title: Broad transcriptomic impact of Sorafenib and its relation to the antitumoral properties in liver cancer cells

status: Public on Feb 24 2022

city: seville

first: laura

last: Contreras Bernal

state: Seville

address: c/ Antonio Maura Montaner s/n. IBiS

department: Genetic

country: Spain

institute: University of Seville

summary: Hepatocellular carcinoma (HCC) is the fourth most frequent cause of cancer-related mortality worldwide. While ablation, resection and orthotopic liver transplantation are indicated at an early stage of the disease, Sorafenib (Sfb) is the current most administrated first-line treatment for advanced HCC, even thought its therapeutic benefit is limited as a consequence of the appearance of resistances. Deep knowledge on the molecular consequences of Sfb-treatment is essentially required for optimizing novel therapeutic strategies to improve the outcomes for patients with advanced HCC. In this study, we analysed differential gene expression changes in two well characterized HCC cell lines upon a Sfb-treatment, demonstrating that both lines responded similarly to the treatment. Our results provide valuable information on the molecular action of Sfb on diverse cellular fundamental processes such as DNA repair, translation and proteostasis and identify rationalization issues that could give a different therapeutic perspective to Sfb.

overall_design: Examination of trasncriptome of two differents hepatocellular carcinoma cell lines, HepG2 and SNU423. Three biological replicates were used for HepG2 cells and two for SNU423.

first: Laura

last: Contreras

first: Alfonso

last: Rodriguez-Gil

first: Jordi

last: Muntane

first: Jesus

last: de la Cruz


title: Chronic isoprenaline/phenylephrine vs. exclusive isoprenaline stimulation in mice: critical contribution of alpha1-adrenoceptors to early cardiac stress responses

status: Public on Feb 23 2022

city: Mannheim

first: Christiane

last: Vettel

address: Ludolf-Krehlstr. 13-17

department: Experimentelle Pharmacologie Mannheim

country: Germany

institute: Heidelberg University

type: Expression profiling by high throughput sequencing

summary: Mice were subjected to either isoprenaline (ISO, 30 mg/kg*d) or isoprenaline and phenylephrine (ISO/PE, 30 mg/kg*d each) for a period of 4 days via osmotic minipumps. At that timepoint, both ISO and ISO/PE treated animals showed a similar increase in heart weight to tibia length ratios. ECG-telemetry data collected from other individuals indicate a similar increase heart rate and normal blood pressure after 4 days of both ISO and ISO/PE exposure. Cardiac function was not assessed at that particular timepoint.

overall_design: Cardiac bulk from control, ISO and ISO/PE treated mice

first: Julio

last: Cordero

first: Thomas

last: Wieland


title: Tumor infiltrating exhausted CD8+ T cells dictate divergent survival outcomes in pre- versus post-menopausal estrogen receptor-positive breast cancer

city: Duarte

first: Peter

middle: P

last: Lee

state: CA

address: 1500 E. Duarte Rd.

department: Immuno-Oncology

country: USA

institute: Beckman Research Institute at City of Hope

summary: CD8+ tumor infiltrating lymphocytes (TILs) are associated with improved survival in triple negative breast cancer (TNBC), yet have no association with survival in estrogen receptor-positive (ER+) BC. The basis for these contrasting findings remains elusive. We identify subsets of BC tumors infiltrated by CD8+ T cells with characteristic features of exhausted T cells (TEX). Tumors with abundant CD8+ TEX exhibit a distinct tumor microenvironment marked by amplified interferon-γ signaling related pathways and higher PD-L1 expression. Paradoxically, high levels of CD8+ TEX TILs associate with decreased overall survival ER+ BC patients, but not TNBC patients. Moreover, high tumor expression of a CD8+ TEX signature identifies dramatically reduced survival in pre-menopausal, but not post-menopausal, ER+ BC patients. Finally, we demonstrate the value of a tumor TEX signature score in identifying high-risk pre-menopausal ER+ BC patients amongst those with intermediate Oncotype Dx breast recurrence scores. Our data highlight the complex relationship between CD8+ TILs, interferon-γ signaling, and estrogen receptor status in BC patient survival. This work identifies pre-menopausal ER+ BC patients with high levels of tumor infiltrating CD8+ TEX as a high-risk subset that may benefit from immunotherapy strategies.

overall_design: We employed single cell sequencing of patient CD8+ T cells from 10 different BC patients, including 9 primary tumors, 2 T+LNs, 3 NCBTs, and 7 matched PBMCs samples. CD8+ T cells stained for PD-1, CD39, CD103, CD69, CD137, and CCR7 were single cell index sorted for downstream whole transcriptome analysis. Unbiased Seurat cluster analysis found CD8+ T cells to be composed of four major clusters with discrete gene expression patterns.

first: Weihua

last: Guo

first: Colt

middle: A

last: Egelston


title: The control of transcriptional memory by stable mitotic bookmarking

status: Public on Feb 25 2022

city: Montpellier

first: Maelle

last: Bellec

address: 1919 route de mende

country: France

institute: CNRS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To maintain cellular identities during development, gene expression profiles must be faithfully propagated through cell generations. The reestablishment of gene expression patterns upon mitotic exit is thought to be mediated, in part, by mitotic bookmarking by transcription factors (TF). However, the mechanisms and functions of TF mitotic bookmarking during early embryogenesis remain poorly understood. In this study, taking advantage of the naturally synchronized mitoses of Drosophila early embryos, we provide evidence that the pioneer-like transcription factor GAF acts as stable mitotic bookmarker during zygotic genome activation. We report that GAF remains associated to a large fraction of its interphase targets (37%). Mitotically-bound loci include cis-regulatory sequences of key developmental genes, with both active and repressive chromatin signatures. GAF mitotic targets are globally accessible during mitosis and a subset is also mitotically bookmarked via histone acetylation (H4K8ac). By monitoring the kinetics of transcriptional activation in living embryos, we provide evidence that GAF binding establishes competence for rapid activation upon mitotic exit.

overall_design: GAF and H4K8ac ChIP-seq was performed on 1-2h30 interphase and mitotic embryos to determine the targets of GAF and H4K8ac in interphase and mitotic chromatin.

first: Jeremy

last: Dufourt

first: George

last: Hunt

first: Helen

last: Lenden-Hasse

first: Antonio

last: Trullo

first: Amal

last: Makrini

first: Marie

last: Lamarque

first: Marissa

last: Gaskill

first: Heloise

last: Faure-Gautron

first: Mattias

last: Mannervik

first: Melissa

last: Harrison

first: Jean

middle: C

last: Andrau

first: Cyril

last: Favard

first: Ovidiu

last: Radulescu

first: Mounia

last: Lagha


title: CMTR1 is recruited to transcription start sites and has enhanced influence over ribosomal protein and histone genes [ChIP-seq]

city: Glasgow

first: Shang

last: Liang

address: Garscube Estate

country: United Kingdom

institute: CRUK Scotland Institute

summary: We investigated the gene-specificity of mRNA cap methyltransferase CMTR1 and its impact in RNA expression. In this ChIP-seq experiment,  we investigated the genome-wide chromatin binding profiles of CMTR1 in mouse embryonic stem cells. We demontrated that CMTR1 binds to the transcription start site (TSS) correlating with RNA polymerase II (RNAP II) levels, with predominant binding at histone genes and ribosomal protein (RP) genes. Moreover, the repression of CMTR1 expression resulted in a loss of RNAP II binding at the TSS.

overall_design: CMTR1 and RNMT ChIP (chromatin immunoprecipitation) libraries were prepared from the CRISPR-Cas9 HA-GFP knock-in (KI) mouse embryonic stem cell lines were generated in which endogenous RNMT and CMTR1 were expressed as N-terminal HA-GFP fusion proteins. The control ChIP and RNAP II ChIP libraries were prepared from the parental stem cell line E14 of the CMTR1/RNMT KI cell lines. For RNAP II ChIP, cells treated with the control scramble siRNA and CMTR1 specific siRNAs for 36 hours. Cells were cross-linked by 1% formaldehyde for 10 min. Then the glycine was added to quench the reaction. The cell lysates were prepared as described (Varshney et al., 2018).The chromatin was sonicated in Bioruptor (Diagenode) at high power for 20 min (30 s on/off, 20 cycles). 25-50 micrograms of the sonicated chromatin were used for each IP. 50μl (10%) from each diluted extract for IP were taken as the inputs. For ChIP using anti-HA beads, 20μL of anti-HA magnetic beads (Pierce) were added to lysates from CMTR1/RNMT KI cells (as IPs) and E14 cells (as control) for 4°C overnight incubation. For RNAP II ChIP, 2μg of anti-Rpb1 (CST 14958) were added to lysates from E14 cells for 4 °C overnight reaction before the incubation with protein G Dynabeads (Life Technologies) for additional 2 hours. The beads were washed and eluted as described (Varshney et al., 2018) before the proteinase K treatment and reverse crosslinking at 42 °C overnight. The eluted DNA was purified by the QIAquick PCR purification kit (QIAGEN).

first: Victoria

middle: H

last: Cowling


title: Next Generation Sequencing Facilitates Quantitative Analysis of Vector and GOLPH3 Transcriptomes

city: Shenzhen

first: Liyun

last: Gong

address: Nanhai Road 3688 number

country: China

institute: Shenzhen University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived HCT-116 cell transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis.
Methods: HCT-116 cell mRNA profiles of HCT-116-GOLPH3-Vector and HCT-116-GOLPH3-Overepression were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays.
Results: RNA sequencing (RNA-seq) was used to investigate gene expression in HCT-116-PMSCV-Vector and HCT-116-PMSCV GOLPH3 cells, while Gene Ontology (GO) was used to annotate the various functional genes. By comparing the differentially expressed genes, we noticed that GOLPH3 was associated with EMT. Gene set enrichment analysis (GSEA) analysis of the RNA-seq results based on the GSE77953 dataset was performed to investigate the biological functions of HCT-116-PMSCV-Vector and HCT-116-PMSCV-GOLPH3 cells. The findings suggested that GOLPH3 expression was positively associated with colon cancer cell autophagy. Signal pathway enrichment was next analyzed based on the differential expression of genes between HCT-116-PMSCV-Vector and HCT-116-PMSCV-GOLPH3 cells, as examined by RNA-seq. Notably, GOLPH3 has correlated with the PI3K/Akt signaling pathway.
Conclusions: Our study represents the first detailed analysis of HCT-116 cell transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: mRNA profiles of HCT-116-GOLPH3-Vector and HCT-116-GOLPH3-Overexpression

first: Li-Yun

first: Yi

last: Yang

first: Zeyao

last: Zhu

first: Yu

last: Chen


title: CMTR1 is recruited to transcription start sites and has enhanced influence over ribosomal protein and histone genes [RNA-seq]

summary: We investigated the gene-specificity of mRNA cap methyltransferase CMTR1 and its impact in RNA expression. In this RNA-seq experiment,  we used siRNA to knockdown the endogenous CMTR1 protein to investigate its role in mouse embryonic stem cells. We demonstrated that the repression of CMTR1 expression resulted in a loss of RNA expression, particularly of histone and ribosomal protein genes.

overall_design: Sequencing of total RNA from the mouse embryonic stem cells treated with the control scramble siRNA and CMTR1 specific siRNAs for 36 hours.


title: CMTR1 is recruited to transcription start sites and has enhanced influence over ribosomal protein and histone genes

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

overall_design: Refer to individual Series


title: Identification of surface antigens that define human pluripotent stem cell-derived PRRX1 positive limb-bud-like mesenchymal cells

city: okayama

first: Takeshi

last: Takarada

state: okayama

address: 2-5-1 Shikata-cho

department: Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

country: Japan

institute: Okayama university

summary: Compare the gene expression profiles of PRRX1 positive LBM-like cells and PRRX1 low Day 4 cells.

overall_design: RNA samples extracted from PRRX1 positive LBM-like cells from PRRX1 low Day 4 cells.

first: Daisuke

last: Yamada

first: Masahiro

last: Nakamura


title: Atmospheric particulate matter aggravates CNS demyelination via TLR-4/NF-κB-mediated microglia pathogenic activities

city: Xi'an

first: Yuan

last: Zhang

address: No. 620, West Chang'an Avenue, Chang'an District

institute: Shaanxi Normal University


title: Atmospheric particulate matter aggravates CNS demyelination via TLR-4/NF-κB-mediated microglia pathogenic activities [RNA-seq]

summary: Atmospheric Particulate Matter (PM) is one of the leading environmental risk factors for the global burden of disease. Increasing epidemiological studies demonstrated that PM plays a significant role in CNS demyelinating disorders; however, there is no direct testimony of this, and yet the molecular mechanism by which the occurrence remains unclear. Using multiple in vivo and in vitro strategies, in the present study we demonstrate that PM exposure aggravates neuroinflammation, myelin injury, and dysfunction of movement coordination ability via boosting microglial pro-inflammatory activities, in both the pathological demyelination and physiological myelinogenesis animal models. Indeed, pharmacological disturbance combined with RNA-seq and ChIP-seq suggests that TLR-4/NF-κB signaling mediated a core network of genes that control PM-triggered microglia pathogenicity. In summary, our study defines a novel atmospheric environmental mechanism that mediates PM-aggravated microglia pathogenic activities, and establishes a systematic approach for the investigation of the effects of environmental exposure in neurologic disorders.

overall_design: RNA from PBS- or PM-treated microglia

first: Bing

last: Han


title: An RNA Polymerase III General Transcription Factor Engages in Cell Type-Specific Chromatin Looping

status: Public on Feb 22 2022

city: Parma

first: Roberto

last: Ferrari

state: Parma

address: Parco Area delle Scienze 23/A

department: Department of Chemistry, Life Sciences and Environmental Sustainability

country: Italy

institute: University of Parma

summary: Transcription factors (TFs) bind DNA in a sequence-specific manner and have been proven to serve as anchors to the 3D genome organization. These TFs are generally cell type-specific factor and/or developmental master regulators. General TFs (GTFs) which serve RNA polymerase recruitment to specific promoter sequences, however, can be part of very large protein complexes but their roles in genome architecture have not been carefully explored. Here, we used a bio-informatic approach of ChIP-seq and Hi-C data analysis to depict the role of one GTF of the RNA polymerase III system (TFIIIC) in several human cell lines, both normal and transformed. We find that TFIIIC occupancy within the genome mainly occurs at specific regions which largely correspond to Alu elements but also at characteristic classes of repetitive elements (REs) such as MIR, FLAMC and ALR/alpha, depending on the cell’s developmental origin. We then show that these TFIIIC-enriched regions are involved in cell type-specific DNA looping within the genome and do not depend on colocalization with the master architectural protein CTCF. This work extends previous knowledge about the role of TFIIIC as a bona fide genome organizer whose action can lead to cell type-dependent 3D genome looping via binding to REs.

overall_design: Examination of the role of TFIIIC in 3D genome organization

first: Lara

middle: I

last: de Llobet Cucalon

first: Chiara

last: Di Vona

first: Marco

last: Morselli

last: Vezzoli

first: Barbara

last: Montanini

first: Martin

last: Teichmann

first: Susana

last: De la Luna


title: Cell-Specific Transcriptomic Analysis of CRH+ cells Identifies Unique Cellular Responses to Chronic Stress

city: Toronto

first: Etienne

last: Sibille

state: Ontario

address: RM,133, 250 college street

department: Neuroscience of Aging and Depression

country: Canada

institute: Center for Addiction and Mental Health

summary:
Rationale: A previous transcriptome meta-analysis revealed significantly lower levels of corticotropin-releasing hormone (CRH) mRNA in corticolimbic brain regions in major depressive disorder (MDD) subjects. Rodent studies show that cortical CRH is mostly expressed in GABAergic neurons; however, the characteristic features of CRH+ cells in human brain cortex and their association with MDD are largely unknown.
Methods: Subgenual anterior cingulate cortex (sgACC) of human subjects without brain disorders were labeled using fluorescent in situ hybridization (FISH) for CRH and markers of excitatory (SLC17A7), inhibitory (GAD1) neurons, as well as markers of other interneuron subpopulations (PVALB, SST, VIP). MDD-associated changes in CRH+ cell density and cellular CRH expression (n=6/group) were analyzed. RNA-sequencing was performed on sgACC CRH+ neurons from comparison and MDD subjects (n=6/group), and analyzed for group differences.
Results: About 80% of CRH+ cells were GABAergic and 17.5% were glutamatergic. CRH+ GABAergic neurons co-expressed VIP (52%), SST (7%), or PVALB (7%). MDD subjects displayed lower CRH mRNA levels in GABAergic neurons relative to comparison subjects without changes in cell density. CRH+ neurons show transcriptomic profile suggesting lower excitability and less GABA release and reuptake. Further analyses suggested that these molecular changes are not mediated by altered glucocorticoid feedback and potentially occur downstream for a common modulator of neurotrophic function.
Summary: CRH+ cells in human sgACC are a heterogeneous population of GABAergic neurons, although largely co-expressing VIP. MDD is associated with reduced markers of inhibitory function of CRH+ neurons.

overall_design: Examination of gene expression in CRH+ cell from post-mortem subgenual anterior cortex of individuals with Major Depressive Disorder or healthy controls

first: Hyunjung

last: Oh

first: Dwight

middle: F

last: Newton

middle: L


title: A PRC2-KDM5B-stemness regulatory axis sustains tumorigenicity of acute myeloid leukemia [ChIP-Seq]

city: Durham

first: Arum

last: Kim

state: NC

address: Medical Sciences Research Building III  3 Genome Ct

institute: Duke University

summary: Acute myeloid leukemias (AMLs) with the NUP98-NSD1 or MLL gene rearrangement (MLL-r) share transcriptomic profiles featured with stemness-related gene signatures and display poor prognosis in the clinic. However, the molecular underpinnings of AML aggressiveness and stemness remain far from clear. Here, we report that the enzymatic activity of Polycomb Repressive Complex 2 (PRC2) is crucial for maintenance of tumorigenicity in NUP98-NSD1+ AML, consistent to its role in MLL-r AML. Transcriptomic analysis revealed Kdm5b, a lysine demethylase gene carrying the “bivalent domain” chromatin feature in AML, to be directly repressed by PRC2. While ectopic expression of Kdm5b suppressed AML growth, its depletion in AML not only promoted tumorigenicity but also significantly attenuated anti-AML effects by PRC2 inhibitors, thus demonstrating an involvement of the PRC2-|Kdm5b axis for AML oncogenesis. Lower KDM5B expression is positively correlated with poorer prognosis of human AML patients. RNA-seq, ChIP-seq and CUT&RUN based genomic profilings also showed that Kdm5b directly binds to and represses AML stemness genes. In contrast to an essential involvement for its various chromatin-associating domains, Kdm5b’s demethylase function was found to be dispensable for AML suppression, indicating a scaffold role in assembling gene-repressive complexes. Collectively, this study describes a molecular axis involving histone modifiers (PRC2 and Kdm5b) for sustaining the malignant features of AML, implicative of potential therapeutics.

overall_design: Examination of genome-wide binding for Kdm5b, Flag-tagged NUP98-NSD1 and H3K4me3 in the Flag-NUP98-NSD1+ murine AML cells.

first: Zhihong

last: Ren

first: Greg

last: Wang


title: Modelling human zygotic genome activation in 8C-like cells in vitro

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: The remodelling of the epigenome and transcriptome of the fertilised oocyte to establish totipotency in the zygote and developing embryo is one of the most critical processes in mammalian embryogenesis. Zygotic or embryonic genome activation (ZGA, EGA) in the 2-cell embryo in mouse, and the 8-cell embryo in humans, constitutes the first major wave of transcription. Failure to initiate ZGA leads to developmental defects, and contributes to the high attrition rates of human pre-implantation embryos. Due to limitations in cell numbers and experimental tractability, the mechanisms that regulate human embryonic genome activation in the totipotent embryo remain poorly understood. Here we report the discovery of human 8-cell like cells (8CLCs) specifically among naïve embryonic stem cells, but not primed pluripotent cells. 8CLCs express ZGA marker genes, such as ZSCAN4, LEUTX and DUXA, and their transcriptome closely resembles that of the 8-cell human embryo. 8-cell like cells reactivate 8-cell stage specific transposable elements such as HERVL and MLT2A1, and are characterized by upregulation of the methylation regulator DPPA3. 8CLCs show reduced SOX2 protein levels and can be identified based on expression of the novel protein marker TPRX1 in vitro. Overexpression of the transcription factor DUX4 not only increases ZGA-like transcription, but also enhances TPRX1+ 8CLCs formation. The discovery of 8CLCs provides a unique opportunity to model and manipulate human ZGA-like transcriptional programs in vitro, and will provide critical functional insights into one of the earliest events in human embryogenesis in vivo.

overall_design: Single-cell RNA expression profiling of naïve HNES1 hPSCs (10X).

first: Jasmin

last: Taubenschmid-Stowers

first: Maria

last: Rostovskaya

first: Ricard

last: Argelaguet

first: Wolf

last: Reik


title: A PRC2-KDM5B-stemness regulatory axis sustains tumorigenicity of acute myeloid leukemia [CUT&RUN]

overall_design: Examination of the genome-wide binding of GFP-tagged Kdm5b in the HEK293 stable expression cells by GFP CUT&RUN. Non-GFP cells serve as negative control.


title: A PRC2-KDM5B-stemness regulatory axis sustains tumorigenicity of acute myeloid leukemia

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Atmospheric particulate matter aggravates CNS demyelination via TLR-4/NF-κB-mediated microglia pathogenic activities [ChIP-seq]

first: Yuan

last: Zhang

overall_design: ChIP-seq of PBS- or PM-treated microglia

first: Bing

last: Han


title: Regulation of group 3 innate lymphoid cells by Setd2

city: Shanghai

first: Ju

last: Qiu

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

summary:
This SuperSeries is composed of the SubSeries listed below.
To determine the molecular regulation of different subsets of ILC3s by Setd2, small intestinal NKp46- ILC3s (Thy1highCD45low NKp46-) and NKp46+ ILC3s (Thy1highCD45low NKp46+) were purified from littermate Rag1-/-;Setd2f/f or Rag1-/-;Rorc-cre;Setd2f/f mice. Cells were subjected to RNA-seq and ATAC-seq analyses.


title: Whole transcriptome analysis of liver tissue from SAMP8 mice treated with the Alzheimer’s disease drug J147

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

summary: Alzheimer’s disease (AD) drug discovery has rarely been addressed in the context of aging even though sporadic AD accounts for 99% of the cases. Previous phenotypic screens based upon old age-associated brain toxicities identified the potent AD drug candidates CMS121 and J147, whose mechanisms were investigated through an integrative multi-omics approach (PMID: 31742554; GSE101112). This study aimed to further reveal drug J147's role involved in liver metabolism during disease progression.

overall_design: 9 month-old (young) and 13 month-old (old) SAMP8 mice were fed with vehicle diet, another group of SAMP8 mice were fed with J147 for 4 months and sacrified at their 13 month-old age. RNA were extracted from liver tissue.

first: Antonio

last: Currais

first: Devin

last: Kepchia

first: Ling

last: Huang


title: Regulation of group 3 innate lymphoid cells by Setd2 [ATAC-seq]

summary: To determine the molecular regulation of different subsets of ILC3s by Setd2, small intestinal NKp46- ILC3s (Thy1highCD45low NKp46-) and NKp46+ ILC3s (Thy1highCD45low NKp46+) from Setd2-deficient and control mice were subjected to assay for ATAC-seq.

overall_design: Biological duplicates of 50000 ILC3s sorted by flow cytometry from the small intestine of 8 week old Rag1-/-;Setd2f/f or Rag1-/-;Rorc-cre;Setd2f/f mice were subjected to ATAC-seq analysis.

first: Jiali

last: Chang


title: Regulation of group 3 innate lymphoid cells by Setd2 [RNAseqILC3]

summary: To determine the molecular regulation of different subsets of ILC3s by Setd2, small intestinal NKp46- ILC3s (Thy1highCD45low NKp46-) and NKp46+ ILC3s (Thy1highCD45low NKp46+) from Setd2-deficient and control mice were subjected to assay for RNA-seq.

overall_design: Biological duplicates of 500000 ILC3s sorted by flow cytometry from the small intestine of 8 week old Rag1-/-;Setd2f/f or Rag1-/-;Rorc-cre;Setd2f/f mice were subjected to RNA-seq analysis.


title: A PRC2-KDM5B-stemness regulatory axis sustains tumorigenicity of acute myeloid leukemia [RNA-Seq]

overall_design: Examination of transcriptome profiles using the NUP98-NSD1+ murine AML cells after treatment with the PRC2 enzymatic inhibitor (UNC1999 or JQEZ5), relative to DMSO, or after depletion of Kdm5b (shKdm5b), relative to the vector control (shEV). Examination of transcriptome profiles using the MLL-AF9+ murine AML cells after ectopic expression of Kdm5b, either WT or H499A-mutated, relative to the vector control (EV).


title: Normal human urothelial cells infected with BK polyomavirus (BKPyV) in the presence or absence of interferon gamma (IFNg)

city: York

first: Simon

middle: Charles

last: Baker

address: Wentworth Way, Heslington

department: Biology Department

institute: University of York

summary: mRNAseq data for differentiated and mitotically-quiescent Normal Human Urothelial (NHU) cells at 14 days post infection (dpi) with BKPyV

overall_design: NHU cells from seven independent donors were differentiated (according to PMID: 15784840) and infected with BKPyV (Dunlop strain) at a multiplicity of infection of 1. RNA was collected in Trizol reagent at 14dpi. In some cultures, at 7dpi 200U/mL IFNg was added for the 7-14dpi culture period.

first: Andrew

middle: S

last: Mason

first: Jennifer

last: Southgate


title: Cytokine profile of ascites derived from patients with peritoneal carcinomatosis

city: Singapore

first: Johnny

middle: Chin-Ann

last: Ong

state: Singapore

address: 11 Hospital Drive

department: Division of Surgical Oncology

country: Singapore

institute: National Cancer Centre Singapore

summary:
Characterizations of ascites proteome from ovarian PC and gastric PC have demonstrated that ascites contains elevated pro-tumorigenic factors. Reasoning that the composition of ascitic fluid might offer insight into the memory of key biological events occurring intra-abdominally, we hypothesized that paracrine factors essential for survival and growth of peritoneal deposits are secreted into and circulate within ascitic fluid.
Our data suggest that ascites contains biologically active ligands capable of supporting cellular functions of cancer cells.

overall_design: We subjected ascites derived from patients with colorectal peritoneal carcinomatosis (n=4) and a patient with benign serous cystadenofibroma (n=1) to R & D Proteome Profiler human cytokine array.

first: Josephine

last: Hendrikson

first: Ong

last: Johnny


title: Chlamydomonas CHT7 Represses DNA Replication and Mitotic Genes Counteracting CDK-Stimulated Cell Division

city: East Lansing

first: Christoph

last: Benning

state: MI

address: 612 Wilson Rd, Plant Research Laboratories

institute: MSU-DOE Plant Research Laboratory

summary: The transcriptome of a Chlamydomonas mutant, cht7, was compared with those of the two control strains. The CHT7 protein has been shown to play a role in regulating the transition into and out of a nitrogen-induced cell-cycle resting state, quiescence. To further clarify the role of CHT7 in cell cyle regulation, we performed RNA-seq to investigate the transcriptomic dynamics of photoautotrophically grown, synchronized cells of cht7 and the two controls at different stages of the cell cycle.

overall_design: The three strains, 6145c/Wild type (Control 1), CHT7-HA::cht7 (Control 2), and cht7, were grown photoautotrophically (12h: 12h Light: Dark) to synchronize them. Samples for RNA-seq were harvested at different timepoints representing different stages of the cell cycle. There are three major sets of samples: ZT samples represent cells undergoing a normal cell division cycle (ZT0: G0, ZT6: G1, ZT10 and 12: S/M). ND samples represent cells in the quiescence state. NR samples represent cells after resupply of nitrogen, resuming the cell division cycle.

first: Yang-Tsung

last: Lin

first: Tomomi

last: Takeuchi

first: Brian

last: Youk

first: James

last: Umen

first: Barbara

middle: B

last: Sears


title: WNT11 is a novel ligand for ROR2 in human breast cancer

city: Göttingen

first: Darius

last: Wlochowitz

address: Goldschmidtstr. 1

institute: Institute of Bioinformatics


title: WNT11/ROR2 signaling is associated with tumor invasion and poor survival in breast cancer

status: Public on Feb 21 2022

summary: Breast cancer has been associated with activation of the WNT signaling pathway, although the underlying molecular mechanisms are still unclear. In order to understand the molecular basis of these observations, we overexpressed ROR2 in human breast cancer cell lines and characterized them by RNA-Sequencing. High levels of ROR2 were associated with defects in cell morphology and cell-cell-contacts leading to increased tumor invasiveness. Using gene expression analysis we demonstrated an upregulation of several non-canonical WNT ligands in ROR2-overexpressing breast cancer cells, in particular WNT11. Knockdown of WNT11 reversed the pro-invasive phenotype and the cellular changes in ROR2-overexpressing cells. Taken together, our studies revealed a novel auto-stimulatory loop in which ROR2 triggers the expression of its own ligands, e.g. WNT11, resulting in enhanced tumor invasion associated with breast cancer metastasis.

overall_design: Human breast cancer cells (MCF-7, SK-BR-3 and BT-474) were transfected either with an empty vector (pcDNA) or with a hROR2 overexpression plasmid (pROR2). To gain further insight into additional pathways regulated specifically by ROR2/WNT11, we characterized ROR2-overexpressing MCF-7 cells with siRNA-mediated WNT11 knockdown by RNA-Seq.

first: Kerstin

last: Menck

first: Saskia

last: Heinrichs

first: Maren

last: Sitte

first: Helen

last: Noeding

first: Andreas

last: Janshoff

first: Hannes

last: Treiber

first: Torben

last: Ruhwedel

first: Bawarjan

last: Schatlo

first: Christian

last: von der Brelie

first: Stefan

last: Wiemann

first: Tobias

last: Pukrop

first: Tim

last: Beißbarth

first: Claudia

last: Binder

first: Annalen

last: Bleckmann


title: Regulatory perturbations of ribosome allocation in bacteria reshape the growth proteome with a trade-off in adaptation capacity

city: Cuernavaca

first: Jose

last: Utrilla

state: Morelos

address: Av. Universidad sn

department: Centro de Ciencias Genómicas

country: Mexico

institute: Universidad Nacional Autonoma de México

summary: Bacteria regulate their cellular resource allocation to enable their fast growth-adaptation to a variety of environmental niches. We studied the ribosomal allocation, growth and expression profile of two sets of fast-growing mutants of Escherichia coli K-12 MG1655. Mutants with 3 copies of the stronger ribosomal RNA operons grew faster than the wild-type strain in minimal media and show similar phenotype to previously studied rpoB mutants. All of them displayed increased ribosomal content, a longer diauxic shift and a reduced activity of the aceBAK operon, indicative of repressed gluconeogenic pathways. Transcriptomic profiles of fast-growing mutants showed common downregulation of hedging functions and upregulated growth functions. Proteome allocation estimations showed an increase in the growth-related proteome for fast-growing strains, but not an increased cellular budget for recombinant protein production.  These results show that two different regulatory perturbations (rRNA promoters or rpoB mutations) increasing ribosomal allocation optimize the proteome for growth with a concomitant fitness cost.

overall_design: mRNA of exponentially growing E. coli mutants in M9 minimal medium supplemented with glucose

first: César

last: Martínez-Ortiz

first: David

last: Hidalgo

first: José


title: Transcriptomic and network analyses reveal immune modulation by endocannabinoids in approach/avoidance traits

status: Public on Feb 19 2022

city: Rome

first: Daniela

last: Laricchiuta

state: Rome

address: Via del fosso di fiorano, 64

department: Preclinical neuroscience

institute: IRCCS Fondazione Santa Lucia

summary: Approach and avoidance (A/A) tendencies are stable behavioral traits in responding to rewarding and fearful stimuli. They represent the superordinate division of emotion and individual differences in such traits are associated with disease susceptibility. The neural circuitry underlying A/A traits is retained to be the cortico-limbic pathway including the amygdala, the central hub for the emotional processing. Furthermore, A/A-specific individual differences are associated with the activity of the endocannabinoid system (ECS) and especially of CB1 receptors whose density and functionality in amygdala differ according to A/A traits. ECS markedly interacts with the immune system (IS). However, how the interplay between ECS and IS is associated with A/A individual differences is still ill-defined. To fill this gap, here we analyzed the interaction between the gene expression of ECS and immune system (IS) in relation to individual differences. To unveil the deep architecture of ECS-IS interaction, we performed cell-specific transcriptomics analysis. Differential gene expression profiling, functional enrichment and Protein-Protein Interaction network analyses were performed in amygdala pyramidal neurons of mice showing different A/A behavioral tendencies. Several altered pro-inflammatory pathways were identified as associated with individual differences in A/A traits, indicating the chronic activation of the adaptive immune response sustained by the interplay between endocannabinoids and the IS. Furthermore, results showed that the interaction between the two systems modulates synaptic plasticity and neuronal metabolism in individual-difference specific manner. Deepening our knowledge about ECS/IS interaction may provide useful targets for treatment and prevention of psychopathology associated with A/A traits.

overall_design: RNA extracted by amygdala pyramidal neurons of 9 B6.Cg-Tg(Thy1-YFP)HJrs/J (Thy1-YFP; Jackson Laboratories, Maine, USA) transgenic mice

first: Andrea

last: Termine

first: Carlo

last: Fabrizio

first: Juliette

last: Gimenez

first: Anna

last: Panuccio

first: Francesca

last: Balsamo

first: Noemi

last: Passarello

first: Silvia

last: Caioli

first: Luana

last: Saba

first: Marco

last: De Bardi

first: Francesco

last: Della Valle

first: Valerio

last: Orlando

first: Laura

last: Petrosini


title: Expression data of peritoneal carcinomatosis human cell lines co-treated with patient derived ascites and ligand inhibitor

first: Johnny

last: Ong

summary:
Characterizations of ascites proteome from ovarian peritoneal carcinomatosis (PC) and gastric PC have demonstrated that ascites contains elevated pro-tumorigenic factors. Reasoning that the composition of ascitic fluid might offer insight into the memory of key biological events occurring intra-abdominally, we hypothesized that paracrine factors essential for survival and growth of peritoneal deposits are secreted into and circulate within ascitic fluid. Our data from cytokine array profile suggest that ascites contains biologically active ligands capable of supporting cellular functions of cancer cells.
To decipher downstream signalling pathways activated in cancer cells when exposed to ascites, we performed gene expression analysis of Colo-205 cells upon exposure to PC ascites and ligand inhibitor.

overall_design: Colo-205 cells were treated with high PAI-1 cell free ascites (CFA), low PAI-1 CFA and FBS control (no PAI-1) in the presence of a PAI-1 inhibitor, TM5441. In this experiment, high PAI-1 CFA corresponds to PC085 while low PAI-1 CFA corresponds to PC249.

first: Josephine

last: Hendrikson

first: Ong

last: Johnny


title: Evolutionarily Conserved Inhibitory uORFs Sensitize Hox mRNA Translation to Start Codon Selection Stringency

city: Baltimore

first: James

state: MD

address: 725 N Wolfe St, 714 PCTB

department: Molecular Biology and Genetics

institute: Johns Hopkins

summary: Translation start site selection in eukaryotes is influenced by context nucleotides flanking the AUG codon and by levels of the eukaryotic translation initiation factors eIF1 and eIF5. In a search of human genes, we identified 5 Hox gene paralogs initiated by AUG codons in conserved suboptimal context as well as 13 Hox genes that contain evolutionarily conserved upstream open reading frames (uORFs) that initiate at AUG codons in poor sequence context. We analyzed published CAGE-seq data and generated CAGE-seq data from mRNAs from mouse somites. These data demonstrate that the 5’ leaders of Hox mRNAs of interest contain conserved uORFs, are much shorter than reported, and lack previously proposed IRES elements. We show that the conserved uORFs inhibit Hox reporter expression and that altering the stringency of start codon selection by overexpressing eIF1 or eIF5 modulates the expression of Hox reporters. We also show that modifying ribosome homeostasis by depleting a large ribosomal subunit protein or treating cells with sublethal concentrations of puromycin leads to lower stringency of start codon selection. Thus, altering global translation can confer gene-specific effects through altered start codon selection stringency.

overall_design: nAnT-iCAGE sequencing data from somite/neural tubes isolated from three E11.5 C56BL/6J mouse embryos

first: Ivaylo

last: Ivanov

first: Chen-Ming

last: Fan

first: Andrew

middle: E

last: Firth

first: Chune

last: Cao

first: Rachel

last: Green

first: Thomas

last: Dever


title: Post-transcriptional regulation can harness genome instability and provide phenotypic robustness during fitness gain in the human parasite Leishmania donovani

city: Paris

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

summary: Genome instability has been recognized as a driver in Leishmania fitness gain in response to environmental change or chemotherapy. How genome instability generates beneficial phenotypes despite potential deleterious gene dosage effects is unknown. Here we address this important open question applying experimental evolution and integrative systems approaches on parasites adapting to in vitro culture. Phenotypic analyses of parasites from early and late stages of culture adaptation revealed an important fitness tradeoff, with selection for accelerated growth (fitness gain) impairing differentiation of infectious metacyclic parasites, hence infectivity (fitness costs). Comparative genomics, transcriptomics and proteomics analyses revealed a complex regulatory network driving parasite fitness, with genome instability causing gene dosage-dependent changes in proteins linked to post-transcriptional regulation. These in turn caused gene dosage-independent changes in transcripts associated with fitness tradeoff, including coordinated degradation of flagellar transcripts and stabilization of coding and non-coding RNAs regulating ribosomal biogenesis and protein translation, including small nucleolar RNAs (snoRNAs).

overall_design: Comparative genomic, transcriptomic and proteomic analyses to study fitness gain and fitness cost of Leishmania donovani during culture adaptation

last: Piel

first: Hugo

last: Varet

first: Caroline

last: Proux

first: Pascale

last: Pescher

first: Gerald

last: Späth


title: Transcriptome of ASXL1-mutant and ASXL1-wildtype chronic myelomonocytic leukemia

city: Rochester

first: Mrinal

middle: M.

last: Patnaik

state: MN

address: 200 First Street SW

department: Division of Hematology

institute: Mayo Clinic

summary: We report the gene expression of human chronic myelomonocytic leukemia by performing whole transcriptome shotgun sequencing of bone marrow mononuclear cells of patients with chronic myelomonocytic leukemia.

overall_design: Comparison of gene expression between ASXL1-mutant and ASXL1-wildtype chronic myelomonocytic leukemia.

middle: M


title: Dynamic Control of Chromatin-associated m6A Methylation Regulates Nascent RNAs Stability

first: Yang

last: Shi

address: NO. 138, Yi-Xue-Yuan Road

institute: Fudan university

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

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Myofibroblast YAP/TAZ activation is a key step in organ fibrogenesis

first: Jeff

last: Wrana

address: 600 University Avenue

institute: Lunenfeld-Tanenbaum Research Institute

summary: Fibrotic diseases account for nearly half of all deaths in the developed world. Despite its importance, the pathogenesis of fibrosis remains poorly understood. Recently, the two mechanosensitive transcription cofactors YAP and TAZ have emerged as important profibrotic regulators in multiple murine tissues. Despite this growing recognition, a number of important questions remain unanswered, including which cell types require YAP/TAZ activation for fibrosis to occur and the time course of this activation. Here, we present a detailed analysis of the role that myofibroblast YAP and TAZ play in organ fibrosis and the kinetics of their activation. Using analyses of cells, as well as multiple murine and human tissues, we demonstrated that myofibroblast YAP and TAZ were activated early after organ injury and that this activation was sustained. We further demonstrated the critical importance of myofibroblast YAP/TAZ in driving progressive scarring in the kidney, lung, and liver, using multiple transgenic models in which YAP and TAZ were either deleted or hyperactivated. Taken together, these data establish the importance of early injury-induced myofibroblast YAP and TAZ activation as a key event driving fibrosis in multiple organs. This information should help guide the development of new antifibrotic YAP/TAZ inhibition strategies.

overall_design: Analysis of 18 archival human transplant kidney biopsies with 12 normal control samples.

first: Xiaolin

last: He

first: Monica

last: Tolosa

first: Tianzhou

last: Zhang

first: Santosh Kumar

last: Goru

first: Luisa Ulloa

last: Severino

first: Paraish

last: Misra

first: Caitríona

last: McEvoy

first: Lauren

last: Caldwell

first: Stephen

middle: G

last: Szeto

first: Feng

last: Gao

first: Xiaolan

last: Chen

first: Cassandra

last: Atin

first: Victoria

last: Ki

first: Noah

last: Vukosa

first: Catherine

last: Hu

first: Christopher

last: Yip

first: Adriana

last: Krisova

first: Jeffrey

first: Darren

last: Yuen


title: Effects of social defeat stress on colonic epithelial transcriptome

status: Public on Feb 18 2022

city: Columbus

first: Michael

last: Bailey

state: OH

address: 700 Children's Drive, W410

department: Center for Microbial Pathogenesis

institute: Abigail Wexner Research Institute at Nationwide Children's Hospital

summary: This study assessed the effects of social defeat stress on the murine colonic epithelial transcriptome

overall_design: Mice were exposed to repeated social defeat (2 hrs per day, 6 days).  CD45-EpCAM+ colonic epithelial cells were then isolated from the mice for RNA Sequencing

middle: T


title: Transcriptional response to amphetamine in Drosophila dopamine transporter (DAT) loss-of-function mutant

city: New York

first: Sergey

last: Kalachikov

state: NY

address: NWC Bld, 550 West 120th Street Rm 1002

department: Chemical Engineering

institute: Columbia University

summary: We used Drosophila genetic and behavioral models to examine AMPH-induced transcriptional changes in DAT-dependent manner, as those would be the most relevant to the stimulatory effects of the drug in the brain. We previously showed that flies respond to AMPH by increasing their locomotor activity and decreasing their sleep in a dopamine-dependent manner. Flies that carry a loss-of-function mutation in the gene encoding the Drosophila DAT homolog (dDATfmn, henceforth referred to as DAT mutants) exhibit heightened activity levels at baseline, consistent with increased levels of extracellular dopamine caused by the impairment of reuptake. In this study we compared gene expression changes in response to AMPH in brains of isogenic w1118 strain (WT) and DAT mutants. We found genes involved in the control of mRNA translation to be significantly upregulated in response to AMPH in a DAT-dependent manner.

overall_design: WT and DAT flies were divided into treatment and control groups resulting in four experimental groups: WT-AMPH, WT-Vehicle for the WT and DAT-AMPH, DAT-Vehicle for the DAT mutant. Each group was housed in polycarbonate tubes containing food consisting of 1% agar and 3% sucrose delivered in water (vehicle) or AMPH solution (10 mM) for 48 hours. Flies were continuously monitored for movement by a single infrared beam in the center of the tube using Trikinetics Drosophila Activity Monitors (TriKinetics, Waltham, MA). Four replicates from each of the four groups were used for subsequent whole brain RNA-Seq gene expression analysis. To ensure sufficient read coverage, we performed two, and in one case, three sequencing runs, except for the samples M1_3_WT0 and M4_17_DAT10, where a single run was sufficient.

first: Caline

last: Karam

first: Yuchao

last: Zhang

first: Jonathan

last: Javitch

first: Colin

last: Hodgkinson

first: Qiaoping

last: Yuan

first: Rony

last: Panarsky

first: David

last: Goldman


title: Role of the cellular factor CTCF in the regulation of Bovine Leukemia Virus latency and three-dimensional chromatin organization

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute


title: Tet enzymes are required for mammalian embryonic hematopoiesis

first: Meelad

last: Dawlaty

state: New York

address: 1301 Morris Park Ave, Price 419, Bronx

department: Genetics

institute: Albert Einstein College of Medicine

type: Methylation profiling by high throughput sequencing

summary: In this study we have examined the role of Tet enzymes in regulation of embryonic Endothelial cells (ECs) and Hematopoietic stem and progenitor cells (HSPCs). We have performed transcriptomic and methylation analyses of Tet deficient and wild type ECs and HSPCs isolated from E11.5 embryonic aorta-gonad-mesonephros (AGM) to identify differentially expressed genes and differentially methylated regions.

overall_design: Endothelial cells (CD31+C-Kit-) and Hematopoietic stem and progenitor cells (CD31+C-Kit+) were isolated by FACS from E11.5 aorta-gonad-mesonephros (AGM)  (Tet1/2/3 F/F +/Rosa26-CreER and littemate control Tet1/2/3 F/F +/+, Tamoxifen E7.5) RNA and DNA were extracted from ECs or HSPCs at the same time using QIAGEN All Prep DNA/RNA Micro Kit (QIAGEN, cat. no.80284).  Gene expression profiling by RNA-seq: RNA-seq libraries were prepared first by amplifying RNA using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara, cat. no.634889) and then libraries were prepared using Nextera XT DNA Library Preparation Kit (illumine, cat.no.15055293). Three technical replicates from three independent batches of cells were used. The libraries were then subjected to 75 bp paired-end sequencing (Illumina NextSeq 500 platform) at the Einstein Epigenomics core. Whole genome bisulfite sequecing (WGBS): WGBS library construction was done using Pico Methyl-Seq TM Library Prep Kit (ZYMO research, cat. no.D5455 for IIIumina-based Sequencing). The libraries were sequenced using Novagene Hiseq 4000 platform. 150 bps paired-end reads were sequenced and data were analyzed as detailed in methods section.

first: Qin

last: Tang

first: Liyang

last: Ma


title: RNA-Seq in porcine ovaries treated with recombinant pig follicle-stimulating hormone (rpFSH)

city: Hangzhou

first: Haiguang

last: Mao

state: Zhejiang

address: Yuhangtang Road 866

institute: Zhejiang University

summary: To identify the DE mRNA and lncRNA between the recombinant pig follicle-stimulating hormone traetment group and control grooup.

overall_design: Ten gilts with the same genetic background were divided into 2 groups (reFSH treatment group and control group) with 5 gilts in each group. All the experiment gilts were born in the same day, raised in the same breeding environment, and fed by the diet according to the Nutrient Requirements of Swine Eleventh Revised Edition 2012. At 210 days of age, altrenogest was administered uniformly for 18 consecutive days, and each pig was fed 20 mg per day. After 18 days, all the pigs were stopped feeding altrenogest for 2 days. The guilts of rpFSH treatment group were injected 1000 IU per pig, and the control group were injected the same volume of normal saline. The ovary samples of the selected pigs were collected at 234 days of age after removing surface follicles and immediately frozen in liquid nitrogen to isolate RNA.

first: Mao

last: Haiguang

first: Wang

last: Jinbo

first: Qi

last: Lili

last: Mengting


title: Role of the cellular factor CTCF in the regulation of Bovine Leukemia Virus latency and three-dimensional chromatin organization [4C-seq]

summary: Bovine Leukemia Virus (BLV)-induced tumoral development is a multifactorial phenomenon which remains incompletely understood. Here, we highlight the critical role of the cellular CCCTC-binding factor (CTCF) both in the regulation of BLV transcriptional activities and in the deregulation of the three-dimensional (3D) chromatin architecture surrounding the BLV integration site. We demonstrated the in vivo recruitment of CTCF to three conserved CTCF binding motifs along the BLV provirus. Next, we showed the localization of CTCF to transitions in the histone modifications profile along BLV genome as well as its implication in the repression the 5’Long Terminal Repeat (LTR) promoter activity, thereby contributing to viral latency, while favoring the 3’LTR promoter activity. Finally, we demonstrated that BLV integration deregulated host cellular 3D chromatin organization through the formation of viral/host chromatin loops. Altogether, our results highlight CTCF as a new critical effector of BLV transcriptional regulation and BLV-induced physiopathology.

overall_design: 4C-contact profiles of 2 BLV-infected ovine cell lines (L267 and YR2)

first: Maxime

last: Bellefroid

first: Anthony

last: Rodari

first: Mathilde

last: Galais

first: Sjoerd

last: Tjalsma

first: Lorena

last: Nestola

first: Estelle

last: Plant

first: Erica

last: Vos

first: Sara

last: Cristinelli

first: Benoit

last: Van Driessche

first: Caroline

last: Vanhulle

first: Amina

last: Ait-Ammar

first: Arsène

last: Burny

first: Angela

last: Ciuffi

first: Wouter

last: de Laat

first: Carine

last: Van Lint


title: Identifying dormant Nfatc1-marked stem/progenitor cells as an important contributor for mammary lobuloalveoli formation

city: Beijing

first: Ruiqi

last: Liu

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

institute: China Agricultural University

summary: The Mammary gland undergoes complicated epithelial remodeling to form lobuloalveoli during pregnancy, in which basal epithelial cells remarkably increase to form a basket-like architecture. However, it remains largely unknown how dormant mammary basal stem/progenitor cells involve in lobuloalveolar development. Here, we show that Nfatc1 expression marks a rare population of mammary epithelial cells with the majority being basal epithelial cells. Nfatc1 reporter-marked basal epithelial cells are relatively dormant mammary stem/progenitor cells. Although Nfatc1 reporter-marked basal epithelial cells show limited contribution to the homeostasis of mammary epithelium, they divide rapidly during pregnancy and contribute to lobuloalveolar development. Furthermore, Nfatc1 reporter-marked basal epithelial cells are preferentially used for multiple pregnancies. Using single-cell RNA-seq analysis, we identify multiple functionally distinct clusters within the Nfatc1 reporter-marked cell-derived progeny cells during pregnancy. Taken together, our findings underscore Nfatc1 reporter-marked basal cells as dormant stem/progenitor cells that contribute to mammary lobuloalveolar development during pregnancy.

overall_design: Examination of Nfatc1-marked cells at 8-week-old and Nfatc1-marked cell-derived prognanythe at pregnancy day 14.5

first: Huan

last: Hu

first: Zhengquan

last: Yu

first: Cong

last: Lv


title: ChIP-Seq in DU-145 (ATCC  HTB-81) Prostate Cancer Cells of FOSL1, TAZ, TEAD1, YAP

status: Public on Feb 17 2022

first: Yu

last: Chen

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

summary: Genome-wide mapping of FOSL1, YAP, TAZ and TEAD1 binding sites in DU145 cells

overall_design: Genome occupancy profiling of FOSL1, YAP, TAZ, and TEAD1 was performed in DU145 cells

first: Ekta

last: Khurana

first: Chen

middle: K

last: Wong

first: Duo

last: Xu


title: Muscle GR and BMAL1 epigenomic binding at ZT4 after vehicle versus prednisone pulse at ZT0

city: Cincinnati

first: Mattia

last: Quattrocelli

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: Exogenous glucocorticoids interact with the circadian clock, but little attention is paid to their time of intake. Here we investigated the epigenetic effects of prednisone in  muscle when pulsed as single 1mg/kg i.p. dose in mice WT mice at ZT0, i.e. when endogenous corticosterone is low.  At 4-hours post-injection (ZT4), we performed ChIP-seq analysis in muscle tissue for the glucocorticoid receptor (GR), as well as BMAL1, clock factor active in the light-phase. We also performed ChIP-seq for RNApol-II to quantitate changes in RNApol-II recruitment. We repeated the GR and RNApol-II analyses in muscles from BMAL1-knockout mice.

overall_design: 3 samples BMAL-WT muscle + vehicle; 3 samples BMAL-WT muscle + prednisone; 3 samples BMAL-KO muscle + vehicle; 3 samples BMAL-KO muscle + prednisone. Each sample was ~10 ng immunoprecipitated chromatin from 2 pooled quadriceps muscles of one mouse. Primary antibodies: rabbit polyclonal anti-GR (ABclonal #A2164), rabbit polyclonal anti-RNApol-II (A11181) and mouse monoclonal anti-BMAL1 (DSHB # PCRP-ARNTL-1C12).

first: Elizabeth

last: McNally


title: ChIP-Seq in MSK-PCa3 Prostate Cancer Organoids of FOSL1, TAZ, TEAD1, YAP

summary: Genome-wide mapping of FOSL1, YAP, TAZ and TEAD1 binding sites in MSK-PCa3 cells

overall_design: Genome occupancy profiling of FOSL1, YAP, TAZ, and TEAD1 was performed in MSK-PCA3 cells


title: Integrated molecular profiling of patient-derived ovarian cancer models identifies clinically relevant signatures and tumor vulnerabilities.

city: San Giovanni rotondo

first: Valentina

last: Melocchi

state: Foggia

address: Viale Padre Pio 7

department: ISBReMIT - Institute for Stem-cell Biology, Regenerative Medicine and Innovative Therapies

institute: Casa Sollievo della Sofferenza Hospital - IRCCS

summary:
Epithelial ovarian cancer (EOC) is the most lethal gynecological tumor in developed countries and is characterized by high biological and molecular heterogeneity. High-grade serous ovarian carcinoma (HGSOC) is the most frequent and intractable form of the disease, mainly due to its rapid dissemination into the abdominal cavity, a process that is tightly linked to peritoneal ascites.
Despite several studies provided insights into the genetic and epigenetic alterations relevant in EOC, the precise molecular alterations involved in tumor onset and progression remain largely unknown. Here we provide an experimental framework to perform a comprehensive investigation of molecular alterations relevant in HGSOC and ovarian cancer stem cells (OCSC) biology.
We relied on a well characterized experimental set derived from human HGSOC-associated ascites and consisting of primary tumor cells, OCSC-enriched spheroids and serially propagated patient-derived xenografts, in order to define genetic and transcriptional signatures associated to specific HGSOC evolutionary trajectories.
Such signatures exhibited prognostic value in a large cohort of HGSOC patients and allowed to define PI3K signaling as a novel vulnerability in OCSCs. Thus, our approach proved effective for the identification of druggable targets in HGSOC ascites, which is a major player in relapse and poor prognosis.

overall_design: mRNA sequencing was performed on 8 samples derived from a single human ascites. Samples analysed are human ascites (N=1), cultured ovarian cancer cells (N=3) and ascites from patient-derived xenograft (N=4).

first: Giuseppe

last: Testa

first: Fabrizio

last: Bianchi

first: Ugo

last: Cavallaro


title: Neuronal–Glial Communication Perturbations in Murine SOD1G93A Spinal Cord

first: Paul

middle: Francis

last: Gugger

address: 435 E 30th St

department: Medicine

institute: NYU Langone Health

summary: Amyotrophic lateral sclerosis (ALS) is an incurable disease characterized by proteinaceous aggregate accumulation and neuroinflammation culminating in rapidly progressive lower and upper motor neuron death. To interrogate cell-intrinsic and inter-cell type perturbations in ALS, single-nucleus RNA sequencing was performed on the lumbar spinal cord in the murine ALS model SOD1G93A transgenic and littermate control mice at peri-symptomatic onset stage of disease, age 90 days. This work uncovered perturbed tripartite synapse functions, complement activation and metabolic stress in the affected spinal cord; processes evidenced by cell death and proteolytic stress-associated gene sets. Concomitantly, these pro-damage events in the spinal cord co-existed with dysregulated reparative mechanisms. This work provides a resource of cell-specific niches in the ALS spinal cord and asserts that interwoven dysfunctional neuronal-glial communications mediating neurodegeneration are underway prior to overt disease manifestation and are recapitulated, in part, in the human post-mortem ALS spinal cord.

overall_design: Single-nucleus RNA-seq data were generated for three male and three female mice of each B6.Cg-Tg(SOD1*G93A)1Gur/J amyotrophic lateral sclerosis-like and C57BL/6J wild-type control mice, for a total of 12 mice. One replicate of each sex/genotype combination was included in each of three 10X Genomics batches, each sample within a batch containing unique nuclear hashtag oligos to enable demultiplexing in silico.

first: Michael

last: MacLean

first: Raquel

last: López-Díez

first: Carolina

last: Vásquez

first: Ann

last: Schmidt


title: Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus [smallRNA-Seq]

city: Edinburgh

last: Bayne

address: Alexander Crum Brown Road

department: Institute of Cell Biology

institute: University of Edinburgh

type: Non-coding RNA profiling by high throughput sequencing

summary: small RNA-seq was performed to identify differences in small RNA complement between wild type and Dcr1 deficent cells in Schizosaccharomyces japonicus.

overall_design: Two biological replicates of small RNA profiles in WT and dcr1D

first: Elliott

last: Chapman


title: Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus [ChIP-Seq]

summary: ChIP-seq was performed to identify differences in H3K9me2 profiles between wild type and Dcr1 deficent cells in Schizosaccharomyces japonicus.

overall_design: Two biological replicates of ChIP-Seq profiles in WT and dcr1D, using antibodies against total histone H3 and histone H3K9 dimethylation


title: GLUT3/SLC2A3 is an endogenous marker of hypoxia in prostate epithelial and prostate cancer cells.

status: Public on Feb 16 2022

city: Tucson

first: Gregory

middle: C.

last: Rogers

state: Arizona

address: 1515 N. Campbell Ave.

department: Department Cellular & Molecular Medicine

institute: University of Arizona Cancer Center

summary: The microenvironment of solid tumors is dynamic and frequently contain pockets of low oxygen levels (hypoxia) surrounded by regions of normal oxygen levels.  Indeed, a compromised vascular is a is hallmark of the tumor microenvironment, creating gradients of hypoxia.  Notably, hypoxia associates with increased metastasis and poor survival in patients.  Therefore, to aid therapeutic decisions and better understand hypoxia's role in cancer progression, it is critical to identify endogenous biomarkers of hypoxia to spatially phenotype oncogenic lesions in human tissue, whether precancerous, benign, or malignant.  Here, we characterize the glucose transporter GLUT3/SLC2A3 as a biomarker of hypoxia prostate epithelial cells and prostate tumors.  Transcriptomic analyses of hypoxic immortalized prostate epithelial cells revealed a highly significant increase in GLUT3 expression.  GLUT3 upregulation was also detected by immunostaining in hypoxic prostate epithelial cells and prostate cancer cell lines.  Additionally, GLUT3 dramatically co-localized with the hypoxia-marker pimonidazole in xenograft tumors formed from prostate cancer cells and showed distinct concentration gradients within patient-derived xenograft tumors from primary and metastatic prostate cancer.  Compared to established hypoxia-response genes, GLUT1 and CA9, GLUT3 shows a higher degree of hypoxia labeling within tumor tissue and may serve as a alternative endogenous biomarker of hypoxia.

overall_design: Coparison of transcriptome of RWPE1 cells in nomoxia to transcriptome of RWPE1 cells in hypoxia

first: John

last: Ryniawec

first: Matthew

middle: R

last: Coope

first: Emily

last: Loertscher

first: Vignesh

last: Bageerathan

first: Diogo

last: de Oliveira Pessoa

first: Noel

middle: A

last: Warfel

first: Anne

last: Cress

first: Megha

last: Padi

middle: C


title: The Cdkn2a gene product ARF is a critical regulator of IFNb mediated Lyme arthritis

city: Salt Lake City

first: Jinze

last: Li

state: UT

address: 15 North Medical Drive #1100

department: Pathology

institute: UNIVERSITY OF UTAH

summary: Lyme disease is caused by infection with Borrelia burgdorferi, with a spectrum of clinical disorders. Murine studies with B6 and C3H mice have demonstrated that genetic differences in the host response play an essential role in regulating the severity of Lyme arthritis. C3H mice generate a robust induction of type I IFN response in joint tissue at one week of infection which leads to severe Lyme arthritis at 4 weeks post-infection, while B6 mice develop mild disease without a type I IFN profile. We used a forward genetic approach and identified B. burgdorferi arthritis- associated locus 1 (Bbaa1) on Chr4, which includes type I IFN cluster. B6.C3-Bbaa1 congenic mice display more severe Lyme arthritis than B6 mice. The blocking of type I IFN receptor and the IFNb subtype in Bbaa1 mice suppressed arthritis back to B6 level, so we concluded the Bbaa1 locus intrinsically controls IFNb production, and the differential expression of IFNb controls the severity of Lyme arthritis.  However, the IFNb genes of C3H and B6 mice are identical, prompting focus on other genetic factors within the Bbaa1 locus as regulators of IFNb. Reciprocal radiation chimeras between B6.C3-Bbaa1 and B6 mice revealed myeloid cells in the joint tissue as IFNb initiators. Advanced congenic lines were generated to reduce the genetic contribution from C3H Bbaa1 region. RNA-seq of bone marrow-derived macrophages (BMDMs) from B6 and advanced interval specific recombinant congenic lines, ISRCL3 and ISRCL4, revealed novel candidates that may regulate Ifnb. In this study, we identify the Cdkn2a gene encoded ARF as a critical regulator of IFNb mediated Lyme arthritis, and investigate mechanistic interactions that modulate IFNb expression in Lyme arthritis development.

overall_design: BMDM's from B6, ISRCL4 and ISRCL3 mice were treated with B. burgdorferi for 0hr, 3hr or 6hr in order to identify genes (protein coding and non-coding RNAs) that are expressed in the Bbaa1 locus from 87.968-94.68Mbps. Genes expressed in this region will be candidates for further identification of the gene that regulates IFNb. Gene expression were compared between control group, B6, and ISRCL4/ISRCL3 congenic mice.

first: Ying

last: Ma

first: Jackie

last: Paquette

first: James

middle: F

last: Zachary

first: Cory

last: Teuscher

first: Janis

middle: J

last: Weis


title: Role of the cellular factor CTCF in the regulation of Bovine Leukemia Virus latency and three-dimensional chromatin organization [ChIP-seq]

first: Peter

last: Krijger

overall_design: Input, CTCF and Rad21 ChIP-seq profiles of 2 BLV-infected ovine cell lines (L267 and YR2)  and 1 ovine PBMC

first: Maxime

last: Bellefroid

first: Anthony

last: Rodari

first: Mathilde

last: Galais

middle: H

first: Sjoerd

last: Tjalsma

first: Lorena

last: Nestola

first: Estelle

last: Plant

first: Erica

last: Vos

first: Sara

last: Cristinelli

first: Benoit

last: Van Driessche

first: Caroline

last: Vanhulle

first: Amina

last: Ait-Ammar

first: Arsène

last: Burny

first: Angela

last: Ciuffi

first: Wouter

last: de Laat

first: Carine

last: Van Lint


title: Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus

first: Elizabeth

last: Bayne

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

overall_design: Refer to individual Series


title: Integrative functional transcriptomic analyses implicate shared molecular circuits in sensorineural hearing loss

city: Kunming

first: Junjun

last: Hao

address: No.17 Longxin Road

institute: Kunming Institute of Zoology

summary: Aging, noise exposure, and ototoxic drugs represent the three main causes of SNHL, leading to substantial similarities in pathophysiological characteristics of cochlear degeneration.  Although the common molecular mechanisms are widely assumed to underlie these similarities, its validity lacks systematic examination.  To address this question, we generated three SNHL mouse models from aging, noise exposure, and cisplatin ototoxicity and constructed gene coexpression networks for the cochlear transcriptome data across different hearing-damaged stages.

overall_design: The cochleae were harvested from controls (2-month-old mice), aging-induced SNHL (8-month-old and 12-month-old mice), noise-induced SNHL (2-month-old female mice after being exposed to noise for one hour and 2-month-old mice after being exposed to noise for 24 hours), and cisplatin-induced SNHL (2-month-old mice after being injected with cisplatin for one day and 2-month-old mice after being injected with cisplatin for three days).  An individual’s bilateral cochleae were collected as a biological replicate.  To ensure the reliability and repeatability of our data, at least three replicates were required.

first: Peng

last: Chen


title: Next Generation Sequencing Analysis of Healthy donors and rhumatoid arthritis patients with or without anti-TNF-treatment

city: le kremlin bicetre

first: audrey

last: paoletti

address: 78 rue du general Leclerc

institute: inserm U1184

summary: Introduction: We previously reported a specific defect of rheumatoid arthritis (RA) monocyte polarization to anti-inflammatory M2-like macrophages related to increased miR-155 expression in all RA patients except those receiving adalimumab (ADA). In this longitudinal study, we examined whether different tumor necrosis factor inhibitors were able to restore monocyte polarization to M2-like macrophages and their effect on the transcriptomic signature. Methods: M2-like polarization induced by human serum AB was studied in 7 healthy donors and 20 RA patients included in the ABIRA cohort before and 3 months after starting ADA or etanercept (ETA). The differential gene expression of M2- and M1-related transcripts was studied in macrophage-derived monocytes after differentiation. Results: At baseline, RA monocytes showed a defect of polarization to M2-like macrophages as compared with healthy donor monocytes, which was negatively correlated with disease activity. M2-like polarization from circulating monocytes was restored only with ADA and not ETA treatment. The transcriptomic signature demonstrated downregulation of M2-related transcripts and upregulation of M1-related transcripts in active RA. In patients receiving ADA, the transcriptomic signature of M2- related transcripts was restored. Conclusion: This longitudinal study demonstrates that ADA but not ETA is able to restore the M2-like polarization of monocytes that is defective in RA

overall_design: For this study we analyzed 5 patients per group (3group HD/ MTX-RA and ADA-MTX) but we excluded 2 samples after quality control

first: Audrey

last: Paoletti

first: Bineta

last: Ly

first: Samuel

last: Bitoun

first: Gaëtane

last: Nocturne

first: Elodie

last: Rivière

first: Jessica

last: Manson

first: Andrea

last: Matucci

first: Marc

last: Pallardy

first: Niek

last: De Vries

first: Xavier

last: Mariette


title: CD226 and TIGIT cooperate in the differentiation and maturation of human Tfh cells

first: Christian

last: Forst

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: The goal was to determine the impact of CD155 signaling through CD226 and TIGIT on Tfh differentiation and function based on gene expression.

overall_design: CD4 T cells derived from tonsils (Sorted Tfh, pre-Tfh and Naïve cells) were stimulated with L cells expresing CD155 in the presence or absence of CD226 blocking antibodies or controls.

first: Motoko

last: Yasutomi

first: Allison

last: Christiaansen

first: Naoko

last: Imai

first: Natalia

last: Martin-Orozco

middle: V

first: Gang

first: Hideki

last: Ueno


title: Bone Marrow Stroma-induced Transcriptome and Regulome Signatures of Multiple Myeloma [ATAC-seq]

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Multiple myeloma (MM) is a hematological cancer with inevitable drug resistance. MM cells interacting with bone marrow stromal cells (BMSCs) undergo substantial changes in transcriptome and develop de novo drug resistance. As a critical component in transcriptional regulation, how chromatin landscape is transformed in MM cells and regulates the transcriptional response to BMSCs remains elusive. We profiled transcriptome and regulome for MM cells using a transwell coculture system with BMSCs. The transcriptome and regulome of MM cells from the upper transwell resembled MM cells coexisting with BMSCs from the lower chamber but were distinctive to monoculture. BMSC-induced genes were enriched in JAK2/STAT3 signaling pathway, unfolded protein stress, signatures of early plasma cells, and response to proteasome inhibitors. Genes with accessibility increased at multiple regulatory sites were preferentially induced by BMSCs and enriched in response to drug and unfavorable prognostic markers from several MM patient cohorts. We proposed JUNB and ATF4::CEBPβ as candidate transcription factors (TFs) that modulated the BMSC-induced transformation of regulome linked to the response to external stimuli. Together, we characterized BMSC-induced transcriptome and regulome signatures of MM cells and prioritized TFs for future study to depict epigenetic mechanisms of BMSC-induced drug resistance in MM.

overall_design: To define BM stroma-induced transcriptome and regulome signatures of MM cells, we utilized an in vitro transwell coculture system, where MM cells (MM.1S or RPMI8226) resided in both the upper transwell and the lower chamber where adhesive BMSCs (HS5) co-existed. We profiled transcriptome by RNA-Seq and regulome by Omni-ATAC for MM cells in the upper transwel, MM cells in the lower chamber, and MM cells in monoculture.

first: Sebastian

last: Dziadowicz

first: Lei

last: Wang

first: Halima

last: Akhter

first: Drake

last: Aesoph

first: Sharma

last: Tulika

first: Lori

last: Hazlehurst


title: Bone Marrow Stroma-induced Transcriptome and Regulome Signatures of Multiple Myeloma [RNA-seq]


title: Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus [RNA-Seq]

first: Elizabeth

last: Bayne

summary: RNA-seq was performed to identify transcripts differentially expressed in Schizosaccharomyces japonicus cells lacking Dcr1.

overall_design: Three biological replicates of RNA profiles in WT and dcr1D

first: Elliott

last: Chapman


title: Collagen10a1-Cre;Rosa26-tdTomato Bone marrow colony forming units

city: Durham

first: Matthew

middle: J.

last: Hilton

address: 450 Research Drive, LSRC B321C

institute: DUKE UNIVERSITY SCHOOL OF MEDICINE

summary: To assess if descendants of the hypertrophic chondrocytes behaved as skeletal stem and progenitor cells, we performed colony unit formation. We observed a near equal proportion of colonies derived from hypertrophic chondrocytes (tomato+) and derived from other sources (likely periosteum). We performed bulk RNA-sequencing on 3 colonies from each origin to compare the gene profiles and potential differentiation capacity or niche support.

overall_design: Col10a1-Cre;R26-tdTomato, Tomato + and Tomato - colonies 10 days post plating

first: Jason

last: Long

first: Abigail

last: Leinroth

first: Yihan

last: Liao

first: Yinshi

last: Ren

first: Anthony

last: Mirando

first: Tuyet

last: Nguyen

first: Wendi

last: Guo

first: Deepika

last: Sharma

first: Colleen

last: Wu

first: Kathryn

middle: S

last: Cheah

first: Courtney

last: Karner

first: Douglas

last: Rouse


title: Collagen10-Cre;Rosa26-tdTomato bone marrow single cell RNA-sequencing

summary: In order to assess the descendants of hypertrophic chondrocytes, we utilized Collagen10-Cre;Rosa26-tdTomato mouse bone marrow harvested at 2 months of age by centrifugation and light Collagenase II digestion. After sequencing and downstream analysis using Seurat, we observed clusters of cells with gene profiles matching classically defined skeletal stem and progenitor cells as well as CXCL12 abundant reticular (CAR) cells. These cells appear to be upstream of both osteoblasts and adipocytes. We conclude that hypertrophic chondrocytes dedifferentiate to this progentior stage before further differentiation.

overall_design: 10X Genomics Single cell RNA-sequencing of bone marrow reporter positive cells.


title: Comparison of Pectobacterium carotovorum RC5297 transcription profiles depending on presence or absence of the PcaRCI RM system

status: Public on Feb 15 2022

city: Dunedin

first: Peter

middle: Charles

last: Fineran

state: Otago

address: 720 Cumberland Street

department: Department of Microbiology and Immunology

country: New Zealand

institute: University of Otago

summary: This project aimed to investigate the transcriptomic differences between a Pectobacterium carotovorum wild-type strain (RC5297) and a derivative in which a restriction-modification system, termed PcaRCI, is knocked out. The aim was to identify genes whose expression might be regulated through methylation by the methyltransferase of the RM system.

overall_design: Examination of two different bacterial strains (P. carotovorum RC5297 wild type and P. carotovorum RC5297 PcaRCI RM knockout) with five replicates each (ten samples in total)

first: Nils

last: Birkholz

first: Simon

last: Jackson

first: Robert

middle: D

last: Fagerlund


title: Effects of dietary fat on neurodevelopmental outcomes in normal birth weight and intrauterine growth restricted piglets

city: Frederiksberg

first: Xiaoyu

last: Pan

address: Dyrlægevej 68

department: Department of Veterinary and Animal Sciences

country: Denmark

institute: University of Copenhagen

summary: Breast milk has shown neurodevelopmental advantages compared to infant formula, especially in IUGR infants, which may relate to the fat source. This study aimed to compare neurodevelopmental outcomes in normal birth weight (NBW) and intrauterine growth restricted (IUGR) piglets fed a formula diet with either a vegetable oil (VEG) or bovine milk fat source (MILK). Results showed that total plasma lipids were increased by feeding the MILK diet. 82% and 11% of lipid species were differentially expressed between dietary groups in plasma and hippocampus, respectively, with slight agreement between the plasma and brain lipidome. The MILK diet was most effective in increasing brain lipid accretion, mainly comprising phospholipids. Absolute regional brain weights, grey and white matter volumes, and behavior and motor function scores were lower in IUGR piglets with no effects of diet. Cognitive function and gene expression profiles were similar for dietary and weight groups, and overall only minor interactive effects between diet and weight were observed. In conclusion, dietary fat source influenced the plasma and to a lesser degree the hippocampal lipidome, but was unable to improve on IUGR induced brain structural and functional impairments.

overall_design: Three-day old term born NBW and IUGR piglets were fed a VEG or MILK diet for 3 weeks in a 2×2 factorial study design. Behaviour, cognitive and motor functional tests were conducted from day 7-20. Plasma and brain tissue were collected for lipidomics, MRI and RNA sequencing.

first: Nicole

middle: L

last: Henriksen

first: Karina

last: Asmussen

first: Ping-Ping

last: Jiang

first: Line

last: Christensen

first: Richard

last: Sprenger

first: Christer

last: Ejsing

first: Stanislava

last: Pankratova

first: Thomas

last: Thymann


title: Collagen10-Cre;Rosa26-tdTomato e16.5 single cell RNA-sequencing

first: Matthew

last: Hilton

state: NC

summary: In order to assess the descendants of hypertrophic chondrocytes, we utilized Collagen10-Cre;Rosa26-tdTomato mouse total bone isolated at e16.5 by Collagenase II digestion after mechanical digestion and soft tissue removal. After sequencing and downstream analysis using Seurat, we observed clusters of cells with gene profiles matching classically defined chondrocytes, skeletal stem and progenitor cells (SSPCs), and osteoblasts. Trajectory analysis reveals that the SSPCs lie intermediate to the transition of chondrocyte to osteoblast. We conclude that hypertrophic chondrocytes dedifferentiate to this progenitor stage before further differentiation.

overall_design: 10X Genomics Single cell RNA-sequencing of total bone e16.5 reporter positive cells.

first: Jason

last: Long

first: Abigail

last: Leinroth

first: Yihan

last: Liao

first: Yinshi

last: Ren

first: Anthony

last: Mirando

first: Tuyet

last: Nguyen

first: Wendi

last: Guo

first: Deepika

last: Sharma

first: Colleen

last: Wu

middle: M


title: Metastasis-relevant cellular constrictions as determinants for resistance to cell death and cancer aggressiveness

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

institute: Genomics Consulting

summary: How mechanical stress might influence the resistance of cancer cells to cell death is currently unknown. To address this, we mimicked the mechanical constrictions that cancer cells might encounter when invading through rich tumoral stroma or undergoing intra- and extravasation. We found that extreme constrictional migration (ECM) but not compression increases the resistance of breast cancer cells to anoikis, a variant of apoptosis triggered by loss of cell adhesions. We also found that Inhibitory of Apoptosis Proteins (IAPs) are responsible for ECM-triggered resistance to anoikis. Together with enhanced cell motility and resistance to natural killer-mediated immune-surveillance, we show that anoikis resistant ECM mechanically-challenged cancer cells have a marked advantage to form lung metastatic lesions. Taken together, our study connects the constrictional mechanical stress typically characterizing the metastatic colonization with the resistance to cell death, while therapeutically targeting the IAPs by SMAC mimetics could counteract anoikis resistance in breast cancer cells.

overall_design: A Transwell assay was performed to distinguish cells that are subject to constriction (also refered to as “down” or “Bottom” cells throughout the text), from those that do not migrate (also refered to as “up” or “Top” control cells). RNA sequencing from control and mechanically-challenged MDA-MB-231 cells was done by the CRCL Cancer Genomics core facility. Sequencing was performed using the NextSeq500 Illumina sequencer in 75 bp paired-end.

first: Deborah

last: Fanfone

first: Gabriel

last: Ichim


title: Investigating the role of Dicer-dependent transfer RNA-derived small RNAs in gene expression regulation

city: Oxford

first: Monika

last: Gullerova

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary: We used sequencing analyses to identify small RNAs that are generated in a Dicer-dependent manner and the genes that are dysregulated upon Dicer knockdown at the mRNA level, and upon Drosha, Dicer and Ago2 knockdown at the chromatin level in HEK293 cells. We found that levels of tRNA-derived sRNAs decreased alongside microRNAs upon Dicer knockdown. Many genes are dysregulated at the chromatin levels when Dicer and Ago2 levels are reduced, indicating that Dicer and Ago2 can regulate genes directly or indirectly at the transcriptional level. Drosha knockdown, on the other hand, has a marginal effect on RNA levels at the chromatin.

overall_design: sRNA and mRNA profiles of HEK293 wt and Dicer knockdown cells were generated by deep sequencing, in triplicates; chromatin-associated RNA profiles of HEK293 wt, Drosha, Dicer and Ago2 knockdown cells were generated by deep sequencing, in duplicates.

first: Sheng

last: Pong

first: Margarita

last: Schlackow

first: Natalie

last: Ng

first: Kaspar

last: Burger


title: Expression data from mouse thymus

city: San Antonio

first: Ann

last: Griffith

address: 7703 Floyd Curl Drive

department: Microbiology, Immunology and Molecular Genetics

institute: UT Health San Antonio

summary:
Previous studies have shown that extensive transciptional changes occur in the thymus as the tissue atrophies during aging, and that atrophy is delayed in catalase transgenic (mCat Tg, tg) mice. These studies address whether the transciptional profile of medullary thymic tissue  in aged mCat Tg mice retains characteristics of the young medullary tissue or not.
We used microarrays to detail transciptional profiles in aged mCat Tg mouse thymus to compare to gene expression in aged wild type mice.

overall_design: 12 month old mCat tg mouse thymi were snap frozen for RNA extraction and hybridization on Affymetrix microarrays. Whole medullary tissue from the middle third of the thymus was isolated by microdissection after snap freezing, 20 micron sectioning, fixation in acetone:ethanol, staining in ethanol:hematoxylin, and dehydration through graded ethanol, all done at ice cold temperatures.

first: Thomas

last: Venables


title: Angioplasty induces epigenomic remodeling in injured arteries

status: Public on Feb 14 2022

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

summary: Neointimal hyperplasia (IH) is a primary etiology of stenotic vascular diseases. It is perpetuated principally by smooth muscle cell proliferation. Epigenome-scale studies concerning IH have been confined to in vitro models, and the IH-underlying epigenetic mechanisms remain poorly understood. The current study has integrated information from in vivo epigenomic mapping, conditional knockout, gene transfer and pharmacology in rodent models of IH. The data from injured (IH-prone) rat arteries revealed a surge of genomewide occupancy by H3K27me3, a gene repression mark. This was unexpected in the traditional view of prevailing post-injury gene activation rather than repression. Further analysis illustrated a shift of H3K27me3 enrichment to anti-proliferative genes, from pro-proliferative genes where gene activation mark H3K27ac instead accumulated. In accordance, H3K27ac and its reader BRD4 co-enriched at Ezh2 governing its expression. Moreover, H3K27me3 writer EZH2 positively regulated another recently identified pro-IH chromatin modulator UHRF1. Thus, results unravel injury-induced loci-specific H3K27me3 redistribution in the epigenomic landscape entailing BRD4->EZH2->UHRF1 hierarchical regulations, and may guide translation to treat IH given that these players are pharmaceutical targets.

overall_design: ChIPseq was performed on injured and uninjured rats for 4 histone markers.

first: Lian

middle: W

last: Webb

first: Hatice

last: Gulcin Ozer


title: Exercise-generated β-aminoisobutyric acid (BAIBA) reduces cardiomyocytes metabolic stress and apoptosis caused by mitochondrial dysfunction through the miR-208b/AMPK pathway

city: Changchun

first: Yanan

last: Yu

state: Jilin

address: Xiantai Street  No.126

department: Department of Rehabilitation

institute: China-Japan Union Hospital

summary:
Objective: To explore the protective effects of exercise-derived β-aminoisobutyric (BAIBA) on apoptosis and energy metabolism in rats with heart failure.
Methods: A rat model of heart failure after myocardial infarction (MI) was started by ligating the left anterior descending branch of the coronary artery, the anterior descending branch of the rats in the SHAM group was only threaded and not ligated. Exercise intervention was given to rats with heart failure. The possible mechanisms by which exercise affected cardiac remodeling after MI were investigated using color ultrasound, HE, Masson, and TUNEL staining, and the detection of apoptosis-associated factors in cardiac tissue. High-throughput sequencing and mass spectrometry were used to measure the production of BAIBA and to explore its protective effects and molecular mechanisms. An in vitro model of apoptosis was created by the application of H2O2 to induce mitochondrial dysfunction. This was then transfected with miR-208b analogue and miR-208b-inhibitor. Apoptosis-related proteins were detected by Western blotting (WB), and ATP production was also assessed. After intervention with BAIBA and compound C, assessments were made of apoptosis, mitochondrial function, lipid uptake, utilization of related proteins, ATP changes, alterations in membrane potential (δψm), and changes in reactive oxygen species (ROS).
Results: Compared with the control heart failure (HF) group, exercise improved the function of mitochondria, reversed the expression of apoptosis-related proteins, and increased ATP production. In both the normal and heart failure groups, exercise significantly increased the production of BAIBA. It was shown that BAIBA played a similar role to exercise in ameliorating heart failure. Transcriptome analysis confirmed that the expression of miR-208b was increased after BAIBA intervention, and transfection with miR-208b analogue increased both the expression of apoptosis-related proteins and energy metabolism in H9C2 cells induced by H2O2. Combined analysis of the transcriptome and metabolome identified AMPK as a target for BAIBA to improve metabolic stress. Cell experiments further confirmed that BAIBA increased AMPK phosphorylation and had a protective effect on downstream fatty acid uptake, oxidative efficiency, and mitochondrial function, which could be counteracted by the AMPK inhibitor compound C.
Conclusion: Exercise-induced BAIBA can reduce the metabolic stress and apoptosis induced by mitochondrial dysfunction through the miR-208b/AMPK pathway.

overall_design:
Rats with heart failure, treated with exercise or BAIBA.
Examining 3 conditions，each with 3 replicates

first: Weiwei

last: Chen


title: Comprehensive transcriptome analysis of heart tissues in the sugen/hypoxia rats with/without treatment of chrysin

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

institute: University of Toyama

summary: Pulmonary arterial hypertension (PAH) is a progressive disease characterized by pulmonary vascular remodeling leading to increased pulmonary vascular resistance and right ventricular (RV) hypertrophy, resulting in RV failure. RV dysfunction is a complex process that leads to cardiomyocyte hypertrophy, fibrosis, inflammation, angiogenesis, and metabolic changes. In patient with PAH, the adaptation of the RV to high pulmonary arterial pressures is the most important determinant of prognosis. However, the underlying molecular mechanism of adverse RV remodeling and dysfunction is poorly understood, and there are no currently approved therapies that improve RV function. Chrysin (5,7-dihydroxyflavone) is a phytochemical, which is a flavonoid widely present in plant sources. In various experimental models chrysin has shown to exert cardio-protective effects through its antioxidant and anti-inflammatory effects. In this study, we performed a comprehensive analysis of gene expression changes in heart tissues of rats under hypoxic conditions with chrysin treatment using RNA sequencing (RNA-seq).

overall_design: mRNA profiles of heart tissues were generated by RNA sequencing using the NextSeq 500 (Illumina).

first: Takayuki

last: Kobayashi

first: Yoshitoshi

last: Kasuya

first: Koichiro

last: Tatsumi


title: Whole lung transcriptome from lung epithelial IRE1α knockout mice

city: San Francisco

first: Vincent

last: Auyeung

state: CA

institute: University of California, San Francisco

summary: This experiment sought to characterize the whole lung transcriptional changes induced by loss of IRE1a function in the lung epithelium. Mice were Shh(Cre/+) IRE1a(fl/fl) on the C57BL/6 background, and had loss of IRE1a function in the epithelium based on XBP1 splicing activity. Lungs from uninjured mice were harvested, flash-frozen, homogenized, and RNA isolated by Trizol extraction.

overall_design: Principal treatment groups are: IRE1α epithelial knockout (Shh Cre/+ IRE1α fl/fl, 5 mice) and IRE1α flox (Shh +/+ IRE1α fl/fl, 5 mice).

first: Dean

last: Sheppard

first: Feroz

last: Papa


title: Lung epithelial transcriptional responses to bleomycin and effects of IRE1α or TGFβ inhibition

summary: This experiment sought to characterize the epithelial-specific transcriptional response in the bleomycin model of lung fibrosis, and the contribution of IRE1a and the TGFb-activating integrin avb6 to this response. "Ribotag" mice were crossed to ShhCre mice, both on the C57BL/6 background to generate experimental cohorts. Mice used for the experiment conditionally expressed HA-tagged ribosomal protein Rpl22 in the epithelium. Mice were exposed to intranasal bleomycin (3 U/kg) on day 1 and subsequently treated with the IRE1a kinase inhibitor KIRA8 (50 mg/kg daily), or the anti-integrin beta6 antibody 3G9 (10 mg/kg on day 1 and day 4). Treatment controls were either drug vehicle (3% ethanol, 7% Tween80, and 90% saline) or the inert antibody Axum8 in saline). Lungs were harvested on day 7 after bleomycin exposure, flash-frozen, and later homogenized under native conditions with cycloheximide. An aliquot of the “input” homogenate was removed and total RNA purified by Qiagen RNeasy Mini and is representative of the whole-lung transcriptome/translatome.  The remaining homogenate was subjected to immunoprecipitation of HA-tagged polysomes, followed by RNA purification by Qiagen RNeasy Micro, and is representative of the lung epithelial transcriptome/translatome.

overall_design: Factorial design. Principal treatment groups are: Saline/Control (6 mice), Bleomycin/Control (9 mice), Bleomycin/KIRA8 (5 mice) and Bleomycin/3G9 (4 mice). Each mouse has a corresponding whole lung and epithelial library.


title: Physiological and Molecular Characterization of an Oxidative Stress-Resistant Saccharomyces cerevisiae Strain Obtained by Evolutionary Engineering

city: Istanbul

first: Halil

middle: ibrahim

last: KISAKESEN

state: Istanbul

address: ITU MOBGAM, SARIYER

department: Molecular Biology, Genetics and Biotechnology

country: Turkey

institute: Istanbul Technical University

summary: Oxidative stress is a key attribute that one should considered when using yeast cells for industrial applications due to its direct impact on yeast growth, viability, and productivity. However, little information is currently available regarding the molecular mechanisms of oxidative stress induction and the antioxidant response to increased reactive oxygen species (ROS) in yeasts. In this study, we generated experimentally evolved and genetically stable oxidative stress-resistant S. cerevisiae strain. This evolved strain has elevated trehalose and glycogen production, and up-regulated gene expression profile for that related to stress response, transport, carbohydrate, lipid and co-factor metabolic processes, protein phosphorylation, cell wall organization or biogenesis. In contrast, down-regulated genes were related to ribosome and RNA processing, nuclear transport, tRNA, cell cycle etc. In addition to that, comparative physiological, transcriptomic, and genomic analyses revealed that this oxidative stress resistant strain was also cross-resistant against other stress types including heat, freeze-thaw, ethanol, copper, and salt stress. Single variants identified via whole genome sequencing were primarily related to stress response, cell wall organization, carbohydrate metabolism/transport which support the physiological and transcriptomic results.  Overall, this shed light how yeast cells can cope with oxidative stress pressure using their complex molecular mechanisms for the stress resistance and hints on how oxidative stress resistant S. cerevisiae strain can be generated for industrial applications.

overall_design: Oxidative stress resistant Saccharomyces cerevisiae (H7) mutant strain and reference strain were grown in yeast minimal medium. When cultures’ Optical Density (OD600) reached to about 1, which correspond to the logarithmic growth phase of the yeast cells, total RNA isolation was carried out by using RNeasy Mini Kit (Qiagen). The experiment was performed triplicates. Whole-genome microarray analysis was carried out by using Agilent DNA Microarray Technology.

first: Nazli

middle: K

last: Ozsen

first: Mevlut

last: Arslan

middle: I

last: Kisakesen

first: Zeynep

middle: P

last: Cakar