title: High-throughput transcriptomics platform for screening hepatotoxicants

city: Singapore

first: Fan

last: Lee

address: 31 Biopolis Way, The NANOS, #06-01

country: Singapore

institute: Institute of Bioengineerng and Nanotechnology

summary: We introduce a new high-throughput transcriptomics (HTTr) platform comprised of a collagen sandwich primary rat hepatocyte culture and the TempO-Seq assay for screening and prioritizing potential hepatotoxicants. We selected 14 chemicals based on their risk of drug-induced liver injury (DILI) and tested them in hepatocytes at two treatment concentrations. HTTr data was generated using the TempO-Seq whole transcriptome and S1500+ assays. The HTTr platform exhibited high reproducibility between technical replicates (r>0.9) but biological replication was greater for TempO-Seq S1500+ (r>0.85) than for the whole transcriptome (r>0.7). Reproducibility between biological replicates was dependent on the strength of transcriptional effects induced by a chemical treatment. Despite targeting a smaller number of genes, the S1500+ assay clustered chemical treatments and produced gene set enrichment analysis (GSEA) scores comparable to those of the whole transcriptome. Connectivity mapping showed a high-level of reproducibility between TempO-Seq data and Affymetrix GeneChip data from the Open TG-GATES project with high concordance between the S1500+ gene set and whole transcriptome. Taken together, our results provide guidance on selecting the number of technical and biological replicates and support the use of TempO-Seq S1500+ assay for a high-throughput platform for screening hepatotoxicants.

overall_design: Primary rat hepatocytes freshly isolated from male Wistar rats (250-300 g) were maintained in collagen sandwich in 96-well plates, and treated with 14 chemicals at two concentrations. To examine technical reproducibility, each treatment was performed in triplicate in culture medium containing 0.5 % DMSO for 24 h. To examine biological reproducibility, the entire experiment was repeated using hepatocytes isolated from another individual with library construction and sequencing independently performed from the first batch of samples.

first: Imran

last: Shah

first: Yun

last: Soong

first: Jiangwa

last: Xing

first: Inn

last: Ng

first: Farah

last: Tasnim

first: Hanry

last: Yu


title: Mouse T-cell dysfunction induced in chronic LCMV infection

status: Public on Sep 01 2021

city: Montreal

first: Jean-Sebastien

last: Delisle

state: Quebec

address: 5415 Boulevard de l'Assomption

country: Canada

institute: Centre de recherche de l'Hôpital Maisonneuve-Rosemont

type: Expression profiling by high throughput sequencing

summary: We report the changes in mRNA profile of activated and dysfunctional LCMV-specific T cells.

overall_design: mRNA profile of mouse gp33-specific T cells harvested at day 8 compared to day 30 of LCMV clone 13 infection.

first: Dave

last: De Sousa

first: Salix

last: Boulet

first: Nathalie

last: Labrecque


title: Effects of durvalumab alone or combined with tremelimumab on preexisting cells in the tumor microenvironment

city: Gaithersburg

first: Yinong

last: Sebastian

address: One MedImmune Way

country: USA

institute: Medimmune

summary: Immune checkpoint blockade with anti–PD-1/L1 or anti–CTLA-4 therapies has shown promising results across multiple cancer types, but the mechanisms within the tumor microenvironment (TME) have not been fully characterized. We used single-cell RNA sequencing to investigate the effects of anti–PD-L1 monoclonal antibody (mAb) durvalumab (D) alone and combined with an anti–CTLA-4 mAb, tremelimumab (T), on distinct subsets of immune cells. Upon treatment with D or D+T, two NSCLC tumors showed elevated IFNγ responses, although they differed in magnitude of response but differed in other areas. Our results highlight that D and D+T in the TME have some consistent effects across tumors but also exhibit tumor-specific effects depending on composition and functional state of immune cells in the TME at time of treatment. This complex tumor-specific interplay of diverse immune subtypes in the TME is critical to better understand patient response to immunotherapy.

overall_design: Two tumors were treated by Durva and Durva+Treme and underwent single cell sequencing. RNA sequencing of 97 advanced-stage non–small-cell lung carcinoma (NSCLC) biopsies from a nonrandomized phase 1b/2 clinical trial (1108/NCT01693562) were profiled to identify expression of genes of interest.

first: Yashaswi

last: Shrestha


title: Gene profiles of Chinese Spring and CDC commander during embryogenesis

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

institute: Agriculture and Agri-Food Canada

summary: We present an atlas of global gene expression covering embryo, endosperm and seed coat development in Chinese Spring and CDC commander, providing insights into the evolution of gene expression in embryogenesis and grain development of hexaploid and tetraploid wheat species.

sample_organism:
Triticum aestivum
Triticum turgidum

platform_organism:
Triticum aestivum
Triticum turgidum

overall_design: We investigate the dynamics and evolution of gene expression throughout seven stages of embryo development (including the two cell, pre-embryo, transition, leaf early, leaf middle, leaf late and mature embryo), two stages of endosperm (transition stage endosperm and leaf late stage endosperm), and one pericarp stage (leaf early stage pericarp) across Chinese Spring and CDC commander, two replicates for each stage.

first: Daoquan

last: Xiang

first: Raju

last: Datla


title: HDAC9 Complex Inhibition Improves Smooth Muscle Dependent Arterial Stenosis

city: Boston

first: SAUMYA

last: Das

state: MA

address: 185 Cambridge Street

institute: MGH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Patients with heterozygous missense mutations in the ACTA2 or MYH11 genes are known to exhibit thoracic aortic aneurysm (TAA) and a risk of early onset aortic dissection. However, less common phenotypes involving arterial obstruction are also observed, including coronary and cerebrovascular stenotic disease. Recently an epigenetic complex containing the histone deacetylase HDAC9 and the long noncoding RNA, MALAT1 was implicated in pathologic vascular smooth muscle cell phenotypic changes in aneurysmal disease, however its involvement in stenotic disease has not been explored. Herein we implicate the HDAC9-MALAT1 complex in transcriptional silencing of contractile associated gene products, known to undergo downregulation in stenotic lesions. Furthermore, neointimal formation was inhibited in Hdac9 or Malat1 deficient mice with preservation of contractile protein expression. Pharmacologic targeting of the complex through either MALAT1 antisense oligonucleotides or inhibition of the methyltransferase EZH2 reduced neointimal formation. In conclusion, we report the implication of the HDAC9-MALAT1 complex in stenotic disease and demonstrate that pharmacologic therapy based on epigenetic targets can ameliorate arterial obstruction in an experimental system.

overall_design: ChipSep analysis of ACTA2 mutants versus wild type human smooth muscle cells.

first: Ashish

middle: S

last: Yeri


title: Genome-wide maps of histone modifications in the SV40 virus

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

summary: In order to better understand the nature of the changes in chromatin structure which occur during encapsidation, we have analyzed SV40 virions and minichromosomes for the organization of nucleosomes carrying specific histone tail modifications and RNA Polymerase II (RNAPII) and report here evidence that encapsidation leads to a reorganization of chromatin structure within the regulatory region of the virus and relief of the repression of early transcription.

overall_design: Examination of ChIP-seq profiles of the histone modifications H3K4me1, H3K4me2, H3K4me3, H3K9me1, H3K9me2, H3K9me3, H3K20me1, H4K20me1, HH4, HH3, and RNA polymerase, in wild-type (776) SV40 mini-chromosomes and virions.

first: Meera

middle: A

last: Kumar

first: Karine

last: Kasti

first: Lata

last: Balakrishnan

first: Barry

last: Milavetz


title: Transcriptomic profiling of remote area 7 days after infarct

city: Cold Spring Harbor

first: Carlos

last: Martí-Gómez

email: carlos199m1@gmail.com, martigo@cshl.edu

state: New York

address: 1 Bungtown Rd

department: Quantitative Biology

institute: Cold Spring Harbor Laboratory

summary: This dataset is part of a study aimed to characterized and analyze the alternative splicing profiles in several models of cardiac disease and compare the changes and regulatory mechanisms to those happening during  mouse heart development.

overall_design: High throughtput sequencing of poly-A selected RNA from remote area of 2 infarcted and 2 uninjured mice. Infarcts were induced by permanent ligation of the Left Anterior Descending coronary artery.

first: Marina

last: López-Olañeta

first: Pablo

last: García-Pavía

first: Fátima

last: Sánchez-Cabo

first: Enrique

last: Lara-Pezzi


title: Gene expression profiling of late reprogramming stages during in vitro reprogramming of mouse embryonic fibroblasts (MEFs) to induced pluripotent stem cells (iPSCs)

city: Leuven

first: Kian

middle: Peng

last: Koh

state: Select...

address: Herestraat 49, O&N IV - box 804

country: Belgium

institute: KULeuven

summary: The generation of  induced pluripotent stem cells (iPSCs) involves activation of the endogenous pluripotency circuitry and global DNA demethylation late in reprogramming, but temporal resolution of these events are insufficient using existing stage markers. Here, we generated murine transgenic lines harboring dual fluorescent reporters reflecting cell-state specific expression of the master pluripotency factor Oct4 and the 5-methylcytosine dioxygenase Tet1. By assessing reprogramming intermediates based on dual reporter patterns, we identified a sequential order of Tet1 and Oct4 gene activation at proximal and distal regulatory elements following pluripotency entry. A transient phase of global gene repression accompanies full activation of Tet1, precedes activation of meiotic and gametogenesis genes, and distinguishes phases of global DNA demethylation reminiscent of germ-line reprogramming.  Loss of Tet1 is compatible with reprogramming towards full Oct4 gene activation, but generates iPSCs with epigenetic defects. Therefore, the transcriptional logic of Tet1 expression signals an epigenetic roadmap towards efficient reprogramming.

overall_design: Transcriptome analysis of parental MEF, late reprogramming intermediate stages and clonally expanded wild type and TET1 knockout (KO) iPSCs all in biological triplicates by RNA-seq.

first: Michela

last: Bartoccetti

first: Xinlong

last: Luo


title: Cancer -associated mutations in XPO1 transform cells through altered nuclear export signal recognition

city: New York

first: Omar

last: Abdel-Wahab

state: NY

address: 1275 York Ave

department: HOPP

institute: MSKCC

summary: Proper nucleocytoplasmic distribution of proteins is essential to cellular homeostasis   but what role the altered nuclear export machinery commonly described in cancer cells plays in cancer initiation is not known. Here, genomic analysis of 42,793 cancers identified recurrent mutational hotspots in XPO1, the main nuclear export receptor in eukaryotic cells. Expression of XPO1 mutations in vivo was sufficient to initiate clonal, B-lymphoproliferative disorders by altering the constellation of proteins exported from the nucleus based on amino acid charge C-terminal to their nuclear export signal. Impaired export of one such protein, the NFkB inhibitor IB enhanced NFkB signaling, a pathway frequently activated by somatic mutations in cancers enriched in XPO1 mutations. These data identify change-of-function mutations in nuclear export as novel drivers of tumorigenesis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Changes in amino acid charges created by mutations in XPO1 lead to sequence-specific effects on nuclear export signal recognition and promote malignant transformation.

first: Justin

last: Taylor

first: Maria

last: Sendino

first: Alex

last: Gorelick

first: Alessandro

last: Pastore

first: Alexander

middle: V

last: Penson

first: Matthew

middle: T

last: Chang

first: Connor

last: Stewart

first: Lillian

last: Bitner

first: Akihide

last: Yoshimi

first: Stanley

middle: C

last: Lee

first: Myriam

last: Boukhali

first: Wilhelm

last: Haas

first: Rajesh

last: Soni

first: Ron

last: Hendrickson

first: Gorka

last: Prieto

first: Jose-Antonio

last: Rodriguez


title: True 5-methylcytosine profiling of late reprogramming stages during in vitro reprogramming of mouse embryonic fibroblasts (MEFs) to induced pluripotent stem cells (iPSCs)

first: Kian

last: Koh

type: Methylation profiling by high throughput sequencing

overall_design: Base-resolution methylome analysis of parental MEF, 5 late reprogramming intermediate stages and clonally expanded wild type and TET1 knockout (KO) iPSCs by oxidative whole genome bisulphite sequencing.

first: Michela

last: Bartoccetti

first: Xinlong

last: Luo


title: Expression data of Tfh cells in hepatitis B patients

city: Changchun

first: Yong

last: Liu

address: 71 Xinmin Avenue, Chaoyang District

country: China

institute: The First Hospital of Jilin University

summary:
Tfh cells can help B cells to produce high-affinity antibodies. To date, no study has examined the status or the biological significance of circulating TFH cells in the treatment response of patients with CHB to standard PEG-IFN-α therapy
To explore the molecular mechanisms underlying the differential biological activities of Tfh cells from CHB patients with distinct therapeutic response to PEG-IFN-α

overall_design: We isolated Tfh cells from 7 CHB patients after 48-week PEG-IFN-α treatment, including 1 complete response, 2  incomplete response, and 4 non-response patients


title: Dynamics of Tet1 and Oct4 gene activation identify temporally distinct late stages in reprogramming of induced pluripotency

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

overall_design: Refer to individual Series


title: Adipocytes induce melanoma plasticity by sensitizing cells to TGFb

city: Tel Aviv

first: Carmit

last: Levy

address: Ramat Aviv

department: Human Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

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

summary: Transcriptome analysis of: 1- WM1716 melanoma cell line transfected with scrambled control or with miR-211. 2- WM3682 cell line mono-cultured or co-cultured  with adipocytes.

platform_organism:
Homo sapiens
synthetic construct

overall_design:
Exp.1.We analyzed RNA from WM1716 melanoma line, which were stably transfected with scrambled control or miR-211, using Affymetrix Clarioum S Human Array platform. No techinical replicates were performed.
Exp.2.We analyzed RNA from WM3682 melanoma line, which were mono-cultured orco-cultured with adipocytes for 5 days, using Affymetrix Clarioum S Human Array platform. Two biological replicates were performed.

first: Tamar

last: Golan

first: Roma

last: Parikh


title: STAT3 promotes melanoma metastasis by CEBP-induced repression of the MITF pigmentation pathway

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Metastatic melanoma is hallmarked by its ability to switch oncogenic MITF expression. Here we tested the impact of STAT3 on melanoma onset and progression in association with MITF expression levels. We established a mouse melanoma model for deleting Stat3 specifically in melanocytes with specific expression of human hyperactive NRASQ61K in an Ink4a deficient background. Mice with tissue specific Stat3 deletion showed an early onset of disease, but displayed significantly diminished lung metastasis. Whole genome expression profiling also revealed a reduced invasion phenotype, which was functionally confirmed in 3D melanoma model systems. Notably, loss or knockdown of STAT3 in mouse or human cells resulted in up-regulation of MITF and induction of cell proliferation. Mechanistically we show that STAT3 induced CEBPa/b expression was sufficient to suppress MITF transcription. Epigenetic analysis by ATAC-seq confirmed that STAT3 enabled CEBPa/b binding to the MITF enhancer region thereby silencing it. We conclude that STAT3 is a metastasis driver able to antagonize the MITF oncogene via direct induction of CEBP family member transcription facilitating RAS-RAF-driven melanoma metastasis.

overall_design: ATAC sequencing of mouse melanoma cell lines with Stat3 knockout and respective wild type controls.

first: Alexander

last: Swoboda

first: Robert

last: Soukup

first: Katharina

last: Kinslechner

first: Bettina

last: Wingelhofer

first: David

last: Schörghofer

first: Christina

last: Sternberg

first: Ha

last: Pham

first: Maria

last: Vallianou

first: Jaqueline

last: Horvath

first: Dagmar

last: Stoiber

first: Lukas

last: Kenner

first: Lionel

last: Larue

first: Valeria

last: Poli

first: Friedrich

last: Beermann

first: Takashi

last: Yokota

first: Stefan

last: Kubicek

first: Thomas

last: Krausgruber

first: André

middle: F

last: Rendeiro

first: Rainer

last: Zenz

first: Boris

last: Kovacic

first: Fritz

last: Aberger

first: Markus

last: Hengstschläger

first: Peter

last: Petzelbauer

first: Mario

last: Mikula

first: Richard

last: Moriggl


title: Gestational choline supplementation improves cross-generational mood by epigenetic upregulation of Nr3c1 [RRBS]

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

summary: Environmental cues during gestation could exert transgenerational effects on behavior mainly through changes in epigenetic marks such as DNA methylation. However, the role of histone modifications in the inheritance of acquired phenotypes remains largely unknown in mammals. Here, we report that gestational choline supplementation (GCS) in maternal mice exerts anxiolytic effects on male offspring across 2 generations. Correspondingly, GCS-induced H3K9 hyperacetylation in the Nr3c1 promoter in male hippocampus leads to upregulation of Nr3c1 and its encoded protein, glucocorticoid receptor (GR), across 2 generations through the male germline. Furthermore, inhibition of CREB-binding protein (CBP) histone acetyltransferase (HAT) function restored GCS-induced epigenetic and behavioral alterations, suggesting that CBP function as a HAT to increase Nr3c1 expression through H3K9 hyperacetylation. Thus, GCS-induced GR upregulation through CBP-mediated H3K9 hyperacetylation in the Nr3c1 promoter is associated with anxiolytic behavior in male offspring, highlighting the role of histone modification in acquired phenotypes across mammalian generations.

overall_design:
RRBS libraries for the hippocampi of F1m-GCS and F1m-CON were constructed as previously described(Cai et al., 2015; Gu et al., 2011). Briefly, 500 ng of genomic DNA was digested with 20 units of MspI (NEB, USA) in a 20 μl reaction for 20 h at 37 °C. After purification, the digested products were blunt-ended, and then dA was added, followed by methylated-adapter (Illumina, USA) ligation. To obtain DNA fractions in 40-120 bp and 120-220 bp range of MspI-digested products, two ranges (160-240 bp and 240-340 bp) of adapter-ligated fractions were excised from 2% agarose gel. The size-selected DNA was bisulfite-treated for two rounds using EpiTect Bisulfite Kit (Qiagen, German) following the manufacturer’s standard protocol. The final libraries were generated by amplification with HiFi HotStart Uracil + ReadyMix PCR kit (KAPA, USA). The quality and quantity were analyzed by an Agilent 2100 Bioanalyzer (Agilent Technologies, USA) and qPCR, respectively. Illumina HiSeq 2000 was used to sequence the libraries according to the manufacturer’s protocol.
After removal of the adaptor sequences and trimming of low quality sequences by using cutadapt, the reads from each of the biological replicates were aligned to mouse mm10 reference genome as well as the size-selected MspI fragments generated by our in silico simulation. Because of the strand specificity of DNA methylation, two rounds of alignments were carried out, i.e. the bisulfite converted reads were aligned to the genome sequences termed the “T genome” with each cytosine converted to thymine and in the meanwhile the reads were also aligned to the genome sequences termed the “A genome” with each guanine converted to adenosine. The alignments were carried out with BGI SOAPaligner verison2.21(Li et al., 2009) with default parameters, allowing up to five mismatches for successful mapping. Both replicates showed near complete (> 99%) bisulfite conversion of non-CpG cytosine (data not shown).
The DNA methylation levels in Nr3c1 and Crebbp promoters in the hippocampi of F1m-GCS and F1m-CON mice were examined by DNA bisulfate conversion and PCR amplification and Sequencing using the EZ DNA Methylation-GoldTM Kit (Zymo Research, USA) following the manufacturer’s standard protocol.

first: Yan

last: Wang

first: Zhong-Sheng

last: Sun


title: Gestational choline supplementation improves cross-generational mood by epigenetic upregulation of Nr3c1 [ChIP-Seq]

overall_design: Libraries of ChIP DNA were constructed using the NEXT flex™ Illumina ChIP-Seq Library Prep Kit (Bioo Scientific, USA) following the manufacturer’s instructions with modifications. Sequenced reads were mapped to the UCSC mouse mm10 reference genome using Bowtie (version 1.0.0) with specific settings(Langmead et al., 2009). We used the function “callpeak” in Model-based Alignment of ChIP-Seq version 2 (MACS2) (Feng et al., 2012) to call peaks of H3K9ac occupancy with default parameters. MACS2 compares the number of H3K9ac-enriched sequence tags in a given window (200 bp) with the number of tags in surrounding windows and with the number of tags in the same region of the input DNA library. Different peaks of H3K9ac occupancy between CON- and SUP-treated cells were called by the function “bdgdiff” in MACS2 and visualized by the Integrative Genomics Viewer(Thorvaldsdottir et al., 2013).


title: Gestational choline supplementation improves cross-generational mood by epigenetic upregulation of Nr3c1


title: Gestational choline supplementation improves cross-generational mood by epigenetic upregulation of Nr3c1 [RNA-Seq]

overall_design:
Total RNA was extracted from the hippocampi of F1m-GCS and F1m-CON mice using the RNeasy Mini Kit (QIAGEN, Germany). The RNA quality was assessed using the Bioanalyser 2100 RNA 6000 Nano Kit (Agilent Technologies, USA). mRNA-Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 (Illumina, USA), and transcriptomes were sequenced using the Hiseq 2000 Sequencing System (Illumina) in paired-end mode.
Sequencing adapters and low quality sequencing reads were excluded using the Trim Galore program (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). TopHat2(Kim et al., 2013) was used to align the reads to the University of California Santa Cruz (UCSC) mouse mm10 reference genome, allowing up to two mismatches and a Phred-scaled mapping quality ≥ 4. The bioconductor package edgeR(Robinson et al., 2010) was used to identify genes that were differentially expressed between CON and GCS groups based on the number of mapped paired-end reads for each gene counted by the Python package HTSeq (http://www.htseq.org/). The genes for which p values and false discovery rate (FDR) values were below 0.05 were considered differentially expressed between CON and GCS groups. The same RNA-seq and analysis protocols were performed on CON- and SUP-treated HT22 cells.


title: An integrative map of transcriptional responses to exercise in non-muscle organs

city: Solna

first: Estelle

last: Proux-Wéra

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Science for Life laboratory

summary:
Global gene expression was measured with Affymetrix in seven organs after 3 weeks swimming and control (non swimming) C57BL6 male mice, 14wks old ( by the end of the study).
We used microarrays to detail the global programme of gene expression indicative of adaptatie changes occuring in seven tissues, skeletal muscle (quadricepts), liver, kidney, subcutaneous and visceral white adipose tissues, spleen, brain, after 3 weeks of swimming

overall_design: C57Bl/6 mice, 11-12 weeks old were acclimated to the swimming protocol by daily swim sessions, which gradually increased by 10 min over the course of 9 days. After the acclimatization period, the mice were made to swim for 3 weeks, twice per day, for 90 min, with 4 hours rest between the sessions. The first swimming session was at 9AM and the second at 3PM

first: Anastasia

last: Georgiadi

first: Pontus

last: Boström


title: Mesenchymal Stromal Cell-Derived Exosomes Attenuate Myocardial Ischemia-Reperfusion Injury through miR-182-Regulated Macrophage Polarization

city: Nanjing

first: Biao

last: Xu

state: Jiangsu

address: No. 321 Zhongshan Road

department: Department of Cardiology

institute: Drum Tower Hospital, Medical School of Nanjing University

type: Non-coding RNA profiling by high throughput sequencing

summary: Aims: Mesenchymal stem cells (MSCs) gradually become attractive candidates for cardiac inflammation modulation, yet understanding of the mechanism remains elusive. Strikingly, recent studies indicated that exosomes secreted by MSCs might be a novel mechanism for the beneficial effect of MSCs transplantation after myocardial infarction. We therefore explored the role of MSC-derived exosomes (MSC-Exo) in the immunomodulation of macrophages after myocardial ischemia-reperfusion and its implications in cardiac injury repair. Methods and Results: Exosomes were isolated from the supernatant of MSCs using a gradient centrifugation method. Administration of MSC-Exo through intramyocardial injection after myocardial ischemia reperfusion reduced infarct size and alleviated inflammation level in heart and serum. Systemic depletion of macrophages with clodronate liposomes abolished the curative effects of MSC-Exo. MSC-Exo modified the polarization of M1 macrophages to M2 macrophages both in vivo and in vitro. miRNA-sequencing of MSC-Exo and bioinformatics analysis implicated miR-182 as a potent candidate mediator of macrophage polarization and TLR4 as a downstream target. Diminishing miR-182 in MSC-Exo partially attenuated its modulation of macrophage polarization. Likewise, knock down of TLR4 also conferred cardioprotective efficacy and reduced inflammation level in a mouse model of myocardial ischemia/reperfusion. Conclusion: Our data indicates that MSC-Exo attenuates myocardial ischemia/reperfusion injury via shuttling miR-182 that modifies the polarization state of macrophages. This study sheds new light on the application of MSC-Exo a potential therapeutic tool for myocardial ischemia/reperfusion injury.

overall_design: small RNA sequencing of murine mesenchymal stromal cell-derived exosomes to find abundant miRNA

first: Jinxuan

last: Zhao


title: Single-cell RNA sequencing analysis reveals the relationship of bone marrow and osteopenia in type 1 diabetic mice

status: Public on Aug 31 2021

city: Hangzhou

first: Linlin

state: Zhejiang

address: Yuhangtang Road No.866

department: Department of Basic Medicine Sciences

institute: Zhejiang University

summary: Type 1 diabetes (T1D) is a multifactorial autoimmune disease characterized by the destruction of pancreatic beta (β) cells and resultant hyperglycaemia. Broad knowledge about the genetics, epidemiology, and clinical management of T1D has been achieved, but the cell varieties in the bone marrow during T1D remain poorly understood. Here, we performed a single-cell RNA sequencing analysis of whole bone marrow cells from healthy (group C) and STZ-induced T1D (group D) mice for the first time, presenting a profile of the bone marrow cells and revealing the changes in immune cells in bone marrow. The bone marrow cells in both groups C and D were divided into 12 clusters, and there were 249 differentially expressed genes (DEGs). Compared with group C, the proportion of CD45+ immune cells in group D was not changed much. However, the diversity of CD45+ immune cells between groups C and D were greatly affected. There was a large increase in the proportion of bone marrow neutrophils (BM-neutrophils) and a large decrease in the proportion of B lymphocytes in group D. Furthermore, it was confirmed by X-ray and micro-CT analyses that osteopenia occurred in group D mice. Finally, we investigated the correlation between immune cells and osteopenia. The results of single-cell flow cytometry and correlation analysis showed that the ratio of BM-neutrophils/B lymphocytes was negatively correlated with osteopenia in T1D mice. Thus, precise regulation of the immune cells in the bone marrow may contribute to a better understanding of the treatment of T1D and the prevention of T1D-induced osteopenia.

overall_design: Single-cell RNA sequencing analysis of bone marrow from normal and STZ-induced type 1 diabetic mice

first: Chuan

last: Xiang

first: Xingjia

first: Jinjie

last: Zhong


title: Differential expression of circulating exosomal miRNAs between rotator cuff tear patients with and without shoulder stiffness

city: Shanghai

first: Yaying

state: Please Select

address: 12# Middle Wulumuqi Road, Jing'an District

institute: Huashan Hospital, Fudan University

summary: We harvested the blood samples from rotator cuff tear patients with and without shoulder stiffness.Then, circulating exosomes were harvested, and the miRNAs content was analyzed with an aim to idenfity differentially expressed miRNAs.

overall_design: 3 rotator cuff tear patients without shoulder stiffness and 3 with stiffness were recurited and blood samples were collected. By ultra-centrifugation and miRNA sequencing, the differentially expressed miRNAs were identified.

first: Jiwu

last: Chen


title: The RNA-binding protein ESRP1 modulates the expression of RAC1b in colorectal cancer cells [HCA24]

city: Grugliasco

first: Ugo

last: Ala

state: TO

address: L.go Paolo Braccini 2

country: Italy

institute: University of Turin

summary:
Colorectal cancer (CRC) ranks third for incidence and second for number of deaths among cancer types worldwide. Poor patient survival, due to inadequate response to currently available treatment regimens, points out to the urgent requirement for personalized therapy in CRC patients. Our aim was to provide mechanistic insights into the pro-tumorigenic role of the RNA-binding protein ESRP1, which is highly expressed in a subset of CRC patients. We show that, in CRC cells, ESRP1 binds to and has the same trend in expression as RAC1b, a well-known tumor promoter. Thus, RAC1b may be a potential therapeutic target in ESRP1-overexpressing CRC.
RNA binding proteins are well recognized as critical regulators of tumorigenic processes through their capacity to modulate RNA biogenesis, including alternative splicing, RNA stability and mRNA translation. The RNA binding protein Epithelial Splicing Regulatory Protein 1 (ESRP1) can act as tumor suppressor or promoter in a cell type- and disease context-dependent manner. We have previously shown that elevated expression of ESRP1 in colorectal cancer cells can drive tumor progression. To gain further insights into the pro-tumorigenic mechanism of action of ESRP1, we performed cDNA microarray analysis on two colorectal cells lines modulated for ESRP1 expression. Intriguingly, RAC1b was highly expressed, both at mRNA and protein levels, in ESRP1-overexpressing cells, while the opposite trend was observed in ESRP1-silenced CRC cells. Moreover, RAC1 and RAC1b mRNA co-immunoprecipitate with ESRP1 protein. Silencing of RAC1b expression significantly reduced the number of soft agar colonies formed by ESRP1-overexpressing cells, suggesting that ESRP1 acted, at least partially, through RAC1b in its tumor-promoting activities in CRC cells. Thus, our data provide molecular cues on targetable candidates in CRC cases with high ESRP1 expression.

overall_design: RNA from 2 conditions was analyzed. Every condition is represented by a duplicate.

first: Enzo

last: Medico

first: Daniela

last: Cantarella

first: Marta

last: Manco

first: Sharmila

last: Fagoonee

first: Fiorella

last: Altruda


title: EZH2 depletion potentiates MYC degradation in neuroblastoma and small-cell lung cancer

city: wuhan

first: song

last: zemin

address: no.185 the road of eastlake

institute: wuhan university

summary: Efforts to therapeutically target EZH2 have generally focused on inhibition of its methyltransferase activity, although it remains less clear whether this is the central mechanism whereby EZH2 promotes cancer. We demonstrate that EZH2 interacts with both MYC family oncoproteins, C-MYC and N-MYC, and promotes their stabilization in a methyltransferase-independent manner. By competing against the SCFFbw7 ubiquitin ligase to bind MYC, EZH2 counteracted Fbw7-mediated MYC polyubiquitination and proteasomal degradation. Depletion, but not enzymatic inhibition, of EZH2 induced robust MYC degradation and inhibited tumor cell growth in MYC-driven neuroblastoma and small-cell lung cancer. These findings unveil the MYC family proteins as critical EZH2 oncogenic effectors and EZH2 pharmacologic degraders as potential MYC-selective cancer therapeutics, pointing out that MYC-driven cancers may develop inherent resistance to canonical EZH2 enzymatic inhibitors currently in clinical development.

overall_design: Determination of binding profile of MYCN and Pol II in EZH2 knockdown  and control SK-N-BE2 cells.

first: Guoliang

last: Qing

first: Liyuan


title: single cell RNA sequencing of CD8+CD44+GP33+ T cells from spleen and  intraepithelial lymphocytes from small intestine at day 30 post LCMV Arm infection

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: During acute infections, CD8+ T cells form various memory subpopulations to provide long-lasting protection against reinfection. Central memory (TCM), Effector memory (TEM), and long-lived effector (LLE) cells are circulating memory populations with distinct plasticity, migration patterns, and effector functions. Tissue-resident memory (TRM) cells permanently reside in the frontline sites of pathogen entry and provide tissue-specific protection upon reinfection. Here, using scRNA-seq and bulk RNA-seq, we examined the different and shared transcriptomes and regulators of TRMs with other circulating memory populations. Furthermore, we identified heterogeneity within the TRM pool from small intestine and novel transcriptional regulators that may control the phenotypic and functional heterogeneity of TRM cells during acute infection. Our findings provide a resource for future studies to identify novel pathways for enhancing vaccination and immunotherapeutic approaches.

overall_design: Two samples (CD8+CD44+GP33+ T cells from spleen and  intraepithelial lymphocytes from small intestine) were prepared using 10x Genomics Chromium platform

first: Yao


title: Single-cell transcriptomics reveals core regulatory programs that determine the heterogeneity of circulating and tissue-resident memory CD8+ T cells


title: Gene-metabolite network analysis revealed tissue specific accumulation of therapeutic metabolites in Mallotus japonicus

city: Chiba

first: Mami

last: Yamazaki

address: Inohana 1-8-1, Chuo-ku

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Chiba University

summary: In this study, we performed LC-QTOF-MS-based metabolomics and RNA-seq based transcriptome analysis using seven tissues of M. japonicus.

overall_design: Examination of 7 tissues of Mallotus japonicus

first: Kazuki

last: Saito

first: Hideyuki

last: Suzuki

first: Michimi

last: Nakamura

first: Masami

last: Yamamoto

first: Tetsuya

last: Mori

first: Ryo

last: Nakabayashi

first: Amit

last: Rai

first: Megha


title: THP-1 cell lines: reference data for classification of THP-1 cells (expression)

city: Tsukuba

first: Fumio

last: Kasai

address: Koyadai 3-1-1

institute: RIKEN

summary:
THP-1 is a representative leukemia cell line, and has been widely used all around the world since its establishment in Japan in 1980.
Differences in THP-1 cells have been reported; however, the THP-1 cell lines have not been accurately classified.

overall_design: Transcriptome patterns of four THP-1 cell lines available from JCRB and RIKEN BRC in Japan; JCRB0112, JCRB0112.1 (corresponding to ATCC TIB-202), RCB1189 (corresponding to DSMZ ACC-16) and RCB3686, have been compared by microarrays.


title: RB-loss determines selective resistance and novel vulnerabilities in breast cancer modelsRB loss

city: Buffalo

first: Ram

middle: Mohan

last: Nambiar

address: 665 Elm Street

institute: Roswell Park

summary:
The retinoblastoma tumor suppressor (RB1) plays a critical role in coordinating multiple pathways that impact on tumor initiation, disease progression, and therapeutic responses.   Here we interrogated the effect of CDK4/6 inhibitor in combination with mTOR inhibtor. Also, we interrogtaed the efffect of AURK and WEE1 inhibition in ER+ breast cacner models
While the RB-pathway has been purported to exhibit multiple mutually exclusive events, only RB1 is mutually exclusive with multiple genetic events that deregulate CDK4/6 activity.  Using an isogenic ER+ breast cancer model with targeted RB1 deletion, we identified gene expression features that link CDK4/6 activity and RB-dependency (CDK4/6-RB integrated signature).   We also investigated the role of RB on apoptotic pathway.
Single copy loss on chromosome 13q encompassing the RB1 locus is prevalent in many cancers, and is associated with reduced expression of multiple genes on 13q including RB1, and inversely related to the CDK4/6-RB integrated signature supporting a genetic cause/effect relationship.
To probe the broader implications on tumor biology, we investigated genes that are positively and inversely correlated with the CDK4/6-RB integrated signature.   This approach defined tumor-specific pathways that could represent new therapeutic vulnerabilities associated with RB-pathway activity.

overall_design: MCF7 wild type and RB knockout cells were exposed to DMSO and Palbociclib (250 nM). Following 48 hours exposure, RNA was extracted from these cells using RNeasy plus kit (Quiagen) according to manufacturer's protocol and then subjected to RNA sequence analysis.

first: Vishnu

last: Kumarasamy

first: Hana

last: Rosenheck

first: Erik

last: Knudsen

first: Agnieszka

middle: K

last: Witkiewicz


title: THP-1 cell lines: reference data for classification of THP-1 cells

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


title: RNA-sequencing of CD34+ hemopoietic stem cell differentiation towards macrophages and dendritic cells

city: Didcot

first: Leonie

middle: Francina Hendrina

last: Fransen

state: Oxfordshire

address: CRCE

department: Toxicology

country: United Kingdom

institute: PHE

summary: CD34+ hemopoietic stem cells were differentiated towards macrophages (MCcd34) and dendritic cells (DCcd34) and characterized using RNA-Sequencing to identify differences between the cell types. Differences in expression levels of MCcd34 and DCcd34 were used to suggest possible explanations of differences in responses to chemicals (paraquat) between the cell types.

overall_design: RNA profiles of CD34+ hempoietic stem cells and differentiation of these cells towards macrophage and dendritic cell populations

middle: H

first: Martin

middle: O

last: Leonard


title: Age-related gene expression changes in seeded tauopathy

city: St Lucia

first: Jay

last: Rasmussen

state: QLD

address: Building 79

department: Queensland Brain Institute

country: Australia

institute: University of Queensland

summary: Wildtype mice at either 3 or 12 months old were subjected to intrahippocampal injection with sarkosyl insoluble brain extracts from either human control or Alzheimer's disease brain. Mice were incubated for 1, 3 or 5 months and then sacrificed. The hippocampus from one hemisphere was used to extract total RNA that was then subjected to polyA-selection and whole transcriptome sequencing. 3 and 12 month old animals were processed in seperate batches and comparisons between control and Alzheimer's disease injected animals from each timepoint were conducted

overall_design: whole mouse transcriptome analysis of different timepoints and ages of mice with and without tauopathy

first: Geoffrey

middle: J

last: Faulkner


title: Position Specific Alternative Splicing and Gene Expression Profiles along the Tonotopic Axis of Chick Cochlea

city: Louisville

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

institute: University of Louisville

summary: We performed an RNA-Seq experiment for three sample groups on base, middle, and apex regions of chick cochlea to identify genes and splicing events whose regulation mechanisms are associated with tonotopy.

overall_design: We conducted transcriptome-wide gene expression profiling and AS analysis using high-throughput sequencing. Post-hatch day 1 chickens were euthanized by carbon dioxide inhalation followed by decapitation. The head was hemi-sectioned and the cochlea duct was isolated in cold DEPC-treated PBS. The basilar papilla was dissected from the cochlear duct and divided into three pieces: base, middle, and apex. Each piece was collected separately and quickly frozen to minimize RNA degradation. Total RNA from 12 chickens (24 cochleas) were used for 3 biological replicates for each region.

first: Heiyeun

last: Koo

first: Jae

middle: Y

first: Jinwoong

last: Bok

first: Juw

middle: W

last: Park


title: KLF5 on dexamethasone-mediated atrophy in mouse satellite cells

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

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

overall_design: Refer to individual Series


title: Skeletal muscle-targeted delivery of Fgf6 protects mice from diet-induced obesity and insulin resistance

first: Hong

last: Zhang

address: 600 Yishan Road, Xuhui  District

institute: Shanghai Diabetes Institute

summary: Obesity, a major healthcare issue, is characterized by metabolic abnormalities in multiple tissues, including the skeletal muscle. Although dysregulation of skeletal muscle metabolism can strongly influence the homeostasis of systemic energy, the underlying mechanism remains unclear. We found promoter hypermethylation and decreased gene expression of fibroblast growth factor 6 (FGF6) in the skeletal muscle of individuals with obesity using high-throughput sequencing. Reduced binding of the cyclic AMP responsive element binding protein-1 (CREB1) to the hypermethylated cyclic AMP (cAMP) response element, which is a regulatory element upstream of the transcription initiation site, partially contributed to the downregulation of FGF6 in patients with obesity. Overexpression of Fgf6 in mice skeletal muscle stimulated protein synthesis, activating the mammalian target of rapamycin (mTOR) pathway, and prevented the increase in weight and the development of insulin resistance in high-fat diet-fed mice. Thus, our findings highlight the role played by Fgf6 in regulating skeletal muscle hypertrophy and whole-body metabolism, indicating its potential in strategies aimed at preventing and treating metabolic diseases.

overall_design: mRNA profiles of gastrocnemius muscles injected with AAV9-FGF6 and AAV9-Control for one month

first: Bo

last: Xu

first: Cheng

last: Hu

first: Weiping

last: Jia


title: Comparative Transcriptomics on cellular reactions to short-term hypergravity [Microarray]

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

summary: Jurkat T cells have been lysed after exposure to 15 minutes of 9g in a ground-based pipette centrifuge. The RNA samples were parallely analyzed with RNA-Seq and microarray transcriptomics.

overall_design: 1 hypergravity condition (9g, 15 minutes). 1 ground control condition with exact same setup including aspiration of cells into pipettes and lysis after 15 minutes, but without hypergravity. 4 samples per condition.

first: Christian

last: Vahlensieck

first: Oliver

last: Ullrich


title: Phytosterol accumulation results in ventricular arrhythmia, impaired cardiac function and death

city: SOUTH SAN FRANCISCO

first: Tracy

last: Yamawaki

state: California

address: 1120 VETERANS BLVD.

institute: AMGEN, INC.

summary: Heart failure (HF) and cardiac arrhythmias share overlapping pathological mechanisms that act cooperatively to accelerate disease pathogenesis.  Cardiac fibrosis is associated with both pathological conditions.  Our previous work identified a link between phytosterol accumulation, cardiac fibrosis and death in a mouse model of phytosterolemia, a rare disorder characterized by elevated circulating phytosterols and increased cardiovascular disease risk.  Here, we uncover a previously unknown pathological link between phytosterols and cardiac arrhythmias in the same animal model.  Phytosterolemia resulted in inflammatory pathway induction, premature ventricular contractions (PVC) and ventricular tachycardia (VT).  Both pharmacological and genetic inhibition of phytosterol absorption prevented the induction of both pathways.  Inhibition of phytosterol absorption reduced inflammation and cardiac fibrosis, improved cardiac function, reduced the incidence of arrhythmias and increased survival in a mouse model of phytosterolemia.  Collectively, this work identified a pathological mechanism whereby elevated phytosterols result in inflammation and cardiac fibrosis leading to impaired cardiac function, arrhythmias and sudden death.  These phytosterolemia-associated comorbidities provide novel insight into the underlying pathophysiological mechanism that predispose these patients to increased risk of sudden cardiac death.

overall_design: Heart tissue RNA-seq of vehicle- or Ezetimibe-treated of ABCG5/8 NPC1L1 TKO and ABCG5/8 male mice.

first: Hongfei

last: Ge

first: Gongxin

last: Liu

middle: M

first: Caroline

last: Tao

first: Shawn

last: Alexander

first: Kimberly

last: Ly

first: Preston

last: Fordstrom

first: Artem

last: Shkumatov

first: Chi-Ming

last: Li

first: Sridharan

last: Rajamani

first: Mingyue

last: Zhou

first: Brandon

last: Ason


title: The RNA-binding protein ESRP1 modulates the expression of RAC1b in colorectal cancer cells  [COLO320DM]

first: Ugo

last: Ala

first: Enzo

last: Medico

first: Daniela

last: Cantarella

first: Marta

last: Manco

first: Sharmila

last: Fagoonee

first: Fiorella

last: Altruda


title: Comparative Transcriptomics on cellular reactions to short-term hypergravity

first: Cora

last: Thiel


title: The histone chaperone Anp32e regulates memory formation, transcription and dendritic morphogenesis by regulating steady-state H2A.Z binding in neurons

city: Mississauga

first: iva

last: zovkic

state: ON

address: 3359 Mississauga road North

institute: University of Toronto Mississauga

summary: Rapid removal of the histone variant H2A.Z from neural chromatin is a key step in learning-induced gene expression and memory formation, but the molecular mechanisms underlying learning-induced H2A.Z removal are unknown. Anp32e was recently identified an H2A.Z-specific histone chaperone that removes H2A.Z from nucleosomes in dividing cells, but whether it plays a similar role in non-dividing neurons is unknown. Moreover, prior studies only investigated effects of Anp32e on H2A.Z binding under steady state-conditions, such that its effect on H2A.Z removal under stimulus-induced conditions is unknown. Here, we show that Anp32e regulates H2A.Z binding in neurons under steady-state conditions, but that stimulus-induced H2A.Z removal is largely independent of Anp32e. In assessing the functional consequences of Anp32e, we showed that its depletion leads to H2A.Z-dependent impairment in dendritic arborization in cultured hippocampal neurons, as well as impaired recall of contextual fear memory and transcriptional regulation. Together, these data indicate the Anp32E regulates behavioral and morphological outcomes by preventing H2A.Z accumulation in chromatin rather than by regulating activity-mediated H2A.Z dynamics.

overall_design:
ChIP-seq dataset:1)ChIP against H2A.Z in control (shScr) neurons along with inputs; 2)ChIP against H2A.Z in shAnp32e neurons along with inputs; 3) ChIP from shScr neurons treated with 55mM KCl for 30 min along with inputs; 4)ChIP from shAnp32e neurons treated with 55mM KCl for 30 min along with inputs
RNA-seq dataset in primary hippocampal neurons infected with shScr, shAnp32e and shAnp32e+shH2afz

first: Iva

last: Zovkic


title: MENS efficacy in STZ-induced DM

city: Hsinchu

first: Yong Chun

last: Luo

address: Boai Street

country: Taiwan

institute: National Chiao Tung University

summary: In previous studies, microcurrent electrical nerve stimulation (MENS) has been also used for pain control and muscular growth, but no literatures study the effects and mechanisms of MENS for DM management. Here we analyzed the effect of MENS and MENS mechanisms using phenotype data and omics data of mouse animal model. The results showed MENS regulated diabetes-related pathways to lower blood glucose.

overall_design: Mice were seperated to three groups: control, STZ, STZ+MENS mice. STZ mice were treated with MENS for 6 consecutive weeks. RNA was perpared from liver and analyzed through microarray which was performed by Phalanx Biotech Group Inc. using Phalanx Mouse OneArray® v2 technology (MOA 2.1).

first: Yong-Chun

first: Sing-Han

last: Huang

first: Jinn-Moon

last: Yang


title: RNA-seq experiment of Calreticulin-mutated patients

city: Florence

first: Paola

last: Chiarugi

state: Florence

address: Viale Morgagni 50

department: Department of Experimental and Clinical Biomedical Sciences

institute: University of Florence

summary: We report the feature count (from HTSeq) of 6 calreticulin-mutated patients and 3 healty control.

overall_design: We examinated the gene expression of calreticulin mutated patients compared to 3 healty control.

first: Simone

last: Romagnoli

first: Majola

last: Balliu

first: Niccolò

last: Bartalucci

first: Laura

last: Calabresi

last: Guglielmelli

first: Alessandro

last: Vannucchi


title: Leveraging the Mendelian Disorders of the Epigenetic Machinery to Systematically Map Functional Epigenetic Variation

city: Baltimore

first: Teresa

middle: Romeo

last: Luperchio

state: MD

address: 733 N Broadway

department: Department of Genetic Medicine

institute: Johns Hopkins School of Medicine


title: The natural compound atraric acid suppresses androgen-regulated neo-angiogenesis of castration-resistant prostate cancer through angiopoeitin2

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

summary: Castration-resistant prostate cancer (CRPC) is an incurable form of prostate cancer (PC) and a major therapeutic challenge. Here, we show that the natural compound, atraric acid (AA), inhibits besides the androgen receptor (AR) those AR-mutants that confer therapy resistance to AR-antagonists indicating a different mode of AR-antagonism. AA induces cellular senescence and inhibits intratumoral angiogenesis and CRPC tumour growth in treated xenograft mice. RNA-seq reveals an upregulated angiogenic transcriptional pathway by androgen. In line with this, conditioned medium from CRPC cells induces angiogenesis in two in vitro models using primary human endothelial cells. By employing immune arrays and mass-spec analyses, we found that androgens induced secretion of pro-angiogenic factors pinpointing to angiopoeitin2 (ANGPT2). The senescence-associated secretory phenotype revealed reduced ANGPT2 secretion by AA. Accordingly, immune-depletion of ANGPT2 or blocking ANGPT2-receptors inhibits angiogenesis. Our data propose AA as potential anti-PCa compound and ANGPT2 pathway as novel therapeutic target for CRPC.

overall_design: Transcriptional profile of C-42 cells upon androgen treatment

first: Marzieh

last: Ehsani

first: Kimia

last: Mirzakhani

first: Seyed

first: Francesco

last: Neri

first: Aria

last: Baniahmad


title: THP-1 cell lines: reference data for classification of THP-1 cells [genome]

first: Fumio

last: Kasai

summary:
THP-1 is a representative leukemia cell line, and has been widely used all around the world since its establishment in Japan in 1980.
Differences in THP-1 cells have been reported; however, the THP-1 genomes have not been accurately characterized.

overall_design: Genome profiles of four THP-1 cell lines available from JCRB and RIKEN BRC in Japan; JCRB0112, JCRB0112.1 (corresponding to ATCC TIB-202), RCB1189 (corresponding to DSMZ ACC-16) and RCB3686, have been compared by microarrays.


title: OTX2 homeoprotein regulates adult choroid plexus activity

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

summary: Choroid plexus secretes cerebrospinal fluid important for brain development and homeostasis. The OTX2 homeoprotein is critical for choroid plexus development and remains highly expressed in adult choroid plexus. Through RNA sequencing analyses of constitutive and conditional knockdown adult mouse models, we reveal putative roles for OTX2 in choroid plexus function, including cell signaling and adhesion, and show that it regulates the expression of factors secreted into cerebrospinal fluid, notably transthyretin. We also show that Otx2 expression impacts choroid plexus immune and stress responses, and also affects splicing which leads to changes in mRNA isoforms of proteins implicated in oxidative stress response and DNA repair. Through mass spectrometry analysis of OTX2 protein partners in the choroid plexus, and in known non-cell autonomous target regions such as visual cortex and subventricular zone, we identified putative targets involved in cell adhesion, chromatin structure and RNA processing. Thus, OTX2 retains important roles in choroid plexus function and brain homeostasis throughout life.

overall_design: transcriptome profile of several Otx2 mutants using RNA-Seq

first: Anabelle

last: Planques

first: Vanessa

last: Moreira

first: David

last: Benacom

first: Clémence

last: Bernard

first: Laurent

last: Jourdren

first: Corinne

last: Blugeon

first: Florent

last: Dingli

first: Damarys

last: Loew

first: Alain

last: Prochiantz

first: Ariel

middle: A

last: Di Nardo


title: DNA methylation of neural differentiation from human adipose derived stem cells

city: Badalona

first: Manel

last: Esteller

state: Barcelona

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

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

summary: DNA methylation from three protocols for neural-like cells derived from adipose stem cells (hASC)

overall_design: The study aimed to compare the DNA methylation differences between three culture media for the differentiation of neural-like cells from human adipose-derived stem cells (hASC) using methylation array technology (450K, Illumina). The identified differently methylated CpG were further analyzed in funcoitnal assays to study their implicatoin on the differentiatin processes.

first: Maria

last: Berdasco

first: Consolación

last: Melguizo


title: Cardiac-specific β-catenin deletion dysregulates energetic metabolism and mitochondrial function in perinatal cardiomyocytes

city: Kyiv

first: Oksana

last: Piven

address: 150 Akad. Zabolotnogo str.

department: Human Genetics

country: Ukraine

institute: Institute of Molecular Biology and Genetics

summary: β-Catenin signaling pathway regulates cardiomyocytes proliferation and differentiation, though its involvement in metabolic regulation of cardiomyocytes remains unknown. We used one-day-old mice with cardiac-specific knockout of β-catenin and neonatal rat ventricular myocytes treated with β-catenin inhibitor to investigate the role of β-catenin metabolism regulation in perinatal cardiomyocytes. Transcriptomics of perinatal β-catenin-ablated hearts revealed a dramatic shift in the expression of genes involved in metabolic processes. Further analysis indicated an inhibition of lipolysis and glycolysis in both in vitro and in vivo models. Finally, we showed that β-catenin deficiency leads to mitochondria dysfunction via the downregulation of Sirt1/PGC-1α pathway. We conclude that cardiac-specific β-catenin ablation disrupts the energy substrate shift that is essential for postnatal heart maturation, leading to perinatal lethality of homozygous β-catenin knockout mice.

overall_design: Heart mRNA profile of newborn (P1) mice with cardiospecific homozygous knockout of β-catenin and control mice.

first: Volodymyr

last: Balatskyi

first: Vasyl

last: Vaskivskyi

first: Anna

last: Myronova

first: Diana

last: Avramets

first: Larysa

last: Macewicz

first: Tetiana

last: Ruban

first: Roman

last: Nikolaev

first: Dar'ya

last: Kucherenko

first: Oleksandr

last: Soldatkin

first: Iryna

last: Lushnikova

first: Galyna

last: Skibo

first: Cecilia

last: Winata

first: Pawel

last: Dobrzyn


title: Analysis of effects of KLF5 on dexamethasone-mediated atrophy in mouse satellite cells [RNA]

first: Ichiro

last: Manabe

institute: Chiba University

summary: We analyzed effects of dexamethasone (Dex) on primary satellite cells (SCs) purified from control and MCK-Cre:Klf5f/f mice.

overall_design: RNA-seq profiling of effects of dexamethasone on primary satellite cells

first: Oishi

last: Yumiko

first: Manabe

last: Ichiro


title: Methylomes of Geobacter sulfurreducens Grown on Different Terminal Electron Acceptors

city: Fuzhou

first: Zhenhua

last: Shi

state: Fujian

address: No.15 Shangxiadian Road

institute: Fujian Agriculture and Forestry University

summary: The Geobacter species evolved respiratory versatility to utilize a wide range of terminal electron acceptors. To explore this adaptive mechanism, Fe(III) citrate, hydrous ferric oxide, and fumarate were selected as electron acceptors, and the methylome and metabolome of Geobacter sulfurreducens PCA grown on each electron acceptor were investigated via third-generation, single-molecule real-time DNA sequencing.Results showed that the patterns of 4-methylcytosine (m4C) and 6-methyladenine (m6A) modification were all varied in different electron acceptor cultures. Moreover, genes (e.g., GSU0466 and GSU1467) with low expression levels generally had high methylation levels. These findings suggest that m4C and m6A modifications play a role in the adaption of G. sulfurreducens to diverse electron acceptors, and DNA methylation may be involved in the adaption mainly via gene expression regulation.

overall_design: The methylomes of Geobacter sulfurreducens PCA grown on electron acceptors of Fe(III) citrate, hydrous ferric oxide, and fumarate were investigated via third-generation, single-molecule real-time DNA sequencing, respectively.


title: Leveraging the Mendelian Disorders of the Epigenetic Machinery to Systematically Map Functional Epigenetic Variation - ATAC-seq

first: Teresa

last: Luperchio

summary: The Mendelian Disorders of the Epigenetic Machinery (MDEMs) have emerged as a class of Mendelian disorders caused by loss-of-function variants in epigenetic regulators. Although each MDEM has a different causative gene, they exhibit several overlapping disease manifestations. Here, we hypothesize that this phenotypic convergence is a consequence of common abnormalities at the epigenomic level, which directly or indirectly lead to downstream convergence at the transcriptomic level. This implies that identifying abnormalities shared across multiple MDEMs could pinpoint locations where epigenetic variation is causally related to disease phenotypes. To test our hypothesis, we perform a comprehensive interrogation of chromatin (ATAC-Seq) and expression (RNA-Seq) states in B cells from mouse models of three MDEMs (Kabuki types 1&2 and Rubinstein-Taybi syndromes). We build on recent work in covariate-powered multiple testing to develop a new approach for the overlap analysis, which enables us to find extensive overlap primarily localized in gene promoters. We show that disruption of chromatin accessibility at promoters often leads to disruption of downstream gene expression, and identify a total of 463 loci and 249 genes commonly disrupted across the three MDEMs. As an example of how widespread dysregulation leads to specific phenotypes, we show that subtle expression alterations of multiple, directly relevant genes, collectively contribute to IgA deficiency in KS1 and RT. In contrast, we predict that KS2 does not have IgA deficiency, and confirm this pattern in mice. We propose that the joint study of MDEMs offers a principled approach for systematically mapping functional epigenetic variation in mammals.

overall_design: ATAC-seq of CD19+ B cells in mouse models of Kabuki Syndrome 1, Kabuki Syndrome 2, and Rubenstein-Taybi Syndrome 1

middle: R

first: Leandros

last: Boukas


title: Genome-wide DNA methylation profiling in Atherosclerotic plaques

city: Beijing

first: Hang

last: Yang

state: Beijing

address: No.1 West Beichen Road,Chaoyang District

institute: CAS

type: Methylation profiling by genome tiling array

summary: Genome wide Methylation profiling of DNA extracted from plaques of atherosclerotic plaque samples (n=14) and of controls (n=4). The Illumina Infinium HumanMethylation450 or HumanMethylation850 BeadChip was used representing potentially methylated CpG sites throughout the genome.

overall_design: Bisulphite converted DNA from the 18 samples(n=4 controls, n=8 stable plaques and n=6 unstable plaques) were hybridized to the Illumina Infinium Human Methylation450 or Methylation850 Beadchip

first: Jingyi

last: Ren


title: Leveraging the Mendelian Disorders of the Epigenetic Machinery to Systematically Map Functional Epigenetic Variation - RNA-seq

overall_design: RNA-seq of CD19+ B cells in mouse models of Kabuki Syndrome 1, Kabuki Syndrome 2, and Rubenstein-Taybi Syndrome 1


title: Comparison analysis of transcriptome profiles between tumor cells before or after immune editing

city: Seoul

first: SUYEON

last: KIM

address: IN-CHONRO 73

department: BIOCHEMISTRY

country: South Korea

institute: KOREA UNI.

summary: To gain insight into the differential expressed genes in immune edited tumor cell lines, we performed genome-wide RNA-sequencing analysis (RNA-seq) in parental P0 (CaSki-P0) and immune edited P3 (CaSki-P3) cells.

overall_design: We established a highly immune-resistant cervical cancer cell line, CaSki P3 (termed P3), which was generated from its immune susceptible parental cell line CaSki P0 (termed P0) through three rounds of in vitro selection by mixing P0 cells pulsed with the MART-1 peptide together with MART-1-specific CTLs.

first: Suyeon

last: Kim

first: Tae


title: Transcriptional profilling of Plasmodium falciparum parasites with disrupted PfNot1.1 (PF3D7_1103800) or PfNot1.2 (PF3D7_1417200)

city: Singapore

first: Ying

last: Liu

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary:
The study aims to investigate functions of two PfNOT1 paralogues in regulating gene expression in the malaria parasite, P. falciparum.
To achieve this goal, the transcriptional profilling of parasites lacking  PfNot1.1 or PfNOT1.2 was analyzed by microarray technology.

overall_design: The endogenous PfNot1.1 was disrupted and PfNot1.2 was conditionally knocked down. Transcriptional profiling of the mutated parasites and the wildtype line was assessed at six timepoints across one parasite's intraerythrocytic life cycle.

first: Zbynek

last: Bozdech

first: Mark

last: Featherstone


title: Two's Company: Epigenome bias in the seed of the allopolyploid Brassica napus

city: Winnipeg

last: Belmonte

state: Manitoba

address: 50 Sifton Rd

department: Biological Sciences

country: Canada

institute: University of Manitoba

overall_design: For WGBS: 3 bio-replicates each of globular and mature green seeds. For sRNA-seq: 3 bio-replicates each of ovule, globular, heart, mature green, and dry seed.

first: Deirdre

last: Khan

first: Dylan

last: Ziegler

first: Isobel

last: Parkin

first: Steven

last: Robinson


title: Transcriptome analyses of Atlantic salmon (Salmo salar L.) erythrocytes infected with piscine orthoreovirus (PRV)

status: Public on Aug 30 2021

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Piscine reovirus (PRV) is a causative agent of heart and skeletal muscle inflammation in Atlantic salmon, which is propagated in red blood cells (RBC). Here, transcriptome analyses of PRV infected erythrocytes showed strong and complex innate antiviral responses.

overall_design: RBC were isolated from fish challenged with PRV, blood was sampled after 5 and 7 weeks (n = 4 at both time-points).

first: Maria

last: Dahle

first: Øystein

last: Wessel


title: Novel Mechanisms of Antibiotic Resistance in Mismatch Repair-Deficient Pseudomonas aeruginosa hypermutators

city: Bethesda

first: Augusto

last: Dulanto Chiang

state: Maryland

address: 9000 Rockville Pike

country: USA

institute: NIAID

summary: Using in vitro directed evolution, we show that mismatch repair-deficient Pseudomonas aeruginosa can engage novel resistance mechanisms to ceftazidime-avibactam.

overall_design: Whole-genome and RNA sequencing of P. aeruginosa isolates passaged under ceftazidime/avibactam selection.

first: Prashant

middle: P

last: Patil

first: Lidia

last: Beka

first: Jung-Ho

last: Youn

first: Adrien

last: Launay

first: Robert

last: Bonomo

first: Pavel

last: Khil

first: John

last: Dekker


title: Hepatocyte-Specific Transcriptional Profiling of the Hepatic Fasting Response

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: We generated transcriptional profiles of fasting-induced changes of in vivo hepatocytes using the INTACT methodology.

overall_design: We subjected female HEP-INTACT mice to an overnight fast starting at the onset of the mouse active phase, ZT12, and after 16h livers were collected for INTACT followed by RNA-seq analyses of isolated hepatocytes. Ad libitum fed control mice were sacrificed at the same time point to account for diurnal variations in gene expression.

first: Søren

last: Fisker Schmidt

first: Thomas

last: Schwarzmayr

first: Stephan

last: Herzig


title: Hepatocyte-Specific Genomic Profiling of the Hepatic Fasting Response

summary: We generated profiles of fasting-induced changes in the genomic landscapes of in vivo hepatocytes using the INTACT methodology.

overall_design: We subjected female HEP-INTACT to an overnight fast starting at the onset of the mouse active phase, ZT12, and after 16h livers were collected for INTACT followed by ATAC-seq analyses of isolated hepatocytes. Ad libitum fed control mice were sacrificed at the same time point to account for diurnal variations.


title: Single-cell profiling of photoreceptor cells in adult zebrafish

city: Saint Louis

first: Joseph

middle: C.

last: Corbo

state: MO

address: 660 S. Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

summary: Vertebrate vision is mediated by two kinds of photoreceptors, rods and cones, responsible for dim- and bright-light vision, respectively. Gene expression differences among cone subtypes remain poorly understood compared with rods. We generated single-cell transcriptome data using a droplet-based approach to reveal the extent of gene expression diversity among adult zebrafish photoreceptor subtypes. Populations of photoreceptor cells were enriched by using the transgenic zebrafish lines, Tg(rho:EGFP)ja2Tg and Tg(gnat2:EGFP)ja23Tg, which express GFP in rods and all cone subtypes, respectively. By analyzing the single-cell transcriptomes, we found that in addition to the four canonical zebrafish cone types (ultraviolet, blue, green and red), there exist subpopulations of green and red cones in the ventral retina that express red-shifted opsin paralogs (opn1mw4 and opn1lw1). This work lays a foundation for future studies aimed at understanding how molecular differences among cone subtypes affect photoreceptor function.

overall_design: GFP-positive cells collected from two transgenic zebrafish, Tg(rho:EGFP)ja2Tg and Tg(gnat2:EGFP)ja23Tg were combined into one sample. A small percentage of GFP-negative cells was also included in the sample.


title: Transcriptome analysis of first-of-a-kind lines of conditionally immortalized human atrial cardiomyocytes (hiAMs)

city: Leiden

first: Antoine

last: de Vries

address: Albinusdreef 2

department: Cardiology

country: Netherlands

institute: Leiden University Medical Center

summary: Using conditional immortalization, we generated the first lines of human cardiomyocytes with preserved cardiomyogenic differentiation capacity. These human immortalized Atrial Myocytes (hiAMs) display strict control over proliferation and differentiation, allowing massive (quadrillion-fold) expansion followed by differentiation towards fully functional (i.e. excitable and contractile) human atrial cardiomyocytes. Here, we characterized the transcriptome of three hiAM monoclones during proliferation (D0) and after differentiation (D12) using RNA-sequencing.

overall_design: Total RNA of hiAM monoclones 2.38, 2.52 and 2.90 was sequenced during proliferation (D0) and after differentiation (D12). Per monoclone and time point, three replicates were used.

first: Niels

last: Harlaar

first: Daniël

last: Pijnappels


title: The effects of metformin on the early LPS response of macrophages

city: Jersey City

middle: S

last: Postler

state: New Jersey

address: 95 Greene Street 5-018

department: Discovery Science

institute: International AIDS Vaccine Initiative

summary: Metformin is a front-line drug in the treatment of type-2 diabetes mellitus (T2DM). In addition to its antigluconeogenic and insulin-sensitizing properties, it has emerged as a potent inhibitor of the inflammatory response of macrophages. Specifically, metformin has been shown to reduce transcript levels of Il1b, the gene encoding the pro-inflammatory cytokine interleukin (IL)-1b, during long-term exposure of macrophages to the bacterial cell-wall component lipopolysaccharide (LPS). However, the extent to which metformin affects the early transcriptional response to LPS has never been investigated. Here, we show that metformin affects transcript levels of a large yet selective subset of LPS-responsive genes after only two hours of LPS exposure, mostly counteracting the effect of LPS rather than enhancing it. The affected genes are implicated in a variety of biological functions, in particular cellular movement and trafficking. Intriguingly, metformin affects transcript levels of Il1b at this early time point as well, but through a molecular mechanism fundamentally different from the regulation observed after longer exposure. While down-regulation of Il1b by metformin during the late stages of the LPS response has been shown to rely on stabilization of hypoxia-inducible factor (HIF)-1α and production of IL-10, Il1b inhibition at the early stage requires AMP-activated protein kinase (AMPK) activation but is independent of HIF-1α and IL-10. These results reveal an unexpected complexity in the anti-inflammatory properties of metformin and demonstrate that Il1b is down-regulated by distinct mechanisms in the early and late stages of the LPS response.

overall_design: Bone-marrow-derived macrophages from WT C57Bl/6 mice were either left untreated, stimulated with 100 ng/ml LPS for 2 h or pretreated with 5 mM metformin for 6 h and then stimulated with 100 ng/ml LPS for 2 h.

first: Vincent

last: Peng

first: Dev

last: Bhatt

first: Sankar

last: Ghosh


title: Identification of circular RNAs related to vascular endothelial proliferation, migration and angiogenesis after spinal cord injury using microarray analysis

city: Hangzhou

first: XIN

last: YE

state: China

address: No.3 Qingchun East Road

department: Department of Neurosurgery

country: China

institute: SIR Run Run Shaw Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang

summary: To further evaluate the role of circRNAs in SCI, we elucidated circRNA expression profiles related to vascular endothelial proliferation, migration and angiogenesis during the early stages of secondary injury in a mouse model of SCI.

overall_design: Microarray analysis was performed to investigate the circRNA expression patterns in mouse spinal cord three days after SCI. Bioinformatic analyses, including GO enrichment analysis, KEGG pathway analysis, and circRNA-miRNA-mRNA network construction, were conducted to explore the role of circRNA dysregulation in vascular endothelial proliferation, migration and angiogenesis following SCI.

first: Xin

last: Ye

first: Fengdong

last: Zhao


title: Differential recruitment of Ser2/5 phosphorylated RPB1, a component of the elongating RNAPII, in Plasmoidium falciparum parasite with disrupted PfNot1.1 (PF3D7_1103800).

first: Ying

last: Liu

type: Genome binding/occupancy profiling by array

summary:
The study aims to investigate the role of PfNOT1.1  in transcription in the malaria parasite, P. falciparum. To achieve this goal, the recruitment of RPB1 was assessed by chromatin immunoprecipitatiion and microarray technology
The endogenous PfNot1.1 was disrupted. DNA bound by Ser2/5-P RPB1 (ChIP DNA) was immunoprecipitated by Ser2/5-P RPB1 antibody in the PfNot1.1 knockout line and the wildtype line at six timepoints across one parasite's intraerythrocytic life cycle. ChIP DNA and Input genomic DNA were analyzed by microarray.

overall_design: RNAPII recruitment was compared between the PfNot1.1 knockout line and the wildtype line.

first: Zbynek

last: Bozdech

first: Mark

last: Featherstone


title: Gene expression profiling in melanised sites of Atlantic salmon fillets

status: Public on Aug 28 2021

first: Aleksei

last: Krasnov

summary: Black spots, which deteriorate quality of Atlantic salmon fillets represent a significant problem for commercial aquaculture. These areas are characterized with accumulation of melanomacrophages, occasional formation of granulomas and substitution of skeletal muscle with connective tissue. Transcriptome analysis was performed to elucidate the origin and the character of inflammation in the melanized foci of skeletal muscle.

overall_design: Nine individuals were analyzed. Despite variation in the appearance of spots the gene expression profiles were similar.

last: Larsson

first: Turid

last: Mørkøre


title: Mutant U2AF1-Induced Alternative Splicing of H2afy (macroH2A1) Regulates B-Lymphopoiesis in Mice

city: St Louis

first: Matthew

last: Walter

state: MISSOURI

address: 660 South Euclid Avenue

department: Oncology

summary: Acquired spliceosome gene mutations are among the most common genetic alterations in myelodysplastic syndromes (MDS). Here we present evidence that H2AFY(macroH2A1), a histone H2A variant, is a functional target that is alternatively spliced by mutant U2AF1(S34F), a spliceosome gene. Expression of H2AFY1.1, a H2AFY splice-isoform that is reduced by U2AF1(S34F) expression, rescues the reduction in B-cells observed in U2AF1(S34F) mice. Human MDS samples with U2AF1 mutations have a similar reduction in B-cells. Collectively, our data suggest that altered splicing of H2AFY contributes to MDS pathogenesis.

overall_design: B-cell biased-lymphoid progenitors were isolated from H2afy+/+ and H2afy-/-mice for RNA-seq. First, bone marrow cells were enriched for c-Kit+ cells using Cd117 MicroBeads on the autoMACS Pro Separator (Miltenyi Biotec). Subsequently, cells were stained according to the staining scheme described above, and BLPs were sorted by FACS (Moflo, Beckman Coulter) directly into the lysis buffer of NucleoSpin RNA XS kit (MACHEREY-NAGEL). RNA was isolated per manufacturer’s instructions. Per sample, RNA equivalent of 5000-15000 BLPs from 2-3 mice were pooled. Total RNA integrity and concentration were assessed using a 2100 Bioanalyzer and an RNA 6000 Pico kit (Agilent). Double stranded-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer’s protocol. cDNA was fragmented using a Covaris E220 sonicator using duty cycle 10, intensity 5, cycles/burst 200, time 180 seconds. Fragments were sequenced on Illumina HiSeq-3000 using single reads extending 50 bases. Reads were aligned to mouse mm9 reference genome using Hisat2(version2.0.6) and following analyses were prefomed using DESeq2 in R

first: Sanghyun

last: Kim

first: Sridhar

middle: N

last: Srivatsan


title: Dysregulation of principal circulating miRNAs in Nonhuman Primates following ischemic stroke

status: Public on Aug 27 2021

first: Haiping

address: 45 Changchun Street

institute: Xuanwu Hospital of Capital Medical University

summary: Despite the recent interest in plasma microRNA (miRNA) biomarkers in acute ischemic stroke patients, there is limited knowledge about the miRNAs directly related to stroke itself due to the multiple complications in patients, which has hindered the research progress of biomarkers and therapeutic targets of ischemic stroke. Therefore, in this study, we compared the differentially expressed miRNA profiles in the plasma of three rhesus monkeys pre- and post-cerebral ischemia. After cerebral ischemia, RFAM sequence category revealed increased ribosomic RNA (rRNA) and decreased transfer RNAs (tRNAs) in plasma. Of the 2049 miRNAs detected after cerebral ischemia, 36 were upregulated, and 76 were downregulated (fold change ≥2.0, P <0.05). For example, Mml-miR-191-5p, miR-421, miR-409-5p, and let-7g-5p were found to be significantly overexpressed, whereas mml-miR-128a-5p_R-2, miR-431_R-1, and let-7g-3p_1ss22CT were significantly downregulated. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that these differentially expressed miRNAs were implicated in the regulation of ubiquitin-mediated proteolysis and signaling pathways in cancer, glioma, chronic myeloid leukemia, and chemokine signaling. miRNA clustering analysis showed that mml-let-7g-5p and let-7g-3p_1ss22CT, which share three target genes (RB1CC1, GNG5, and CXCR4), belong to one cluster, were altered in opposite directions following ischemia. These data suggest that circulating mml-let-7g may serve as a therapeutic target for ischemic stroke.

overall_design: ischemic stroke: before ischemia, after ischemia

first: Jian

last: Chen

first: Yuyou

last: Huang

first: Yuqian

last: Li

first: Junfen

last: Fan

first: Rongliang

last: Wang

first: Ziping

last: Han

first: Zhenhong

last: Yang

first: LongFei

last: Wu

first: Di

first: Yumin

last: Luo

first: Xunming

last: Ji


title: Analysis of accessible chromatin regions in response to dexamethasone mediated-atrophy in mouse satellite cells [ATAC]

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

country: Japan

summary: We analyzed the accessible chromatin regions globally in response to dexamethasone in primary mouse satellite cells (SCs)

overall_design: ATAC-seq profiling of effects of dexamethasone on primary satellite cells

first: Oishi

last: Yumiko

first: Manabe

last: Ichiro


title: Expression and tumour-promoting effect of tyrosine phosphatase receptor type N (PTPRN) in human glioma

status: Public on Aug 29 2021

city: Tianjin

first: Bo

address: JIZHAOROAD 6#

institute: Tianjin medical university

summary: To study the molecular mechanism of the effects of PTPRN on glioma cell proliferation and metastasis.

overall_design: Effect of PTPRN knockdown on the transcriptome of U87 glioma cells


title: Genome-wide maps of colorectal cancer diagnosis and toxicity of capecitabine-based chemotherapy.

city: Shanghai

first: Wansheng

address: 415 Fengyang Road

department: Department of Pharmacy

institute: Changzheng Hospital, Second Military Medical University

summary: Background: Capecitabine-based adjuvant chemotherapy is the first-line treatment for patients with colorectal cancer (CRC). Although this therapy generally reduces the incidence of CRC recurrence and mortality, it can cause various chemotherapy-related adverse events (CRAEs), one of the most frequent of which is hand-foot syndrome (HFS). Most of the currently available HFS prediction markers focus on the pharmacokinetic parameters of drugs or their metabolites, yet our understanding of the biomolecular mechanism of HFS remains limited.  Methods: We conducted an integrated multi-omics analysis of 63 Chinese patients with colorectal cancer (CRC) who had chemotherapy related adcerse effect (CRAE) records during adjuvant chemotherapy. The metabolomic profiles for each of plasma, urine, and colorectal tissue as well as profiles for colorectal-tissue transcriptomics and genome methylation were analyzed based on samples collected before and during surgery.  Results: Susceptibility to HFS was found to be associated with profibrotic changes in several aspects of cellular biochemistry and physiology, characterized by reduced nucleotide salvage (indicating potential tissue damage, elevated spermine release, increased M2 macrophage polarization, and hypermethylation of genes for collagen formation. All these aspects were found to promote fibrosis, even before patients received chemotherapeutic drugs or developed any HFS symptoms. Additionally, we developed and validated relevant biomarkers with reasonably good discrimination performance and a high AUROC (area under the receiver operating characteristic curve) value, i.e., from 0.848 to 1.000.  Conclusions: Our results demonstrate that a profibrotic phenotype characterized by multi-omics variation in colorectal tissue, plasma, and urine is closely related to the susceptibility to chemotherapy-induced HFS. Our findings provide a better understanding of the molecular mechanism underlying HFS.

overall_design: There are 57 patients with different grade of Hand-Foot Syndrome were analyzed, no replicate was included.

first: Mingming


title: Genome-wide maps of colorectal cancer diagnosis and toxicity of capecitabine-based chemotherapy [methylation array]

summary:
Background: Capecitabine-based adjuvant chemotherapy is the first-line treatment for patients with colorectal cancer (CRC). Although this therapy generally reduces the incidence of CRC recurrence and mortality, it can cause various chemotherapy-related adverse events (CRAEs), one of the most frequent of which is hand-foot syndrome (HFS). Most of the currently available HFS prediction markers focus on the pharmacokinetic parameters of drugs or their metabolites, yet our understanding of the biomolecular mechanism of HFS remains limited.
Methods: We conducted an integrated multi-omics analysis of 63 Chinese patients with colorectal cancer (CRC) who had chemotherapy related adverse effect (CRAE) records during adjuvant chemotherapy. The metabolomic profiles for each of plasma, urine, and colorectal tissue as well as profiles for colorectal-tissue transcriptomics and genome methylation were analyzed based on samples collected before and during surgery.
Results: Susceptibility to HFS was found to be associated with profibrotic changes in several aspects of cellular biochemistry and physiology, characterized by reduced nucleotide salvage (indicating potential tissue damage, elevated spermine release, increased M2 macrophage polarization, and hypermethylation of genes for collagen formation. All these aspects were found to promote fibrosis, even before patients received chemotherapeutic drugs or developed any HFS symptoms. Additionally, we developed and validated relevant biomarkers with reasonably good discrimination performance and a high AUROC (area under the receiver operating characteristic curve) value, i.e., from 0.848 to 1.000.
Conclusions: Our results demonstrate that a profibrotic phenotype characterized by multi-omics variation in colorectal tissue, plasma, and urine is closely related to the susceptibility to chemotherapy-induced HFS. Our findings provide a better understanding of the molecular mechanism underlying HFS.

overall_design: Bisulphite converted DNA from the 56 samples were hybridised to the Illumina Infinium Human MethylationEPIC Beadchip


title: Vitis vinifera embryogenic callus epigenomics (small RNA data)

city: Blenheim

first: Darrell

middle: Karl

last: Lizamore

state: Marlborough

address: 85 Budge St

country: New Zealand

institute: Bragato Research Institute

summary: Plants regenerated from tissue culture frequently show somaclonal variation. In this study we compared the transcriptomic and epigenetic state of embryogenic callus of grapevine with leaves from mature grapevine plants. In particular, we focussed on the expression of transposable elements and changes in siRNA abundance and genome-wide methylation in these tissues.

overall_design: Comparison of gene and transposable element transcription, small RNA and DNA methylation in embryogenic callus cells with leaf tissue

first: Chris

last: Winefield


title: Vitis vinifera embryogenic callus epigenomics (RNA-seq)

middle: K

first: Ross

last: Bicknell


title: The mRNA decay analysis of Plasmodium falciparum parasites with disrupted PfNot1.1 (PF3D7_1103800) at 24 hour post-invasion.

first: Ying

last: Liu

summary:
The study aims to investigate functions of PfNOT1.1 in regulating mRNA decay in the malaria parasite, P. falciparum.
To achieve this goal, transcription was blocked by actinomycin D (actD) and the transcriptional profilling of parasites was analyzed by microarray technology.

overall_design: The endogenous PfNot1.1 was disrupted. The transgenic line and the wildtype line were treated with actD to block transcription or DMSO as a control for four hours. Transcriptional profiling of initial parasites at 24 hpi, parasites treated with actD and parasites treated with DMSO was assessed by microarray.

first: Zbynek

last: Bozdech

first: Mark

last: Featherstone


title: Vitis vinifera embryogenic callus epigenomics (WGBS data)


title: Tumor microbiome contributes to an aggressive phenotype in the basal-like subtype of pancreatic cancer

first: Wei

last: Guo

state: Shanghai

address: Yueyang road 320, Shanghai

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

summary: Despite the uniform mortality in pancreatic adenocarcinoma (PDAC), clinical disease heterogeneity exists with limited genomic differences. A highly aggressive tumor subtype termed basal-like was identified to show worse outcomes and higher inflammatory responses. Here, we focus on the microbial effect in PDAC progression and present a comprehensive analysis of the tumor microbiome in different PDAC subtypes. Tumors from 62 resectable PDAC patients were subjected to metagenomic sequencing and RNA-seq.

overall_design: Analysis of the landscape of gene expression in pancreatic adenocarcinoma. Data include 62 primary PDAC tumors.

first: Xiangyin

last: Kong

first: Shiwei

first: Gang

last: Jin


title: Glycolytic preconditioning in astrocytes mitigates trauma-induced neurodegeneration

status: Public on Aug 26 2021

city: Dallas

first: Peter

last: Douglas

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

summary: Reducing mitochondrial electron transport induces a Warburg-like shift to accommodate for the energetic burden caused by brain trauma without overwhelming mitochondrial cellular respiration and cellular redox to salvage dopaminergic neurons. This metabolic shift is evident in the transcriptional upregulation of key genes in the Pyruvate Dehydrogenase Complex and glycolytic pathway.

overall_design: Age-matched, 10 week old Surf1+/+ and Surf1-/- mouse brains were harvested and single nuclei preps were submitted for sequencing.

first: Genevieve

last: Konopka

first: Karthigayini

last: Sivaprakasam

first: Rene

last: Fonseca


title: RNA-seq analysis in WT and rpb1-CTD-S2A strains

city: Oxford

first: Krzysztof

last: Kus

address: South Parks Rd

department: Biochemistry

country: United Kingdom

institute: University of Oxford

summary: We report calibrated transcriptome of rpb1-CTD-S2A and WT of S. pombe cells. Phosphorylation of the RNA polymerase II (Pol II) C-terminal domain on heptad Y1S2P3T4S5P6S7 coordinates key events during transcription and when its deregulation leads to defects in transcription and RNA processing. Here we report that alanine substitution of all Ser2 in CTD result in increased antisense transcription.

overall_design: RNA sequencing in WT and rbp1-CTD-S2A strains

first: Dong-hyuk

last: Heo

last: Kuś

first: Tea

last: Kecman

first: Sue

last: Tan-Wong

first: Nikolay

last: Zenkin

first: Lidia

last: Vasiljeva


title: Efficacy of BET protein proteolysis targeted chimera-based combinations against novel patient-derived models of Richter Transformation-Diffuse Large B-Cell Lymphoma

city: Houston

first: Kapil

last: Bhalla

address: 1515 Holcombe Blvd

department: Leukemia

institute: MD Anderson Cancer Center

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

overall_design: Refer to individual Series


title: Chromatin Accessibility and Regulatory Vocabulary Across Indicine Cattle Tissues

city: St. Lucia

first: Antonio

last: Reverter

state: QLD

address: 306 Carmody Road

department: Agriculture and Food

country: Australia

institute: CSIRO

summary: We have generated open-chromatin profiles for liver, muscle, and hypothalamus of indicine cattle through ATAC-seq. Using robust methods for motif discovery, motif enrichment and transcription factor binding sites, we identified potential master regulators of the epigenomic profile in these three tissues, namely HNF1, MEF2 and NFYA factors, respectively. Integration with transcriptomic data allowed us to predict their target genes showing a significant recovery of confirmed targets across species.

overall_design: ATAC-seq in liver, muscle and hypothalamus in indicine cattle.

first: Pamela

last: Alexandre

first: Marina

last: Naval-Sanchez

first: Moira

last: Menzies

first: Loan

middle: T

last: Nguyen

first: Laercio

last: Porto-Neto

last: Fortes


title: Efficacy of BET protein proteolysis targeted chimera-based combinations against novel patient-derived models of Richter Transformation-Diffuse Large B-Cell Lymphoma [ATAC-Seq]

summary: RichterTransformation (RT) develops in CLL as an aggressive, therapy resistant diffuse large B cell  lymphoma  (RT-DLBCL),  commonly clonally  related (CLR) to the antecedent CLL. Lack  of available pre-clinical models has hampered development of novel therapies for RT-DLBCL. Here,we report the profiles of genetic  alterations,  active  enhancers, gene-expressions and  anti-lymphoma drug-sensitivity patterns of first-ever established, patient-derived xenograft models of RT-DLBCLs,  including CLR  and  clonally  unrelated  (CLUR) to  antecedent  CLL. The  CLR  and CLUR RT-DLBCL cells display active enhancers, higher single-cell RNA-Seq-determined mRNA, and protein-expressions of IRF4, TCF4 and BCL2. This correlated with higher sensitivity to BET inhibitor and BET-PROTAC-based combinations with ibrutinib or venetoclax, including improved in vivo tumor burden and survival in the PDX model of CLR-RT-DLBCL.

overall_design: Examination of chromtin accessibility by ATAC-Seq analysis in Diffuse Large B cell Lymphoma PDX cells

first: Warren

last: Fiskus


title: Efficacy of BET protein proteolysis targeted chimera-based combinations against novel patient-derived models of Richter Transformation-Diffuse Large B-Cell Lymphoma [RNA-Seq]

overall_design: Examination of mRNA expression changes due to 8 hours treatment with BET inhibitor (OTX015) or BET-PROTAC (ARV-771) by RNA-Seq analysis in Diffuse Large B cell Lymphoma PDX cells


title: A Single Cell Atlas of MMRd and MMRp Colorectal Cancer

city: Jerusalem

first: Matan

last: Hofree

address: The Edmond J. Safra, Givat Ram Campus

department: School of Computer Science and Engineering | The Lautenberg Center for Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

summary: Immune responses to cancer are highly variable, in particular colorectal cancer tumors with mismatch repair-deficiency (MMRd) show an elevated presence and activity of immune cells as compared to mismatch repair proficient tumors. To understand the immune response patterns, and key differences between these types of colorectal cancer, we transcriptionally profiled 371,223 tumor and adjacent normal cells from 28 MMRp and 34 MMRd patients. Unsupervised analysis identified 88 cell subsets, from 7 distinct cell lineages, and an associated compendium of 204 gene expression programs. Examination of these programs revealed extensive transcriptional and spatial reprogramming, characteristic to MMRd and MMRp tumors.

overall_design:
A single cell expression study of primary treatment-naive colorectal cancer from MMR deficient, MMR proficient, and adjacent tumour samples.
***RNA-Seq raw data will be available through dbGaP (controlled access) due to patient privacy concerns: phs002407.v1.p1
Matan,Hofree

first: Karin

last: Pelka

first: Joanthan

middle: H

last: Chen

first: Ana

middle: C

last: Anderson

first: Orit

last: Rozenblatt-Rosen

first: Aviv

last: Regev

first: Nir

last: Hachoen


title: Efficacy of BET protein proteolysis targeted chimera-based combinations against novel patient-derived models of Richter Transformation-Diffuse Large B-Cell Lymphoma [ChIP-Seq]

overall_design: Examination of Acetylated K27  histone H3 modification and BRD4  occupancy by ChIP-Seq analysis in Diffuse Large B cell Lymphoma PDX cells


title: The Carcinogenome Project

city: Boston

first: Stefano

last: Monti

state: MA

address: 25 Buick Street

department: Computational Medicine

institute: Boston University

summary:
We generated a large toxicogenomics resource comprising ∼11,000 expression profiles corresponding to ~500 chemicals, each annotated with carcinogenicity and genotoxicity information, and profiled in HepG2 (human hepatocellular carcinoma cell line) and MCF10A cells at multiple doses and replicates.

The Platform is GPL20573: Broad Institute Human L1000 epsilon
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL20573

For questions or assistance with this dataset, please email the CMap support team at: clue@broadinstitute.org

overall_design:
We prioritized chemicals with long-term rodent liver and breast carcinogenicity annotation (derived from the Carcinogenic Potency Database (CPDB)) for inclusion in this experiment. Additional chemicals without carcinogenicity annotation were included on the basis of interest to the Superfund Research Program (environmental toxicants), presence in controversial commercial products (included for predictive purposes), and evidence of binding to the aryl hydrocarbon receptor (AhR), as the AhR is an important mediator of xenobiotics, including carcinogens.

Detailed cell culture, plating, treatment and lysis protocols are described in https://assets.clue.io/resources/sop-cell.pdf. Briefly, HepG2  (ATCC® HB-8,065™), MCF10A parental and TP53-/- (Horizon, cat# HD 101-005), were used with medium RPMI1640 (10040CV; Mediatech) supplemented with 10% v/v fetal bovine serum (F4135; Sigma-Aldrich), 1× penicillin-streptomycin-glutamine (Invitrogen 10378016), and incubated at humidified 5% CO2 atmosphere at 37°C. Cell cultures were plated with 4,000 cells (45μL of growth medium) per well on 384-well plates (3707; Corning) and incubated for 24 h before treatment. Cells were treated with 5μL of 1:100 diluted 1,000× stock compound plates to final volume of 50μL and incubated for 24 h before lysis.

Each chemical perturbation for the HEPG2 screen was administered at six doses in triplicate wells per dose and chemical combination, starting from 40μM maximum dose (40 mM stock diluted 1:1,000) for NTP chemicals and 20μM for chemicals procured from Sigma-Aldrich, in series of two-fold dilutions. The sole exception to the standard dosage was 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), which had a starting dose of 50 nM due to its extreme potency. Each chemical perturbation for the MCF10A was administered at three doses (100, 33, 10μM) in triplicate wells. The vehicle control used was DMSO with final dose of 14.1 mM. Four positive controls were used (vorinostat, geldanamycin, mitoxantrone, withaferin-a) each in final doses of 10, 3.33, and 1.00μM, respectively.

Following treatment and lysis, the gene expression of the HepG2 and MCF10A cells was profiled using the L1000 platform, a high-throughput assay that measures the expression of ∼1,000 landmark genes and computationally infers the expression of nonmeasured transcripts.

For each perturbation and landmark gene, we computed the change in gene expression following the perturbation using a moderated z-score procedure as described in the CMap–L1000 workflow. Differential expression values were calculated as moderated z-scores for each landmark gene and each unique perturbation (chemical and dose combination) perturbation, collapsed to a single value across replicates (Subramanian et al. 2017).

Each GEO sample (GSM) represents 1-3 replicates of the same treatment.

Raw data files can be analyzed at: https://github.com/cmap/cmapJ where the Broad Institute of MIT and Harvard provided the Connectivity Map software for Java to read and store lxb and GCTX files.