear translocation and is required for optimal AhR target gene regulation. These observations reveal ARNT as a central modulator of AhR activity predicated on the status of the ARNT isoform ratio and suggest that ARNT-based therapies are a viable option for tuning the immune system to target immune disorders.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Karpas 299 cells were propagated in RPMI-1640 medium (Corning, 15-041-CV) complete with 10% FBS (Atlanta Biologicals, S11550) and 2 mM GlutaMAX (Gibco, 35050-061) at 37 °C, 5% CO2. Hepa-1c1c7 cells were cultured in MEM Alpha (1X) + 2 mM GlutaMAX (Gibco, 32561-037) with 10% FBS at 37 °C, 5% CO2. Stable BpRc1 cells, an Arnt-null variant of Hepa-1c1c7 cells, were cultured in DMEM (Corning, 15-018-CV) with 10% FBS, 2 mM GlutaMAX, and 2 mg/mL puromycin (Invivogen, ant-pr) at 37 °C, 5% CO2. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) (Cerilliant, ED-901-C), a high affinity AhR ligand, was used to activate the AhR pathway in samples that include TCDD in the label. TCDD was added to a final concentration of 10 nM and incubated for 2 hours, followed by total RNA collection.

first: Luke

last: Bourner

first: Israel

last: Muro

first: Amy

last: Cooper

first: Barun

middle: K

last: Choudhury

first: George

last: Golovko

first: Casey

middle: W

last: Wright


title: Expression profilling of C. glabrata response to fluconazole in distinct growth conditions. Role of the Coregulator Pgd1 in such response.

city: Lisbon

first: Miguel

middle: Cacho

last: Teixeira

address: Avenida Rovisco Pais 1

department: Institute for Bioengineering and Biosciences

country: Portugal

institute: Instituto Superior Tecnico

summary: The goal of this study is to compare the C. glabrata transcriptome profile (RNA-seq) upon exposure to the antifungal fluconazole in either liquid or solid medium and assess differential antifungal response. The role of the coregulator PGD1 is clarified through comparison of the transcriptome profiles of WT and PGD1 mutant cells. mRNA profiles of WT and ∆pgd1 were generated by deep sequencing, in triplicate, using Illumina NextSeq. The sequence reads that passed quality filters were analyzed with TopHat followed by HTSeq.

overall_design: Yeast mRNA profiles after 1h fluconazole exposure (liquid growth) or 24h fluconazole exposure (solid growth) WT and ∆pgd1 cells were generated by RNA-Seq, in triplicate, using Illumina NextSeq

first: Mónica

last: Galocha

first: Pedro

last: Pais

middle: C


title: Control of regulatory T cell function by the non-oxidative pentose phosphate pathway

city: shang hai

first: Qi

last: Liu

address: 280 S. Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

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

overall_design: Refer to individual Series


title: Toxicogenomics studies reveal common and specific pathways in pulmonary, hepatic, and neuronal cell models.

first: Chiara

last: Urani


title: Reduction N6AMT1-mediated 6mA DNA modification promotes tumor progression [MeDIP-seq]

city: Tianjin

first: Ping

last: Wang

address: No22.Qixiangtai Rd.,Heping Dist

institute: Tianjin Medical University

type: Methylation profiling by high throughput sequencing

summary: Background: DNA N6-methyladenosine (6mA) as a novel epigenetic signaling modification in humans and has been implicated in progression and tumorigenesis of several cancers. However, the function and mechanisms of 6mA in breast cancer (BC), the most common cancer among women, are unclear. Methods: The clinical role of 6mA was investigated by immunohistochemical (IHC) staining and Kaplan-Meier analysis of BC and their normal tissues. 6mA immunoprecipitation (IP) sequencing, mRNA sequencing and bioinformatics analysis were used to screen and validate the direct targets of 6mA. Results: Decreases in N6AMT1 correlated with the extent of 6mA in BC tissues and predicted a worse overall survival of BC patients. Knockdown N6AMT1 markedly reduced 6mA in DNA and promoted the proliferation and migration of BC in vivo and in vitro, whereas overexpression of N6AMT1 had the opposite effect, indicating N6AMT1 is a functional methyltransferase for DNA 6mA and relates with gene transcription. Critical negative regulators of the cell cycle, such as RB1, P21, REST and TP53 were identified as targets of N6AMT1 in BC. Conclusion: These results suggest N6AMT1 enhances DNA 6mA levels to repress tumor progression via transcriptional regulation of cell cycle inhibitors.

overall_design: Global 6mA profiles of MDA-MB-453 cells by transfected with siRNAs for N6AMT1 (n=2) or Controls (n=2).

first: Jiongyu

last: Chen

first: Yixuan

last: Zhuang

first: Jinfeng

last: Ning

first: Wei

first: Yiteng

last: Huang

first: Xueqiong

last: Lin

first: Lin

last: Peng

first: Donghong

last: Zhang


title: Transcriptome and proteome analysis in LUHMES cells overexpressing alpha-synuclein

city: Hannover

first: Matthias

last: Hoellerhage

address: Klinik für Neurologie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

summary: Differential transcriptome analysis in LUHMES cells overexpressing human wild-type alpha-synuclein or GFP

overall_design: Total RNA was obtained from LUHMES cells that were transduced with adenoviral vectors to overexpress human wild-type alpha-synuclein or GFP under a CMV promoter four days after transduction

last: Höllerhage

first: Günter

last: Höglinger


title: The spliceosome is an exploitable vulnerability in RB1-mutant cancer

city: Houston

first: Yao

last: Yu

address: 1155 Pressler

institute: UT MD Anderson Cancer Center

summary: RB transcriptional corepressor 1 (RB1) is frequently mutated in human cancers, we discover a new target of oncogenic stress in RB1-mutant cells.

overall_design: RNA-seq, ChIP-seq and WES are used to profile RB1 mutant fibroblasts, RB1 mutant iPSC derived mesenchyma stem cell, osteoblast and osteosarcoma cancer cell lines.

first: Jian

last: Tu

first: Dung-Fang

last: Lee


title: Transcriptomics analysis investigate the molecular mechanisms of carnosol on t-BHP induced Human retinal microvascular endothelial cells (HRMECs)

first: Yue

last: Ren

address: Beijing University of Chinese Medicine

institute: Beijing University of Chinese Medicine

summary:
Purpose: Transcriptomics analysis provides a genome-wide digital gene expression profile, which reveals the regulation of gene transcription at the overall level. This study aimed to investigate the underlying mechanism of carnosol against t-BHP-induced Human retinal microvascular endothelial cells (HRMECs) oxidative stress injury.
Methods: HRMECs were treated with 10 μM carnosol for 24 h, followed by 300 μM t-BHP for 4 h to simulate the oxidative stress environment in vitro. Oligo dT was used to generate the cDNA library. After constructing the cDNA library, the quality of the library was detected with Agilent biological analyzer, and the cDNA was sequenced with Illumina.
Conclusions: Our data provide a systematic perspective for the mechanism of carnosol against HRMECs oxidative stress injury, which lay a foundation for further study on carnosol.

overall_design: Three treatments were considered, namely normal group, model group (t-BHP), administration group (carnosol). Each group contained three biological replicates.

first: Yanan

first: Kaiyang

first: Zhan

last: Shu

first: Tianyi

last: Lv

first: Zijun

first: Wenqing

last: Feng

first: Yanling


title: Reduction N6AMT1-mediated 6mA DNA modification promotes tumor progression

first: Ping

last: Wang


title: Analysis of genes regulated by neural activity in D. melanogaster

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

summary: To identify genes upregulated by neural activity in the brain of Drosophila melanogaster, we have performed comprehensive gene expression profiling analysis. Samples were prepared from unstimulated animals (1-1 to 1-4) and aniamals which experienced induced neural activity (sample 2-1 to 2-4).

overall_design: Neural activity-induced gene in D. melanogaster brain was searched by comparing control (w/o stimulation)and experimental (with artificial neural activity) samples. Four independent samples were prepared for each condition.

first: Kiya

last: Taketoshi

first: Takayanagi-Kiya

last: Seika


title: Comparative analyses of erythroid cells from ES cells and cord blood CD34+ cells reveal mechanisms for defective expansion and enucleation of ES cell-derived erythroid cells

city: New York

first: Xiuli

last: An

address: 310 E 67th St

institute: New York Blood Center

summary: We used both RNA-seq and ATAC-seq analyses to uncovered mechanisms for the limited expansion and impaired enucleation in ES CD34+ cell-derived orthochromatic erythroblasts

overall_design: Examination the differences of gene expression and chromatin accessibility between ES CD34+ cell-derived orthochromatic erythroblasts and CB CD34+ cell-derived orthochromatic erythroblasts.


title: ChIP-seq analyses of human odontoblast-like (OD) cells transfected with siRNA for IKBz

city: Okayama

first: Shigeki

last: Suzuki

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Operative Dentistry

institute: Okayama University

summary: Enforced enhancement of H3K4me3 and H3K27ac, active chromatin marks, by inhibiting histone demethylases and deacetylases is positively linked with hard tissue formation by inducing matrix synthesis and osteo/odontogenic differentiation. However, the key endogenous epigenetic modifier of odontoblasts to regulate the expression of the genes coding dentin extracellular matrix (ECM) proteins has not been identified yet. We herein focused on IκBζ, which was originally identified as transcriptional regulator for NF-B and recently regarded as the local epigenetic modifier by independently on NF-B, and demonstrated that the IκBζ null mice exhibited thicker dentin width and narrower pulp chamber with aged mice having more drastic phenotypes. At 6 months old, dentin fluorescent labeling exhibited that dentin synthesis was significantly accelerated in the incisors of IκBζ null mice. In molars of IκBζ null mice, aggressive reactionary dentin adjacent to pulp horn was exhibited. Mechanistically, COL1A2 and COL1A1 collagen genes were increased in the odontoblasts rich fraction of IκBζ null mice than that of wild type in vivo and human odontoblasts-like cells transfected with siRNA for IκBζ than the control siRNA transfected cells in vitro. Further, the direct binding of IκBζ to COL1A2 promoter suppressed COL1A2 expression and the local active chromatin status marked with H3K4me3. By whole-genomic identification of H3K4me3 enrichments revealed that ECM and ECM organization-related gene loci were selectively activated by the knockdown of IκBζ, which consistently resulted in the up-regulation of these genes. Collectively, these results indicated that IκBζ is the key negative regulator of dentin formation in odontoblasts since the deletion of IκBζ expression enhanced dentin formation by inducing dentin ECM and ECM organization-related gene expression via altering the local chromatin status marked by H3K4me3. Therefore, IκBζ is a potential target for improving the clinical outcomes of dentin regeneration therapies such as pulp capping and pulp revitalization procedures.

overall_design: Comparison of the H3K4me3 and H3K27me3 peaks between control siRNA- and si-IKBz-transfected OD cells.

first: Hanu

last: Yuan

first: Satoru

last: Yamada


title: Effects of glucose on gene expression of human dental pulp cells under odontogenic differentiation

city: Bangkok

first: Nakarin

last: Kitkumthorn

address: Yothee road

department: Oral Biology

country: Thailand

institute: Mahidol University

summary: Human dental pulp cells have the ability to differentiate into odontoblast cells under various stimuli. The objective of our study is to investigate the efffects of glucose on gene expression of human dental pulp cells that under go odontogenic differentiation. Expression microarray were performed to identify the genes that were affected by short-term and long-term exposure to high glucose levels.

overall_design: Human dental pulp cells were cultures in Low glucose (LG) or High glucose (HG) cultured medium under odontogenic inducing conditions. On culture day 1 and days14  RNA were collected.Three independent experiments were performed at each time using different donors for each experiment.

first: Narakin

last: Kitkumtorn

first: Rudee

last: Surarit

first: Sivaporn

last: Horsophonphong


title: LncRNA and mRNA expression data from TMZ-resistant cell line

status: Public on Mar 30 2022

city: Shenzhen

first: Zhou

last: Jian

address: Shenzhen

institute: Shenzhen University

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

summary:
The discovery of long non-coding RNAs (lncRNAs) has improved the understanding of development and progression in various cancer sub-types. However, the role of lncRNAs in temozolomide (TMZ) resistance in glioblastoma (GBM) remains largely undefined.
In this present study, the differential expression of lncRNAs were identified between U87 and U87TR (TMZ-resistant) cells and to find potential therapeutic targets of GBM for improving the survival of patients.

overall_design: TMZ-sensitive cell line U87 and TMZ-resistant cell line U87TR were used for RNA extraction and hybridization on microarrays. Using the gene expression microarray data, we sought to assess the mRNA and lncRNA expression profiles in U87 and U87TR.

first: Jian

last: Zhou

first: Ningbo

last: Xu

first: Wenhui

last: Tang

first: Hongbo

last: Guo


title: Small RNA profile of 4 biofluids from healthy individuals B [EXR-KWANG1jo8Fqz-AN]

city: Seattle

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Endogenous and exogenous extracellular RNAs will be characterized in four body fluids (plasma, serum, CSF and saliva) collected at the same time from 134 healthy subjects ranging in age from 31 to 101 years old.  Small RNAs contained in these samples will be profiled by small RNA-seq using unfractionated biofluids and purified extracellular vesicles.

overall_design: smRNA-seq of plasma, serum, CSF and saliva samples from 134 healthy individuals, no replicates

first: David

last: Galas

first: Elaine

last: Peskind

first: Saroja

last: Somasundaram

first: Alton

last: Etheridge

first: Nikita

last: Sakhanenko

last: Baxter


title: Angiotensin II disrupts the cytoskeletal architecture of human urine-derived podocytes and results in activation of the renin-angiotensin system

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

summary: High blood pressure is one of the major public health problems which causes severe disorders in several tissues including the human kidney. One of the most important signaling pathways associated with the regulation of blood pressure is the renin-angiotensin system (RAS), with its main mediator angiotensin II (ANGII). Elevated levels of circulating and intracellular ANGII and aldosterone lead to pro-fibrotic, -inflammatory and -hypertrophic milieu that causes remodelling and dysfunction in cardiovascular and renal tissues. Furthermore, ANGII has been recognized as major risk factor for the induction of apoptosis in podocytes, ultimately leading to chronic kidney disease (CKD).    In the past, disease modeling of kidney-associated malignancies was extremely difficult, as the derivation of kidney originated cells is very challenging. Here we describe a differentiation protocol for reproducible differentiation of SIX2-positive urine derived renal progenitor cells (UdRPCs) into mature podocytes bearing typical foot processes. The UdRPCs-derived podocytes show the ability to execute Albumin endocytosis and the activation of the renin-angiotensin system by being responsive to ANGII stimulation. Our data reveals the ANGII dependent downregulation of NPHS1 and SYNPO, resulting in the disruption of the complex podocyte cytoskeletal architecture, as shown by immunofluorescence-based detection of α–ACTININ. In the present manuscript we confirm and propose UdRPCs as a unique cell type useful for studying nephrogenesis and associated diseases. Furthermore, the responsiveness of UdRPCs-derived podocytes to ANGII implies potential applications in nephrotoxicity studies and drug screening.

overall_design: The transcriptomes of UdRPC-derived podocytes with and without Angiotensin II treatment were compared by microarray analysis (PrimeView Human Gene Expression Array, Affymetrix, Thermo Fisher Scientific).

first: Lars

last: Erichsen

first: James

last: Adjaye


title: Small RNA profile of 4 biofluids from healthy individuals


title: RNAseq of GL261 tumor endothelial cells from wild type and Eltd1-/- mice

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

institute: Uppsala University

summary: Eltd1 is widely expressed in endothelial cells. We have reported that the expression of Eltd1 is highly up-regulated in glioma vessels. Other studies have shown that Eltd1 is up-regulated in vessels in other types of tumors, and has been suggested as a vascular target for anti-angiogenesis therapy. However, the role of Eltd1 in vessels is largely unknown. We isolated endothelial cells from healthy brain tissue and GL261 tumor tissue, and analyzed the role of Eltd1 in tumor angiogenesis by analyzing the endothelial gene profile from wild type and Eltd1-/- mice.

overall_design: We injected GL261 intracranially to C57BL/6 wild type and Eltd1-/- mice. Tumors were dissected under a stereological microscope. To isolate endothelial cell mRNA from heathy brain tissue and tumor tissue, we took advantage of the mouse that expressing a fusion eGFP-L10a ribosomal protein under control of the VE-cadherin promoter, and crossed it with the Eltd1-/- mouse. Using translating ribosome affinity purification (TRAP) strategy, endothelial specific mRNA was isolated and were further prepared for RNAseq analysis.

first: Hua

last: Huang

first: Maria

last: Georganaki

first: Anna

last: Dimberg


title: Hepatic transcriptome analysis after acute and chronic glucocorticoid exposure combined with androgen receptor antagonism.

status: Public on Mar 28 2022

city: Leiden

first: Jacobus

middle: Cornelis

last: Buurstede

state: Zuid-Holland

address: Albinusdreef 2

department: Endocrinology

country: Netherlands

institute: Leiden University Medical Center

summary:
Aim: We investigated the effect of acute and chronic glucocorticoid exposure on the hepatic transcriptome and its dependency on active androgen signaling.
Methods: Adult male mice were used in the experiments. For the chronic exposure, mice were implanted with CORT (20mg) or vehicle pellets and administered ENZA (40mg/kg/day) or solvent via oral gavage. For the acute exposure, mice were pre-treated with ENZA (40mg/kg/day) or solvent every 12 hours for 24 hours via oral gavage and subsequently subcutaneously injected with 3mg/kg CORT or vehicle. Livers of all animals were dissected after 3 hours and snap-frozen. Next, total RNA was isolated and send for 100bp paired-end sequencing by BGI.

overall_design: Hepatic mRNA profiles of male mice studying glucocorticoid-androgen crosstalk.

first: Onno

last: Meijer

first: Jan

last: Kroon


title: Obesity Potentiates TH2 Immunopathology Via Dysregulation of PPARg

status: Public on Mar 29 2022

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary: Clinically, obesity is strongly associated with severe TH2 immunopathology, though the physiological, cellular, and molecular underpinnings of this association remain obscure. We demonstrate that obese mice are susceptible to severe atopic dermatitis (AD), a major manifestation of TH2 immunopathology and disease burden in humans. Mechanistically, we show that dysregulation of the nuclear hormone receptor peroxisome proliferator-activated receptor gamma (PPARg) in T cells is a causal link between obesity and the increased TH2 immunopathology. We find that PPARg directly controls a cellular metabolic transcriptional program that restrains nuclear gene expression of the chief TH2 effector cytokines interleukin-4 (IL-4) and interleukin-13 (IL-13). Accordingly, thiazolidinediones (TZDs), potent PPARg agonists, robustly protect obese mice from TH2 immunopathology. Collectively, these findings establish PPARg as a molecular link between obesity and TH2 immune homeostasis and identify TZDs as novel therapeutic candidates for TH2 immunopathology.

overall_design: ChIP-seq experiments were conducted multiple times, but only one replicate was used for this publication.  Input was used for background subtraction.  Single end sequencing yielded 13.23M 100bp reads. Bowtie 2 was used for alignment with mm10.  Peak calling, motif analyses, and other data analysis were performed using HOMER, a software suite for ChIP-seq analysis. The methods are freely available at http://biowhat.ucsd.edu/homer/. Only tags that mapped uniquely to the genome were considered for further analysis.

first: Sagar

last: Bapat

first: Christopher

last: Liddle


title: A genome-wide CRISPR activation screen identifies PRRX2 as a regulator of enzalutamide resistance in prostate cancer

city: Chicago

first: Sarki

last: Abdulkadir

state: IL

address: 303 E Superior St

institute: Northwestern University


title: H3K36 Dimethylation Shapes the Epigenetic Interaction Landscape by Directing Repressive Chromatin Modifications in Embryonic Stem Cells

city: Santiago de Compostela

first: Carmen

last: Rivas

address: Avda Barcelona

department: CIMUS

country: Spain

institute: Universidad de Santiago de Compostela

summary: Epigenetic modifications on the chromatin do not occur in isolation. Chromatin associated proteins and their modification products form a highly interconnected network, and disturbing one component may rearrange the entire system. We see this increasingly clearly in epigenetically dysregulated cancers. It is important to understand the rules governing epigenetic interactions. Here, we use the mouse embryonic stem cell (mESC) model to describe in detail the relationships within the H3K27-H3K36-DNA methylation subnetwork. In particular, we focus on the major epigenetic re-organization caused by deletion of the histone 3 lysine 36 methyltransferase NSD1, which in mESCs deposits nearly all of the intergenic H3K36me2. Although disturbing the H3K27 and DNA methylation (DNAme) components also affects this network to a certain extent, the removal of H3K36me2 has the most drastic effect on the epigenetic landscape, resulting in full intergenic spread of H3K27me3 and a substantial decrease in DNAme. By profiling DNMT3A and CHH methylation (mCHH), we show that H3K36me2 loss upon Nsd1-KO leads to a massive re-distribution of DNMT3A and mCHH away from intergenic regions and towards active gene bodies, suggesting that DNAme reduction is at least in part caused by redistribution of de novo methylation. Additionally, we show that pervasive acetylation of H3K27 is regulated by the interplay of H3K36 and H3K27 methylation. Our analysis highlights the importance of H3K36me2 as a major determinant of the developmental epigenome and provides a framework for further consolidating our knowledge of epigenetic networks.

sample_organism:
Drosophila melanogaster
Mus musculus

platform_organism:
Drosophila melanogaster
Mus musculus

overall_design: WGBS, RNA-seq, and ChIP-seq for histone H3 post-translational modifications in mouse embryonic stem cells (mESC).

first: Haifen

last: Chen

first: Bo

last: Hu

first: Cynthia

last: Horth

first: Eric

last: Bareke

first: Phillip

last: Rosenbaum

first: Sin

middle: Y

last: Kwon

first: Jacinthe

last: Sirois

first: Daniel

middle: N

last: Weinberg

first: Chao

last: Lu

first: William

last: Pastor

first: Jacek

last: Majewski


title: Control of regulatory T cell function by the non-oxidative pentose phosphate pathway [ATAC-seq]

first: Qi

last: Liu

address: 280 S. Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

summary: Non-oxidative pentose phosphate pathway (PPP) is a crucial gatekeeper of glucose catabolism in metabolic tissues. However, its role in regulatory T cells (Tregs) remains unknown. Here we report deleting transketolase (TKT), an indispensable enzyme of non-oxidative PPP, in Tregs caused a fatal auto-immune disease in mice. TKT deletion impaired suppressive capability without disturbing Treg cell number. Mechanistically, TKT deficiency caused Treg metabolic remodeling with decreased glucose catabolism, activated fatty acid and amino acid catabolism and uncontrolled oxidative phosphorylation. Moreover, excessive ammonia from deregulated amino acid catabolism impaired mitochondrial fitness while reduced α-ketoglutarate/succinate ratio led to DNA hypermethylation, limiting functional gene expression and suppressive activity of TKT-deficient Tregs. Therefore, our study identifies non-oxidative PPP as a new pathway for controlling Treg function.

overall_design: 50,000 CD4+CD25+YFP+ Tregs were isolated from 7-week-old chimeric female WT and cKO mice by FACS and washed once with 50 μl cold PBS buffer. Supernatant was discarded by centrifugation at 500 g, 4oC for 5 min. Lysed the cell pellet in 50 μl cold lysis buffer (10 mM NaCl, 10 mM pH7.4 Tris-HCl; 0.5%NP-40 and 3mM MgCl2) and centrifuge immediately at 500g, 4°C for 10 min. Transposition reaction and purification PCR amplification were performed using Nextera XT DNA Library Preparation Kit (Illumina, Cat. #FC-131-1096) and Qiagen MinElute PCR Purification Kit (Qiagen, Cat. #28004). Illumina Novaseq 6000 was used for sequencing.

first: Xuemei

last: Tong


title: Correcting altered immunological responses in obesity restores efficacy of targeted biologic therapy for inflammatory disease

city: San Francisco

first: Alexander

last: Marson

address: 1650 Owens Street

institute: Gladstone-UCSF Institute of Genomic Immunology

summary: Decades of work have elucidated cytokine signaling and transcriptional pathways that control T cell differentiation and have led the way to targeted biologic therapies that are effective in a range of autoimmune, allergic, and inflammatory diseases. More recent evidence indicates that obesity and other shifts in systemic metabolism can also influence the function of cells in the immune system, although the mechanisms and possible effects on immunotherapy outcomes remain largely unknown. Here, using two models of atopic dermatitis (AD), we show that lean and obese mice mount strikingly different immune responses. Obesity converts the classical AD-associated type 2 T helper cell (TH2)-predominant disease into a more severe disease with prominent TH17 inflammation. In addition to this immunopathologic difference, we observed strikingly divergent responses to biologic therapies targeting TH2 cytokines, which robustly protected lean mice but significantly exacerbated disease in obese mice. Single-cell RNA sequencing (scRNA-seq) coupled with genome-wide binding analysis revealed decreased activity in nuclear receptor PPARg (peroxisome proliferator-activated receptor gamma) activity in TH2 cells from obese mice relative to lean mice. Conditional ablation of PPARg in T cells identified a novel function for PPARg as required for focusing the in vivo TH response towards a TH2-predominant state and preventing aberrant non-TH2 inflammation. Treatment of obese mice with a small molecule PPARg agonist prevented development of TH17 pathology in AD and unlocked robust therapeutic responsiveness to targeted anti-TH2 biologics. These studies reveal the effects of obesity on immunological disease and demonstrate a precision medicine approach to target the immune dysregulation caused by obesity to restore efficacy of a biological immunotherapy.

overall_design: Mice were challenged with MC903-AD on their ears, and lesional CD4+ T cells were isolated by FACS sorting on Day 10 of the challenge for single cell sequencing using the 10X platform.

first: Sagar

middle: P

last: Bapat

first: Cody

last: Mowery

first: Ronald

last: Evans

first: Ye

last: Zheng


title: Small RNA profile of 4 biofluids from healthy individuals C [EXR-KWANG15hiHRW-AN]

first: Kai

last: Wang

first: David

last: Galas

first: Elaine

last: Peskind

first: Saroja

last: Somasundaram

first: Alton

last: Etheridge

first: Nikita

last: Sakhanenko

last: Baxter


title: Acylation probing of “generic” RNA libraries reveals critical influence of loop constraints on reactivity

city: Stanford

first: Lu

last: Xiao

state: California

address: 369 N-S Axis, Stauffer I, 109

institute: Stanford University

summary: The reactivity of RNA 2’-OH acylation is broadly useful both in probing structure and in preparing conjugates. To date, this reactivity has been analyzed in limited sets of biological RNA sequences, leaving open questions of how reactivity varies inherently without regard to sequence in structured contexts. To investigate, we constructed and probed “generic” structured RNA libraries using homogeneous loop sequences. We employed deep sequencing to carry out a systematic survey of reactivity. We find a wide range of RNA reactivities among single-stranded sequences, with nearest neighbors playing substantial roles. Remarkably, certain small loops are found to be far more reactive on average (up to 4000-fold) than single-stranded RNAs, due to conformational constraints that enhance reactivity. Among loops, we observe large variations in reactivity based on size, type, and position. The results lend insights into RNA designs for achieving high-efficiency local conjugation and provide new data to refine structure analysis.

overall_design: 12 samples are analyzed, including replicates for each conditions: (1) A-case RNA library treated with 200mM NAIN3 (duplicate); (2) A-case RNA library treated with 25mM 1M7 (duplicate); (3) A-case RNA library treated DMSO (duplicate, as control); (4) U-case RNA library treated with 200mM NAIN3 (duplicate); (5) U-case RNA library treated with 25mM 1M7 (duplicate); (6) U-case RNA library treated DMSO (duplicate, as control).

first: Linglan

last: Fang

first: Eric

last: Kool


title: Generation and characterisation of pre-neural progenitors and neural crest from human embryonic stem cells.

status: Public on Mar 27 2022

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

summary: The spinal cord emerges from a niche of neuromesodermal progenitors (NMPs) formed and maintained by Wnt/FGF signals in the posterior end of the embryo. NMP-like cells can be generated from human pluripotent stem cells providing a promising source for spinal cord replacement therapies. However, these progenitors are often transient and unable to produce the full range of rostrocaudal spinal cord identities in vitro. Here we report the generation of NMP-derived pre-neural progenitors (PNPs). These PNPs maintain pre-spinal cord identity by co-expressing the transcription factors SOX2 and CDX2, while losing the mesodermal potential of NMPs by downregulating TBXT. They gradually adopt more posterior identity by activating collinear HOX gene expression, and in parallel undergo an epithelial-to-mesenchymal transition to give rise to neural crest (NC) cells with corresponding rostrocaudal identity.

overall_design: Bulk mRNA sequencing was completed using 47 RNA samples extracted from differentiated WA09 hESCs. Each experiment (n=3) consisted of 12 time-points: undifferentiated WA09 human embryonic stem cells (t0), NMPs-likes cells (36h) and PNPs/NC cells (P1-P10). P9 samples contain 2 experimental repeats.  Four additional samples were collected during each experiment: At passage 5 and passage 8 mesenchymal (MES) or epithelial (EPI) cells were enriched by selective detachment.

first: Fay

last: Cooper

first: George

middle: E

last: Gentsh

first: Andreia

last: Bernardo

first: Jim

last: Smith


title: Progression from the preleukemic stage to acute leukemia in TAL1/SCL-LMO1 transgenic mice

city: Montreal

first: mathieu

last: tremblay

state: QC

address: 2950 Chemin de Polytechnique, pav marcelle-coutu 1432

country: Canada

institute: Université de Montréal/IRIC

summary: The TAL1/SCL and LMO1 oncogenic transcription factors establish a pre-leukemic state by reprogramming thymocytes into self-renewing pre-leukemic stem cells (pre-LSCs). Pre-TCR signaling accelerates the progression to T-cell acute lymphoblastic leukemia (T-ALL). To directly address the importance of pre-TCR signaling in driving progression to T-ALL, we leverage on Cd3-deficient mice in which pre-TCR signaling and progression through β-selection is abrogated.  In the absence of pre-TCR signaling in Cd3ε-deficient SCL-LMO1 transgenic mice, T-ALL onset is delayed by 150 days. Despite the absence of pre-TCR/CD3 signaling in these mice, we show that leukemic thymocytes exhibit the gene expression profiles of thymocytes that have undergone β-selection, i.e. exhibiting a re-activation of pre-TCR-driven proliferation signature, and a down regulation of HEB/TCF12 target genes.  Lastly, monoallelic deletion of Heb is sufficient to accelerate T-ALL onset in Cd3ε-deficient SCL-LMO1 transgenic mice. Together, these results underscore the role of HEB/TCF12 as a tumor suppressor in T-ALL.

overall_design: Gene expression comparison of Cd3e-deficient non-transgenic thymocytes, with pre-leukemic Cd3-deficient TAL1/SCL-LMO1 transgenic thymocytes, and leukemic TAL1/SCL-LMO1 transgenic thymocytes in the absence (Cd3ε-/-) or presence (Cd3ε+/+) of preTCR signaling.

first: Diogo

middle: F

last: Veiga

first: Mathieu

last: Tremblay

first: Sabine

last: Herblot

first: Patrick

last: Gendron

first: Sébastien

last: Lemieux

first: Trang

last: Hoang


title: JunB plays a crucial role in the development of regulatory T cells by increasing a sensitivity to interleukin-2

city: Tokyo

first: Takaharu

last: Katagiri

address: 5-21-16 Omori-Nishi,Ota-ku

department: Biochemistry

institute: Toho University School of Medicine

summary: The AP-1 transcription factor JunB is crucial for multiple biological processes, such as placental development and bone homeostasis. We recently reported that JunB plays an essential role in development of Th17 cells, and thus Junb-deficient mice are resistant to experimental autoimmune encephalomyelitis. However, the role of JunB in CD4+ T cells under other inflammatory disease conditions is unknown. Here we show that mice lacking JunB in CD4+ T cells (Junbfl/flCd4-Cre mice) were more susceptible to dextran sulfate sodium (DSS)-induced colitis, a disease model induced by innate immune cells. While the Th17-associated genes Il17a and Il22 are shown to be protective against DSS-induced colitis, their expression was not impaired in the colon of Junbfl/flCd4-Cre mice. In addition to the defect in Th17 development, the colon of Junbfl/flCd4-Cre mice exhibited reduction in regulatory T (Treg) cells. Junb-deficient CD4+ T cells needed high concentration of IL-2 for differentiating into Treg cells in vitro because of their hyporesponsiveness to IL-2. Mechanistically, JunB directly up-regulated expression of CD25, the α−chain of high affinity IL-2 receptor, thereby increasing a sensitivity to IL-2 under Treg-inducing conditions. We uncover a crucial role for JunB in development of Treg cells and defense against an epithelial cell damage-induced colitis.

overall_design: To further characterize the Treg cells in Junbfl/flCd4-Cre mice, we performed genome-wide transcriptome analysis using total RNA prepared from in vitro differentiated Treg cells.

first: Soh

last: Yamazaki

first: Hiroyasu

last: Nakano


title: RNA sequencing  of tomato seedlings infected with Fusarium responding to an Artemissia Absinthium essential oil

status: Public on Mar 25 2022

city: Madrid

first: Marta

last: Berrocal-Lobo

state: Madrid

address: Antonio Nováis 10, s/n

department: System and Natural Resources

institute: School of Forestry Engineering and Natural Resources

summary: Tomato seedlings with coated seeds of 12days responding to an Artemissia Absinthium essential oil shows increased tolarance to Fusarium

overall_design: Tomato seeds were coated with an Artemissia absinthium essential oil growth and inoculated with Fusarium oxysporum sp. oxysporum radicis lycopersici, sampling tissues after 12 days of inoculation, for RNAseq analysis, three independent biological samples were sampled  from three independent experiments.

first: César

last: Poza-Carrión

first: Azucena

last: González-Coloma

first: MaríaFé

last: Andrés


title: A Novel platform for single-cell RNA-sequencing and its application in genome medicine

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

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

overall_design: Refer to individual Series


title: Targeting Xist with compounds that disrupt RNA structure and X-inactivation

city: hopkinton

first: barry

last: kesner

state: ma

address: 1 chamberlain street

institute: molecular biology

summary: Although >98% of our genome is noncoding, nearly all drugs on the market target one of ~700 disease-related proteins. The historical reluctance to invest in noncoding RNA stems partly from requirements for drug targets to adopt a single stable conformation. Most RNAs can adopt several conformations of similar stabilities. RNA structures also remain challenging to determine. Nonetheless, an increasing number of diseases is now being attributed to noncoding RNA and the ability to target them would vastly expand the chemical space for drug development. Here we devise a screening strategy and identify small molecules that hit the non-coding RNA prototype, Xist. The X1 compound has drug-like properties and binds specifically to Xist’s RepA motif in vitro and in vivo. SAXS analysis reveals that RepA can adopt multiple conformations but favors one structure in solution. X1 binding reduces RepA’s conformational space, displaces cognate interacting protein factors (PRC2, SPEN), suppresses H3K27 trimethylation, and blocks initiation of X-inactivation. X1 inhibits cell differentiation and growth in a female-specific manner. Thus, RNA can be systematically targeted by drug-like compounds that disrupt RNA structure and epigenetic function.

overall_design:
Day 5 TST cells are subjected to drug or control and then used in three deep sequencing analyses, RNA sequencing, H3K27me3 ChIP, and Suz12 ChIP.

Please note that RAb5-*.div.RAb5-*bw files were generated from both input and ChIP samples, and are linked to the corresponding ChIP-Suz12* sample records.

first: Rodrigo

last: Aguilar

first: Kerrie

middle: B

last: Spencer

first: Barry

last: Kesner

first: Noreen

last: Rizvi

first: Maulik

middle: D

last: Badmalia

first: Tyler

last: Mrozowich

first: Jonathan

last: Mortison

first: Carlos

last: Rivera

first: Graham

first: Julia

last: Burchard

first: Peter

last: Dandliker

first: Trushar

middle: R

last: Patel

first: Elliott

last: Nickbarg

first: Jeannie

last: Lee


title: Fusion protein-driven IGF-IR/PI3K/AKT signals deregulate Hippo pathway promoting oncogenic cooperation of YAP1 and FUS-DDIT3 in myxoid liposarcoma

city: Heidelberg

first: Cihan

last: Erkut

address: Im Neuenheimer Feld 581

department: Applied Functional Genomics

institute: German Cancer Research Center

summary: Myxoid liposarcoma (MLS) represents a common subtype of liposarcoma molecularly characterized by a recurrent chromosomal translocation that generates a chimeric FUS DDIT3 fusion gene. The FUS-DDIT3 oncoprotein has been shown to be crucial in MLS pathogenesis. Acting as a transcriptional dysregulator, FUS-DDIT3 stimulates proliferation and interferes with adipogenic differentiation. As the fusion protein represents a therapeutically challenging target, a profound understanding of MLS biology is elementary to uncover FUS DDIT3-dependent molecular vulnerabilities. Recently, a specific reliance on the Hippo pathway effector and transcriptional co-regulator YAP1 was detected in MLS; however, details on the molecular mechanism of FUS-DDIT3-dependent YAP1 activation, and YAP1's precise mode of action remain unclear. In elaborate in vitro studies, employing RNA interference-based approaches, small-molecule inhibitors, and stimulation experiments with IGF-II, we show that FUS-DDIT3-driven IGF-IR/PI3K/AKT signaling promotes stability and nuclear accumulation of YAP1 via deregulation of the Hippo pathway. Co-immunoprecipitation and proximity ligation assays revealed nuclear co localization of FUS-DDIT3 and YAP1/TEAD in FUS-DDIT3-expressing mesenchymal stem cells and MLS cell lines. Transcriptome sequencing of MLS cells demonstrated that FUS DDIT3 and YAP1 co-regulate oncogenic gene signatures related to proliferation, cell cycle progression, apoptosis, and adipogenesis. In adipogenic differentiation assays, we show that YAP1 critically contributes to FUS-DDIT3-mediated adipogenic differentiation arrest. Taken together, our study provides mechanistic insights into a complex FUS-DDIT3-driven network involving IGF-IR/PI3K/AKT signals acting on Hippo/YAP1, and uncovers substantial cooperative effects of YAP1 and FUS-DDIT3 in the pathogenesis of MLS.

overall_design: siRNA-mediated knockdown of FUS-DDIT3 and YAP1 in MLS 402-91

first: Ruth

last: Berthold

first: Claudia

last: Scholl

first: Stefan

last: Fröhling

first: Wolfgang

last: Hartmann


title: ESCRT-I controls lysosomal membrane protein homeostasis and restricts MCOLN1-dependent TFEB/TFE3 signaling.

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

summary: Within the endolysosomal pathway in mammalian cells, ESCRT complexes facilitate degradation of membrane proteins from limiting membranes of late endosomes. Recent studies revealed that yeast ESCRT proteins also sort for degradation, ubiquitinated proteins from vacuolar membrane. However, whether mammalian ESCRTs perform similar function at lysosomes remained unknown. Here, we studied the involvement of mammalian ESCRT-I in maintaining lysosomal membrane homeostasis and its implication in lysosome-related signaling. We show that ESCRT-I restricts the size of lysosomes and promotes degradation of lysosomal Ca2+ channel, MCOLN1 protein. ESCRT-I depletion induced transcriptional response related to MiT-TFE signaling and cholesterol biosynthesis, pointing to lysosomal dysfunction. The lack of ESCRT-I promoted abnormal cholesterol accumulation on lysosomes and activated TFEB/TFE3 transcription factors in Ca2+-MCOLN1-dependent, but lipid-independent manner. Hence, our study provides evidence that ESCRT-I maintains lysosomal homeostasis and elucidates MiT-TFE regulatory mechanism activated in response to ESCRT-I deprivation

overall_design: The aim of the study was to analyze by RNA sequencing the transcriptional changes upon single siRNA-mediated depletion of two core component of ESCRT-I complex, Tsg101 or Vps28 subunit. As a model, human colorectal RKO cell line was used. 3 biological replicates were prepared for each experimental condition. The conditions were: 1/RKO transfected with non -targeting siRNA (siCtrl#1), 2/ RKO transfected with non-targeting siRNA (siCtrl#2), 3/ RKO transfected with siRNA targeting TSG101, sequence #1 (siTsg101#1), 4/ RKO transfected with siRNA targeting TSG101, sequence #2 (siTsg101#2), 5/ RKO transfected with siRNA targeting VPS28, sequence #1 (siVps28#1), 6/ RKO transfected with siRNA targeting VPS28, sequence #2 (siVps28#2). siCtrl#1-transfected cells served as the reference sample.

first: Marta

last: Wróbel

first: Ewelina

last: Szymańska

first: Noga

last: Budick-Harmelin

first: Krzysztof

last: Kolmus

last: Goryca

first: Michalina

last: Dąbrowska

first: Agnieszka

last: Paziewska

first: Michał

first: Jarosław

last: Cendrowski

last: Miączyńska


title: Analysis of transcriptomic responses of genotoxic and non-genotoxic stress in human lymphoblastoid TK6 cells

city: Berlin

first: Katrin

last: Kreuzer

address: Max-Dohrn-Str. 8-10

department: Food Safety

institute: German Federal Institute for Risk Assessment

summary:
Purpose: Toxicogenomics analyses may provide information about DNA-damaging properties of test compounds but are not routinely used for identification of a genotoxic potential. In this study, p53 wild type TK6 cells were exposed to six food-relevant genotoxic and four non-genotoxic compounds to elucidate genotoxic mechanism.
Method: Transcriptomic responses were analyzed using RNA sequencing technology

overall_design: Examination with a total of 31 samples, thereof 4 control samples and 27 samples in 9 treatment groups in triplicates

first: Albert

last: Braeuning

first: Heike

last: Sprenger


title: Analysis of Wild Type and Whsc1-/- small intestine Transcriptomes

city: shanghai

first: jiale

middle: jia

last: ren

state: shanghai

address: yueyang road 320

department: shanghai institute of nutrition and health

institute: CAS

summary: Histone dimethyl transferase WHSC1 drives the transcription of MHC-I machinery in mouse and human colorectal cancer cells (CRCs); thus, WHSC1 downregulation potentiates CRCs to escape from cytotoxic CD8+ T cell responses. WHSC1 directly interacts with MHC-I transactivator, NLRC5 to selectively stimulate MHC-I gene expression. Thus, silencing Whsc1 diminished MHC-I level, impaired anti-tumor immunity and blunted immunotherapy efficacy.

overall_design: RNA-seq:Small intestine mRNA profiles of 3-monthe old wild type (WT) and Whsc1 -/- mice

first: Jiale

last: Ren

first: Ni

last: Li

first: Siyu

last: Pei

first: Yannan

last: Lian

first: Jiacheng

last: Guo


title: Defining Essential Regulators of Naïve Human Pluripotent Cell Reprogramming

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: Defining how human pluripotent cell identity is controlled and in particular how naïve pluripotency is acquired during cell reprogramming is crucial for the future applications of pluripotent stem cells. However, the regulatory pathways of naïve cell reprogramming remain incompletely understood. Here, we used genome-wide CRISPR-Cas9 screening to identify novel regulators of primed to naïve pluripotent stem cell reprogramming, including genes that are essential for reprogramming and genes that impede reprogramming and whose targeted deletion led to enhanced reprogramming. Integrated analysis defined specific chromatin complexes and signalling pathways as critical regulators of naïve reprogramming, and were largely distinct from regulators of somatic cell reprogramming. Mechanistically, PRC1.3 and PRDM14 are jointly required to transcriptionally repress developmental and gene regulatory factors to ensure naïve cell reprogramming. Additionally, small molecule inhibitors of reprogramming impediments increased the efficiency of naïve cell reprogramming, and are of practical benefit that can improve on current reprogramming methods. Taken together, we have identified novel regulators controlling the establishment of naïve pluripotency in human cells, which will open up new ways to exploit the full potential of pluripotent stem cells. These results also provide new insights into mechanisms that destabilise and reconfigure cell identity during cell state transitions.

overall_design: We generated RNA-seq and PCGF3 and RING1B ChIP-seq datasets in naïve and primed human pluripotent stem cells.

first: Amanda

middle: J

last: Collier

first: Adam

last: Bendall

first: Charlene

last: Fabian

first: Andrew

last: Malcolm

first: Katarzyna

last: Tilgner

first: Claudia

last: Semprich

last: Wojdyla

first: Paola

middle: S

last: Nisi

first: Kamal

last: Kishore

first: Valar

last: Franklin

first: Clive

last: D’Santos

first: Kathrin

last: Plath

first: Kosuke

last: Yusa

first: Peter

last: Rugg-Gunn


title: Small RNA profile of 4 biofluids from healthy individuals (EVs) [EXR-KWANG1Nb3oPN-AN]

city: Seattle

first: Kai

last: Wang

address: 401 Terry Ave N

institute: Institute for Systems Biology

summary: Endogenous and exogenous extracellular RNAs will be characterized in four body fluids (plasma, serum, CSF and saliva) collected at the same time from 134 healthy subjects ranging in age from 31 to 101 years old.  Small RNAs contained in these samples will be profiled by small RNA-seq using unfractionated biofluids and purified extracellular vesicles.

overall_design: smRNA-seq of plasma, serum, CSF and saliva samples from 134 healthy individuals, no replicates

first: David

last: Galas

first: Elaine

last: Peskind

first: Saroja

last: Somasundaram

first: Alton

last: Etheridge

first: Nikita

last: Sakhanenko

last: Baxter


title: Single-cell RNA-seq analysis of cells from degenerating and non-degenerating intervertebral discs from the same individual reveals new biomarkers for intervertebral disc degeneration

first: Alain

last: Pacis

address: 740 Dr Penfield Ave

institute: Canadian Centre for Computational Genomics (C3G)

summary: Low back pain continues to be a major public health problem worldwide. In this study, we used single-cell transcriptomic analysis to identify new specific biomarkers for nucleus pulposus (NP) and annulus fibrosis (AF) cells and to define cell populations within non-degenerating and degenerating human intervertebral discs (IVD). Freshly isolated human NP and AF cells were separately isolated from non-degenerating (nD) and degenerating (D) discs of the same individual. Isolated cells were subjected to droplet-based single-cell RNA sequencing (scRNA-Seq) using 10X Genomics platform. A total of 3134 (AFD), 3182 (AFnD), 3665 (NPD) and 3918 (NPnD) individual cells were profiled from nD and D discs respectively.

overall_design: Single-cell RNA-seq analysis of human NP and AF cells from non-degenerating (nD) and degenerating (D) discs of the same individual.

first: Hosni

last: Cherif

first: Matthew

last: Mannarino

first: Jiannis

last: Ragoussis

first: Oded

last: Rabau

first: Jean

middle: A

last: Ouellet

first: Lisbet

last: Haglund


title: Lichen secondary metabolites inhibit Wnt/β-catenin pathway in glioblastoma cells and improve the anticancer effects of temozolomide

status: Public on Mar 23 2022

city: Poznan

first: Marcin

last: Rucinski

address: Swiecicki 6

department: Histology and Embriology

institute: Poznan University of Medical Science

summary:
Lichens are a source of secondary metabolites with significant pharmacological potential. Data regarding their possible application in glioblastoma (GBM) treatment are, however scarce. The study aimed to analyze the mechanism of action of six lichen secondary metabolites: atranorin, caperatic acid, physodic acid, squamatic acid, salazinic acid, and lecanoric acid using two- and three-dimensional GBM cell line models. The Parallel Artificial Membrane Permeation Assay was used to predict the blood-brain barrier penetration ability of the tested compounds. Their cytotoxicity was analyzed using MTT test on A-172, T98G, and U-138 MG cells. Flow cytometry was applied for the analysis of oxidative stress, cell cycle distribution, and apoptosis, whereas qPCR and microarrays detected the induced transcriptomic changes.
Our data confirm the ability of lichen secondary metabolites to cross the blood-brain barrier and exert cytotoxicity against GBM cells. Moreover, the compounds generated oxidative stress, interfered with the cell cycle, and induced apoptosis in T98G cells. They also inhibited Wnt/β-catenin pathway, and this effect was even stronger in case of a co-treatment with temozolomide. Transcriptomic changes in cancer related genes induced by caperatic acid and temozolomide were the most pronounced. Lichen secondary metabolites, in particular caperatic acid should be further analyzed as potential anti-GBM agents.

overall_design: The T98G spheroids were exposed to the influence of lichen secondary metabolites for 48 h and subjected to microarray analysis. A pairwise scatter plot analysis was performed to determine the general profiles of the whole gene expression in the control (1), TMZ 100 μM (2), atranorin 25 μM + TMZ 100 μM (3), caperatic acid 50 μM + TMZ 100 μM (4), physodic acid 25 μM + TMZ 100 μM (5), squamatic acid 25 μM + TMZ 100 μM (6), salazinic acid 50 μM + TMZ 100 μM (7) and lecanoric acid 100 μM + TMZ 100 μM (8) experimental groups.

first: Aleksandra

last: Majchrzak-Celińska

first: Robert

last: Kleszcz

first: Elżbieta

last: Studzińska-Sroka

first: Agnieszka

last: Łukaszyk

first: Anna

last: Szoszkiewicz

first: Ewelina

last: Stelcer

first: Karol

last: Jopek

first: Judyta

last: Cielecka-Piontek

first: Violetta

last: Krajka-Kuźniak


title: Next Generation Sequencing Facilitates Quantitative Analysis of  Transcriptomes in The White Adipose Tissues of Wild Type (WT) and Adipose-tissue-specific Ces1d knockout (Ces1d FKO) mice

city: Houston

first: Yulin

last: Dai

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

summary:
The goal of this study is to analyze the white adipose tissue transcriptome profiling (RNA-seq) of the wild type and adipose-tissue-specific Ces1d knockout mice.
Methods: White adipose tissue mRNA profiles of 14-week-HFD-fed wild-type (WT) and Ces1d adipose tissue knockout mice were collected.  Total RNA quality was measured using Agilent RNA 6000 Pico kit (#5067-1513) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). The samples with RNA integrity number (RIN) greater than 7 were used for library preparation. Libraries were prepared with KAPA mRNA HyperPrep (KK8581, Roche) and KAPA UDI Adapter Kit 15μM (KK8727, Roche) following the manufacturer’s instructions. The pooled libraries (n = 10) were paired-end sequenced using 75-cycle High Output Kit v2.5 (#20024907, Illumina, Inc., USA) on Illumina NextSeq 550 System. We used ultrafast universal RNA-seq aligner STAR (v2.5.3a) to conduct the read alignment to mouse reference genome GRCm38. Gene read counts were calculated through setting the argument –quantMode to “GeneCounts” to let STAR count number of uniquely-mapped reads per gene from the GencodeM15 reference.
Groups: WT, Sample 1-5;  Ces1d FKO, Sample 6-10

overall_design: White adipose tissue mRNA profiles of HFD fed wild type (WT) and adipose-tissue-sepecific Ces1d knokout  mice were generated by deep sequencing(n=5)

first: Li

last: Gang

last: Xin

first: Yang

last: Li

first: Sun

last: Kai


title: Bulk RNA-seq analysis of control and siMPI TWNT-4 cells

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: The purpose of this study was to identify the changes in gene expression that occur in TWNT-4 human hepatic stellate cells in response to depletion of mannose phosphate isomerase enzymatic activity.

overall_design: Bulk RNA sequencing of TWNT-4 human hepatic stellate cells treated with a control vector or one that encodes an siRNA targeting MPI (siMPI). Biological replicates were included. *samples labled S7 and S9 are controls; S8 and S10 are MPI knockdown cells

last: Edepli

first: Jaim

last: Chu