title: Exploring molecular profiles of calcification in aortic vascular smooth muscle cells and aortic valvular interstitial cells

city: Milwaukee

first: Joy

last: Lincoln

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: Cardiovascular calcification can occur in vascular and valvular structures and is commonly associated with calcium deposition and tissue mineralization leading to stiffness and dysfunction. Based on shared risk factors and end stage pathologies, calcific aortic valve disease (CAVD) and coronary artery calcification (CAC) are often considered as one disease, and similarly treated. However, the clinical conditions associated with each phenotype can be different, suggesting multifaceted pathologies. To better understand diversity in molecular and cellular processes that underlie calcification in vascular and valvular structures, we exposed aortic vascular smooth muscle cells (AVSMCs) and aortic valve interstitial cells (AVICs) to calcific stimuli including high (2.5mM) phosphate and osteogenic media (OM) treatments in vitro. Consistent with clinical observations made by others, we show that AVSMCs are more susceptible to calcification than AVICs, and this process is mediated by cell-specific and treatment-specific molecular responses. RNA-seq analysis demonstrates that in response to calcific-stimuli, both AVSMCs and AVICs activate a robust ossification-program, although the signaling pathways, cellular processes and osteogenic-associated markers involved are diverse. In addition, VIC-mediated calcification appears to involve biological processes related to osteo-chondro differentiation and down regulation of actin cytoskeleton genes, that are not observed in VSMCs. Furthermore, are findings suggest that signaling pathways involved in cardiovascular cell calcification are dependent on the calcific-stimuli, including a requirement of PI3K signaling for OM-induced calcification, and not 2.5mM Phosphate. Together, this study provides a wealth of information suggesting that the pathogenesis of cardiovascular calcifications may be significantly more diverse than previously appreciated.

overall_design: Porcine aortic valve interstitial cells (pAVICs) and aortic vascular smooth muscle cells (pAVSMCs) were cultured as previously described and harvested either 3 (d3) or 5 (d5) days after treatment in conditioned media (CM), osteogenic media (OM), or 2.5mM phosphate (Pi). 200ng total RNA was extracted using the RNeasy Mini Kit from Qiagen (#74104), quantified using NANOdrop, and sent to Psomagen, Rockville, MD for analyses. Amplified cDNA libraries suitable for sequencing were prepared from 200 (ng) of DNA-free total RNA using the Universal Plus mRNA-Seq Library Prep Kit (NuGEN Technologies, Inc. #0508-96).  The RNA Integrity Number (RIN) was determined using Ribogreen on a TapeStation to measure concentration and quality, with a value of >7.0 meeting threshold. Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep kit and sequenced on an Illumina platform. Raw FASTQs were split into files containing ~40,000,000 total reads and checked for quality using the FASTX-Toolkit. The reads were filtered (removing sequences that did not pass Illumina’s quality filter) and trimmed based on the quality results (3 nucleotides at the left end of the R1 reads and 1nt at the left end of the R2 reads). Trimmed reads were mapped to reference genome (Sus Scrofa, GCF_000003025.6_Sscrofa11.1) with HISAT2. After the read mapping, Stringtie was used for transcript assembly. Expression profiles were calculated for each sample and transcript/gene as read count and FPKM (Fragment per Kilobase of transcript per Million mapped reads).

first: Julie

middle: R

last: Kessler

first: Theresa

last: Bluemn

first: Samuel

last: DeCero

first: Punashi

last: Dutta

first: Kaitlyn

last: Thatcher

first: Donna

last: Mahnke

first: Makenna

middle: C

last: Knas

first: Hail

middle: B

last: Kazik

first: Vinal

last: Menon


title: Responses of Atlantic cod to high water temperature and bacterial infection

status: Public on Aug 01 2023

city: Ås

first: Aleksei

last: Krasnov

state: Viken

address: Øreveien, 47B

country: Norway

institute: Nofima AS

summary: Aquaculture is one of the fastest growing food production sectors in the world and further expansion is expected throughout the 21st century. However, climate change is threatening the development of the sector and action is needed to prepare the industry for the coming challenges. Using downscaled temperature projections based on the Intergovernmental Panel on Climate Change (IPCC) climate projection (Shared Socioeconomic Pathway, SSP2-4.5), we analysed potential future temperatures at a selected Atlantic cod (Gadus morhua L.) farm site in Northern Norway. Results showed that the farming area may experience increased temperatures the next 10–15 years, including more days with temperatures above 17°C.  Based on the predicted future conditions, we designed a study with Atlantic cod (Gadus morhua L.) to evaluate effects from high temperature alone and in combination with Fransicella noatunensis infection. Fish were kept at 12°C and 17°C for eight weeks and samples of skin and spleen collected at different timepoints were analysed with transcriptomics, histology, scanning electron microscopy and immunohistochemistry.

overall_design: Atlantic cod, produced at the Center of Marine Aquaculture (Nofima, Norway), were transferred to The Aquaculture Research Station (Tromsø, Norway). Fish were kept for acclimatization for 4 weeks in flow-through tanks at 8 oC, and fed Amber Neptun (Skretting, Norway). Temperature increase was performed in two stages. First the fish were acclimated to 12oC for one week. Second, 120 fish were distributed in 4 tanks, 30 fish per tank, and temperature in two tanks increased to 17 oC. Temperature in the two remaining tanks were kept at 12oC. After acclimatization, fish were moved to the challenge facility at the station where they were kept in 200 L tanks with similar conditions. First day after transfer (T0), three fish from each tank were killed by an overdose of anaesthetics and sampled. At week 8, fish were challenged by cohabitation with Francisella noatunensis (type strain NCIMB 14265).

first: Elisabeth

last: Ytteborg

first: Krasnov

last: Aleksei


title: ATM-inhibitor AZD1390 is a radiosensitizer for breast cancer CNS metastasis

city: Los Angeles

first: Bodour

last: Salhia

state: CA

address: 1450 Biggy St 2nd floor, Los Angeles, CA 90033

department: Department Of Translational Genomics

country: USA

institute: University of Southern California

type: Expression profiling by high throughput sequencing

summary:
Purpose: Central nervous system (CNS) metastasis has remained a major source of mortality for breast cancer patients. This is largely driven by the inability of current therapeutics to penetrate the blood brain barrier (BBB) and the lack of preclinical models for testing new therapies. Here we study the efficacy of AZD1390, a BBB penetrating ataxia-telangiectasia mutated (ATM) inhibitor, as a radiosensitizer for breast cancer CNS metastasis treatment.
Experimental Design: Three PDX tumors including 2 HER2+ and 1 triple negative breast cancer (TNBC) harboring TP53 mutations, were implanted subcutaneously in the flank of mice to assess tumor growth inhibition by AZD1390 combined with radiation. Animal survival was further assessed by implanting the best responding PDX model orthotopically in the brain.
Results: Pretreatment with AZD1390 followed by radiation therapy inhibited growth of PDX tumors implanted in the flank, and improved survival in orthotopic models with average survival 222 days compared to 123 days in controls. Adjuvant administration of AZD1390 had no further benefits. While the combination therapy resulted in sustained tumor inhibition, sporadic regrowth was observed in in some mice 50-100 days post-treatment in all models. Gene expression analysis comparing these tumors with complete responders demonstrated changes in upregulation of multiple oncogenic proteins, which are potential drivers of tumor growth after treatment.
Conclusions: Our results demonstrate that AZD1390 effectively sensitizes breast cancer CNS metastasis to radiation therapy in TP53 mutant tumors. This study demonstrates the potential of using AZD1390 as a novel therapeutic agent for patients with breast cancer CNS metastasis.

overall_design: RNA-seq profiling of tumors after combiation of AZD1390 and radiation therapy

first: Ben-Yi

last: Tew

first: Alex

middle: J

last: Kalfa

first: Zeyi

last: Yang

first: Kyle

last: Hurth

first: Thomas

last: Simon

first: Eric

last: Abnoosian

first: Stephen

middle: T

last: Durant

first: Petra

last: Hamerlik


title: Differential gene expression in IFNg+ and IFNg- IL-15 primed NK cells after anti-NK1.1 stimulation [IFNgReporter_RNA-seq]

city: SAINT LOUIS

first: Megan

last: Cooper

state: MISSOURI

address: MPRB, 6th floor, 4905 Childrens Place

department: Pediatrics

institute: Washington University in St Louis

summary:
We isolated splenic NK cells and cultured them for 3 days in 100 ng/ml IL-15.
Next, we stimulated the cells with plate-bound anti-NK1.1 for 6 hours and sorted YFP+ (IFNg+) and YFP- (IFNg-) populations.
We then performed gene expression profiling analysis using data obtained from RNA-seq from unstimulated, YFP+ or YFP- NK cells.

overall_design: RNA-seq

first: Maria

last: Cimpean

middle: A


title: Gene expression of myeloid lineage cells reveals a role for myeloid progenitor cells in mammary gland fibrosis in obesity

city: Madison

first: Lisa

last: Arendt

state: WI

address: 2015 Linden Drive

department: Comparative Bioscience

institute: University of Wisconsin-Madison

summary: Obesity enhances macrophage recruitment in to mammary adipose tissue and increases fibrosis.  We isolated monocytes/macrophages and myeloid progenitor cell populations from the mammary gland and queried gene expression of fibrosis related genes to assess the contribution of each population to fibrosis within the mammary gland.

overall_design: Mice were randomized to received either a low-fat diet or high-fat diet to induce obesity  (n=3/group), and monocytes/macrophages and myeloid progenitor cells were isolated using FACS from the mammary glands of lean and obese mice to examine gene expression changes due to obesity.


title: ASCL1 is activated downsrteam of ROR2/CREB signaling pathway to support lineage plasticity [ChIP-seq]

city: Vancouver

first: Amina

last: Zoubeidi

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Lineage plasticity has been shown to be a form of therapy-induced drug resistance. In prostate cancer, androgen receptor (AR) pathway inhibitors have led to accretion of tumor relapse with loss of AR signaling and a shift from a luminal state to an alternate program. Although different genomic and epigenomic aberrations have been correlated with lineage reprogramming, the molecular and signaling mechanisms orchestrating the development of lineage plasticity under the pressure of AR-targeted therapies are not fully understood. Here, a survey of receptor tyrosine kinases (RTKs) identified ROR2 as the top-upregulated RTK following AR pathway inhibition, which feeds into lineage plasticity by promoting stem cell-like and neuronal networks. Mechanistically, we demonstrated that ROR2 activates the ERK/CREB signaling pathway to modulate the expression of the lineage commitment transcription factor, ASCL1. Collectively, our findings nominate ROR2 as a potential therapeutic target to reverse the ENZ-induced plastic phenotype and potentially re-sensitize tumors to AR pathway inhibitors.

overall_design: ChIP-seq for AR in 16D cell line with or without DHT treatment, ChIP-seq for H3K27Ac in 16D and NCI-H660

first: Nakisa

last: Tabrizian

first: Shaghayegh

last: Nouruzi

first: Cassandra

last: Cui

first: Maxim

last: Kobelev

first: Takeshi

last: Namekawa

first: Ishana

last: Lodhia

last: Talal

first: Olena

last: Sivak

first: Dwaipayan

last: Ganguli


title: ASCL1 is activated downsrteam of ROR2/CREB signaling pathway to support lineage plasticity [RNA-seq]

overall_design: Deciphering ROR2 dependent prostate cancer stage specific gene expression profile by RNAseq.


title: ASCL1 is activated downsrteam of ROR2/CREB signaling pathway to support lineage plasticity.

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of C2C12 myotubes after adenoviral expression of Crebrf

city: San Francisco

first: Phillip

middle: Anthony

last: Dumesic

address: 513 Parnassus Ave, HSW1119

department: Diabetes Center

institute: University of California, San Francisco

summary:
Purpose: identify global changes in gene expression in C2C12 myotubes caused by an increase in Crebrf.
Methods: Triplicate replicates of differentiated C2C12 myotubes expressing either Gfp or Crebrf for 3 days after transduction. After assessing RNA quality with Agilent Bioanalyzer, mRNAs were enriched by poly-A pull-down. Then, sequencing libraries constructed with Illumina TruSeq RNA prep kit were sequenced using. We multiplexed samples in each lane, which yields targeted number of single-end 75 bp reads for each sample, as a fraction of 180 million reads for the whole lane. Sequence reads were mapped back to the Drosophila genome (flybase genome annotation version r6.30) using STAR. With the uniquely mapped reads, we quantified gene expression levels using Cufflinks (FPKM values). Next, differentially expressed genes between experimental and control data were analyzed with DESeq2.
Results: Gene set enrichment analysis reveals oxidative phosphorylation and interferon response as the top up- and down-regulated gene sets, respectively, upon Crebrf expression.  The glycolysis gene set is also reduced.  These gene expression findings parallel our metabolic observations in Seahorse analysis.
Conclusions: Our study indicates that CREBRF is a strong regulator of muscle metabolism in C2C12 myotubes

overall_design: C2C12 myotubes were transduced by adenovirus encoding Gfp or Crebrf and RNA was isolated and analyzed by deep sequencing, in replicate, using Illumina HiSeq2000.

first: Perrimon

last: Norbert

first: Pedro

last: Saavedra


title: Immune microenvironment and molecular mechanism of oral lichen planus [bullk RNA-Seq]

city: Chengdu

first: Hao

last: Xu

state: China

address: No.17 section3 renmin south road, chengdu

country: China

institute: Sichuan university

summary: Oral lichen planus (OLP) is a poorly understood chronic inflammatory mucocutaneous disease and is associated with many systemic diseases, which may lead to the erosion of oral mucosa and bring physical and psychological disorders to patients. However, the pathogenesis and immune microenvironment of OLP with different clinical subtypes are unclear. therefore, this study established a clinical cohort of OLP with 1-year follow-up and obtained the clinical information and bulk RNA-seq files to explore the immune microenvironment and molecular mechanism of oral lichen planus with different clinical subtypes. Based on the erosion of oral mucosa in the biopsy, the participants of OLP were divided into two groups, non-erosive OLP (NEOLP) and erosive OLP (EOLP). According to whether erosion occurred in oral mucosa more than three times and a remission period of less than 3 months within a one-year follow-up, OLP was divided into two groups, recalcitrant erosive OLP (REOLP) and stable OLP (SOLP).

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data for non-erosive OLP (NEOLP) and erosive OLP (EOLP), and recalcitrant erosive OLP (REOLP) and stable OLP (SOLP).

first: Maofeng

last: Qing

first: Qianhui

last: Shang

first: Qianming

last: Chen


title: DOT1L deletion impairs the development of cortical Parvalbumin-expressing interneurons

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 23

country: Germany

institute: University of Freiburg

summary: Our group has reported that the histone methyltransferase DOT1L is necessary for proper cortical plate development and layer distribution of glutamatergic neurons, however, its specific role on cortical interneuron development has not yet been explored. Here, we demonstrate that DOT1L affects interneuron development in a cell-autonomous manner. Deletion of Dot1l in MGE-derived interneuron precursor cells results in an overall reduction and altered distribution of GABAergic interneurons in the cortical plate at postnatal day (P) 0. Furthermore, we observed an altered proportion of GABAergic interneurons in the cortex and striatum at P21 with a significant decrease in Parvalbumin (PVALB)-expressing interneurons. Altogether, our results indicate that reduced numbers of cortical interneurons upon DOT1L deletion results from altered postmitotic differentiation/maturation.

overall_design: Assessment of DOT1L role in the development of cortical interneurons at E14.5.

first: Esther

last: Maier

first: Arquimedes

last: Cheffer

first: Marta

last: Garcia Miralles

first: Ipek

last: Akol


title: Time series scRNAseq analysis in mouse and human informs optimization of rapid astrocyte differentiation protocols

city: New York

first: Paul

last: Frazel

state: NY

address: 435 E 30th St

institute: NYU Langone Medical Center

summary: Macroglia (astrocytes and oligodendrocytes) are required for normal development and function of the central nervous system, yet many questions remain about their emergence in the brain and spinal cord. Here we used single-cell RNA sequencing (scRNAseq) to analyze over 298,000 cells and nuclei during macroglia differentiation from mouse embryonic and human induced pluripotent stem cells. We computationally identify candidate genes involved in fate specification of glia in both species, and report heterogeneous expression of astrocyte surface markers across dif- ferentiating cells. We then used our scRNAseq data to optimize a previous mouse astrocyte differentiation protocol, decreasing the overall protocol length and complexity. Finally, we used multiomic, dual single nuclei (sn)RNAseq/snA- TACseq analysis to uncover potential genomic regulatory sites mediating glial differentiation. These datasets enable future optimization of glial differentiation protocols and provide insight into human glial differentiation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Overall, single-cell RNA and ATAC sequencing of time points during glial differentiation in human and mouse stem cells. Some time points were replicated as discussed in manuscript. Multiomic (dual snRNAseq + snATACseq) analysis of mouse astrocytes given either BMP4/FGF1 or CNTF growth factor treatments for 5,7, or 9 days total.

middle: W

first: Shane

last: Liddelow


title: The function of Trim71 in supporting cell reprogramming and hair cell regeneration

city: Baltimore

first: Angelika

last: Doetzlhofer

state: MD

address: 855 North Wolfe St

department: Neuroscience

institute: Johns Hopkins University School of Medicine

summary: Employing an organoid based assay, we show that lentiviral overexpression of human TRIM71 in stage P5 cochlear epithelial cells restores their capacity to proliferate and form hair cells. RNA-sequencing and cell-based assays reveal that similar to LIN28B, TRIM71 overexpression activates the expression of pro-growth genes and inhibits pro-differentiation genes resulting in the reprogramming of supporting cells into progenitor like cells.

overall_design: Cochlear epithelial cells isolated from stage P5 wild type mice were used to establish organoid cultures as previously described (DOI: 10.1073/pnas.2000417117). Before plating, equal amount of cells were infected with control lentivirus expressing mCherry only or lentivirus expressing human TRIM71 and mCherry. At 10 days of expansion, RNA was extracted and RNA samples were processed using Illumina's TruSeq stranded Total RNA kit, per manufacturer's recommendations, using the UDI indexes. The samples were sequenced on the NovaSeq 6000, paired end, 2x50 base pair reads.   Three independent samples from three different animals were analyzed.

first: Xiaojun

last: Li

first: Charles

last: Morgan


title: Gene expression profile at single cell level of cardiac derived cells (CDCs) from the adult mouse hearts

city: Augusta

first: Yaoliang

last: Tang

state: GA

address: 1460 Laney Walker Blvd.

department: Medicine

institute: Augusta University

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of CDCs in the mouse hearts

overall_design: Cardiac-derived Lin-  non-cardiomyocytes of the BL6 mice were isolated by magnetically-activated cell sorting (MACS) using mouse lineage cell depletion kit and analyzed using scRNAseq.

first: Yan

last: Shen


title: Elafin as a Prognostic Marker in Esophageal Squamous Cell Carcinoma: A Pilot Study using Three-Dimensional Imag-ing and Genomic Profiling

city: Kaohsiung

first: Ming-Tsang

last: Wu

address: No.100, Shih-Chuan 1st Road, Sanmin Dist

department: Research Center for Environmental Medicine

country: Taiwan

institute: Kaohsiung Medical University

summary: Esophageal cancers are globally the sixth deadliest malignancy, with limited curative options. The association of high serum elafin levels, a molecule produced by epithelial cells, with esophageal squamous cell carcinoma (ESCC) risk is established, but its link to poor ESCC prognosis remains unclear. To explore this question, we first used three-dimensional confocal imaging to create a model of the spatial distribution of elafin inside locoregional ESCC tissues. Then, after analyzing data ob-tained from whole-genome microarrays for ESCC cell lines and their more invasive sublines, we performed in vitro experiments using RNA sequencing to identify possible elafin-related pathways. Three-dimensional tissue imaging showed elafin distributed as an interweaved-like fibrous structure in the stroma of tissue obtained from patients with high serum levels of elafin and poorer prognoses. By contrast, the signal was confined inside or around the tumor nest in patients who had lower serum levels and better survival. The analysis of a TCGA dataset revealed that higher levels of elafin mRNA in stage I–IIIA ESCC patients were associated with shorter survival. The in vitro studies revealed that elafin promoted ESCC cell proliferation, migration, and invasion via the epithelial–mesenchymal transition pathway. Thus, elafin inhibition could potentially be used therapeutically to improve survival in patients with locoregional ESCC.

overall_design: Comparative gene expression profiling analysis of RNA-seq data between elafin(PI3) overexpression and knockout in human ESCC cell lines

first: Wei-Chung

first: Chun-Chieh

first: Yu-Peng

last: Liu

first: Guan-Yu

last: Zhuo

first: Yao-Kuang

last: Wang

first: Yi-Hsun

first: Chu-Chih

first: Yin-Han

first: I-Chen


title: Immune microenvironment and molecular mechanism of oral lichen planus with different clinical subtypes

first: Hao

last: Xu


title: Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma [BCR-Seq]

city: Jerusalem

first: Miriam

middle: I.

last: Rosenberg

address: Edmond Safra Campus

department: Genetics

country: Israel

institute: Hebrew University of Jerusalem, Givat Ram

summary: Two percent of children with Neuroblastoma, a pediatric solid tumor of the peripheral nerve ganglia, develop Opsoclonus Myoclonus Ataxia Syndrome (OMAS), a paraneoplastic disease characterized by devastating cerebellar and brainstem-directed autoimmunity, but typically with outstanding cancer-related outcomes. Here, we compared tumor transcriptomes and tumor infiltrating T- and B-cell repertoires from a cohort of OMAS subjects with neuroblastoma to a set of controls from 13 low- and 13 high-risk non-OMAS associated neuroblastoma tumors.

overall_design:
Here, we compared tumor transcriptomes and tumor infiltrating T- and B-cell repertoires from a cohort of OMAS subjects with neuroblastoma to a set of controls from 13 low- and 13 high-risk non-OMAS associated neuroblastoma tumors.
>>> Adaptive Biotechnologies (service provider) did not provide FASTQ files due to proprietary content. <<<

middle: I

first: John

middle: M

last: Maris


title: Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma [RNA-Seq]

overall_design: Here, we compared tumor transcriptomes and tumor infiltrating T- and B-cell repertoires from a cohort of OMAS subjects with neuroblastoma to a set of controls from 13 low- and 13 high-risk non-OMAS associated neuroblastoma tumors.


title: MAF functions as a pioneer transcription factor that initiates and sustains oncogenesis

city: London

first: Nikolaos

last: Trasanidis

address: Hammersmith Campus, Commonwealth Building, 4th Floor,, Du Cane Road, Imperial College London

department: Department of Immunology and Inflammation,

country: United Kingdom

institute: Imperial College London

summary: Here we report the use of high-throughput sequencing technologies (RNA-seq, ATAC-seq, ChIP-seq) to identify the molecular programme of the transcirption factor c-MAF (MAF) in parental  (MM1.S, JJN3, H929), MAF-depleted (MM1S, JJN3) and MAF-overexpressing (MM1S, U266)  multiple myeloma (MM) cells . We performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) against MAF in naive MM cells , and against MAF, H3K27ac and H3K4me1 in MAF-overexpressing cells. Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) was performed on MAF-overexpressing U266 myeloma cells. In addition, we identifed the transcriptome of MAF-depleted myeloma cells 3 days after lentiviral transduction with MAF-targeting shRNA and scbl control. Our integrated -omics approach provides a comprehensive characterization of the role and function of MAF in myeloma cells and provides novel insights towards the discovery and design of molecular targets for precision therapy against MAF-overexpressing MM.

overall_design: Identification of the transcriptional and epigenomic programme of MAF in MM1S, JJN3, H929 and MAF-overexpressing U266 multiple myeloma cells using ChIP-seq, ATAC-seq and RNA-seq.

first: Alexia

last: Katsarou

first: Anastasios

last: Karadimitris


title: Micro RNA Expression data from DU145 shDCUN1D1

city: Cape Town

first: Luiz

middle: F

last: Zerbini

address: Wernher and Beit Building (South), Anzio Road

country: South Africa

institute: ICGEB

summary: Defective in Cullin Neddylation 1 Domain Containing 1 (DCUN1D1) is an E3 ligase for neddylation, a post translational process similar to, and that runs in parallel with the ubiquitin proteasome pathway. Although being established as an oncogene in various squamous cell carcinomas, the role of DCUN1D1 in prostate cancer has not been explored. Here we used microarray analysis to determine the set of genes regulated by DCUN1D1 in prostate cancer cells. Using the prostate cancer DU145 cell line as model, and a lentivirus encoding shRNA-DCUN1D1, we generated DCUN1D1 knockdown cell lines. Microarray analysis identified deregulation of key gene expression, cellular growth and proliferation, developmental, cell death and cancer pathways as possible mechanisms mediated by DCUN1D1 in prostate cancer.

overall_design: Total RNA was isolated from DU145 stabley transduced with lentivirus expresssing shRNA against DCUN1D1 or GFP (control) and hybridized to HT Human U133 gene .

first: Manoj

last: Bashin

first: Towia

last: Libermann

first: Xuesong

last: Gu


title: Th17 signaling in asthma: relevance for psychopathology and neuroinflammation

city: Seattle

first: Kimberly

last: Dill-McFarland

state: WA

address: 750 Republican St

department: Allergy and Infectious Diseases

institute: University of Washington

summary: Asthma influences brain health both functionally (emotions) and structurally (neurodegeneration). Although airway inflammation is proposed to initiate afferent communications with the brain, the associated patterns of airway inflammation and gene-expression profiles are not established. Here, we investigate associations of gene expression in response to allergen challenge in the lung with functional magnetic resonance imaging (fMRI) in the brain.

overall_design: Segmental bronchial provocation with allergen (SBP-Ag) was used to provoke airway inflammation and retrieve airway cells to characterize cellular responses by RNA-sequencing to determine gene-expression profiles. Differential gene-expression was assessed by cell deconvolution modular analysis coupled with linear modeling. Functional magnetic resonance imaging (fMRI) assessed brain function; data were acquired at baseline and 48h following SBP-Ag. Activation in brain regions of interest (amygdala, insula and anterior cingulate cortex) was correlated with inflammatory patterns of airway cell gene-expression.

first: Matthew

last: Altman

first: Stephane

last: Esnault

first: Nizar

middle: N

last: Jarjour

first: William

last: Busse

first: Melissa

last: Rosenkranz


title: Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma


title: Gene expression profiles of an ALK-fusion driven cell line and its derivatives resistant to crizotinib alone or resistant to crizotinib plus afatinib

status: Public on Jul 31 2023

city: Aurora

first: Robert

last: Doebele

state: CO

address: 12801 E. 17th Ave, Building RC1-S, Rm L18-8401A

department: Devision of Medical Oncology

institute: University of Colorado Anschutz Medical Campus

summary: Despite the initial benefit of the tyrosine kinase inhibitors targeting ALK gene fusions in non-small cell lung cancer, resistance to ALK inhibitors is almost inevitable. To determine the acquired resistance mechanism to ALK inhibition, we generated crizotinib-resistant ALK lines by chronically treating H3122 cells (driven by EML4-ALK) with an ALK inhibitor, crizotinib for approximately 3 months. RNA-seq and differential expression analyses were performed to determine the transcriptional changes of H3122-CR cells in comparison to parental H3122 cells. Because we demonstrated EGFR could mediate the early adaptive resistance to crizotinib, we further explored the mechanism that contributes to the resistance to the combination of crizotinib and afatinib. H3122-CAR (crizotinib and afatinib-resistant) cells were generated by treating them with a combination of crizotinib and afatinib for approximately 6 months and then profiled by RNA-seq to determine the associated transcriptional reprogramming.

overall_design: Three biological replicates of H3122-CR cells (resistant to crizotinib, named H3122-CR1, 2, and 3) and two biological replicates of H3122-CAR cells (resistant to crizotinib plus afatinib, named H3122-CAR1 and H3122-CAR3) were generated. RNA was isolated from H3122 parental line and each resistant cell line in triplicates and subjected to RNA-seq.

last: Chen


title: A branching model of lineage differentiation underpinning the neurogenic potential of enteric glia  (Single-cell ATAC-seq data for enteric glial cells)

first: Vassilis

last: Pachnis

address: 1 Midland Rd

department: Development and Homeostasis of the Nervous System Laboratory

institute: The Francis Crick Institute

summary: Glial cells have been proposed as an endogenous source of progenitors for the treatment of neural deficits. However, the cellular and molecular mechanisms underpinning the neurogenic potential of certain populations of adult glial cells, are not known. Using single cell transcriptomic profiling, we show here that enteric glial cells represent a cell state attained by autonomic neural crest cells as they transition during development along a linear default differentiation trajectory that allows them to retain neurogenic potential while acquiring a gene expression profile associated with their role in neuronal support and immunomodulation. Key neurogenic loci in early enteric nervous system progenitors remain in open chromatin configuration in mature enteric glia, thus facilitating neuronal differentiation under appropriate conditions. Molecular profiling and gene targeting of enteric glial cells in a novel cell culture system of enteric neurogenesis and a gut injury model, demonstrated that neuronal differentiation of glia is driven by transcriptional programs employed in vivo by early progenitors. Our work provides mechanistic insight into the dynamic regulatory landscape underpinning the development of intestinal neural circuits and generates a platform for advancing glial cells as therapeutic agents for the treatment of neural deficits.

overall_design: We performed scATAC-seq of nGFP+ cells isolated from tunica muscularis preparations from 8 week old Sox10CreERT2(SER93);Rosa26-nuclearGFP mice that had been injected with tamoxifen (2 doses of tamoxifen at 100 μg/g of body weight 10 days prior isolation).

first: Anna

last: Laddach

first: SongHui

last: Chng

first: Reena

last: Lasrado

first: Fränze

last: Progatzky

first: Michael

last: Shapiro

first: Alek

last: Erickson

first: Marisol

last: Sampedro-Castaneda

first: Artem

last: Artemov

first: Ana

last: Bon-Frauches

first: Eleni-Maria

last: Amaniti

first: Jens

last: Kleinjung

first: Stefan

last: Boeing

first: Sila

last: Ultanir

first: Igor

last: Adameyko


title: TCR-Engineered Lymphocytes Targeting NY-ESO-1: In Vitro Assessment of Cytotoxicity against Tumors

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

country: Russia

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

summary: In this work, we compared the expression profiles of Anti-NY-ESO1- transduced T-cells with Anti-NY-ESO1- transduced T-cells co-cultured with SK-Mel-37.

overall_design: We profiled total RNA from the anti-NY-ESO1-transduced TCR T-cells on NanoString Sprint Platform using Immunology V2 panel.


title: Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma [TCR-Seq]

first: Miriam

last: Rosenberg

first: John

last: Maris


title: Maternal emulsifier consumption programs offspring metabolic and neuropsychological health

city: Barcelona

first: Arnaud

last: Obri

address: C/ del Rosselló, 149

country: Spain

institute: IDIBAPS

summary:
Modern lifestyle is associated with a major consumption of ultra-processed foods (UPF) due to their practicality and palatability. The ingestion of emulsifiers, a main additive in UPFs, has been related to gut inflammation, microbiota dysbiosis, adiposity and obesity.
Maternal unbalanced nutritional habits during embryonic and perinatal stages perturb offspring’s long-term metabolic health, thus increasing obesity and associated comorbidity risk. However, whether maternal emulsifier consumption influences developmental programming in the offspring remains unknown.
Here we show that, in mice, maternal consumption of dietary emulsifiers (1% CMC and 1% P80 in drinking water), during gestation and lactation, perturbs the development of hypothalamic energy balance regulation centers of the progeny, leads to metabolic impairments, cognition deficits and induces anxiety-like traits in a sex-specific manner. Our findings support the notion that maternal consumption of emulsifiers, common additives of UPFs, causes mild metabolic and neuropsychological malprogramming in the progeny. Our data call for nutritional advice during gestation.

overall_design: Total RNA samples from P21 male mice (4 control litters and 5 emulsifiers litters) were processed at the IDIBAPS genomics’ platform for Tapestation quality control and subsequent sequencing. All samples had an RNA integrity number (RIN) > 8. mRNA strand-specific RNA libraries were generated using 200 ng of total RNA using the Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer’s instructions. Libraries were sequenced on an Illumina NextSeq2000 (Illumina) in paired-end mode with a read length of 2×50 bp. Around 40 million of paired-end reads were generated for each sample/condition.

first: Maria

last: Milà-Guasch

first: Sara

last: Ramírez

first: Sergio

last: Rodriguez

first: Júlia

last: Fos-Domènech

first: Lea

last: Dropmann

first: Macarena

last: Pozo

first: Elena

last: Eyre

first: Alicia

middle: G

last: Gómez-Valadés

first: Roberta

last: Haddad-Tóvolli

first: Marc

last: Claret


title: TF binding profiles acquired using ChEC-seq in various TF co-deletion strains

city: Rehovot

first: Naama

last: Barkai

address: Herzl 234

department: Molecular Genetics

institute: Weizmann Institute of Science

summary:
This data set contains ChEC-seq binding profiles of various TF in yeast strains deleted of other TFs. Each sample has a pair-end sequencing file and a processed file (.out) is a genomic signal track after alignment to S.cerevisiae (R64) reference genome. Mapping was done using the read end.
This dataset also contains raw and processed MNase-seq data files for nucleosome occupancy.

Data related to manuscript: The architecture of binding cooperativity between densely bound transcription factors.

overall_design: Binding of 28 TFs in co-deletion of multiple closely-bound TFs, nucleosome profiles of selected strains

first: Offir

last: Lupo

first: Divya

last: Kumar

first: Rotem

last: Livne

first: Michal

last: Chappleboim

first: Idan

last: Levy


title: Genetically modified IL-2 bone marrow-derived myeloid cells reprogram the glioma immunosuppressive tumor microenvironment

city: Columbus

first: Alessandro

last: Canella

state: OH

address: 700 Children’s Drive

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

summary:
Low-Grade Glioma RCAs mice were treated with one dose of Vehicle (PBS) or GEMys-IL2
We analized the tumor-infiltrating immune cells at day 3 post-treatment with GEMys-IL2, or Vehicle.

overall_design: Retro-orbital intravenous injection of Vehicle (80μl of PBS, n=3), or 8x106 GEMys-IL2 (80μl, n=3). Immune cells from the TME were isolated at day 3 post-treatment, and processed for Total RNA extraction and Total RNA sequencing.

first: Matthew

last: Nazzaro

first: Sakthi

last: Rajendran

first: Claire

last: Schmitt

first: Abigail

last: Haffey

first: Giovanni

last: Nigita

first: Diana

last: Thomas

first: Justin

last: Lyberger

first: Gregory

middle: K

last: Behbehani

first: Elaine

last: Mardis

first: Timothy

middle: P

last: Cripe

first: Prajwal

last: Rajappa


title: Gene expression profile at single cell level of in utero and ex vivo peri-implantation mouse embryos

city: Utrecht

first: Peter

last: Zeller

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

summary: We used single cell RNA sequencing (scRNA-seq) to analyze gene expression in mouse embryos reaching peri-implantation stages in utero and ex vivo.

overall_design: E4.5 and E5.25 embryos, dissected from the uterus, and day two and day three embryos, grown in 3E-uterus, were dissociated and analysed using scRNA-seq.

first: Vladyslav

last: Bondarenko

first: Marloes

last: Blotenburg


title: Exploring TCR-like CAR-Engineered Lymphocyte Cytotoxicity against MAGE-A4

first: Roman

last: Perik-Zavodskii

summary: In this work, we compared the expression profiles of Anti-MAGE-A4- transduced T-cells with Anti-MAGE-A4- transduced T-cells co-cultured with SK-Mel-37.

overall_design: We profiled total RNA from the anti-MAGE-A4-transduced TCR T-cells on NanoString Sprint Platform using Immunology V2 panel.


title: Total transcriptome analysis of Candida auris planktonic cells exposed to tyrosol

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

summary: Tyrosol, a secondary metabolite of Candida species, regulates fungal morphogenesis, and its application may represent a novel innovative therapy against emerging multi-resistant fungal superbug such as Candida auris. In the current study, the effects of tyrosol on growth, redox homeostasis, intracellular microelement contents and activities of virulence-related enzymes released by C. auris were examined. To gain further information about the effect of tyrosol exposure, we revealed gene transcriptional changes using total transcriptome sequencing (RNA-Seq). At a concentration of 15 mM, tyrosol significantly decrease the growth of fungal cells within 2 h of its addition (5.6 × 107±1.2 × 107 and 2.5 × 107±0.6 × 107 colony forming unit/mL for control and tyrosol-treated cells, respectively). Furthermore, it enhanced the release of reactive oxygen species as confirmed by a dichlorofluorescein (DCF) assay (7.3 ± 1.8 [nmol DCF (OD640)−1] versus 16.8 ± 3.9 [nmol DCF (OD640)−1]), which was coincided with elevated superoxide dismutase, catalase and glutathione peroxidase activities. Tyrosol exerted in a 37%, 25%, 34% and 55% decrease in intracellular manganese, iron, zinc and copper contents, respectively, compared to control cells. The tyrosol treatment led to a 142 and 108 differentially transcripted genes with at least a 1.5-fold increase or decrease in transcription, respectively. Genes related to iron and fatty acid metabolism as well as nucleic acid synthesis were down-regulated, whereas those related to the antioxidative defence, adhesion and oxoacid metabolic processes were up-regulated. This study shows that tyrosol significantly influences growth, intracellular physiological processes and gene transcription in C. auris, which could highly support the development of novel treatment approaches against this important pathogen.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of tyrosol treated and untreated Candida auris cultures.

first: Noémi

last: Balla

first: Ágnes

first: Fruzsina

last: Kovács

first: Ágota

last: Ragyák

first: Zoltán

last: Tóth

first: Dávid

last: Balázsi

first: Lajos

last: Forgács

first: Aliz

last: Bozó

first: Farah

last: Refai

first: Andrew

last: Borman

first: László

last: Majoros

first: Renátó


title: Single cell profiling of bone marrow adipocytes and bone marrow stromal cells from irradiated mice.

first: Lei

last: Ding

institute: Conlumbia University Irving Medical Center

summary: In order to comprehensively characterize bone marrow mesenchymal cells after myeloablation, single-nuclei RNA sequencing was performed on bone marrow adipocytes and bone marrow stromal cells isolated from sublethally-irradiated mice.

overall_design: Collected bone marrow adipocytes and sorted CD45/Ter119/CD31- cells from the bone marrow of Plin1-creER; tdTomato mice 5 weeks after sublethal irradiation were kept frozen until nuclei isolation. Cells were resuspended and extracted nuclei for single-nuclei RNA-seq (snRNA-seq).

first: L


title: Effect of overexpression of ELAPOR1 on gene expression of colorectal cancer cells

city: Shanghai

first: Chunzhi

last: Qin

address: 1508 Longhang Road, Jinshan District

institute: Jinshan Hospital, Fudan University

summary: To investigate the function of ELAPOR1 in the proliferation and invasion of colorectal cancer cells, we established SW620 cell lines in which ELAPOR1 is stably overexpressed using lentiviruses.

overall_design: We performed transcriptome sequencing of 3 ELAPOR1 groups and 3 vector groups, then analyzed the differentially expressed genes using  bioinformatics.

first: Anzhong

last: Huang

first: Dawei

last: Zhang

first: Binwu

last: Guang


title: Transcriptomic analysis of C. elegans mutants which fail to activate the oomycete recognition response

first: Michalis

last: Barkoulas

address: SAF Building, South Kensington

summary: We used RNA-seq to identify gene expression changes in C. elegans old-1(ok1273) and flor-1(icb93) mutants along with old-1 overexpression transgenic strains

overall_design: Comparative gene expression of oomycete extract treated L4 staged N2, old-1(ok1273) and flor-1(icb93) animals with untreated controls, along with animals overexpressing old-1 under its endogenous promoter (+old-1p::old-1) compared with non-transgenic animals from the same population as control; and animals overexpressing old-1 under epidermal promoter (+dpy-7p::old-1) compared with animals carrying the co-injection marker (hygromycin resistance) as control.

first: Florence

last: Drury

first: Manish

last: Grover

first: Mark

last: Hintze


title: Functional characterization of Alzheimer´s disease genetic variants in microglia

city: SAN FRANCISCO

first: Yin

last: Shen

state: CALIFORNIA

address: 513 Parnassus Ave

department: Department of Neurology

institute: UCSF

summary: Alzheimer’s disease (AD) is an age-related neurodegenerative progressive disorder affecting 10% of people over 65. Less than 5% of patients have known causal genetic mutations while the exact cause of AD for the majority of patients, especially the late onset form, is unknown. Large scale epigenomic studies revealed that disease associated SNPs are highly enriched in cell-type-specific cis-regulatory elements. In AD, SNPs are more significantly enriched in the regulatory regions of myeloid lineages rather than the neuronal cells. However, how AD SNPs affect microglia enhancers, and more interestingly differentially affect state-specific enhancers such as activated upon stimulation, e.g. viral infection, remain largely unexplored. In this study we identified cis-regulatory elements in both resting and IFN-beta stimulated microglia and further functionally characterized how regulatory SNPs lead to immune response dysregulation in the pathogenesis of AD.

overall_design: Examination of chomatin interactions in both resting and IFN-beta stimulated human iPSC derived microglia

first: Xiaoyu

last: Yang


overall_design: We pooled iPSC derived microglia, monocyte derived dendritic cells, monocyte derived macrophages, and fresh monocytes without or with treatment of IFNβ (100U/mL) for 6 hours in scRNA-seq. Each of these 4 cell types/ 2 conditions were labeled with individual hashtag (HashTAG001-008), pooled and loaded to 2 lanes of 10X Chromium. Sequencing data from each lane was processed separately and then aggregated using the Cell Ranger.


title: β3-adrenergic receptor on tumor-infiltrating lymphocytes sustains IFN-γ-dependent PD-L1 expression and impairs anti-tumor immunity in a murine model of neuroblastoma

city: Firenze

first: Gianluca

last: Mattei

state: FI

address: Via di S. Marta, 3

country: Italy

institute: Università degli Studi di Firenze

summary: A distinctive feature of neuroblastoma (NB) tumors is their ability to secrete neuroendocrine mediators such as catecholamines, which through β-adrenergic receptors ligation may influence different signaling pathways in the tumor microenvironment (TME). Here, we aimed to investigate whether the β3-AR modulation affected the host immune system response to NB tumor. In a murine syngeneic NB model, pharmacological β3-AR antagonism lead to an immune response reactivation and reduced tumor growth through the involvement of PD-1/PD-L1 signaling axis. Indeed, β3-AR blockade on tumor infiltrating lymphocytes (TILs) dampened their ability to secrete IFN-γ and reduced PD-L1 expression on NB tumor cells, preventing the establishment of an immune suppressive TME. Furthermore, genomic analysis on NB patients showed that high ADRB3 gene expression correlates with poor clinical outcome. Overall, these findings indicate that β3-AR is able to sustain an immune suppressive TME in NB via PD-1/PD-L1 crosstalk, and suggest that targeting β-adrenergic signaling in NB could represent a new strategy to overcome immune escape gateway.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NB murine tumors (derived from N2A tumor cells in A/J mice) treated with vehicle or SR59230A

first: Gennaro

last: Bruno

first: Alessia

last: Boaretto

first: Maura

last: Calvani


title: Genetic reporter for live tracing fluid flow forces during cell fate segregation in mouse blastocyst development

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

institute: Peking University

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

overall_design: Refer to individual Series


overall_design: We performed a pooled CRISPRi screen to functionally characterize putative cCREs at 5 AD risk loci, including TREM2, PICALM, BIN1, INPP5D, and SLC24A4/RIN3). The screen was repeated on two independent microglia differentiations.


title: Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis

city: Bei Jing

first: Hsiang-Ying

last: Lee

state: Bei Jing

address: Yiheyuan Road

summary: Erythropoiesis in mammalian involves chromatin compaction which is initiated in the early stage of terminal differentiation. The proper condensation of chromatin is essential for the subsequent enucleation of erythroblast, but the characteristics of chromatin compaction and chromatin architecture changes in erythropoiesis are poorly understood. Here, we show that the formation of H3K9me3 long-range interactions which mediated heterochromatin three-dimensional rewiring participant in human erythroid chromatin condensation. TADs structure attenuated and boundary strength weakened globally but selectively maintaining in active chromatin region during terminal erythropoiesis. We demonstrate that the erythroid master regulators GATA1 safeguard the active chromatin structure and ensure the appropriate gene expression, under the chromatin condensation of human terminal erythropoiesis

overall_design: Hi-C was performed on human Pro-, Ortho-erythroblast, KO-GATA1 and KO-control samples, and each sample has 2 replicates. The KO-KLF1 sample only has one replicate.

first: Dong

last: Li

first: Fan

last: Wu

first: Shuo

last: Zhou


overall_design: Examination of chromatin accessibility (ATAC-seq) in both resting and IFN-beta stimulated human iPSC and ESC-derived microglia


title: Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis [RNA-seq]

overall_design: RNA-seq was performed on Pro-erythroblasts and Orthochromatic erythroblast of human using cells cultured from cord blood CD34+ cells. Each sample has 2 replicates.


title: Genetic reporter for live tracing fluid flow forces during cell fate segregation in mouse blastocyst development [scRNA-seq]

summary: We performed single-cell RNA-seq in cultured embryos under shaking and static condition using Klf2-H2Bmcherry mice to screen an effective force reporter.

overall_design: Here we performed single cell RNA-seq analysis for isolating TE or ICM cells from shaking and static E3.5 mouse embryo

first: Xin

first: Yanzhu

last: Yue

first: Youdong

last: Zhang

first: Yuanhui

last: Liao

first: Min

last: Liu

first: Yingjie

last: Luo

first: Shu

last: Gao

first: Yunkun

last: Bian

first: Kexin

last: Xian

first: Aibin

last: He


first: Yin

last: Shen

overall_design: Examination of gene expression with RNA-seq in both resting and IFN-beta stimulated human iPSC and ESC-derived microglia.

first: Xiaoyu

last: Yang


title: ChIP-seq analysis for endogenous TFEB in EndoC-βH1 upon amino acid starvation

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

summary: Endogenous TFEB occupancy in human pancreatic beta cells undergoing nutrients depletion was evaluated using ChIPseq analysis to identify bona-fide TFEB targets

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for endogenous TFEB in EndoC-βH1 upon amino acid starvation in two biological replicates, each with its own input.

first: Margherita

last: Mutarelli

first: Susanna

last: D’Ambrosio

first: Gennaro

last: Tufano

first: Marcella

last: Cesana


title: Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis [HiChIP]

first: Hsiang-Ying

last: Lee

overall_design: GATA1-HiChIP and KLF1-HiChIP libraries were constructed on D12 erythroblast cells. H3K9me3-HiChIP libraries were constructed on human Pro-E and Ortho-E cells. And each sample has 2 replicates.

first: Dong

last: Li

first: Fan

last: Wu

first: Shuo

last: Zhou


title: Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis [CUT&RUN]

overall_design: CUT&RUN was performed on human Pro- and Ortho-erythroblast for H3K9me3, H3K27ac, KLF1, PolII, CTCF, SMC3, GATA1, and each sample has 2 replicates.


title: Male specific impact of parental care on gene expression in nucleus accumbens

city: Charlottesville

first: Joshua

last: Danoff

state: VA

address: 485 McCormick Road

institute: University of Virginia

summary: Mammalian infants depend on parental care for survival, with numerous consequences for their behavioral development. We investigated the epigenetic and neurodevelopmental mechanisms mediating the impact of early parental care on social behavior development in prairie voles. We find widespread male specific differential expression of genes related to synaptic transmission and autism in the nucleus accumbens.

overall_design: RNA-sequencing analysis of gene expression in bulk tissue nucleus accumbens of prairie voles raised in different early life environments

middle: S

first: Erin

last: Ramos

first: Taylor

middle: D

last: Hinton

first: Allison

last: Perkeybile

first: Andrew

last: Graves

first: Graham

last: Quinn

first: Aaron

middle: R

last: Lightbody-Cimer

first: Juozas

last: Gordevičius

first: Milda

last: Milčiūtė

first: Robert

last: Brooke

first: C

last: Carter

first: Karen

middle: L

last: Bales

first: Alev

last: Erisir

first: Jessica

last: Connelly


title: Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis [Mnase-seq]

first: Hsiang-Ying

last: Lee

overall_design: MNase-seq was performed on Pro-erythroblasts and Orthochromatic erythroblast of human using cells cultured from cord blood CD34+ cells. Each sample has 2 replicates.

first: Dong

last: Li


title: Transcriptome profile of ENDOC-BH1 cells silencing TFEB and TFE3 (siTFEB/TFE3) or controls

first: Rossella

last: De Cegli

summary: To analyze gene expression differences between cells silenced for TFEB and TFE3 vs. Controls, under growing conditions (GC) vs. Fasting conditions (Fast)

overall_design: Total RNA was extracted from n=4 for each conditions.

first: Adrien

last: Pasquier


title: Heterochromatin rewiring and domain disruption-mediated chromatin compaction during erythropoiesis [ATAC-sq]

overall_design: ATAC-seq was performed on Pro-erythroblasts and Orthochromatic erythroblast of human using cells cultured from cord blood CD34+ cells. Each sample has 2 replicates.

first: Fan

last: Wu

first: Shuo

last: Zhou


title: Transcriptome profile of INS-1E Ctrl and hTFEB OE cells

summary: To analyse gene expression differences between the human TFEB overexpressing cells vs. Controls, under growing conditions (GC) vs. Fasting conditions (Fast)

overall_design: Total RNA was extracted from n=4 for each conditions


title: Transcriptome profile of ENDOC-BH1 cells overexpressing TFEB-V5 or controls

summary: To analyse gene expression differences between the TFEB overexpressing cells vs. Controls, under growing conditions (GC) vs. Fasting conditions (Fast).

overall_design: Total RNA was extracted from n=4 for each condition. Sequencing could only be proceeded for 3 samples for TFEB OE GC.


title: Orchestration of a blood-derived and ADARB1-centred network in Alzheimer's and Parkinson's disease

status: Public on Jul 30 2023

city: Shenyang

first: Zhijie

last: Song

state: Liaoning

address: Huanghe North street No.146

institute: Shenyang Medical College

type: Non-coding RNA profiling by high throughput sequencing

summary: The peripheral immune system is thought to influence the pathogenesis of the central nervous system in Alzheimer’s disease (AD) and Parkinson’s disease (PD). This study aimed to investi-gate the characteristics of peripheral leukocytes in AD and PD by comprehensively analyzing the transcriptomic and metabolic features in the blood (NCONTROL = 15; NAD = 11; NPD = 13). The study found an ADARB1-centered module that was associated with diagnosis, phenethylamine, and glutamate. The module consisted of ADARB1, a vital RNA-editing enzyme, LINC02960, and 109 miRNAs. The study also predicted that the ADARB1 and involved regulators were targeted by miRNAs in the ADARB1 module. The integrated analysis of transcriptome and metabolic panel revealed a central role of ADARB1, miR-199b-5p, miR-26a, miR-450b-5p, miR-34c-5p, glutamate and phenethylamine in the regulatory relationships. The study highlights a set of synergetic non-coding RNA related to ADARB1 in the blood ecosystem of AD and PD with dy-namic glutamate and phenethylamine, providing new insights into the pathogenesis of these diseases.

overall_design:
To better understand the relationship between peripheral blood leukocyte and brain-based epigenetic activity in the context of Alzheimer's disease (AD) and Parkinson's disease (PD), we conducted a pilot study on peripheral blood leukocytes by comprehensively analysing transcriptomic and metabolic features in blood (NCONTROL = 15; NAD = 11; NPD = 13). Using next-generation sequencing, we identified 766 miRNAs and 19,512 mRNAs/lncRNAs after removing low-quality reads and low-abundance RNAs. Using LC-MS/MS, we identified 8 DE metabolites of 7 short-chain fatty acids and 23 neurotransmitters. Using a comprehensive integrative analysis of multi-omics data, we identified an ADARB1-centred co-expression sub-network consisting of ADARB1, LINC02960 and 109 miRNAs simultaneously correlated with diagnosis, glutamate and phenethylamine. A putative interaction within the ADARB1 module was raised in the blood ecosystem of AD and PD.

**RAW data not provided due to relevant law**

first: Qingqing

last: Ding

first: Yan

last: Yang


title: Transcriptome profile of INS-1E Ctrl and DKO cells

summary: To analyse gene expression differences between the TFEB/TFE3 KO cells vs. Controls, under growing conditions (GC) vs. Fasting conditions (Fast)


title: Transcriptome profile of isolated murine islets overexpressing TFEB or controls

summary: To analyse gene expression differences between the TFEB overexpressing islets vs. Controls.

overall_design: Total RNA from isolated islets of single mouse was extracted from n=4 for control and n=3 for TFEB OE mice.


title: Transcriptome profile of ENDOC-BH1 cells and isolated murine islets modulating TFEB expression

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: The effect of KIF11 knockdown on gene expression profile in HepG2 cells

city: Hefei

first: Pengfei

last: Zhang

address: 443 Huang-Shan Road

department: School of Life Sciences

institute: University of Science and Technology of China

summary: High-throughput sequencing is performed to identify the genes whose expression levels were altered when KIF11 is downregulated by lentiviruses-mediated shRNA in HepG2 cells.

overall_design: The expression of KIF11 was knocked down by lentiviruses-mediated shRNA in HepG2. The control and KIF11-deficient HepG2 cells were subjected to High-throughput sequencing and mRNA expression profile data analyzing.

first: Danlei

last: Chen

first: Lianxin

last: Liu


title: HIF-1 regulates pathogenic T cells in lupus skin disease

city: New Haven

first: Alicia

middle: J

last: Little

state: CT

address: 333 Cedar St, PO Box 208059

department: Dermatology

institute: Yale University


title: Effect of overexoression LOC646029 on gene expression in 3AO cells

last: Zhao

address: No.17, Panjiayuan Nanli, South Huawei Road

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

summary: To investigate the function of LOC646029 in ovarian cancer progression, we constructed 3AO cell lines overexpressing LOC646029 and the corresponding empty vector. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.

overall_design: Comparative gene expression profiling of RNA-seq data from 3AO cells expressing LOC646029 and empty vector

first: Yating

last: Wang

first: Xiao

last: Yu

first: Yabing

first: Shi

first: Bin

first: Zhumei

last: Cui

first: Zhihua


title: Genetic reporter for live tracing fluid flow forces during cell fate segregation in mouse blastocyst development

first: Haiqing

last: Xiong

summary: We used a robut low input cell and high throughput in-situ ChIP method to emphasize regulation mechanism among E3.5 klf2, E3.5 klf4 and E12.5 EC klf2.

overall_design: We fused Protein A to the N-terminal of Tn5 to generated Protein A-Tn5 fusion enzyme, the ProteinA-Tn5-complex is enriched through specific antibodies to genomic regions and Tn5 generates indexed chromatin fragments ready for the library preparation and sequencing

first: Youdong

first: Xin

first: Shu

last: Gao

first: Yuanhui

last: Liao

first: Yingjie

last: Luo

first: Min

first: Yunkun

last: Bian

first: Yanzhu

last: Yue

first: Aibin

last: He


title: Unambiguous detection of SARS-CoV-2 subgenomic mRNAs with single cell RNA sequencing

city: New York

first: Brad

last: Rosenberg

address: 1 Gustave L Levy Place, Box 1124

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent responsible for the ongoing pandemic of coronavirus disease 2019 (COVID-19). Single cell RNA sequencing (scRNAseq) studies have been valuable for studying SARS-CoV-2 pathogenesis, but the performance of these methods to detect and quantify viral RNAs has not been evaluated. Here we develop an analysis pipeline, single cell coronavirus sequencing (scCoVseq), to quantify unambiguous reads derived from coronavirus genomic (gRNA) and subgenomic mRNAs (sgmRNAs). We use this method to compare the ability of scRNAseq methods developed by 10X Genomics to detect and quantify SARS-CoV-2 RNAs, with particular focus on sgmRNAs. We find that while sequencing libraries from 10X Genomics Chromium Next Gem Single Cell V(D)J (10X 5') contain more unambiguous reads derived from sgmRNAs due to the presence of reads spanning junctions between the viral 5' leader and sgmRNA open reading frames. We demonstrate that by extending read 1 (R1) of 10X 5' leaders we can further increase the number of unambiguous reads from SARS-CoV-2 sgmRNA resulting in more UMIs per sgmRNA per cell. Using this method, which we call 10X 5' Extended R1, we are able quantify viral sgmRNA production per cell, which we believe will improve understanding regarding the dynamics of coronavirus RNA biogenesis over time and across cell types and viruses. We believe this will improve our understanding of coronavirus pathogenesis.

sample_organism:
Chlorocebus aethiops
Homo sapiens

platform_organism:
Chlorocebus aethiops
Homo sapiens

overall_design: Single cell RNA sequencing of mock and SARS-CoV-2 infected Vero E6 cells performed with either 10X Genomics Chromium Next GEM Single Cell 3' (10X 3') or 10X Genomics Chromium Next GEM Single Cell V(D)J (10X 5').

first: Phillip

last: Cohen


title: High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins (ETS1 and RUNX1)

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

summary: Cooperative DNA-binding by transcription factor (TF) proteins is critical for gene expression regulation in eukaryotes. In the human genome, many regulatory regions contain TF binding sites in close proximity to each other, which can facilitate cooperative interactions. However, binding site proximity does not necessarily imply cooperative binding, as two TFs could also bind independently to each of their neighboring target sites. Currently, the rules that drive cooperative versus independent binding of TFs to neighboring sites are not well understood. In addition, it is oftentimes difficult to infer direct cooperativity between TFs from existing DNA-binding data. Here, we show that in vitro binding assays using DNA libraries of a few thousand genomic sequences with putative cooperative TF binding events can be used to develop accurate models of cooperativity and to gain insights into cooperative binding mechanisms. Using human factors ETS1 and RUNX1 as our case study, we show that the distance and orientation between ETS1 sites are critical determinants of cooperative ETS1-ETS1 binding, while cooperative ETS1- RUNX1 interactions show more flexibility in distance and orientation and can be accurately predicted based on binding affinity and the sequence/shape features of the binding sites. The approach described here, combining custom experimental design with machine learning modeling, can be easily applied to study the cooperative DNA-binding patterns of any TFs.

overall_design: We performed cooperative gcPBM (genome-context protein binding microarray) experiments  for recombinant, full-length, human transcription factors Ets1 and Runx1. Briefly, the PBMs involved binding of GST-tagged Ets1 and/or GST-tagged Runx1 to double-stranded 4x180k Agilent microarrays in order to identify Ets1-Runx1 cooperative binding events. Each genomic DNA sequence represented on the array is present in 8 replicate spots, four for each orientation. We report the PBM signal intensity of Ets1 and/or Runx1 for each spot.


title: High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins (ETS1 only)

overall_design: We performed cooperative gcPBM (genome-context protein binding microarray) experiments  for recombinant, full-length, human transcription factor Ets1. Briefly, the PBMs involved binding of GST-tagged Ets1 to double-stranded 4x180k Agilent microarrays in order to identify Ets1-Ets1 cooperative binding events. Each genomic DNA sequence represented on the array is present in 6 replicate spots, three for each orientation. We report the PBM signal intensity of Ets1 for each spot.


title: High-throughput data and modeling reveal insights into the mechanisms of cooperative DNA-binding by transcription factor proteins


title: Silc1 long noncoding RNA is required for efficient memory formation

status: Public on Jul 29 2023

first: Igor

last: Ulitsky

address: Hertzl St.

institute: Weizmann Institute of Science

summary: A rich repertoire of long noncoding RNAs (lncRNAs) is expressed in the mammalian nervous system, but their significance and functions remain largely unknown. Co-expression analysis, referred to as guilt-by-association, is often used as a proxy for prediction of lncRNA function, but the validity of the assumptions of this approach remains unclear. Here, we study the functions in the central nervous system of Silc1, a lncRNA we previously shown to be important for neuroregeneration in the peripheral nervous system. Silc1 is located in a gene desert ~200 Kb away from its cis-regulated target gene, Sox11. Silc1 is broadly expressed in the adult brain, and surprisingly, in the hippocampus Silc1 and Sox11 are anti-correlated in their expression domains. Despite this, upon exposure to novel environment, Silc1 transcription or its RNA product are important for proper induction of Sox11 mRNA and protein throughout CA1-3, and for proper expression of key Sox11 target genes. Furthermore, an intact Silc1 is required for efficient spatial learning (but notably not for memory retrieval). Silc1 levels decline during aging and in models of Alzheimer’s disease. Overall, we uncover a novel pathway, acting in mature neurons, which need Silc1 to activate Sox11, a transcription factor mostly studied exclusively in the context of immature neurons, and in turn to induce a neuronal growth-associted transcriptional program required for efficient memory formation.

overall_design: RNA-seq and ATAC-Seq from hippocampus following different manipulations and RNA-seq from cultured hippocampus neurons. Single-nucleus RNA sequencing from hippocampus in WT and Silc1-/- hippocampus

first: Rotem

last: Ben-Tov Perry


title: Gene expression profile at single cell level of patient-derived colon fibroblasts induced by different cytokine cocktails to become inflammation-associated fibroblasts (IAFs)

city: Baltimore

first: Rong

last: Li

address: 855 N. Wolfe St., Suite 440.

department: Cell Biology

institute: Johns Hopkins School of Medicine

summary: IAFs are associated with the progression and drug resistance of chronic inflammatory diseases such as inflammatory bowel disease (IBD), but their direct impact on epithelial function and architecture is unknown. One major problem is that IAFs do not persist after in vitro culture. Here we used single cell RNA sequencing (scRNA-seq) to validate and analyze the diversity of different cytokine-induced IAFs.

overall_design: Eight patient-derived colon fibroblast lines were generated and treated with no treatment (earlier passage), no treatment (older passage), IL1β+TNFα, IL4+IL13+TNFα, or TNFα for 96hrs. After treatment, fibroblasts were dissociated and sorted into single cells and analyzed using scRNAseq.

first: Dong

last: Yi

first: Larman

last: Tatianna

first: Li

last: Rong


title: Title Multi-generational mRNA sequence data of pooled Drosophila melanogaster male and female flies from populations selected for long or short night sleep

city: Bethesda

first: Susan

middle: T

last: Harbison

address: 10 Center Drive, Bldg. 10, Rm. 7D13

department: Center for Systems Biology

institute: National Heart Lung and Blood Institute

summary: Our objective was to determine whether gene expression in Drosophila melanogaster selectively bred for long or short night sleep duration changes detectably across generations.  To meet this objective, we performed transcriptional profiling of ten pooled whole adult individuals from four selected populations and two control populations across 13 generations.  We quantified differential expression among selection scheme (long sleep, short sleep, or unselected control), generation (generation 0; then generations 2-13), and sex for each gene.

overall_design: We created four Drosophila melanogaster populations selected for long and short night sleep duration and two unselected control populations. The Sleep Advanced Intercross Population (SAIP) was the outbred starting population used, which originated from lines of the Drosophila Genetic Reference Panel (DGRP) (Serrano Negron et al., G3, 2018, PMID: 29991508).  We selected flies for long and short night sleep for 13 generations under controlled environmental conditions.   We seeded the fly culture bottles with 25 male and 25 female parents each generation. We reared the flies on standard Drosophila food at 25°C, 60% humidity, and a 12:12-hour light:dark cycle. Each generation, we collected 100 virgin males and 100 virgin females from each of the six population bottles and maintained the virgins at 20 individuals to a same-sex vial for four days. We then measured sleep for four days. After the sleep measurements, virgin flies were frozen for RNA extraction at the same circadian time (12:00 pm). For the starting generation (0) and generations 2-13, we randomly froze virgin male and virgin female flies from the sleep assays for RNA extraction.  Ten males and ten females were frozen in two same-sex replicates from each of the six populations to generate 24 mRNA sequence profiles per generation.  RNA was extracted using Qiazol (Qiagen, Hilden, Germany), followed by phenol-chloroform extraction, isopropanol precipitation, and DNase digestion (Qiagen, Hilden, Germany).  To purify RNA, we used Qiagen RNeasy MinElute Cleanup kits (Qiagen, Hilden, Germany). We constructed Poly-A selected stranded mRNA libraries using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA). We added unique barcode adaptors to each sample. We conducted paired end sequencing using pooled libraries on an Illumina HiSeq2500 for a minimum of 38 million 126 base read pairs.  Reads were mapped to FlyBase release 6 version 07 of the Drosophila melanogaster genome.  Mapped reads were counted at the gene level.

first: Caetano

last: Souto-Maior

first: Yazmin

last: Serrano Negron


title: SETD1A function is mediated through interaction with mitotic regulators BuGZ/BUB3 in leukemia [RNA-seq]

city: Chiba

first: Masaki

last: Fukuyo

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

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

summary: The H3K4 methyltransferase SETD1A plays a crucial role in leukemia cell survival through its non-catalytic FLOS domain mediated recruitment of cyclin K and regulation of DNA damage response genes. In this study, we identify a functional nuclear localization signal and interaction partners for the FLOS domain. Our proteomics analysis against FLOS domain-binding partners reveals that the SETD1A FLOS domain binds mitosis-associated proteins BuGZ/BUB3. Targeted inhibition of both cyclin K and BuGZ/BUB3 binding motifs on SETD1A shows synergistic anti-leukemic effects. BuGZ/BUB3 localize to SETD1A-positive promoter-TSS regions and SETD1A-negative H3K4me1-positive enhancer regions adjacent to SETD1A-target genes. The GLEBS motif and intrinsically disordered region of BuGZ are required for both SETD1A binding and the leukemia cell proliferation. Despite the role of BuGZ/BUB3 at mitotic phase, the cell-cycle specific SETD1A restoration study indicates the roles of SETD1A at G1/S phase of cell cycle. Discovery of this complex indicates the indispensable role of the SETD1A-BuGZ axis in cancer.

overall_design:
1) Examination of SETD1A, BuGZ and BUB3 targets in human MOLM-13 leukemia cell line,
2) Examination of BuGZ and SETD1A knockdown in human MOLM-13 leukemia cell line.
3) Examination of SETD1A knockout and rescue in mouse MLL-AF9 leukemia cell line.

first: Takayuki

last: Hoshii

first: Sarah

last: Perlee

first: Sota

last: Kikuchi

first: Bahityar

last: Rahmutulla

first: Atsushi

last: Kaneda


title: The effect of ZSWIM8 knockout on RNA levels in tissues of E18.5 mouse embryos [scRNA-seq]

status: Public on Jul 28 2023

city: Cambridge

first: Charlie

middle: Y.

last: Shi

state: MA

address: 455 Main St.

department: Biology

institute: Whitehead Institute / MIT

summary: MicroRNAs (miRNAs) pair to sites in mRNAs to direct the degradation of these RNA transcripts. Conversely, certain RNA transcripts can direct the degradation of particular miRNAs. This target-directed miRNA degradation (TDMD) requires the ZSWIM8 E3 ubiquitin ligase. Here, we report the function of ZSWIM8 in the mouse embryo. Zswim8–/– embryos were smaller than their littermates and died near the time of birth. This highly penetrant perinatal lethality was apparently caused by a lung sacculation defect attributed to failed maturation of alveolar epithelial cells. Some mutant individuals also had heart ventricular septal defects. These developmental abnormalities were accompanied by aberrant accumulation of >50 miRNAs observed across 12 tissues, which often led to enhanced repression of their mRNA targets.

overall_design: Single-cell RNA sequencing (scRNA-seq) from lungs of Zswim8+/– and Zswim8–/– E18.5 mouse embryos

middle: Y

first: David

last: Bartel


title: Effect of depletion of hepatocellular STAT3 on alcohol-treated liver tissue

city: Guangzhou

last: Lin

address: No.1838, Guangzhou Avenue North

institute: Southern Medical University

summary: To investigate the influence of hepatocellular STAT3 activation on liver under alcohol condiction, mice of Stat3 condictional knock-out in hepatocytes were treated by alcohol for 2 weeks.

overall_design: Comparative liver tissue gene expression profiling analysis of RNA-seq data for Stat3flox/flox;Alb-Cre and its control Stat3flox/flox mice after 2-week alcohol (20% alc/vol, 15 µL/g) daily gavage


title: SETD1A function is mediated through interaction with mitotic regulators BuGZ/BUB3 in leukemia [ChIP-seq]


title: ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development

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


title: The effect of ZSWIM8 knockout on miRNA levels in tissues of E18.5 mouse embryos [sRNA-seq]

overall_design: Small RNA sequencing (sRNA-seq) from tissues of Zswim8+/– and Zswim8–/– E18.5 mouse embryos


title: The effect of ZSWIM8 knockout on RNA levels in tissues of E18.5 mouse embryos [RNA-seq]

summary: MicroRNAs (miRNAs) pair to sites in mRNAs to direct the degradation of these RNA transcripts. Conversely, certain RNA transcripts can direct the degradation of particular miRNAs. This target-directed miRNA degradation (TDMD) requires the ZSWIM8 E3 ubiquitin ligase. Here, we report the function of ZSWIM8 in the mouse embryo. Zswim8-/- embryos were smaller than their littermates and died near the time of birth. This highly penetrant perinatal lethality was apparently caused by a lung sacculation defect attributed to failed maturation of alveolar epithelial cells. Some mutant individuals also had heart ventricular septal defects. These developmental abnormalities were accompanied by aberrant accumulation of >50 miRNAs observed across 12 tissues, which often led to enhanced repression of their mRNA targets.

overall_design: RNA sequencing from tissues of Zswim8+/- and Zswim8-/- E18.5 mouse embryos


title: Next generating sequencing of primary murine WT and Gpr44 knockout leukemia-initiating cells in acute myeloid leukemia (AML) induced by MLL-AF9 oncogene

city: University Park,

first: Sandeep

last: Prabhu

state: Pennsylvania

address: 108 K Animal & Veterinary and Biomedical Sciences (AVBS) Building

department: Veterinary and Biomedical Science

institute: the Pennsylvania State University

summary: Knockout of GPR44 results in increased aggressiveness in AML leukemia-initiating cells, leading to worsened outcome in AML mice

overall_design: mRNA profiles of WT and Gpr44 knockout leukemia-initiating cells (Lin-Sca-1-c-Kit+) isolated from bone marrow of transplanted mice and normal counterparts (Lin-Sca-1-c-Kit+) isolated from bone marrow of WT, Gpr44+/-, Gpr44-/- mice (cells are all female source)

first: Fenghua

last: Qian

first: Robert

last: Paulson


title: SETD1A function is mediated through interaction with mitotic regulators BuGZ/BUB3 in leukemia.


title: Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors [ChIP-seq]

city: Bunkyo-ku

first: Ryuichiro

last: Nakato

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

institute: The University of Tokyo

summary: Cohesin plays vital roles in chromatin folding and gene expression regulation, cooperating with such factors as cohesin loaders, unloaders, and the insulation factor CTCF. Although models of regulation have been proposed (e.g., loop extrusion), how cohesin and related factors collectively or individually regulate the hierarchical chromatin structure and gene expression remains unclear. We have depleted cohesin and related factors and then conducted a comprehensive evaluation of the resulting 3D genome, transcriptome and epigenome data. We observed substantial variation in depletion effects among factors at topologically associating domain (TAD) boundaries and on interTAD interactions, which were related to epigenomic status.

overall_design: Chromatin preparation for ChIP was performed as described (Izumi et al., Nat Genet. 2015, 10.1038/ng.3229). In brief, ~8 × 10^6 RPE cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by an additional 5 min with glycine in PBS added at a final concentration of 125 mM. Fixed cells were lysed in LB1 (50 mM HEPES-KOH, pH 7.4; 140 mM NaCl; 1 mM EDTA; 10% glycerol; 0.5% NP-40; 0.25% Triton X-100; 10 mM dithiothreitol; 1 mM PMSF) on ice. The lysate was washed sequentially with LB2 (20 mM Tris-HCl, pH 8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1 mM PMSF) and LB3 (20 mM Tris-HCl, pH 7.5; 150 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1% Triton X-100; 0.1% sodium deoxycholate; 0.1% SDS; 1× cOmplete protease inhibitor cocktail [Roche]) on ice. The lysate was resuspended in LB3 and sonicated using Branson Sonifier 250D (Branson) for chromatin shearing (12 sec with amplitude setting at 17% of the maximum amplitude, six times). In addition, lysate containing fragmented chromatin was also prepared from ~2 × 10^6 mouse cells (C2C12) with the same procedures. Human cell lysate and mouse cell lysate (as a spike-in internal control) were combined (~4:1 ratio) and incubated with protein A or G Dynabeads (Thermo Fisher Scientific) conjugated with the relevant antibodies for 14 h at 4℃. The beads were then washed five times with cold RIPA wash buffer (50 mM HEPES-KOH, pH 7.4; 500 mM LiCl; 1 mM EDTA; 0.5% sodium deoxycholate; 1% NP-40) and once with cold TE50 (50 mM Tris-HCl, pH 8.0; 10 mM EDTA). Material captured on the beads was eluted with TE50 containing 1% SDS. The eluted material and input were incubated for 6 h at 65℃ to reverse crosslinks and were treated with 100 ng RNaseA (Roche) for 1 h at 50℃, followed by treatment with 100 ng Proteinase K (Merck) overnight at 50℃. The input and ChIP DNA were then purified with a PCR purification kit (Qiagen). DNA from the ChIP and input fractions was end-repaired, ligated to sequencing adaptors, amplified and size-selected using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) and Agencourt AMPure XP (Beckman Coulter). DNA was then sequenced to generate single-end 65-bp reads using the Illumina HiSeq-2500 system.

first: Toyonori

last: Sakata

first: Masashige

last: Bando

first: Katsuhiko

last: Shirahige


title: Liver of alcohol-treated mouse

first: Li

address: No.1838, Guangzhou Avenue North, Guangzhou, China

summary: The mice were administered 20% edible alcohol (15 µL/g) by gavage daily for 2 weeks, while the control group was administered normal saline solution.

overall_design: Liver mRNA profiles of normal saline or alcolhol-treated mice.


title: IKKa kinase coordinates BRD4 and JAK/STAT signaling to subvert DNA damage-based anticancer therapy

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

institute: Hospital del Mar

summary:
Activation of the IKK kinase complex has recurrently been linked to colorectal cancer (CRC) initiation and progression. However, identification of downstream effectors other than NF-B has remained elusive.
Analysis of IKK-dependent substrates after UV-treatment revealed that BRD4 phosphorylation by IKK is required for chromatin-binding dynamics upon damage. Moreover, IKK induces the NF-B-dependent transcription of LIF leading to STAT3 activation, association of BRD4 to STAT3 and recruitment to specific target genes. IKK abrogation results in defective BRD4 and STAT3 function leading to irreparable DNA damage and apoptotic cell death upon different stimuli. Simultaneous inhibition of BRAF-dependent IKK activity or BRD4 and the JAK/STAT pathway enhanced the therapeutic potential of 5-FU plus irinotecan in CRC cells, and is curative in a chemotherapy-resistant CRC xenograft model. Coordinated expression of LIF and IKK is a poor prognosis marker for CRC patients.
Our data uncover a functional link between IKK, BRD4 and JAK/STAT signaling with clinical relevance.

overall_design: 6 samples analyzed, plus two different inputs

middle: E

last: Blay

first: Irene

last: Pecharromán

first: Yolanda

last: Guillén


title: Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors [RNA-seq]

overall_design: Total RNA was isolated using Trizol (Thermo Fisher Scientific) and a Nucleospin RNA kit (Macherey-Nagel). rRNA was removed with the Ribo-Zero Gold rRNA Removal Kit (Illumina), followed by sequencing library preparation with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).


title: Glomerular-tubular crosstalk via cold shock Y-box binding protein-1 in the kidney

status: Public on Jul 27 2023

city: Leipzig

first: Berend

last: Isermann

address: Paul List Str. 13/15

department: Medical Faculty

institute: University of Leipzig

summary: Glomerular-tubular crosstalk within the kidney has been proposed, but the paracrine signals enabling this remain largely unknown. The cold-shock protein Y-box binding protein 1 (YBX1) is known to regulate inflammation and kidney diseases but its role in podocytes remains undetermined. Therefore, we analyzed mice with podocyte specific Ybx1 deletion (Ybx1ΔPod). Albuminuria was increased in unchallenged Ybx1ΔPod mice, which surprisingly was associated with reduced glomerular, but enhanced tubular damage. Tubular toll-like receptor 4 (TLR4) expression, node-like receptor protein 3 (NLRP3) inflammasome activation and kidney inflammatory cell infiltrates were all increased in Ybx1ΔPod mice. In vitro, extracellular YBX1 inhibited NLRP3 inflammasome activation in tubular cells. Co-immunoprecipitation, immunohistochemical analyses, microscale cell-free thermophoresis assays, and blunting of the YBX1-mediated TLR4-inhibition by a unique YBX1-derived decapeptide suggests a direct interaction of YBX1 and TLR4. Since YBX1 can be secreted upon post-translational acetylation, we hypothesized that YBX1 secreted from podocytes can inhibit TLR4 signaling in tubular cells. Indeed, mice expressing a non-secreted YBX1 variant specifically in podocytes (Ybx1PodK2A mice) phenocopied Ybx1ΔPod mice, demonstrating a tubular-protective effect of YBX1 secreted from podocytes. Lipopolysaccharide-induced tubular injury was aggravated in Ybx1ΔPod and Ybx1PodK2A mice, indicating a pathophysiological relevance of this glomerular-tubular crosstalk. Thus, our data show that YBX1 is physiologically secreted from podocytes, thereby negatively modulating sterile inflammation in the tubular compartment, apparently by binding to and inhibiting tubular TLR4 signaling. Hence, we have uncovered an YBX1-dependent molecular mechanism of glomerular-tubular crosstalk.

overall_design: RNA was isolated from whole kidney of wild-type mice (C57Bl/6N) and Ybx1ΔPod and Ybx1PodK2A (Ybx1K2A)  mice at 16 weeks of age.

first: B

first: R

last: Rana


title: Emerging Aeromonas enteric infections: their association with inflammatory bowel disease and novel pathogenic mechanisms

city: Sydney

last: Zhang

state: NSW

address: Botany Street

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary: The intestinal epithelial gene responses to Aeromonas veronii infection and the pathogenic mechanisms were investigated by comparative differential expression analysis

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HT-29 cells with and without Aeromonas veronii treatment, and cells treated with Escherichia coli strain K12 were used as control


title: Gain-of-function genetic perturbationssimultaneouslyacross500 barcoded cancer cell lines

first: Sellers

last: Lab

address: 415 Main St

institute: Broad Institute

summary: Using thisapproach, wequeriedthe pan-cancer vulnerability landscape upon activating 10key pathway nodes, revealing selectiveactivation dependenciesof MAPK and PI3K pathwaysassociatedwith specific biomarkers

overall_design: To profile activation of the curated gene sets across a broad panel of cell lines, we developed a high-throughput method for systematically examining the growth-suppressive effect of ORF expression in ~500 cancer cell lines. We next tested the perturbation effects of 11 ORFs (including GFP as a negative control) by lentiviral infection of each ORF encoding virus into separate pools of 488 cell lines.

first: Liang

last: Chang

first: Matthew

last: Rees

first: Jennifer

last: Roth

first: Melissa

last: Ronan

first: Mustafa

last: Kocak


title: Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors

first: Ryuichiro

last: Nakato

overall_design: Refer to individual Series


title: Gene expression profiling of bone marrow and lung ILC2s

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research (BDR)

institute: RIKEN

summary: We found that CD45, a membrane bound tyrosine phosphatase important for T cell development, negatively regulated ILC2s in a cell-intrinsic manner. ILC2s in CD45-deficient mice exhibited enhanced proliferation and maturation in bone marrow and hyperactivated phenotypes in lung with alteration of cell metabolism.

overall_design: Examination two hundred of ILC2s freshly sorted from bone marrow and lung of CD45-deficient and control mice

first: Guangwei

last: Cui

first: Jianshi

last: Jin

first: Nozomi

last: Hojo

first: Koichi

last: Ikuta


title: Feeding Neurons Integrate Metabolic and Reproductive States in Mice

city: Los Angeles

first: John

middle: Edward

last: van Veen

state: CA

address: 610 Charles E young Dr

department: Integrative Biology and Physiology

institute: UCLA

summary: Metabolic and reproductive processes interact in ways that are important for survival, particularly in mammals that gestate their young. Puberty and reproduction, as energetically taxing life stages, are often gated by metabolic availability in animals with ovaries. How the nervous system coordinates these interactions is an active area of study. We identify somatostatin (SST) neurons of the tuberal hypothalamus as a cell type in the feeding circuitry that alters feeding in a manner sensitive to metabolic and reproductive states in mice. Whereas chemogenetic activation of SST neurons increased food intake across sexes, selective ablation decreased food intake only in female mice during proestrus. Interestingly, this ablation effect was only apparent in animals with a low body mass. Fat transplantation and bioinformatics analysis of SST neuronal transcriptomes revealed white adipose as a key modulator of the effects of SST neurons on food intake. Together, these studies point to a mechanism whereby SST hypothalamic neurons modulate feeding by responding to varying levels of circulating estrogens differentially based on energy stores. This research provides insight into how neural circuits integrate reproductive and metabolic signals and illustrates how gonadal steroid modulation of neuronal circuits can be context-dependent and gated by metabolic status.

overall_design: RNA seq data from neurons FACS isolated from the mouse tuberal hypothalamus. Derived from n=4 male mice and n=4 female mice

first: Megan

last: Massa

first: Rachel

last: Scott

first: Alexandra

last: Cara

first: Laura

last: Cortes

first: Paul

middle: B

last: Vander

first: Norma

last: Sandoval

first: Jae

middle: W

last: Park

first: Sahara

last: Ali

first: Leandro

last: Velez

first: Heui-Bin

last: Wang

first: Shomik

last: Ati

first: Bethlehem

last: Tesfaye

first: Karen

last: Reue

first: J

first: Marcus

last: Seldin

first: Stephanie

last: Correa


title: Functional characterization of Alzheimer´s disease genetic variants in microglia

city: SAN FRANCISCO

first: Yin

last: Shen

address: 513 Parnassus Ave

institute: UCSF


title: Gene expression profiling in prostate cancer cell line LNCaP.

city: Boston

first: Shaoyong

last: Chen

state: Massachusetts

address: 3 Blackfan Circle, CLS-432

department: Hem/Onc

institute: Boston BIB

summary:
Global definition of androgen and anti-androgen effects on LNCaP transcriptomes using Affymetrix U133A oligonucleotide microarray.
LNCaP in androgen-depleted medium was treated with androgen (DHT) and anti-androgen (CPA) for different time points (2 hours, 4 hours, 8 hours, and 24 hours). Untreated or Vehicle (Ethanol) treated samples as control.

overall_design:
Total RNA was extracted from duplicate LNCaP samples using Trizol reagent. Biotin-labeled cRNA was generated and hybridized to Affymetrix U133A oligonucleotide microarrays as described (PMID: 10521349). The expression files were normalized across the arrays, and genes expressed below 10 were filtered out. For each gene, the average expression level in the control samples (no treatment or Vehicle-treated) was set as 1.0, and expression at each time point in the treated samples was expressed as fold change relative to this value.
Submitter states that raw data files are not available.

first: Youyuan

last: Xu

first: Steven

last: Balk

first: Xin

last: Yuan


title: Murine Bone Marrow Erythroid Cells Have Two Branches of Differentiation Defined by the Presence of CD45 and a Different Immune Transcriptome Than Fetal Liver Erythroid Cells

city: Novosibirsk

first: Roman

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

summary:
Ter-119 is a better murine erythroid selection marker than CD71 for bulk immunomics, murine bone marrow and fetal liver erythroid cells have different antimicrobial immune transcriptome signatures, murine bone marrow erythropoiesis is comprised of two branches
In this study, we decided to benchmark erythroid cells’ selection and enrichment markers – CD71 and Ter-119 via bulk immune transcriptomics by Nanostring and perform bulk immune transcriptome profiling of Ter-119+ erythroid cells from the bone marrow and the fetal liver by Nanostring.

overall_design:
We profiled total RNA from either CD71+ erythroid cells (CECs) or Ter-119+ erythroid cells from the bone marrow and Ter-119+ erythroid cells from the fetal liver on NanoString Sprint Platform using Mouse Immunology V1 panel.
We performed mRNA profiling for 561 target genes,  14 housekeeping genes,  8 negative and 6 positive spike-in controls


title: Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors [Hi-C]

first: Ryuichiro

last: Nakato

overall_design: We used the in situ Hi-C protocol as described in Rao et al. (Rao et al., Cell, 2014, 10.1016/j.cell.2014.11.021). In brief, ~3 × 10^6 RPE cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by an additional 5 min with 200 mM glycine in phosphate-buffered saline (PBS). Fixed cells were permeabilized in Hi-C lysis buffer (10 mM Tris-HCl, pH 8.0; 10 mM NaCl; 0.2% Igepal CA630; 1× protease inhibitor cocktail [Sigma]) on ice. The cells were treated with 100 U of MboI (New England Biolabs) for chromatin digestion, and the ends of digested fragments were labeled with biotinylated nucleotides followed by ligation. After DNA reverse crosslinking and purification, ligated DNA was sheared to a size of 300–500 bp using a Covaris S2 focused-ultrasonicator (settings: Duty Cycle, 10%; Intensity, 4; Cycles per Burst, 200; Duration, 55 sec). The ligated junctions were then pulled down with Dynabeads MyOne Streptavidin T1 beads (Thermo Fisher Scientific). The pulled-down DNA was end-repaired, ligated to sequencing adaptors, amplified on beads and purified using Nextera Mate Pair Sample Preparation Kit (Illumina) and Agencourt AMPure XP (Beckman Coulter). DNA was then sequenced to generate paired-end 150-bp reads using the Illumina HiSeq-2500 or X Ten system.

first: Toyonori

last: Sakata

first: Masashige

last: Bando

first: Katsuhiko

last: Shirahige


title: Cutaneous squamous cell carcinoma-derived extracellular vesicles exert an oncogenic role by activating cancer-associated fibroblasts

city: Uppsala

first: Mohamad

middle: Moustafa

last: Ali

state: Uppsala län

address: husargatan 3, Biomedical Center

department: IMBIM

country: Sweden

institute: Uppsala University

summary: In this study, we investigated extracellular vesicle (EVs)-mediated intercellular communication between cutaneous squamous cell carcinoma (cSCC) cells and surrounding stroma cells in tumor microenvironment (TME). Interfering with capacity of cSCC cells to secrete EVs resulted by depletion of RAB27A inhibits cSCC tumor growth in vivo.Transcriptome analysis of tumor xenografts by RNA-seq enabling the identification of both human and mouse transcripts revealed wide-spread changes both in mouse and human cells. Impaired EV-production prominently altered the phenotype of stomal cells, in particular genes related to extracellular matrix (ECM)-formation and epithelial-mesenchymal transition (EMT). This was paralleled by transcriptomic changes in the human tumor cells showing signs of activated p53 pathway and cell apoptosis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mouse xenografts generated by RAB27A-knockdown cutaneous squamous cell carcinoma cells (UT-SCC7) and mouse xenografts generated by control cells.

first: Chen

last: Li

first: Warangkana

last: Lohcharoenkal

middle: M

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last: Xing

first: Andor

last: Pivarcsi