title: The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation

city: Shanghai

first: Luzhang

last: Ji

address: 1239 Siping Rd.

institute: Tongji University

summary: Interphase chromatin is hierarchically organized into higher-order architectures that are essential for gene functions, yet the biomolecules that regulate these 3D architectures remain poorly understood. Here, we show that scaffold attachment factor B (SAFB), a nuclear matrix (NM)-associated protein with RNA-binding functions, modulates chromatin condensation and stabilizes heterochromatin foci in mouse cells. SAFB interacts via its R/G-rich region with heterochromatin-associated repeat transcripts such as major satellite RNAs, which promote the phase sep- aration driven by SAFB. Depletion of SAFB leads to changes in 3D genome organization, including an increase in interchromosomal interactions adjacent to pericentromeric heterochromatin and a decrease in genomic compartmentalization, which could result from the decondensation of pericentromeric heterochromatin. Collectively, we reveal the integrated roles of NM-associated proteins and repeat RNAs in the 3D organization of heterochromatin, which may shed light on the molecular mechanisms of nuclear architecture organization.

overall_design: Refer to individual Series


title: The hematopoietic master transcription factor PU.1 requires its interaction with the SWI/SNF remodeler to access chromatin de novo [ChIP-seq]

status: Public on Nov 17 2019

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg

type: Genome binding/occupancy profiling by high throughput sequencing

summary: PU.1 is a prototype master transcription factor (TF) of hematopoietic cell differentiation with diverse roles in different lineages. Analysis of its genome-wide binding pattern across PU.1 expressing cell types revealed manifold cell type-specific binding patterns. They are not consistent with the epigenetic and chromatin constraints to PU.1 binding observed in vitro, suggesting that PU.1 requires auxiliary factors to access DNA in vivo. Using a model of transient mRNA expression we show that PU.1 induction leads to the extensive remodeling of chromatin, redistribution of partner transcription factors, and rapid initiation of a myeloid gene expression program in heterologous cell types. By probing mutant PU.1 variants for defects in chromatin access and screening for PU.1 proximal proteins in vivo, we found that its N-terminal acidic domain was required for the recruitment of SWI/SNF remodeling complexes, de novo chromatin access and stable binding as well as the redistribution of partner TFs.

overall_design: ChIP-seq data from cells transiently mRNA transfected with the transcription factor PU.1 and mutants thereof

first: Julia

last: Minderjahn


title: Titrating gene expression with allelic series of CRISPR guide RNAs

status: Public on Nov 18 2019

city: Boston

first: Marco

last: Jost

state: MA

address: 77 Ave Louis Pasteur, NRB848

country: USA

institute: Harvard Medical School

type: Expression profiling by high throughput sequencing

summary: Cellular phenotypes arise from the degrees to which different genes are expressed, yet the  ability to monitor these phenotypes is limited by a lack of tools to precisely control gene expression. We  describe the development of allelic series of systematically compromised sgRNAs to titrate expression of human genes with CRISPR interference. Using large-scale measurements of compromised sgRNA activities, we both  identify empirically validated intermediate-activity sgRNAs and derive the factors governing sgRNA activity using deep learning, enabling construction of a compact sgRNA library to titrate expression of ~2,400 essential genes and a genome-wide in silico library. Staging cells along a continuum of essential gene expression levels using sgRNA series  combined with rich single-cell RNA-seq readout reveals expression threshold-specific responses and gene-specific expression-to-phenotype relationships. Our work provides a general tool to control gene expression with applications ranging from tuning of biochemical pathways to identification of suppressors for diseases of dysregulated gene expression.

overall_design: Pooled CRISPR screening experiment with intermediate-activity sgRNAs conducted via Perturb-seq

first: Daniel

middle: A

last: Santos

first: Reuben

last: Saunders

first: Jonathan

middle: S

last: Weissman


title: The hematopoietic master transcription factor PU.1 requires its interaction with the SWI/SNF remodeler to access chromatin de novo

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


title: The hematopoietic master transcription factor PU.1 requires its interaction with the SWI/SNF remodeler to access chromatin de novo [CTV1_TALL_HELP ChIP-seq]

overall_design: ChIP-seq data from cells transiently mRNA transfected with the transcription factor PU.1 and mutants


title: The sulfur stress response caused by sodium hydrosulfide, allicin and diallyl polysulfanes in Bacillus subtilis as revealed by transcriptomics

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

institute: University Medicine Greifswald

summary:
In this study, we compared the transcriptome signatures in response to sodium hydrosulfide (NaHS), allicin and diallyl tetrasulfane (DAS4) exposure in the Gram-positive bacterium Bacillus subtilis. This analysis revealed that NaHS, allicin and DAS4 caused a similar thiol-specific oxidative and
electrophile stress response as well as protein and DNA damage.

platform_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: B. subtilis wild-type cells were grown in Belitsky minimal medium (BMM) to an OD500 of 0.4 and harvested before and 30 minutes after treatment with 2.5 mM NaHS, 90 µM allicin or 92 µM DAS4. Microarray hybridizations were performed with RNA from two biological replicates.

first: Marc

last: Schaffer

first: Khanh-Chi

last: Bui

first: Haike

last: Antelmann


title: Comparative profiling of metastatic 4T1- versus non-metastatic Py230-based mammary tumors in an intraductal model for triple-negative breast cancer.

status: Public on Nov 20 2019

city: Merelbeke

first: Jonas

last: Steenbrugge

address: Salisburylaan 133

department: Veterinary and Biosciences

country: Belgium

institute: Ghent University

summary:
Purpose: Compare the tumor outgrowth and immunology of an immunocompetent 4T1- and Py230-based intraductal model for triple-negative breast cancer (TNBC).

Methods: BALB/c-derived 4T1 and C57BL/6-derived Py230 mammary tumor cells were side-by-side intraductally inoculated in lactating and syngeneic mice, 4T1 and Py230 primary tumors were subsequently resected at 1, 3 and 6 weeks (w) post-inoculation (p.i.), and RNA was isolated from the 4T1 and Py230 primary tumors using in house developed protocols.

Results: The differentially expressed genes in the 4T1 versus Py230 primary tumor datasets at the 3 different time points were categorized into 28 hallmark gene sets using GSEA. Nine hallmarks could be related to tumor immunology and collectively showed a decreased difference in expression over time, although every immunology-related gene set remained most expressed in 4T1 primary tumors across all time points. Seven hallmarks could be related to cellular mitosis and tumor progression and were significantly upregulated at 1 w p.i. in 4T1 primary tumors, whereas at 3 w p.i. they became significantly upregulated in Py230 primary tumors, indicative for enhanced Py230 tumor proliferation. The hallmark epithelial-mesenchymal transition was significantly upregulated at 3 w p.i. in 4T1 compared to Py230 primary tumors, indicative for metastatic progression. Gene sets involved in adipose/stromal processes within the mammary gland were downregulated or weakly expressed at 1 w p.i., but became upregulated at 3 w p.i. in 4T1 compared to Py230 primary tumors, indicating that at the time 4T1 tumor cells were less proliferative compared to Py230 tumor cells, the surrounding stroma and fat tissue were more active in the 4T1- compared to the Py230-based intraductal model. The hallmark androgen response also showed a significantly upregulated expression in Py230 tumors at 3 and 6 w p.i., indicating that androgen signaling is important in invasive Py230 tumors.

Conclusion: Our findings highlight an innovative 4T1- and Py230-based intraductal mouse model for TNBC with a different tumor outgrowth and associated tumor microenvironment. These differential models may broadly represent the clinically observed TNBC diversity and together provide a powerful tool to evaluate therapeutics.

overall_design: RNA was isolated from 4T1 and Py230 primary tumors at 3 different time points (i.e. 1, 3 and 6 w p.i.) using the Rneasy Mini Kit (QiAgen, Valencia, CA, USA). All analyses were done in triplicate. In addition, Matrigel® controls were included for each intraductal model and time point, yielding a total of 36 samples. RNA sequencing was done in collaboration with Oxford Genomics using Illumina’s TruSeq chemistry and a HiSeq4000 (paired end, read length of 75 bp) using 2 lanes aiming for 10 million reads per sample.

first: Niels

last: Vander Elst

first: Kristel

last: Demeyere

first: Olivier

last: De Wever

first: Niek

middle: N

last: Sanders

first: Wim

last: Van Den Broeck

first: Luc

last: Dirix

first: Steven

last: Van Laere

first: Evelyne

last: Meyer


title: The hematopoietic master transcription factor PU.1 requires its interaction with the SWI/SNF remodeler to access chromatin de novo [ATAC-seq]

first: Michael

last: Rehli

overall_design: ATAC-seq data from cells transiently mRNA transfected with the transcription factor PU.1 and mutants

first: Julia

last: Minderjahn


title: Comparison of the RNA expression profiles of CD14+ monocytes (MO) from human peripheral blood with M-CSF macrophages differentiated in the presence of DMSO (MAC) or 50µM cambinol (Camb) for 5 days

status: Public on Nov 15 2019

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

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

country: Spain

institute: Josep Carreras Research Institute (IJC)

summary: Comparison of RNA expression of human peripheral blood monocytes with macrophages differentiated with M-CSF in the presence or absence of cambinol.

overall_design: Total RNA were isolated from three donor-matched MO and M-CSF-differentiated MACs in the presence of DMSO (MAC) or 50µM cambinol (Camb) for 5 days

first: Tianlu

last: Li

first: Antonio

last: Garcia-Gomez

first: Octavio

last: Morante-Palacios

first: Sevgi

last: Ozkaramehmet

first: Evelien

last: Van Dijck

first: Javier

last: Rodríguez-Ubreva

first: Alejandro

last: Vaquero


title: Comparison of the DNA methylation profiles of CD14+ monocytes (MO) from human peripheral blood with M-CSF macrophages differentiated in the presence of DMSO (MAC) or 50µM cambinol (Camb) for 5 days

type: Methylation profiling by genome tiling array

summary: Comparison of DNA methylation of human peripheral blood monocytes with macrophages differentiated with M-CSF in the presence or absence of cambinol.

overall_design: Total DNA were isolated from three donor-matched MO and M-CSF-differentiated MACs in the presence of DMSO (MAC) or 50µM cambinol (Camb) for 5 days


title: RNA sequencing for human induced pluripotent stem cell cardiomyocyte differentiation

city: Aurora

first: Edward

last: Lau

state: CO

address: 12700 E19th Av RCII Rm 8004

department: Medicine/Cardiology

institute: University of Colorado

summary: We apply short-read RNA sequencing technology to identify transcripts expressed during four time points of a human induced pluripotent stem cell derived cardiomyocyte differentiation protocol, corresponding to pluripotent, mesoderm, early cardiomyocyte, and cardiomyocyte cell stages. The RNA-seq reads are used to generate custom protein sequence database for proteogenomic applications and downstream mass spectrometry analysis. We demonstrate that this custom RNA-seq-guided proteomics approach can be used to identify protein isoforms that are differentially regulated during cardiac differentiation.

overall_design: Comparison of transcript expression in three replicates during four time points.

first: Maggie

middle: P

last: Lam


title: The hematopoietic master transcription factor PU.1 requires its interaction with the SWI/SNF remodeler to access chromatin de novo [RNA-seq]

overall_design: RNA-seq data from cells transiently mRNA transfected with the transcription factor PU.1 and mutants


title: Real-time quantitative PCR analysis of OC-C and CH under osteoarthritic condition

status: Public on Nov 14 2019

city: Pittsburgh

first: Zixuan

last: Lin

state: PA

address: 450 Technology Dr

department: Department of Orthopaedic Surgery

institute: University of Pittsburgh

summary: IL-1β (1 ng/ml) was introduced via medium feed to the cartilage side to induce OA-like phenotype in both OC and CH tissue chip. The catabolic, inflammatory and chondrogenic gene expression were compared between these two groups to assess the effect of osseous tissue on chondral tissue under OA condition.

overall_design: qPCR gene expression profiling: catabolic, inflammatory and chondrogenic gene expression of OC-C and CH were compared. Total RNA from each sample was used for gene expression analysis and normalized to RPL13A.

first: Lin

last: Hang

last: Zixuan


title: Real-time quantitative PCR analysis of chondrosupportive activity of bone component in the engineered osteochondral tissue

summary: To explore the influence of subchondral bone on the health of cartilage under normal physiology conditions, we compared the phenotype of OC-C with CH in terms of chondrogenic and hypertrophic gene expression

overall_design: qPCR gene expression profiling: chondrogenic and hypertrophic markers of OC-C and CH were compared with each other.Total RNA from each sample was used for gene expression analysis and normalized to RPL13A.


title: Transcriptional responses of human melanoma cells to EZH2 inhibition

city: Camperdown

first: Stuart

middle: J

last: Gallagher

state: NSW

address: Building 93, RPA Hospital

department: Melanoma Oncology

country: Australia

institute: Centenary Institute

summary:
The epigenetic modifier EZH2 is part of the polycomb repressive complex that suppresses gene expression via histone methylation. Activating mutations in EZH2 are found in a subset of melanoma that contributes to disease progression by inactivating tumor suppressor genes. In this study we have targeted EZH2 with a specific inhibitor (GSK126) or depleted EZH2 protein by stable shRNA knockdown. We show that inhibition of EZH2 has potent effects on the growth of both wild-type and EZH2 mutant human melanoma in vitro particularly in cell lines harboring the EZH2Y646 activating mutation. This was associated with cell cycle arrest, reduced proliferative capacity in both 2D and 3D culture systems, and induction of apoptosis. The latter was caspase independent and mediated by the release of apoptosis inducing factor (AIFM1) from mitochondria. Gene expression arrays showed that several well characterized tumor suppressor genes were reactivated by EZH2 inhibition. This included activating transcription factor 3 (ATF3) that was validated as an EZH2 target gene by ChIP-qPCR. These results emphasize a critical role for EZH2 in the proliferation and viability of melanoma and highlight the potential for targeted therapy against EZH2 in treatment of patients with melanoma.
Tiffen JC, Gunatilake D, Gallagher SJ, Gowrishankar K, Heinemann A, Cullinane C, et al. Targeting activating mutations of EZH2 leads to potent cell growth inhibition in human melanoma by derepression of tumor suppressor genes. Oncotarget 2015;12:12

overall_design: Total RNA was obtained from cultured human melanoma cell lines treated with either EZH2 inhibitor GSK126 (7.5 micromolar)  or DMSO carrier control for either 8 hr or 48 hr and analysed on Illumina HumanHT-12 v4 BeadChip arrays. Four seperate cell lines were treated with all experiments performed in biological duplicates. There are a total of 32 samples.

first: Jessamy

middle: C

last: Tiffen

first: Peter

last: Hersey


title: Real-time quantitative PCR analysis of celecoxib treatment on OC tissue chip

summary: To test the utility of iPSC-derived OC tissue chip in drug screening, Celecoxib, a selective cyclooxygenase 2 (COX-2) inhibitor commonly used to treat OA, was administered to the system. Celecoxib was administered at 10 µM concentration, and showed no noticeable adverse effect on the health of normal chondral tissue. Administration of Celecoxib to both OC-C and OC-B were used to simulate the typically systemic action of Celecoxib, represented by the “SY” group. In addition, we also examined the potential effect of intraarticular (IA) application of Celecoxib in treating OA, by delivery only to OC-C, namely the “IA” group. Normal OC tissues without any treatments served as the control (CL).

overall_design: qPCR gene expression profiling: catabolic, inflammatory and chondrogenic gene expression of CL, OA, SY and IA were compared. Total RNA from each sample was used for gene expression analysis and normalized to RPL13A.


title: Real-time quantitative PCR analysis of osteogenic markers in iMPC with different treatments

summary: To further enhance the osteogenesis of iMPCs, five types of medium were tested: Group 1 (Gr 1),  MM (negative control); Gr 2, OM; Gr 3, OM + 10 nM VitD3; Gr 4, OM + 10 nM VitD3 + 100 ng/ml BMP-7; Gr 5, OM + 10 nM VitD3 + 100 ng/ml BMP-7, with Dex treatment only during the first 14 days.

overall_design: qPCR gene expression profiling:osteogenic markers of Gr1-5 were compared with each other. Total RNA from each sample was used for gene expression analysis and normalized to RPL13A.


title: Real-time quantitative PCR analysis of chondrogenic markers in iMPC with different treatments

summary: Conventional TGF-β3 containing CM showed limited efficacy in promoting iMPCs chondrogenesis, which necessitated the development of a more optimal chondrogenic medium for iMPCs. Classic chondrogenic medium (CM) was compared with optimal chondrogenic medium (CM+BMP6), and basic meidum (BM) were served as control.

overall_design: qPCR gene expression profiling: chondrogenic markers of BM, CM and CM+BMP6 were compared with each other.Total RNA from each sample was used for gene expression analysis and normalized to RPL13A.


title: Osteochondral Tissue Chip Derived from iPSCs: Modeling OA pathologies and Testing Drugs

overall_design: Refer to individual Series


title: Gene expression profiling of GP2+ M cells and other epithelial cells in Peyer's patch

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dymanics Research

country: Japan

institute: RIKEN

summary: To define gene expression profiling of microfold (M) cells in follicle-associated epithelium (FAE), we isolated M cells and other epithelial cells from EpCAM+CD45-CD24- cells of Peyer's patches. The gene expression profilings were clearly different between GP2+ M cells and GP2- epithelial cells.

overall_design: GP2+ M cells and GP2- epithelial cells were sorted from EpCAM+CD45-CD24- fraction of C57BL/6J mouse Peyer's patch

first: Yutaka

last: Nakamura

first: Koji

last: Hase


title: Comprehensive analysis of miRNAs in matrix vesicles

status: Public on Nov 13 2019

city: Hiroshima

first: Tomoko

last: Minamizaki

state: Hiroshima

address: 1-2-3, Kasumi

institute: Hiroshima University

summary: miRNAs in matrix vesicles isolated from the extracellular matrix of MC3T3-E1 cell cultures

overall_design: Matrix vesicles were isolated three times independently from the extracellular matrix deposited by MC3T3-E1 cells with ultracentrifugation.

first: Yuji

last: Yoshiko


title: Different class IIa HDACs repressive complexes regulate specific epigenetic responses related to cell survival in leiomyosarcoma cells

city: udine

first: raffaella

last: picco

address: piazzale kolbe 4

department: department of medical and biological sciences

country: Italy

institute: university of Udine

summary:
Purpose: Define the transcriptional networks supervising class IIa HDAC expression.
Outcome: We demonstrate that MEF2D is the key factor controlling HDAC9 transcription. Comprehensive genome-wide studies demonstrate that HDAC4 and HDAC9 supervise different genetic programs and show both specific and common genomic bindings. Although the number of MEF2-target genes commonly regulated is similar, only HDAC4 represses many additional genes that are not MEF2D targets. HDAC4-/- and HDAC9-/- cells increase H3K27ac levels around the TSS of the respective repressed genes. However, these genes rarely show bindings of the HDACs at their promoters. Frequently HDAC4 and HDAC9 bind intergenic regions. We demonstrate that these regions, recognized by MEF2D/HDAC4/HDAC9 repressive complexes, show the features of active enhancers.

overall_design: 5 clones of SK-UT-1 cells were created: one transfected with Cas9 only as control, two HDAC4-/-  and two HDAC9-/-. Genes were targeted with CRISPR/Cas9 technology. Two replicates per clone were analyzed.

first: Eros

last: Di Giorgio

first: Emiliano

last: Dalla

first: Raffaella

last: Picco

first: Claudio

last: Brancolini


title: ARID1A is a critical regulator of luminal identity and therapeutic response in oestrogen receptor-positive breast cancer (RNA-seq II)

city: New York

first: Sagar

last: Chhangawala

state: NY

address: 1300 York Ave.

department: PBSB

institute: Weill Cornell Medical College

summary: Mutations in ARID1A, a subunit of the SWI/SNF chromatin remodelling complex, are the most common somatic alteration of the SWI/SNF complex across all cancers including oestrogen receptor positive (ER)+ breast cancer. We have recently reported that ARID1A inactivating mutations are present at a high frequency in advanced endocrine resistant ER+ breast cancer. In parallel, to identify mechanisms of resistance to endocrine therapy in breast cancer, we performed an epigenome CRISPR/CAS9 knockout screen that identified ARID1A as the top candidate whose loss determines resistance to the ER degrader fulvestrant. ARID1A knockout cells were found to be less responsive to endocrine therapy compared to intact ARID1A cells in vitro and in vivo. This set of observations in patients’ tumours and in unbiased CRISPR screens led us to explore the epigenetic mechanisms whereby loss of ARID1A may influence breast cancer progression and/or endocrine therapy resistance. ARID1A disruption in ER+ breast cancer cells led to widespread changes in chromatin accessibility converging on loss of the master transcription factors (TFs) that regulate gene expression programs critical for luminal lineage identity. Global transcriptome profiling of ARID1A knockout cell lines and patient samples harbouring ARID1A inactivating mutations revealed an enrichment for basal-like gene expression signatures. The state of increased cellular plasticity of luminal cells that acquire a basal-like phenotype upon ARID1A inactivation is enabled by loss of ARID1A-dependent SWI/SNF complex targeting to genomic sites of the major luminal-lineage determining transcription factors including ER, FOXA1, and GATA3. We also show that ARID1A regulates genome-wide ER-chromatin interactions and ER-dependent transcription. Altogether, we uncover a critical role for ARID1A in the determination of breast luminal cell identity and endocrine therapeutic response in ER+ breast cancer.

overall_design: RNA-seq assay was performed on MCF7 breast cancer cells expressing three distinct sgARID1As or two control sgRNAs

first: Eneda

last: Toska


title: Transcriptome profiling of adult mouse bone marrow endothelial cells

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

summary: We performed RNA sequencing analyses of adult mouse bone marrow endothelial cells. Especially, we investigated gene expression profiling of endothelial cells before and after lethal irradiation or hematopoietic cell depletion. We also analyzed mouse bone marrow endothelial cell subtypes, Apln+ and diaphyseal endothelial cells. Whole bone marrow cells, lineage negative hematopoietic stem and progenitor cells, Lin- Sca1+ cKit+ cells were used as controls for the differential gene expression analyses.

overall_design: Different adult mouse bone marrow cell populations were sorted by flowcytometry (FACS) for RNA sequencing

first: Ralf

middle: H

last: Adams

first: Qi

last: Chen

first: Yang

last: Liu


title: ARID1A is a critical regulator of luminal identity and therapeutic response in oestrogen receptor-positive breast cancer (ChIP-seq II)

overall_design: ChIP-se ssay was performed on MCF7 breast cancer cells expressing three distinct sgARID1As or two control sgRNAs in DMSO treated cells


title: Characterization of the transcriptional landscape of human developing hippocampus by ATAC-seq

city: Beijing

first: Suijuan

last: Zhong

state: Haidian

address: No.19 Xinjiekouwai Street

country: China

institute: Beijing Normal University

summary: Human hippocampus enabled further processing of higher brain functions. However, very little is known about human hippocampus development, which is largely accomplished during fetal stage. Our current study elucidates the transcriptomic profiling of the developing human fetal hippocampus using single-cell RNA-seq (scRNA-seq) and bulk atac-seq, allowing us to reconstruct the order of neurogenesis and their lineage relationships.

overall_design: ATAC sequencing of human fetal hippocampus.

last: ZHONG

first: Qian

last: WU

first: Xiaoqun

last: WANG


title: Erythroblasts from human cord blood

city: Chiba

first: Ryoko

last: Araki

address: Anagawa4-9-1, Inage-ku

institute: National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology

summary: Erythroblasts-rich fraction expanded from three healthy commercial available cord blood mononuclear cells were analyzed.

overall_design: Erythroblats from cord blood, CD34+ cells from cord blood and human dermal fibroblasts were used.

first: Masumi

last: Abe


title: ARID1A is a critical regulator of luminal identity and therapeutic response in oestrogen receptor-positive breast cancer (RNA-Seq)

overall_design: ATAC-seq assay was performed on MCF7 breast cancer cells expressing three distinct sgARID1As or two control sgRNAs in DMSO or fulvestrant treated cells


title: Decoding the development of the human hippocampus

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


title: Dysregulation of RNA splicing in tauopathies

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: Pathological aggregation of RNA binding proteins (RBPs) has emerged as an important driver of multiple neurodegenerative diseases. Since RBP aggregation may result in a loss of normal RBP function, we examined whether dysregulation of RNA metabolism contributes to tauopathies. We find that the PS19 P301S tau mouse model exhibits a dysregulation of RNA splicing that is also apparent upon analysis of human Alzheimer’s disease brain tissues. Dysregulated splicing particularly affected genes involved in synaptic transmission. We also analyzed alternative splicing in PS19 mice crossed to a heterozygous TIA1 background, which has recently been shown to slow disease progression. TIA1 reduction alleviated several of the most significant alternative splicing events for synaptic mRNA transcripts, suggesting that normalization of RBP functions is associated with the neuroprotection. We then used a systems biology approach termed NetDecoder to identify key upstream biological targets, including MYC and EGFR, underlying the transcriptional and splicing changes in the protected compared to tauopathy mice. Importantly, pharmacological inhibition of MYC and EGFR activity in primary neurons overexpressing tau recapitulated the neuroprotective effects of TIA1 reduction. These results demonstrate that dysfunction of RBPs and RNA splicing processes are major elements of the pathophysiology of tauopathies, and identify new potential therapeutic targets for tauopathies.

overall_design: Examination transcriptional profiles of TIA1_het and P301S tau mouse models.

first: Benjamin

last: Wolozin


title: ARID1A is a critical regulator of luminal identity and therapeutic response in oestrogen receptor-positive breast cancer (ATAC-Seq)


title: ARID1A is a critical regulator of luminal identity and therapeutic response in oestrogen receptor-positive breast cancer (ChIP-Seq)

overall_design: ChIP-seq assay was performed on MCF7 breast cancer cells expressing three distinct sgARID1As or two control sgRNAs in DMSO or fulvestrant treated cells

first: Cigall

last: Kadoch


title: Characterization of Zygotic Genome Activation-dependent Maternal mRNA Clearance in Mammals

status: Public on Nov 12 2019

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: A conserved event of the maternal-to-zygotic transition (MZT) in animal embryos is the elimination of a subset of the maternal transcripts that accumulated during oogenesis. In invertebrates and lower vertebrates, a maternally encoded mRNA decay pathway (M-decay) acts before zygotic genome activation (ZGA) while a second pathway, which requires zygotic transcription, subsequently clears additional mRNAs (Z-decay). To date it has not been clear whether a Z-decay pathway is present in mammals. Here, we identify mouse and human maternal transcripts that are degraded after ZGA and show that inhibition of de novo transcription stabilizes these mRNAs in mouse and human embryos. We show that YAP1-TEAD4 transcription factor-mediated transcription is essential for Z-decay in mouse embryos and that TEAD4-triggered zygotic Tut4/7 expression and mRNA 3ʹ-oligouridylation direct Z-decay.

overall_design: WT embryos at zygote and 2-cell stages, siTut4/7 embryos at 2-cell stage for three replicates are performed RNA sequencing.

first: Yezhang

last: Zhu


title: DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing

status: Public on Nov 10 2019

city: Philadelphia

first: Zilu

last: Zhou

address: 3730 Walnut St

institute: University of Pennsylvania

summary: We delineate subclonal expansion in a mouse melanoma models in response to immunotherapy, highlighting the role of neoantigens

overall_design: Examination of subclone differences by single cell RNA sequencing

first: Bihui

last: Xu


title: The MITF-SOX10 regulated long non-coding RNA DIRC3 is a melanoma tumour suppressor

status: Public on Nov 11 2019

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research

summary: The MITF and SOX10 transcription factors regulate the expression of genes important for melanoma proliferation, invasion and metastasis. Despite growing evidence of the contribution of long non-coding RNAs (lncRNAs) in melanoma and other cancers, their functions within MITF-SOX10 transcriptional programmes is poorly investigated. Here, we identify 245 candidate melanoma associated lncRNAs whose loci are co-occupied by MITF-SOX10 and are enriched at active enhancer-like regions. We characterise the function and molecular mechanism of action of one of these lncRNAs, Disrupted In Renal Carcinoma 3 (DIRC3), and show that it operates as a MITF-SOX10 regulated tumour suppressor. DIRC3 depletion in human melanoma cells leads to increased anchorage-independent growth, a hallmark of malignant transformation, whilst melanoma patients classified by low DIRC3 expression have decreased survival. DIRC3 is a nuclear lncRNA that functions locally to activate expression of its neighbouring IGFBP5 tumour suppressor through modulation of chromatin structure and suppression of SOX10 binding to putative regulatory elements within the DIRC3 locus. In turn, DIRC3 dependent regulation of IGFBP5 impacts the expression of genes important for cell metabolism, oxidative phosphorylation and cancer. Our work indicates that lncRNA components of MITF-SOX10 networks are an important new class of melanoma regulators and candidate therapeutic targets.

overall_design: 2 melanoma and 1 melanocyte cell lines were subjected to

first: Colin

middle: R

last: Goding


title: ARID1A is a critical regulator of luminal identity and therapeutic response in oestrogen receptor-positive breast cancer

first: Sagar

last: Chhangawala


title: RNA-seq analysis of SKMEL28 melanoma cells following DIRC3 and IGFBP5 ASO knockdown

status: Public on Nov 08 2019

city: Bath

first: Keith

middle: William

last: Vance

state: Somerset

address: University of Bath

department: Department of Biology and Biochemistry

institute: University of Bath

summary: We identified genes regulated by the DIRC3 long non-coding RNA and its neighbouring tumour suppressor gene IGFBP5 and determined common targets. DIRC3 and IGFBP5 were knocked down by transient transfection of antisense oligonucleotides (ASOs) in the human melanoma cell line Sk-Mel-28. RNA was extracted 72 hours after transfection and polyA selected 150-bp paired end RNA sequencing was performed on the Illumina HiSeq4000 .

overall_design: Comparison of DIRC3 and IGFBP5 ASO knockdown in melanoma cell line SKMEL28

first: Elizabeth

last: Coe

first: Michael

last: Shapiro


title: Different class IIa HDACs repressive complexes regulate specific epigenetic responses related to cell survival in leiomyosarcoma cells.

city: Udine

first: Emiliano

last: Dalla

state: UD

address: Piazzale Kolbe 4

department: Department of Medicine

institute: Università degli Studi di Udine

summary:
Purpose: Define the transcriptional networks supervising class IIa HDAC expression.
Outcome:  We demonstrate that MEF2D is the key factor controlling HDAC9 transcription. Comprehensive genome-wide studies demonstrate that HDAC4 and HDAC9 supervise different genetic programs and show both specific and common genomic bindings. Although the number of MEF2-target genes commonly regulated is similar, only HDAC4 represses many additional genes that are not MEF2D targets. HDAC4-/- and HDAC9-/- cells increase H3K27ac levels around the TSS of the respective repressed genes. However, these genes rarely show bindings of the HDACs at their promoters. Frequently HDAC4 and HDAC9 bind intergenic regions. We demonstrate that these regions, recognized by MEF2D/HDAC4/HDAC9 repressive complexes, show the features of active enhancers.

overall_design: Examination of the H3K27ac histone modification and of MEF2, HDAC4 and HDAC9 binding in SK-UT-1 Leiomyosarcomas cells (WT and HDAC4 or HDAC9 null, mutated using the CRISPR/Cas9 technology).

first: C

last: Brancolini

first: E

last: Di Giorgio


title: Characterization of the transcriptional landscape of human developing hippocampus by scRNA-seq

first: Suijuan

last: Zhong

summary: Human hippocampus enabled further processing of higher brain functions. However, very little is known about human hippocampus development, which is largely accomplished during fetal stage. Our current study elucidates the transcriptomic profiling of the developing human fetal hippocampus using single-cell RNA-seq (scRNA-seq), allowing us to reconstruct the order of neurogenesis and their lineage relationships.

overall_design: Single cell RNA sequencing for 30416 cells from 7 human fetal hippocampus.

first: S

first: Q

last: Wu

first: X

last: Wang


title: RNA-seq analysis of the Innate Lymphoid Cells type 2 (ILC2) or their precursors (ILC2p ) sorted from WT and Tgfbr2-/- mice

status: Public on Nov 09 2019

city: Bethesda

first: Peter

last: Zanvit

email: peter.zanvit@nih.gov, wailim.ku@nih.gov

state: Maryland

address: 30 Convent Drive

department: NIDCR

institute: NIH

summary:
Purpose: The molecular pathways underlying the development of innate lymphoid cells (ILCs) are mostly unknown.
Results: TGF-β signaling programs the development of ILC2s from their progenitors. Specifically, the deficiency of TGF-β receptor II in bone marrow progenitors results in inefficient development of ILC2s, but not ILC1s or ILC3s. We found that hundreds of genes were changed in Tgfbr2-/- ILC2s compared to WT ILC2s (FDR < 0.1 and Fold-Change >1.5). Some ILC2-associated genes including Gata3, Il1rl1 (ST2), Il-5, Atxn1 (Sca1), and Ccr4 were decreased in Tgfbr2-/- ILC2s, according to RNA-seq analysis
Conclusions: TGF-β upregulates the expression of the IL-33 receptor gene Il1rl1 (encoding IL-1 receptor-like 1, also known as ST2) in ILC2p and common helper-like innate lymphoid progenitors (CHILP), at least partially through the MEK-dependent pathway. These findings identify a function of TGF-β in the development of ILC2s from their progenitors.

overall_design: Lamina propria CD45+Lin–CD127+Sca–1+CD25+KIRG1+ ILC2 cells were sorted from tamoxifen or oil-treated Tgfbr2f/fER-Cre+ mice. Bone marrow CD45.2+Lin–CD127+α4β7+CD25+ ILC2p cells were sorted from Tgfbr2-/-/45.1 or Control/45.1 chimeras. RNA was extracted using RNeasy Plus Micro Kit (QIAGEN), and RNA-seq experiments were performed.

first: Li

first: Wai

middle: L

last: Ku

first: Wanjun

last: Chen

first: Keji

last: Zhao


title: Transcription factor Bach2 attenuates T cell receptor induced transcription to control regulatory T cell differentiation and homeostasis [RNA-seq II]

status: Public on Nov 07 2019

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

institute: Monash University

summary: The differentiation and homeostasis of Foxp3+ regulatory T (Treg) cells is strictly controlled by T cell receptor (TCR) signals; however, the molecular regulators of these processes are incompletely known. Here we found that Bach2 was a key regulator of Treg cell differentiation and homeostasis downstream of TCR signalling. Bach2 prevented premature differentiation of fully suppressive effector (e)Treg cells, limited IL-10 production and was required for the development of peripherally induced (p)Treg cells in the gastrointestinal tract. We found that Bach2 attenuated TCR signalling-induced and IRF4-dependent Treg cell differentiation programs. Deletion of IRF4 promoted inducible Treg cell differentiation and rescued pTreg cell differentiation in the absence of Bach2. In turn, loss of Bach2 normalised eTreg cell differentiation of IRF4-deficient Treg cells. Mechanistically, Bach2 counteracted DNA-binding activity of IRF4 and limited chromatin accessibility, thereby attenuating IRF4-dependent transcriptional programs. Thus, Bach2 balanced TCR signalling induced transcriptional activity of IRF4 to maintain Treg cell homeostasis.

overall_design: RNA-sequencing of flow cytometrically sorted splenic Treg cells from Bach2-flox/Foxp3-cre or Foxp3-cre control mice

first: Tom

last: Sidwell

first: Yang

last: Liao

first: Axel

last: Kallies


title: Transcription factor Bach2 attenuates T cell receptor induced transcription to control regulatory T cell differentiation and homeostasis [ChIP-seq]

overall_design: ChIP-sequencing of flow cytometrically sorted naïve CD4 T cells following culture for 72 hours in Treg cell inducing conditions

first: Alex

last: Garnham

first: Gordon

last: Smyth


title: Life-long impairment of glucose homeostasis upon prenatal exposure to psychostimulants.

city: Vienna

first: Tibor

last: Harkany

address: Spitalgasse 4

department: Department of Molecular Neurosciences (Center for Brain Research)

country: Austria

institute: Medical University of Vienna

type: Methylation profiling by high throughput sequencing

summary:
Abstract: Maternal drug abuse during pregnancy is a rapidly escalating societal problem. Psychostimulants, including amphetamine, cocaine and methamphetamine, are amongst the illicit drugs most commonly consumed by pregnant women. Neuropharmacology concepts posit that psychostimulants affect monoamine signaling in the nervous system by their affinities to neurotransmitter reuptake and vesicular transporters to heighten neurotransmitter availability extracellularly. Exacerbated dopamine signaling is particularly considered as a key determinant of psychostimulant action. Much less is known about possible adverse effects of these drugs on peripheral organs, and if in utero exposure induces life-long pathologies. Here, we addressed this question by combining human RNA-seq data with cellular and mouse models of neuroendocrine development. We show that episodic maternal exposure to psychostimulants during pregnancy coincident with the intrauterine specification of pancreatic β cells permanently reduces their ability of insulin production, leading to glucose intolerance in adult female but not male offspring. We link psychostimulant action specifically to serotonin signaling and implicate the sex-specific epigenetic reprogramming of serotonin-related gene regulatory networks upstream from the transcription factor Pet1/Fev as determinants of reduced insulin production.

Synopsis: The abuse of illicit drugs is a major societal problem, including their continued use during pregnancy. Even though harmful effects of commonly-used psychostimulants to the unborn fetus have been postulated, if and how maternal exposure to illicit psychostimulants during pregnancy could reprogram the fetal pancreas and limit glucose metabolism and tolerance for life in affected offspring remain unknown. Here, we combine human and mouse data to outline the sex-specific epigenetic deregulation of serotonin signaling-related gene regulatory networks, which leads to reduced insulin production postnatally.

•        As little as episodic intrauterine psychostimulant exposure is sufficient to permanently limit beta cell function in postnatal female rather than mouse male offspring.
•        The serotonin transporter, rather than the dopamine transporter, is identified as a molecular target of psychostimulants in fetal beta cells and in beta cell-like cellular models.
•        Psychostimulants adversely affect protein serotonylation in beta-cell models.
•        Altered DNA methylation and accessibility link the life-long deregulation of transcription factors and genes shaping serotonin signaling with reduced functionality in beta cells.

overall_design: We studied the DNA methylation landscape in P0 pancreata of mice of both sexes from amphetamine-treated and control dams.

first: Solomiia

last: Korchynska

first: Maria

last: Krassnitzer

first: Katarzyna

last: Malenczyk

first: Rashmi

middle: B

last: Prasad

first: Evgenii

middle: O

last: Tretiakov

first: Sabah

last: Rehman

first: Valentina

last: Cinquina

first: Victoria

last: Gernedl

first: Matthias

last: Farlik

first: Julian

last: Petersen

first: Sophia

last: Hannes

first: Julia

last: Schachenhofer

first: Sonali

last: Reisinger

first: Alice

last: Zambon

first: Olof

last: Asplund

first: Isabella

last: Artner

first: Erik

last: Keimpema

first: Gert

last: Lubec

first: Jan

last: Mulder

first: Christoph

last: Bock

first: Daniela

middle: D

last: Pollak

first: Roman

last: Romanov

first: Christian

last: Pifl

first: Leif

last: Groop

first: Tomas

middle: G

last: Hökfele


title: Transcription factor Bach2 attenuates T cell receptor induced transcription to control regulatory T cell differentiation and homeostasis [RNA-seq]

first: Wei

last: Shi

overall_design: Transcriptional profiling of flow cytometrically sorted naïve CD4+ T cells from wildtype, Bach2-deficient, IRF4-deficient and Bach2/IRF4 double deficient mice, cultured in Treg cell inducing conditions for 0, 24 or 72 hours.

first: Tom

last: Sidwell

first: Yang

last: Liao

first: Alex

last: Garnham

first: Gordon

last: Smyth

first: Axel

last: Kallies


title: Lifecycle transcriptomics of field-droughted sorghum reveals rapid biotic and metabolic responses

city: Berkeley

first: Benjamin

middle: Jeremy

last: Cole

state: CA

address: 1, Cyclotron Road

institute: DOE-Joint Genome Institute

summary: We conducted a large-scale field experiment, imposing pre- and post-flowering drought stress on two genotypes of sorghum across a tightly-resolved time series, resulting in a data set of over 350 transcriptomes root and shoot tissue.

overall_design: RNA-seq on root and shoot tissue of Sorghum exposed to two drought regimes

first: Nelle

last: Varoquaux

first: Cheng

last: Gao

first: Grady

last: Pierroz

first: Christopher

last: Baker

first: Dhruv

last: Patel

first: Mary

last: Madera

first: Tim

last: Jeffers

first: Joy

last: Hollingsworth

first: Julie

last: Sievert

first: Yuko

last: Yoshinaga

first: Judith

last: Owiti

first: Vasanth

last: Singan

first: Stephanie

last: DeGraaf

first: Ling

last: Xu

first: Matthew

last: Blow

first: Maria

last: Harrison

last: Visel

first: Christer

last: Jansson

first: Krishna

middle: K

last: Niyogi

first: Robert

last: Hutmache

first: Devin

last: Coleman-Derr

first: Ronan

last: O’Malley

first: John

middle: W

last: Taylor

first: Jeffery

last: Dahlberg

last: Vogel

first: Peggy

last: Lemaux

first: Elizabeth

last: Purdom


title: Transcription factor Bach2 attenuates T cell receptor induced transcription to control regulatory T cell differentiation and homeostasis [ATAC-seq]

first: Wei

last: Shi

overall_design: ATAC-sequencing of flow cytometrically sorted naïve CD4 T cells following culture for 72 hours in Treg cell inducing conditions

first: Tom

last: Sidwell

first: Yang

last: Liao

first: Axel

last: Kallies


title: Gene expression change after JQ1 treatment in breast cancer cell

city: Guangzhou

first: Jian

state: Guangdong

address: 1023 South Shatai Road

department: Department of Pathology

institute: Southern Medical University

summary: BET bromodomain inhibitors effectively kill several types of cancer cells. However, the underlying mechanism of BET inhibition resistance remains obscure. We sought to identify the gene expression change upon treatment of JQ1, a well-known BET inhibitor, in basal-like breast cancer cells. In this dataset, we used RNA-sequencing to characterize the mRNA expression profiles from DMSO and JQ1-treated MDA-MB-231 breast tumor cells.

overall_design: Total RNA was extracted from JQ1-treated MDA-MB-231 cells for RNA sequencing. DMSO-treated MDA-MB-231 cells were used as control.

first: Shi

last: Jian


title: Transcription factor Bach2 attenuates T cell receptor induced transcription to control regulatory T cell differentiation and homeostasis [ATAC-seq II]

overall_design: ATAC-sequencing of splenic, activated and naïve, non-follicular, conventional and regulatory CD4+ T cell populations nine days following infection with influenzavirus (HKx31)

first: David

last: Chisanga


title: RiboTag enrichment of aBNST nociceptin neurons

status: Public on Nov 04 2019

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

institute: MRC London Institute of Medical Sciences

summary: We report the differential expression of genes in aBNST nociceptin neurons in comparison to the whole aBNST in mice

overall_design: We compare 2 populations (3 mice pooled per population) of aBNST RNA enriched in nociceptin neurons by viral targeted RiboTag. RiboTag enriched RNA is compared with total RNA from each population

first: Dominic

last: Withers


title: HaloTag-based conjugation of proteins to barcoding-oligonucleotides

city: Yokohama

first: Junshi

last: Yazaki

state: Kanagawa Prefecture

address: 1-7-22 Suehirocho, Tsurumi Ward,

institute: RIKEN

summary: We describe the development of a high-sensitivity protein quantification system called HaloTag protein barcoding assay. The assay involves target protein linking to a unique molecule-counting oligonucleotide by click chemistry.

overall_design: The assay involves target protein linking to a unique molecule-counting oligonucleotide by amido-bond or click chemistry.

first: Yusuke

last: Kawashima

first: Taisaku

last: Ogawa

first: Atsuo

last: Kobayashi

first: Mayu

last: Okoshi

first: Takashi

last: Watanabe

first: Suguru

last: Yoshida

first: Isao

last: Kii

first: Shohei

last: Egami

first: Masayuki

last: Amagai

first: Takamitsu

last: Hosoya

first: Katsuyuki

last: Shiroguchi

first: Osamu

last: Ohara


title: Transcription factor Bach2 attenuates T cell receptor induced transcription to control regulatory T cell differentiation and homeostasis

status: Public on Nov 06 2019

first: Wei

last: Shi

overall_design: Refer to individual Series


title: RNA sequencing of uninfected, H37Rv- or Rv0222Ko-infected mouse peritoneal macrophages

status: Public on Nov 03 2019

city: Shanghai

first: Lin

last: Wang

address: 507 Zhengmin Road

institute: Shanghai Pulmonary Hospital

summary: RNA sequencing for 6 samples

overall_design: Examing 3 conditions (uninfected, H37Rv and Rv0222Ko), each with 2 replicates

first: Baoxue

last: Ge


title: RNA-seq data of small cell carcinoma of the bladder (SCCB) /urothelial carcinoma (Non-SCCB) clinical samples, and bladder-PARCB cell lines

status: Public on Nov 02 2019

city: Los Angeles

first: Liang

address: 675 Charles E Young Dr

department: MIMG

institute: UCLA

summary: SCCB or Non-SCCB samples are collected from Archived FFPE

first: Bryan

middle: A

last: Smith

first: Owen

last: Witte

first: Arnold

middle: I

last: Chin

first: Jung

last: Park


title: High nuclease activity of long persisting Staphylococcus aureus isolates within the airways of cystic fibrosis patients protects against NET- mediated killing

status: Public on Nov 01 2019

city: Braunschweig

first: Diego

last: Chaves-Moreno

address: inhoffenstrasse 7

department: Department of Medical Microbiology (MMIK)

institute: Helmholtz Centrum for Infection Research

summary: Staphylococcus aureus is one of the first and most prevalent pathogens cultured from the airways of cystic fibrosis (CF) patients, which can persist there for extended periods. Airway infections in CF patients are characterized by a strong inflammatory response of highly recruited neutrophils. One killing mechanism of neutrophils is the formation of neutrophil extracellular traps (NETs), which capture and eradicate bacteria by extracellular fibers of neutrophil chromatin decorated with antimicrobial granule proteins. S. aureus secretes nuclease, which can degrade NETs. We hypothesized, that S. aureus adapts to the airways of CF patients during persistent infection by escaping from NET-mediated killing via an increase of nuclease activity. Sputum samples of CF patients with chronic S. aureus infection were visualized by confocal microscopy after immuno-fluorescence staining for NET-specific markers, S. aureus bacteria and overall DNA structures. Nuclease activity was analyzed in sequential isogenic long persisting S. aureus isolates, as confirmed by whole genome sequencing, from an individual CF patient using a FRET-based nuclease activity assay. Additionally, some of these isolates were selected and analyzed by qRT-PCR to determine the expression of nuc1 and regulators of interest. NET-killing assays were performed with clinical S. aureus isolates to evaluate killing and bacterial survival depending on nuclease activity. To confirm the role of nuclease during NET-mediated killing, a clinical isolate with low nuclease activity was transformed with a nuclease expression vector (pCM28nuc). Furthermore, two sputa from an individual CF patient were subjected to RNA-sequence analysis to evaluate the activity of nuclease in vivo. In sputa, S. aureus was associated to extracellular DNA structures. Nuclease activity in clinical S. aureus isolates increased in a time-and phenotype-dependent manner. In the clinical isolates, the expression of nuc1 was inversely correlated to the activity of agr and was independent of saeS. NET-mediated killing was significantly higher in S. aureus isolates with low compared to isolates with high nuclease activity. Importantly, transformation of the clinical isolate with low nuclease activity with pCM28nuc conferred protection against NET-mediated killing confirming the beneficial role of nuclease for protection against NETs. Also, nuclease expression in in vivo sputa was high, which underlines the important role of nuclease within the highly inflamed CF airways. In conclusion, our data show that S. aureus adapts to the neutrophil-rich environment of CF airways with increasing nuclease expression most likely to avoid NET-killing during long-term persistence.

overall_design: RNAseq from sputum samples of CF patients collected during their clinical visits

first: Susann

last: Herzog

first: Felix

last: Dach

first: Nicole

last: de Buhr

first: Silke

last: Niemann

first: Jannik

last: Schlagowski

first: Claudia

last: Neumann

first: Jonas

last: Goretzko

first: Angelika

last: Dübbers

first: Peter

last: Küster

first: Holger

last: Schültingkemper

first: Dietmar

last: Pieper

first: Maren

last: Von Köckritz-Blickwede

first: Barbara

last: Kahl


title: Role of Mineralocorticoid Receptor (Nr3c2) in Adipogenesis and Obesity in Male Mice

city: St Louis

first: Charles

last: Harris

state: MO

address: 660 S. Euclid Ave

institute: Washington University School of Medicine in St. Louis

summary:
Increased visceral adiposity and hyperglycemia, two characteristics of metabolic syndrome, are also present in conditions of excess glucocorticoids (GCs). GCs are hormones thought to act primarily via the glucocorticoid receptor (GR). GCs are commonly prescribed for inflammatory disorders, yet their use is limited due to many adverse metabolic side effects. In addition to GR, GCs also bind the mineralocorticoid receptor (MR), but there are many conflicting studies as to the exact role of MR in metabolic disease.  Using MR knockout mice (MRKO), we find that both white and brown adipose depots form normally when compared to wild-type mice at P5.  We created mice with adipocyte-specific deletion of MR (FMRKO) to better understand the role of MR in metabolic dysfunction.  Treatment of mice with excess GCs for 4 weeks, via corticosterone in drinking water, induced increased fat mass and glucose intolerance to similar levels in FMRKO and floxed-control mice.  Separately, when fed a high-fat diet for 16 weeks, FMRKO mice had reduced body weight, fat mass, and hepatic steatosis, relative to floxed-control mice.  Decreased adiposity likely resulted from increased energy expenditure since food intake was not different.  RNA sequencing analysis revealed decreased enrichment of genes associated with adipogenesis in inguinal white adipose of FMRKO mice.  Differentiation of mouse embryonic fibroblasts (MEFs), showed modestly impaired adipogenesis in MRKO MEFs compared to wild-type, but this was rescued upon the addition of peroxisome proliferator-activated receptor gamma (PPARγ) agonist or PPARγ overexpression.  Collectively, these studies provide further evidence supporting the potential value of MR as a therapeutic target for conditions associated with metabolic syndrome.
Method (Chow): At six weeks of age mice were maintained on a chow diet (PicoLab® Rodent Diet 20 5053* [20% protein]) for 16 weeks
Method (High Fat Diet): 6 week-old mice were fed ab libitum with Teklad TD.88137 (21.2% fat [42% kcal fat], 48.5% carbohydrate [34% sucrose by weight], 17.3% protein, and 0.2% cholesterol by weight) for 16 weeks
Method (Corticosterone): 10-11-week-old mice were administered corticosterone via drinking water (100 μg/mL) for 4 weeks, while maintained on a chow diet

overall_design: Examination of inguinal white adipose from Nr3c2-floxed-control (control) and Nr3c2-floxed Adipoq-Cre+ (fat-specific mineralocorticoid receptor knockout, FMRKO) mice on chow diet, high fat diet, or corticosterone-treatment (n=4/group)

first: Daniel

last: Ferguson


title: Gene expression from tuft cells under scopolamine treatment

city: Munich

first: Hans

middle: Carlo

last: Maurer

state: Bavaria

address: Ismaninger Str. 22

department: II. Medizinische Klinik

institute: Klinikum rechts der Isar

summary: In our study, we investigated the effect of muscarinic receptor blockade on murine intestinal stem cell activity and differentiation. Following pharmacologic (scopolamine) and genetic muscarinic receptor interruption (M3R-KO, M1R-KO; Vil-Cre x M3R fl/fl, Vil-Cre x M1R fl/fl mice, respectively), we observe a selective, significant expansion of DCLK1-positive tuft cells. This is primarily sensed by endocrine Prox1-positive cells (Prox1-CreERT2 x M3R fl/fl mice), while Lgr5-positive ISCs respond with a reduction of their cellular activity (Lgr5-EGFP-IRES-CreERT2 x M3R fl/fl mice). To characterize expanding tuft cells in more detail, adult BAC transgenic DCLK1-DTR-ZSgreen reporter mice generated in our lab were treated with scopolamine or sodium chloride as controls (Sham) for 7d and live jejunal EPC-positive/ZSgreen-positive cells sorted. Extracted total RNA from sorted ZSgreen-positive cells of scopolamine- and sham-treated mice was sequenced. Further analysis revealed that expanding tuft cells orchestrate an increase in mucosal acetylcholine, which maintained intracellular signaling pathways such as p-ERK/ERK 1/2 or TCF-1/7. Finally, acute irradiation injury was employed to investigate the importance of this regulatory circuit for tissue homeostasis. Indeed, tissue injury in Vil-Cre x M3R fl/fl mice resulted in a severe reduction of epithelial DCLK1-positive tuft cells, concomitant to reduced mucosal Ach levels as well as intracellular PI3K-/p-ERK levels. Therefore, DCLK1-positive tuft cells appear essential for the maintenance of a regular intestinal cholinergic niche.

overall_design: Bulk gene expression data are presented for sorted DCLK1-DTR-ZSgreen-positive cells from scopolamine treated mice (n=4) or sham treated mice (n=4).

first: Moritz

last: Middelhoff

first: Henrik

last: Nienhüser

first: H

first: Timothy

last: Wang


title: AIB1 and TEAD ChIP-seq

city: Washington

first: Max

middle: Harley

last: Kushner

state: DC

address: 3970 Reservoir Rd NW, NRB E311

department: Oncology

institute: Georgetown University

summary: We report the global occupancy by ChIP-seq of AIB1 and TEAD4 in normal mammary epithelial cells (MCF10A). We performed ChIP and library preparation with the ActiveMotif Low Cell ChIP-seq kit. Data was aligned to Hg38 with BWA-MEM, data was sorted and de-duplicated with SAMTOOLS, and peaks were called with MACS2. Analysis was done with ChIP-seeker in R.

overall_design: Examination of ChIP-seq of 2 target proteins in triplicate, normalized to cell lysate input.

first: Anna

middle: T

last: Riegel


title: Integrative discovery of treatments for high-risk neuroblastoma

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

summary: Neuroblastoma (NB) cells exhibit a complex spectrum of pathway changes associated with oncogene activation, chromosome events, tumor micro-environment and super-enhancer states.  So far, elucidating which pharmaceutical compounds could modulate the activation level of each known pathway in NB cells has not been feasible. We treated 2 patient-derived xenograft (PDX) NB cell lines with different chemical compounds, at 3 different doses (IC50, IC20, and IC10) and 2 time-points (6 and 24h). The whole-transcriptome of the treated cells was analyzed by a cost-effective DRUG-Seq method. Using factor analysis and supervised machine learning, the data was used to build a model that predicts the NB-specific outcome of 19,000+ drugs studied in other (non-NB) cell lines in several drug profiling databases (LINCS, CMap, DepMap).

overall_design:
Two patient-derived xenograft (PDX) NB cell lines treated with different chemical compounds, at 3 different doses (IC50, IC20, and IC10) and 2 time-points (6 and 24h).

Please note that the D1, D2, and D3 (in the sample titles) correspond to IC10, IC20, and IC50, respectively.

first: Elin

last: Almstedt

first: Michael

last: Vanlandewijck

first: Sven

last: Nelander


title: Analysis of RNA-binding protein PSF- and NONO-associated transcripts in breast cancer

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

summary: To examine the role of PSF and NONO in breast cancer cells, PSF- and NONO- associated transcripts were co-immunoprecipitated with PSF and NONO antibodies, respectively. Purified RNAs were analyzed with NGS.

overall_design: Estrogen receptor (ER)-positive breast cancer MCF-7 were treated with 17beta-estradiol (E2) or control vehicle (ethanol), and RNA-binding protein complexes were immunoprecipitated with PSF or NONO antibody, or control IgG. NONO-RNA complexes in ER-negative MDA-MB-231 cells were immunoprecipitated with PSF or NONO antibody or control IgG.

first: Yuichi

last: Mitobe

first: Kaori

last: Iino

first: Kazuhiro

last: Ikeda

first: Kuniko

last: Horie-Inoue

first: Satoshi

last: Inoue


title: Human buffy coat gene expression, custom 250-plex Nanostring panel

city: Rockville

first: Jeffrey

last: Robinson

state: United States

address: 9630 Gudelsky Dr

department: Translational Life Sciences Technology

institute: UMBC

summary:
Buffy coat PBMC RNA expression was tested using a custom Nanostring probe panel, to identify general immune and glucocorticoid receptor-associated immune genes.

ClinicalTrials.gov Identifier: NCT00824941

overall_design:
Buffy coat samples were collected using Lymphoprep density gradient protocol, total RNA extracted with miRVana kit.

Custom 250-plex "ImmunoGC" panel selected genes for: 1) reported glucocorticoid immune responsiveness, 2) immune-cell type specific expression, 3) microRNA processing, and 4) putative stress-associated biomarkers.

first: Wendy

last: Henderson

first: Simon

last: Turkington

first: Christina

last: Boulineaux


title: mRNA-sequencing of 293T-no dice transfected with miR-16, miR-214, or KSHV-miR-K6-5p

city: Chicago

first: Eva

middle: Henriette

last: Gottwein

state: IL

address: 320 E Superior St., Tarry building, Room 6-752

department: Microbiology-Immunology

institute: Northwestern University

summary: The viral miRNA miR-K6-5p encoded by the DNA tumor virus Kaposi’s sarcoma-associated herpesvirus exhibits offset, sequence similarity with the tumor suppressive cellular miR-15/16 family, as well as sharing a short seed match to the cellular miR-214 (nts 2-7). We investigated how gene regulation by the viral miR-K6-5p is related to regulation by these cellular miRNAs by performing transcriptome analysis. mRNA-Seq was done in HEK 293T NoDice cells (Bogerd et al., RNA 2014) lacking Dicer which severely impaired the maturation of miRNAs thereby eliminating confounding effects of endogenously expressed miR-15/16 family. We transfected mature miRNA mimics of miR-16, miR-K6-5p wild-type, a variant of miR-K6-5p with a U at nt 1 instead of a C to control of RISC loading (miR-K6 5’U), miR-214, or a control mimic into NoDice cells, and harvested total RNA 2 days post-transfection.

overall_design: Gene expression changes due to expression of miR-16, miR-214, KSHV-miR-K6-5p were measured by mRNA-sequencing


title: BLISTER safeguards the protein kinase activity of ER stress modulator IRE1A during plant growth and development in Arabidopsis thaliana

city: shanghai

first: zhenghui

last: hong

state: --- Select a state ---

address: dongchuan road NO.800

department: life of science

institute: shanghai jiaotong university

summary: BLI tightly controls the protein kinase activity of IRE1A in plants,and IRE1A plays new roles in plant growth and development

overall_design: Totally 12 samples with four genotypes ,both of which are in triplicates.

first: Zhenghui

last: Hong

first: Jian-Xiang

last: Liu


title: Role of cis-zeatin in root responses to phosphate starvation

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

institute: Centro de Biotecnología y Genómica de Plantas

summary: In this work we show that root illumination influences Pi starvation response, enhancing the root and shoot growth arrest and limiting the root/shoot ratio as well as root hair elongation.  A transcriptomic study in dark-grown roots (DGR) roots identifies several genes that respond to Pi deficiency that were not previously reported. Hormone profiling revealed that Pi starvation reduces the level of trans-Zeatin (tZ) but significantly increases the amount of cis-Zeatin (cZ) and cis-Zeatin Riboside (cZR). We have analyzed the transcriptomic response of Arabidopsis roots to phosphate starvation combined with cis- or trans-zeatin treatments for 8 hours.

overall_design: Random sequencing of poly A RNA from Arabidopsis thaliana wild type roots grown with or withoput phosphate and  treated with cis- or trans-zeatin for 8 hours. Demultiplex trimmed reads.

middle: C


title: Expression data from human keratinocytes after scratch wounds in vitro

first: Helena

last: Topouzi

address: Royal School of Mines, Imperial College, Prince Consort Road

institute: Imperial College London

summary:
In skin homeostasis, dermal fibroblasts are responsible for coordinating the migration and differentiation of overlying epithelial keratinocytes. As hairy skin heals faster than non-hairy skin, we hypothesised that follicular fibroblasts would accelerate skin re-epithelialisation after injury faster than interfollicular fibroblasts. We found that hair follicle dermal papilla fibroblast conditioned media (DPFi CM) could significantly accelerate wound closure compared to controls partly due to the presence of sAXL in this media.
We used microarrays to identify upregulated and downregulated genes in human epidermal keratinocytes incubated with sAXL, DPFi CM and Epilife (keratinocyte growth media;control) after scratch wounds in vitro.

overall_design: 6 well plates were prepared by coating them using the coating matrix kit. Keratinocytes from two patients were seeded at a density of 6000 cells/cm2 using Epilife supplemented with EDGS. At confluency, a p200 pipette tip was used to scratch the well in 4 different regions (in a hashtag), to create a ‘wound’ in the cells. The cells were then washed two times with PBS to remove debris. Conditioned media obtained from DPFi, sAXL, and control with just Epilife supplemented with EDGS were added on the wounded cells. After 6 hours, media was removed, cells were washed in PBS, then RNA was collected using the RNeasy Plus Micro Kit (Qiagen). RNA was used to synthesize first-strand complementary DNA (cDNA) using Nugen Ovation V2. This was then converted to double-stranded cDNA, and used as a template for in vitro transcription to generate cRNA using the Nugen Encore Biotin Module. The cRNA was then transferred for hybridization and scanning onto the GeneChip™ Human Genome U133 Plus 2.0 Array.

first: Claire

last: Higgins


title: Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations [ChIP-Seq]

city: Cambridge

first: Charles

last: Fulco

state: MA

address: 415 Main Street

institute: Broad Institute

summary: Mammalian genomes harbor millions of noncoding elements called enhancers that quantitatively regulate gene expression, but the mechanisms that determine which enhancers regulate which genes are not well understood. Here we describe a high-throughput approach, based on CRISPR interference, RNA FISH, and flow cytometry (CRISPRi-FlowFISH), to perturb enhancers in the genome and apply it to test >3,000 potential regulatory enhancer-gene connections across multiple genomic loci. Seemingly complex patterns of enhancer-gene connections in this dataset can largely be explained by a simple quantitative Activity-by-Contact (ABC) model, in which the effect of a candidate enhancer on a target gene is predicted by the intrinsic activity of the enhancer multiplied by the contact frequency between the enhancer and promoter. This ABC score can identify regulatory enhancer-gene connections and predict their quantitative effects from DNase-Seq, H3K27ac ChIP-seq, and Hi-C measurements. The ABC model can explain even complex regulatory phenomena including the ability of an enhancer to “skip” over one gene to regulate a more distant one. Our approach provides a foundation for dissecting mechanisms of enhancer-gene regulation and predicting enhancer-gene connections across cell types.

overall_design: H3K27ac ChIP-seq was used to profile F2-1 mESCs in 2 technical replicates.

middle: P

first: Joseph

last: Nasser

first: Thouis

last: Jones

first: Glen

last: Munson

first: Drew

last: Bergman

first: Vidya

last: Subramanian

first: Sharon

middle: R

last: Grossman

first: Rockwell

last: Anyoha

first: Tejal

last: Patwardhan

first: Tung

middle: H

last: Nguyen

first: Michael

last: Kane

first: Benjamin

last: Doughty

first: Elizabeth

middle: M

last: Perez

first: Neva

last: Durand

first: Elena

last: Stamenova

first: Erez

middle: L

last: Aiden

first: Eric

middle: S

last: Lander

first: Jesse

last: Engreitz


title: Effect of wrky47 mutation on gene expression in roots

city: Hangzhou

first: Zhong Jie

last: Ding

address: 866# Yuhangtang Rd

institute: Zhejiang University

summary: To identify the potential downstream genes that are regulated by WRKY47 under control or Al treatment.

overall_design: Root samples from WT and wrky47-1 with control or Al treatment

first: Zhong

middle: J


title: The role of plasticity and adaptation on in the incipient speciation of a fire salamander population

status: Public on Oct 31 2019

first: Joana

last: Sabino Pinto

address: Mendelsohnstrasse 4

institute: Technische Universität Braunschweig, Zoologisches Institute

summary: Phenotypic plasticity and local adaptation via genetic change are two major mechanisms of response to dynamic environmental conditions. These mechanisms are not mutually exclusive, since genetic change can establish similar phenotypes to plasticity. This connection between both mechanisms raises the question of how much of the variation observed between species or populations is plastic and how much of it is genetic. In this study, we used a structured population of fire salamanders (Salamandra salamandra), in which two subpopulations differ in terms of physiology, genetics, mate-, and habitat preferences. Our goal was to identify candidate genes for differential habitat adaptation in this system, and to explore the degree of plasticity compared to local adaptation. We therefore performed a reciprocal transfer experiment of stream- and pond-originated salamander larvae and analyzed changes in morphology and transcriptomic profile (using species-specific microarrays). We observed that stream- and pond-originated individuals diverge in morphology and gene expression. For instance, pond-originated larvae have larger gills, likely to cope with oxygen-poor ponds. When transferred to streams, pond-originated larvae showed a high degree of plasticity, resembling the morphology and gene expression of stream-originated larvae (reversion); however the same was not found for stream-originated larvae when transferred to ponds, where the expression of genes related to reduction-oxidation processes was increased, possibly to cope with environmental stress. The lack of symmetrical responses between transplanted animals highlights the fact that the adaptations are not fully plastic and that some level of local adaptation has already occurred in this population. This study illuminates the process by which phenotypic plasticity allows local adaptation to new environments and its potential role in the pathway of incipient speciation.

overall_design: Expression data from: 16 individuals from ponds kept in ponds; 18 individuals from ponds translocated to streams; 13 individuals from streams translocated to ponds; 11 individuals from streams kept in streams; 7 free-swimming pond individuals not manipulated;  7 free-swimming stream individuals not manipulated.

last: Sabino-Pinto

first: Daniel

last: Goedbloed

first: Eugenia

last: Sanchez

first: Till

last: Czypionka

first: Arne

middle: W

last: Nolte

first: Sebastian

last: Steinfartz


title: ABCA7 haplodeficiency disrupts microglial inflammatory responses and membrane trafficking

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary: Carrying premature termination codons in one allele of the ABCA7 gene is associated with an increased risk for Alzheimer’s disease (AD). While the primary function of ABCA7 is to regulate the transport of phospholipids and cholesterol, ABCA7 is also involved in maintaining homeostasis of the immune system. Since inflammatory pathways causatively or consequently participate in AD pathogenesis, we studied the effects of Abca7 haplodeficiency in mice on brain immune responses under acute or chronic conditions. When the acute inflammation was induced through peripheral lipopolysaccharide (LPS) injection in control or heterozygous Abca7 knockout mice, partial ABCA7 deficiency diminished pro-inflammatory responses by impairing CD14 expression in the brain.

overall_design: We used Abca7 heterozygous and control mice. To investigate the relationship between Abca7 and inflammation in the brain, we injected lipopolysaccharide (LPS) into mice and then sacrificed the brains from these mice. Total RNAs of cortical brain were sequenced with Illumina HiSeq 4000 and Reads were mapped to the mouse genome mm10. Raw gene read counts, along with sequencing quality control, were generated using the Mayo Clinic RNA-sequencing analytic pipeline, MAP-RSeq Version 2.1.1.

first: Tomonori

last: Aikawa

first: Yu

last: Yamazaki

first: Masaya

last: Tachibana

first: Madeleine

last: Johnson

first: Casey

last: Anderson

first: Yuka

last: Martens

first: Marie-Louise

last: Holm

first: Yan

last: Asmann

first: Takashi

last: Saito

first: Takaomi

last: Saido

last: Fitzgerald

first: Guojun

last: Bu

first: Takahisa

last: Kanekiyo


title: Molecular characterization of a toxicological tipping point in human induced pluripotent stem cell (hiPSC)-derived endoderm exposed to all-trans retinoic acid (ATRA)

city: Research Triangle Park

first: Thomas

last: Knudsen

state: NC

address: 109 T.W. Alexander Drive (D-143-02)

department: NCCT/ORD

institute: US EPA

summary: Embryonic development commences with the formation of three germ layers from the primitive streak during gastrulation. The endoderm layer gives rise to the gut tube, leading to development of several internal organs, including the thyroid, thymus, lungs, stomach, liver, pancreas, and intestines. We differentiated human induced pluripotent stem cells (hiPSCs) to embryonic endoderm and sought to identify a tipping point at which the developing system did not recover from perturbations caused by exposure to a known teratogen, all-trans retinoic acid (ATRA). Differentiating iPSC-derived endoderm was exposed to five concentrations of ATRA between 0.001 and 10 µM at 6h, 96h, or 192h and assessed for forkhead box A2 (FOXA2) protein expression and global gene transcript expression measured by RNA-sequencing. A tipping point of 17±11 nM was identified where patterns of differentially expressed genes supported a shift in the developmental trajectory away from embryonic endoderm in favor of mesoderm and extraembryonic endoderm.

overall_design: Five concentrations of all-trans retinoic acid (ATRA) between 0.001 and 10 µM were compared to time-matched 0.1% DMSO controls at three timepoints (6h, 96h, and 192h) in differentiating endoderm. Two biological replicates were used. Undifferentiated controls (not in DMSO) were also included in duplicate as internal controls for 6h, 96h, and 144h.

first: Katerine

last: Saili

first: Todor

last: Antonijevic

first: Todd

last: Zurlinden

first: Imran

last: Shah

first: Chad

last: Deisenroth

middle: B


title: RNA-seq of cortical brain from Grin1-exon5 constitutive vs. Grin1-exon5 knockout mice

city: Toronto

first: Michael

last: Salter

state: Ontario

address: 686 Bay Street

department: Neurosciences & Mental Health

country: Canada

institute: Hospital for Sick Children

summary: Here we report bulk RNA transcriptomes of cortical brains from transgenic mice from Grin1-exon5 constitutive vs. Grin1-exon5 knockout mice. Physiologically, Grin1-exon5 positive mice have reduced hippocampal LTP (vs. WT) and are learning and memory (vs. WT) impaired compared to Grin1-exon5 negative mice that have heightened LTP (compared to WT) and better learning and memory (compared to WT).

overall_design: Cortex from adult mice were sequenced using standard Illumina protocols.

first: Ameet

last: Sengar

first: Honbin

last: Li

first: Wenbo

last: Zhang

first: Celeste

last: Leung

first: Arun

middle: K

last: Ramani

first: Ner

last: Saw

first: Yongqian

last: Wang

first: YuShan

last: Tu

last: Brudno

first: Zhengping

last: Jia


title: TFEB activation in macrophages attenuates postmyocardial infarction ventricular dysfunction independently of ATG5-mediated autophagy

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

summary: Lysosomes are at the epicenter of cellular processes critical for inflammasome activation in macrophages, including autophagy and lipid metabolism. Inflammasome activation and IL1-beta secretion are implicated in atherogenesis, ischemic cardiac injury and resultant heart failure; however, little is known about the role of macrophage lysosome function in regulating these processes. We hypothesized that macrophages exhibit lysosome dysfunction in heart failure due to ischemic injury, and that augmentation of macrophage lysosomal biogenesis via macrophage-specific overexpression of transcription factor EB (mf-TFEB) would attenuate ischemic remodeling by modulating macrophage inflammatory responses. In both mice subject to ischemia-reperfusion injury, and human heart tissue from patients with ischemic cardiomyopathy, we find evidence of lysosome insufficiency and autophagic impairment, respectively. Mf-TFEB overexpression significantly attenuated post-IR adverse left ventricular remodeling at 4 weeks without affecting scar size. Mf-TFEB overexpression reduced the relative amounts of pro-inflammatory macrophage populations in the myocardium. RNA sequencing of flow-sorted cardiac macrophages post-IR confirmed that TFEB stimulated a lysosomal transcriptional program in macrophages, and upregulated key targets involved in lysosomal lipid metabolism, which we show are critical for inflammasome suppression. Both TFEB-dependent inflammasome suppression and effects on post-IR remodeling were independent of autophagy. Our findings suggest that TFEB reprograms macrophage lysosomal lipid metabolism to attenuate inflammasome activity and protect against post-ischemic cardiac remodeling and simultaneously shift our understanding of how autophagy and lipid metabolism impact acute inflammation.

overall_design: Macrophages were flow-sorted on the basis of CCR2 overexpression (CCR2pos and CCR2neg). Four TFEB-TG (TFEB expression cassette preceded by a floxed stop sequence) and five TFEB-wt (no expression cassette) cell samples, all lacking Cre (Cre-neg), were compared in order to evaluate mRNAs differentially expressed in response to the presence of the TFEB-TG cassette alone.  After eliminating these mRNAs, TFEB-TG and TFEB-wt samples expressing Cre (mac-TFEB and CX3CR1-Cre) were compared to detect mRNAs differentially expressed in response to TFEB overexpression.

first: Ali

last: Javaheri


title: The histone deacetylase SIRT6 restrains transcription elongation via promoter-proximal  pausing

city: Newark

first: Jean-Pierre

last: Etchegaray

state: NJ

address: 225 University Ave

department: Biological Sciences

institute: Rutgers University

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

overall_design: Refer to individual Series


title: The histone deacetylase SIRT6 controls transcription elongation via promoter-proximal  pausing (PRO-Seq)

city: Boston

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

summary: Transcriptional regulation in eukaryotes commonly occurs at promoter-proximal  regions wherein transcriptionally engaged RNA Polymerase II (Pol II) pauses before  proceeding towards productive elongation. The roles of chromatin in this process  remains poorly understood. Here, we demonstrate that the histone deacetylase SIRT6  regulates transcription elongation by binding to Pol II and anchoring the Negative  ELongation Factor NELF, thereby preventing the release of Pol II towards elongation.  Absence of SIRT6, or conditions of glucose deprivation, lead to increased levels of  acetylated histone H3 at lysines 9 (H3K9ac) and 56 (H3K56ac), activation of the CDK9  kinase, phosphorylation of NELF and Pol II, and recruitment of the transcription factors  MYC and BRD4, the PAF1 Complex, as well as several positive elongation factors, in  turn releasing Pol II into productive elongation. Collectively, we identified SIRT6 as the  first pausing-dedicated histone deacetylase, regulating intragenic H3K9ac and  H3K56ac as critical chromatin modifications modulating transcriptional pausing and  elongation.

overall_design: PRO-seq: Biological replicates were generated using WT (3 replicates) mESC cells, SIRT6-KO (3 biological replicates) and Glucose deprivation (2 replicates).

first: Telmo

last: Henriques

first: Karen

last: Adelman


title: Novel role of proton-secreting epithelial cells in sperm maturation and mucosal immunity

first: Maria

middle: Agustina

last: Battistone

state: Massachusetts

department: Program in Membrane Biology, Center for Systems Biology and Nephrology Division, Department of Medicine

institute: Massachusetts General Hospital. Harvard Medical Scholl

summary: We identify clearly distinct transcriptomic signatures between clear cells from the caput, corpus and cauda regions, which might reflect a more accurate functional characterization of a given specific cell type.

overall_design: Clear cell gene-expression profile based on their location in the epididymis using RNA-sequencing. EGFP+ clear cells were isolated by double cell sorting from the caput, corpus and cauda epididymal regions of B1 V ATPase - EGFP transgenic mice that specifically express EGFP in clear cells.

middle: A

first: Raul

middle: G

last: Spallanzani

first: Alexandra

last: Mendelsohn

first: Diane

last: Capen

first: Anil

middle: V

last: Nair

first: Dennis

last: Brown

first: Sylvie

last: Breton


title: The histone deacetylase SIRT6 controls transcription elongation via promoter- proximal  pausing (RNA-Seq)

overall_design: RNA-seq in WT, Glucose depleted and Sirt6-KO mESC

first: J

first: L

last: Catherine

first: R

last: Mostoslavsky

first: A

last: Goren

first: K

middle: N

last: Ross


title: RNA-Seq analysis of juvenile stages of Ramazzottius varieornatus

city: Tsukuba

first: Yuki

last: Yoshida

state: Ibaraki

address: 1-2 Owashi

department: NIAS

institute: NARO

summary: Tardigrades are microscopic organisms, famous for their tolerance against extreme environments. The establishment of rearing systems of multiple species has allowed for comparison of tardigrade physiology, in particular in embryogenesis. Interestingly, in-lab cultures of limnic species showed smaller variation in hatching timing than terrestrial species, suggesting a hatching regulation mechanism acquired by adaptation to their habitat. To this end, we screened for coordinated gene expression during the development of two species of tardigrades, Hypsibius exemplaris and Ramazzottius varieornatus, and observed induction of the arthropod molting pathway. Exposure of ecdysteroids and juvenile hormone analog affected egg hatching but not embryonic development in only the limnic H. exemplaris. These observations suggest a hatching regulation mechanism by the molting pathway in H. exemplaris.

overall_design: Day 2-7 of juvenile stages of R. varieornatus, three replicates.

first: Kenta

last: Sugira

first: Masaru

last: Tomita

first: Midori

last: Matsumoto

first: Kazuharu

last: Arakawa


title: Photodamage repair pathways contribute to the accurate maintenance of DNA methylome landscape upon UV exposure

city: Strasbourg

first: Jean

last: Molinier

address: 12 rue du General Zimmer

country: France

institute: IBMP-CNRS

type: Non-coding RNA profiling by high throughput sequencing

summary: We report the methylation level of photodamage repair deficient plants 24h upon UV-C exposure. We determined the methlome changes genome wide and at photodamaged sites using NGS approaches.

overall_design: Examination of methylome landscape upon UV-C exposure

first: Stéfanie

last: Graindorge

first: Valérie

last: Cognat


title: miRNA-seq from white blood cells of responders and non-responders (weight loss) to a hypocaloric mediterranean diet

city: Pamplona

first: Fermin

middle: I

last: Milagro

state: Navarra

address: c/ Irunlarrea 1

department: Centre for Nutrition Research

institute: University of Navarra

summary: The objective of the present study is to identify early miRNAomic biomarkers of response to a hypocaloric mediterranean diet (RESMENA study). The RESMENA study (“REducción del Síndrome Metabólico en Navarra”) is a Spanish, randomized controlled and longitudinal trial over a six-month period that aimed to improve the parameters related with Metabolic Syndrome, including body fat composition, biochemistry, inflammation, or oxidative stress. The study was approved by the Research Ethics Committee of the University of Navarra (ref.065/2009). All the participants (n=96) were Caucasian and gave written informed consent for participation in agreement with the Declaration of Helsinki (www.clinicaltrials.gov; NTC01087086). Participants were categorized into “High Responders” (HR), when weight loss was >8%, and “Low Responders” (LR) when weight loss was <8%. White blood cells were separated from whole blood by centrifugation at 1,100 g at 4ºC for 15 min. Total RNA from WBCs isolated before the nutritional intervention was extracted using TRIzol reagent. miRNAs from white blood cells of 6 LR and 5 HR were sequenced using Illumina’s miRNA-Seq following the standardized protocol.

overall_design: miRNAs from white blood cells of two groups of volunteers: 6 low responders (LR) and 5 high responsers (HR) were sequenced using Illumina’s miRNA-Seq protocol. Samples called C06, C26, C48, R03, R20 and R26 are the low responders (LR), whereas C16, C31, C38, R31 and R36 are the high responders (HR).

first: Maria

last: Zulet

first: Marcos

last: Garcia-Lacarte


title: The histone deacetylase SIRT6 controls transcription elongation via promoter- proximal  pausing (ChIP-Seq)

first: Fei

last: Ji

overall_design: ChIP-seq experiments to determine genome wide profiles of multiple histone modifications (H3K36me3, H3K79me2, H3K9ac,H3K56ac), RNA polymerase II and the transcription factor LEO1 component of the PAF1 complex) in WT and SIRT6 KO mouse embryonic stem cells (129 mouse strain).

last: Etchegaray

first: Ji

last: Fei


title: Global analysis of enhancer targets

city: Dallas

first: Gary

last: Hon

state: TX

address: 5323 Harry Hines Blvd, J7.125, Hon Lab

institute: UT Southwestern Medical Center


title: Loss of ANCO1 repression of AIB1/YAP drives breast cancer progression

city: Washington

first: Max

middle: Harley

last: Kushner

address: 3970 Reservoir Rd NW, NRB E311

institute: Georgetown University

summary: We report the role of AIB1 in regulated YAP driven transcription and repression in normal mammary epithelial cells (MCF10A). We generated six cell lines by sequential infection and selection and extracted RNA for sequencing. Data was aligned to Hg38 with STAR and processed with EdgeR.

overall_design: Examination of RNA-seq of 6 cell lines in triplicate

first: Anna

middle: T

last: Riegel


title: Exercise instructs hematopoietic progenitor cells and reduces chronic leukocytosis [RNA-seq]

first: I-Hsiu

last: Lee

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Mass General Hospital/Harvard University

summary: Physical activity modulates communication between fat and the stromal hematopoietic bone marrow niche, leading to changes in hematopoiesis, reduced leukocyte levels and protection from cardiovascular disease.

overall_design: 7-8 weeks old C57BL/6 mice were individually housed and had access to exercise wheels for 6 weeks (Ex), or were housed with igloos (Sed). Another group had access to exercise wheels for 6 weeks followed by a 3 weeks wheel withdrawal (ExSed). mRNA profiles of FACS sorted LSK were generated by deep sequencing, in triplicate, using Illumina NextSeq

first: Matthias

last: Nahrendorf

first: Vanessa

last: Frodermann


title: Global analysis of enhancer targets: Bulk RNA-Seq validation

summary: Single-cell perturbation assays such as Mosaic-seq enable highly multiplexed functional assessment of enhancers in their endogenous genomic context. By introducing a few computational and experimental improvements, we expanded the Mosaic-seq analysis to capture the secondary gene targets of enhancers. Our analysis of >500 putative enhancers in K562 cells demonstrates that many secondary hits are shared among enhancers targeting different transcriptional factors, which reveals an interwoven enhancer-driven gene regulatory network. Together, our data underscore the flexibility of manipulating gene transcription by modifying enhancer activity.

overall_design: In order to validate the differentiated expressed genes identified in the Mosaic-seq experiment, we performed bulk RNA-seq for two enhancer regions, including the enhancer of ARL15 gene (ARL15-enh) and the third enhancer for the MYB gene (MYB-enh-3). For sample preparation, K562-dCas9-KRAB cells were infected with all 10 sgRNAs from each region, respectively. In addition, two non-targeting sgRNAs were used as the negative control. For each sgRNA, two to three biological duplicates were collected at the same time.

first: Shiqi

last: Xie

first: Daniel

last: Armendariz


title: Global analysis of enhancer targets: Mosaic-seq

overall_design: We performed Mosaic-seq on 518 enhancers in K562 cells. We used 10X genomics 3’ V2 kit to prepare the single-cell transcriptome libraries. The sgRNA is expressed by using the CROP-seq design, and a sgRNA enrichment library was also prepared for each single-cell library. In total, we performed ten 10X runs for five different batches, with a total number of > 100K cells sequenced. For the processed data, we uploaded the gene expression matrix (HDF5 format) from 10X cellranger pipeline in together with the sgRNA information of each cell.


title: Expression profile of GATA6 deficient pancreatic islets

city: Seville

first: Anabel

last: Rojas

state: Seville

address: Avda. Américo Vespucio

department: Stem Cell

institute: CABIMER

summary: GATA6 mutations have  been linked to adult-onset diabetes with subclinical or no exocrine insufficiency suggesting an important role for GATA6 in humanβcell physiology. To investigate the role of GATA6 in adult endocrine pancreas, we generated mice in which Gata6 is specifically inactivated in the pancreas. These mice develop glucose intolerance. Islets deficient in GATA6 activity display decreased insulin content and impaired glucose-induced insulin secretion. Gata6-deficient ß cells exhibit ultrastructural abnormalities including increased immature insulin granules, swollen mitochondria and disorganized endoplasmic reticulum. Microarray analysis revealed that loss of GATA6 greatly impacts ß cell specific gene expression.

overall_design:
Expression profile of GATA6 deficient islets and control islets were studied using Gene Chip Mouse Gene 2.0 ST
Three samples of control islets and four samples of Gata6 KO islets were used in this study to compare the gene expression profile using Gene Chip mouse. Each sample contain pooled islets from three mice of two month of age.

first: Laura

last: Villamayor Coronado


title: ID1 mediates escape from TGFβ Tumor Suppression in Pancreatic Cancer

city: New York

first: Joan

last: Massague

state: NY

address: 417 E 68th St

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: We perform ChIPseq, ATACseq, and RNAseq to characterize the role of ID1 in PDA cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIPseq, RNAseq, and ATACseq are used to profile PDA cells

first: Yun-Han

last: Huang


title: Blue Light Sensing in Listeria monocytogenes Is Temperature-Dependent and the Transcriptional Response to It Is Predominantly SigB-Dependent

status: Public on Oct 30 2019

city: Galway

first: Amber

middle: Louise

last: Dorey

state: Galway

address: University Road

department: Microbiology

country: Ireland

institute: National University of Ireland Galway

summary: In this study the global transcriptional response of L. monocytogenes to blue light was elucidated using an RNAseq-based approach. A transcriptomic analysis of the response to sub-lethal levels of blue light found that the changes in transcription were almost entirely SigB-dependent. A mutant where the light sensing mechanism of RsbL was inactivated through an amino acid substitution (Cys56Ala)  was found to have an attenuated response to blue light, but residual activation of SigB-dependent genes suggested that alternative routes for activation of SigB by light are likely to exist.

overall_design: Comparison between wild-type and mutant cells cultured in darkness and in light.

first: Conor

middle: P

last: O'Byrne

first: Bo-Hyung

first: Bjorn

last: Rotter


title: Maintenance of primary hepatocyte functions in vitro by inhibiting mechanical tension-induced YAP activation

city: Shanghai

first: Wenlin

last: Li

address: 800 Xiangyin Road

institute: Second Military Medical University

summary: It has been a long-standing challenge to maintain the functions of hepatocytes in vitro. In the present study, we found that mechanical tension-induced yes-associated protein (Yap) activation triggered hepatocyte dedifferentiation. Alleviation of mechanical tension by confinement of cell spreading was sufficient to inhibit hepatocyte dedifferentiation. Based on this finding, we identified a small molecular cocktail LBDXL through reiterative chemical screening that could maintain hepatocyte functions over the long term and in vivo repopulation capacity by targeting actin polymerization and actomyosin contraction.

overall_design: Hepatocytes mRNA profiles of freshly isolated hepatocytes (FH), freshly isolated Yap-/- hepatocytes (FH Yap-/-), LBDXL hepatocytes at three weeks (LBDXL 3W), BM hepatocytes at three weeks (BM 3W), BM Yap-/- hepatocytes at three weeks (BM 3W Yap-/-), BM hepatocytes at one day (BM 1D) and BM hepatocytes at three days (BM 3D) were generated by deep sequencing, in duplicate, using illumina Hiseq4000

first: Pingxin

last: Sun


title: Tagger–a Swiss army knife for multiomics to dissect cell type-specific mechanisms of gene expression in mice [Nuc-Tag-MeDIP-seq]

city: Tübingen

first: Vikas

last: Bansal

state: BW

address: Otfried Müller Strasse 23

institute: German Center for Neurodegenerative Diseases (DZNE)-Tübingen

summary: We developed a knock-in mouse line that combines four enrichment tools to study gene regulatory networks of the brain and other complex tissues. As a result, chromatin, nascent RNA, translating mRNA and mature miRNA can be purified from specific cell populations. Specifically, we developed "Tagger" – a Cre and/or Flp recombinase-dependent mouse model that expresses four proteins to enable purification of distinct populations of cellular nucleic acids from specific cell types. Upon activation by cell type-directed recombinases, cells of a desired population express: 1) exogenous uracil phoshoribosyltransferase (UPRT) for tagging nascent total RNA with thiol groups upon administration of 4-thiouracil (4TU, TU-Tag), 2) epitope-tagged large ribosomal subunit protein 22 (Rpl22) to co-immunoprecipitate (co-IP) ribosome-bound mRNA (RiboTag), 3) epitope-tagged Argonaute 2 (Ago2, a component of the RNA-induced silencing complex) to co-IP mature miRNA (AgoTag), and 4) nucleus-directed mKate2 red fluorescent protein, providing good tissue penetrating transmission properties for in vivo imaging and a fluorescent nuclear tag (NucTag) for FACS enrichment of nuclei for chromatin studies.

overall_design: For functional validation, Tagger mice were bred to neuron-directed Cre lines: vGluT2-Cre and Gad2-Cre, producing vGluT2-Tagger and Gad2-Tagger mice, respectively. Then, TU-Tag RNA-seq, RiboTag RNA-seq, AgoTag small RNA-seq and NucTag MeDIP-seq from specific cell types and respective controls/input was generated.

first: Lech

last: Kaczmarczyk

first: Stefan

last: Bonn

first: Walker

last: Jackson