title: Effect of Okadaic Acid on gene expression in human pancreatic cells

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary:
Pancreatic ductal adenocarcinoma (PDAC) has a bad prognosis, a fast progression and is difficult to treat, highlighting the need for new therapeutic targets. Aggressive tumors mostly show Epithelial-to-Mesenchymal Transition (EMT). Protein phosphatase type 2A (PP2A) plays a central role in processes of cell survival and proliferation, but the link with EMT and tumor progression is largely unknown. Therefore, we examined expression of a PP2A gene set in five datasets of human PDAC and their association with an aggressive phenotype. Two datasets included PDAC tumor samples and normal pancreatic tissue. In two other datasets, the samples could be classified into clinical/molecular subtypes of EMT-high/aggressive and EMT-low/moderate PDAC. Spearman correlation, hierarchical clustering and ROC-analysis were performed. EMT was also quantified using weighted expression of 8 marker genes. In each study we observed that, compared to normal tissue, (advanced) tumor stage positively and significantly correlated with EMT. EMT-high PDAC showed suppression of PPP2R1B and PPP2R2D expression and upregulation of PPP2R3C, PPP2R5E, STRN, STRN3 and PPP2R2A. A strong link was further found for upregulation of endogenous inhibitors of PP2A (KIAA1524/CIP2A, ARPP19, TIPRL and PPME1) with advanced PDAC. ROC-curve indicates that high expression of PP2A-inhibitors are predictors of aggressive PDAC. This was further investigated in a cell line model of Panc-1 cells made resistant to the PP2A-inhibitor Okadaic acid. Gene expression was determined in cells exposed for 24 hours and resistant cells. In summary, we demonstrate an important association of PP2A inhibition with EMT in advanced human pancreatic cancer.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Panc-1 cells and Okadaic acid (PP2A-inhibitor)-resistant  derivatives (OA-7A and OA-7G).

first: Jos

last: van Pelt

first: Veerle

last: Janssens

first: Chris

last: Verslype


title: Histone H3K27ac extension and intergenic transcription from enhancers activate close erythroid genes in a TAL1-independent manner

status: Public on May 16 2023

city: Busan

first: AeRi

last: Kim

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

country: South Korea

institute: Pusan national university

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [12C-E]

status: Public on May 18 2023

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

type: Methylation profiling by high throughput sequencing

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (12C_201015, 12C_201022, 12D_191024, 12D_191031, 12E_200820, 12E_200827).

first: Hanqing

last: Liu

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

middle: K

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

middle: G

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

first: Michael

last: Nunn

first: Jesse

last: Dixon

first: M

middle: M

last: Behrens


title: Histone H3K27ac extension and intergenic transcription from enhancers activate close erythroid genes in a TAL1-independent manner [ChIP-seq]

summary: Erythroid genes having enhancers in a short distance appear to be transcriptionally activated by histone H3K27ac extension and intergenic transcription that are independent from TAL1.

overall_design: GATA1, TAL1 and H3K27ac ChIP-seq was performed in control, GATA1 and TAL1 knockdown K562 cells.


title: Genome-wide Mapping Implicates 5-Hydroxymethylcytosines in Diabetes and Alzheimer’s Disease

city: Chicago

first: Zhou

last: Zhang

state: IL

address: 680 North Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

summary:
Background: Diabetes mellitus (DM) is a recognized risk factor for dementias, including AD, increasing its odds by two-fold. Because DM is potentially modifiable risk factor, a greater understanding of the mechanisms linking DM to the clinical expression of AD may provide insights into much needed dementia therapeutics. Epigenetics offers a novel approach, and previously under-investigated 5-hydroxymethylcytosines (5hmC) is now emerging as a promising measure to investigate in diabetes related conditions.
Methods: Using 5hmC-Seal, a highly sensitive chemical labeling technique developed by our team, we performed genome-wide profiling of 5hmC in circulating cell-free DNA (cfDNA) and prefrontal cortex tissue from 80 individuals across four groups: AD, DM, DM and AD (AD+DM), and non-AD/non-DM controls. We used differential analysis and machine-learning to explore whether 5hmC and biological pathways might be implicated in DM-associated AD under a balanced design.
Results: We uncovered distinct 5hmC genome-wide signatures and biological pathways associated with AD or AD+DM compared to non-AD/non-DM controls or DM alone. We further demonstrated potential diagnostic value of 5hmC profiling in circulating cfDNA through feature selection based on machine learning.
Conclusions: Genome-wide 5hmC profiling uncovered genomic features and biological pathways linking DM to DM-associated AD. Our findings also demonstrate the potential of utilizing 5hmC in circulating cfDNA as diagnostic biomarkers or disease monitoring tools, with the ultimate goal of preventing or ameliorating DM-associated AD dementia and improving clinical outcomes.

overall_design:
We performed genome-wide profiling of 5hmC in circulating cell-free DNA (cfDNA) and prefrontal cortex tissue from 80 individuals across four groups: AD, DM, DM and AD (AD+DM), and non-AD/non-DM controls.

** Due to the patient privacy policy of Rush Medical Center, the raw data and the diagnosis of each subject are not included here. The raw data and diagnoses can be requested at www.radc.rush.edu and are available with a Data Use Agreement **

first: Wei


title: Effect of deficiency of PINK1 on gene expression during 4-month and 24-month.

city: Seongnam-si

first: Min Heui

last: Ha

address: Pangyo-ro 335

institute: CHA univeristy

summary: To investigate the PINK1 regulates mitochondrial function, we performed the gene expression data for two independent libraries for Pink1-/- and Pink1+/+ mice, at two different time points, 4 and 24 months.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 4month and 24-month mice in Pink1+/+ and Pink1-/- mice.

first: Min

middle: J

last: Sung

first: Hyun-Ju

last: An

first: Man

middle: S

middle: H

first: Hye

middle: Y

last: Jeong


title: Combined oncolytic adenovirus DNX-2401 and anti-PD-checkpoint inhibitor pembrolizumab for recurrent glioblastoma

city: Toronto

first: Vikas

last: Patil

state: Ontario

address: 610 University Ave.

country: Canada

institute: Princess Margaret Cancer Center

summary: Gene expression data for samples included in this trial of DNX2401 and pembrolizumab for recurrent glioma

overall_design:
Observational cohort
CAPTIVE investigators

first: Farshad

last: Nassiri

first: Gelareh

last: Zadeh


title: The endothelial inflammatory repertoire: a multi-omic delineation of cytokine induced endothelial inflammatory states

city: Amsterdam

first: Arie Johan

last: Hoogendijk

address: Plesmanlaan 125

country: Netherlands

institute: Sanquin Research

summary: Vascular endothelial cells (ECs) form a dynamic interface between blood and tissue and play a crucial role in the progression of vascular inflammation. Here, we explored the underlying molecular mechanisms of endothelial-cytokine responses which govern inflammation. Applying an unbiased cytokine library, we determined TNFα and IFNγ induced the largest EC response and had distinct proteomic inflammatory signatures. Moreover, combined TNFα + IFNγ stimulation induced a third synergetic inflammatory state. We employed a multi-omics approach combining (phospho-) proteome, transcriptome and secretome to delineate these inflammatory states and found that endothelial cells contain a wide-array of immune-modulating capacities such as complement proteins, MHCI and MHCII complexes and distinct secretory cytokine production per stimulus. Synergy was regulated through cooperative interplay of transcript induction. This extensive resource describes the intricate molecular mechanisms that are at the basis of endothelial inflammation and supports the adaptive immunomodulatory role of the endothelium in host defense and vascular inflammation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BOEC cells stimulated for TNF, IFNgamma and TNF+IFNgamma upt 24 hours

first: Arie


title: Low-input Nucleus Isolation and Multiplexing with Barcoded Antibodies of Mouse Sympathetic Ganglia for Single-nucleus RNA Sequencing

status: Public on May 15 2023

city: Leiden

first: Monique

last: Jongbloed

address: Einthovenweg 20

department: Cardiology and Anatomy & Embryology

institute: Leiden University Medical Center

summary: The cardiac autonomic nervous system is crucial in controlling cardiac function, such as heart rate and cardiac contractility, and is divided into sympathetic and parasympathetic branches. Normally, there is a balance between these two branches to maintain homeostasis. However, cardiac disease states such as myocardial infarction, heart failure, and hypertension can induce the remodeling of cells involved in cardiac innervation, which is associated with an adverse clinical outcome. Although there are vast amounts of data for the histological structure and function of the cardiac autonomic nervous system, its molecular biological architecture in health and disease is still enigmatic in many aspects. Novel technologies such as single-cell RNA sequencing (scRNA-seq) hold promise for the genetic characterization of tissues at single-cell resolution. However, the relatively large size of neurons may impede the standardized use of these techniques. Here, this protocol exploits droplet-based single-nucleus RNA sequencing (snRNA-seq), a method to characterize the biological architecture of cardiac sympathetic neurons in health and disease. A stepwise approach is demonstrated to perform snRNA-seq of the bilateral superior cervical (SCG) and stellate ganglia (StG) dissected from adult mice. This method enables long-term sample preservation, maintaining an adequate RNA quality when samples from multiple individuals/experiments cannot be collected all at once within a short period of time. Barcoding the nuclei with hashtag oligos (HTOs) enables demultiplexing and the trace-back of distinct ganglionic samples post sequencing. Subsequent analyses revealed successful nuclei capture of neuronal, satellite glial, and endothelial cells of the sympathetic ganglia, as validated by snRNA-seq. In summary, this protocol provides a stepwise approach for snRNA-seq of sympathetic extrinsic cardiac ganglia, a method that has the potential for broader application in studies of the innervation of other organs and tissues.

overall_design: droplet-based snRNAseq of the murine left and right SCG in male (N = 2) and female (N =2)

first: Yang

last: Ge

first: Lieke

last: van Roon

first: H

first: Ruben

last: Methorst

first: Martin

last: Paton

first: Marco

middle: C

last: DeRuiter

first: Szymon

last: Kielbasa


title: Modulation of Polar Auxin Transport Identifies the Molecular Determinants of Source-Sink Carbon Relationships and Sink Strength in Poplar

city: Richland

first: Hugh

middle: D

last: Mitchell

state: Washington

address: 902 Battelle Blvd, P.O. Box 999, MSIN J4-18

department: Computational Biology

institute: Pacific Northwest National Laboratory

summary: Source-to-sink carbon (C) allocation driven by the sink strength, i.e., the ability of a sink organ to import C, plays a central role in tissue growth and biomass productivity. However, molecular drivers of sink strength have not been thoroughly characterized in trees. Auxin, as a major plant phytohormone, regulates the mobilization of photoassimilates in source tissues and elevates the translocation of carbohydrates toward sink organs, including roots. In this study, we used an ‘auxin-stimulated carbon sink’ approach to understand the molecular processes involved in the long-distance source-sink C allocation in poplar. Poplar cuttings were foliar sprayed with polar auxin transport modulators, including auxin enhancers (AE) (i.e., IBA and IAA) and auxin inhibitor (AI) (i.e., NPA), followed by a comprehensive analysis of leaf, stem, and root tissues using biomass evaluation, phenotyping, C isotope labeling, metabolomics, and transcriptomics approaches. Auxin modulators altered root dry weight and branching pattern, and AE increased photosynthetically fixed C allocation from leaf to root tissues. The transcriptome analysis identified highly expressed genes in root tissue under AE condition including transcripts encoding polygalacturonase and β-amylase that could increase the sink size and activity. Metabolic analyses showed a shift in overall metabolism including an altered relative abundance levels of galactinol, and an opposite trend in citrate levels in root tissue under AE and AI conditions. In conclusion, we postulate a model suggesting that the source-sink C relationships in poplar could be fueled by mobile sugar alcohols, starch metabolism-derived sugars, and TCA-cycle intermediates as key molecular drivers of sink strength.

overall_design: 4-5 week-old poplar cuttings were treated with auxin enhancer or inhibitor and harvested for RNAseq analysis at 24 hours and 11 days.

first: Vimal

last: Balasubramanian

first: Albert

last: Rivas-Ubach

first: Tanya

last: Winkler

first: James

last: Moran

first: Amir

last: Ahkami


title: ChIP-seq of histone modifications and EZH2 in the striatum of four-month-old HttQ111/+ and wildtype mice

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

summary: Progressive striatal gene expression changes and epigenetic alterations are a prominent feature of Huntington’s disease (HD), but direct relationships between the huntingtin (HTT) protein and chromatin remain poorly described. Here, using chromatin immunoprecipitation and sequencing (ChIP-seq), we show that HTT reproducibly occupies specific locations in the mouse genome, including thousands of genomic loci that are differentially occupied in striatal tissue from a knock-in mouse model of the HD mutation (B6.HttQ111/+) versus wildtype controls. ChIP-seq of histone modifications, generated in parallel, revealed genotype-specific colocalization of HTT with trimethylation of histone 3 lysine 27 (H3K27me3), a repressive chromatin mark. Near genes that are differentially regulated in HD, greater HTT occupancy in HttQ111/+ vs. wildtype mice predicted increased H3K27me3, reduced histone 3 lysine 4 (H3K4me3), a marker of poised and active promoters, and down-regulated gene expression. Altered huntingtin-chromatin interactions may therefore play a direct role in driving transcriptional dysregulation in HD.

overall_design: Fresh frozen striatal tissue from five male four-month-old HttQ111/+  and age-matched Htt+/+ mice were pooled per replicate for n = 3 samples.  Further processing was performed at Active Motif (Carlsbad, CA).  Tissue was fixed in 1% formaldehyde, lysed, and disrupted with a Dounce homogenizer.  DNA was sonicated to an average fragment length of 300-500bp, and 25ug chromatin plus 200ng Drosophila spike-in chromatin was incubated with antibody targeting EZH2, H3K27me3, H3K4me3, or H3K27ac (Active Motif catalog numbers 39901, 39155, 399159, and 39133, respectively).  Antibody against H2Av was also present in the reaction to ensure efficient pull-down of the spike-in chromatin. Complexes were captured using protein A agarose beads (Invitrogen). Illumina sequencing libraries were prepared from ChIP and Input DNA by end-polishing, dA-addition, and adaptor ligation. Libraries were quantified and sequenced on Illumina’s NextSeq 500 (75nt single end reads). Reads were aligned consecutively to the mouse (mm10) and Drosophila (dm3) genomes using the BWA algorithm (default settings). The number of mouse alignments used in the analysis was scaled to the number of Drosophila spike-in alignments. Peak-calling was performed with MACS and SICER.

first: Jeff

last: Carroll

first: Seth

last: Ament

first: Jocelynn

last: Pearl

last: Cantle


title: Histone H3K27ac extension and intergenic transcription from enhancers activate close erythroid genes in a TAL1-independent manner [RNA-seq]

first: AeRi

last: Kim

overall_design: RNA-seq was performed in control, GATA1 and TAL1 knockdown K562 cells.


title: HDACi and PLK1i synergize in MYC-amplified MB

city: Memphis

first: Gintvile

last: Valinciute

state: TN

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

summary:
We and others have demonstrated that MYC-amplified medulloblastoma (MB) cells are susceptible towards treatment with class I histone deacetylase inhibitors (HDACi). However, single drug treatment with HDACi has shown limited clinical efficacy. We hypothesized that addition of a second compound acting synergistically with HDACi may enhance efficacy. Gene expression changes in HDACi entinostat-treated cells identified, the cell cycle protein PLK1 as a potential second target. Indeed, MYC-amplified tumor cells are highly sensitive towards treatment with ATP-competitive PLK1 inhibitors as monotherapy. Moreover, entinostat and PLK1i in combination act synergistically in MYC-driven MB, exerting cytotoxic effects at clinically relevant concentrations. The downstream effect of both drugs as monotherapy and in combination is exerted via MYC-related pathways, pointing out the potential of MYC amplification as a clinically feasible predictive biomarker for patient selection. While entinostat significantly extended survival of mice implanted with orthotopic MYC-amplified MB PDX, there was no evidence of the improvement of survival when treating the animals with combination. However, further screening of blood-brain barrier penetrating PLK1is is necessary to determine the true potential of the combination.
We use microarry to interrogate the expression differences in vehicle, entinostat, volasertib or combination treated cells.

overall_design: HD-MB03 cells were treated with vehicle, 5 uM enitnostat, 1 uM volasertib or their combination for 6 hours. 3 independent biological replicates were conducted for each of the conditions

first: Jonas

last: Ecker

first: Florian

last: Selt

first: Thomas

last: Hielscher

first: Romain

last: Sigaud

first: Johannes

last: Ridinger

first: Venu

last: Thatikonda

first: Charlotte

last: Gatzweiler

first: Sarah

last: Robinson

first: Julie

last: Talbot

first: Flavia

last: Bernardi

first: Daniel

last: Picard

first: Mirjam

last: Blattner-Johnson

first: Simone

last: Schmid

first: David

middle: T

last: Jones

first: Cornelis

last: van Tilburg

last: Capper

first: Marcel

last: Kool

first: Marc

last: Remke

first: Ina

last: Oehme

first: Martine

middle: F

last: Roussel

first: Stefan

last: Pfister

first: Olivier

last: Ayrault

first: Olaf

last: Witt

first: Till

last: Milde


title: scRNA-seq of HSCs

city: Guangzhou

first: chen

last: minqi

state: Guangdong

address: No.74, 2nd Zhongshan Road

country: China

institute: Sun Yat-sen University

summary: Both mHSCs and nHSCs had activated differentiation genes upon LM challenge; however, mHSCs more robustly increased cell cycle and T lymphocyte-differentiation genes but reduced myeloid-, erythrocyte- and B cell-differentiation genes compared to nHSCs upon LM challenge

overall_design: scRNA-seq on HSCs

first: Meng

last: Zhao


title: Altered granulopoiesis aggravates stroke in the elderly [bulk RNA-seq]

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

summary: Ischemic stroke is one of the leading causes of disability and mortality worldwide, recognizing aging as a prominent risk factor and determinant of dismal outcome. Aging is known to lead to overall frailty due to multifactorial changes, but pathogenic mechanisms underlying poor outcome remain unclear. Here we show that deterioration in elderly stroke is preceded by neutrophil accumulation and clogging in the ischemic brain microcirculation leading to a worse no-reflow phenomenon. With high-dimensional single-cell profiling over time of the brain's, blood's, and bone marrow's immune response, we could delineate after stroke four main neutrophil clusters in the blood whose quantitative and temporal dynamic of release is deranged in the bone marrow of the old. In the elderly, stroke triggers an early surge in the blood of the CD62Llo neutrophil subset characterized by a signature of bone marrow proximity, senescence, and oxidative stress. Functionally, transfer of this neutrophil subset displaying prominent thrombogenic features in young stroke mice leads to increased clogging of the ischemic brain microcirculation, worse no-reflow and outcome. Interrogating the blood leukocyte landscape of a large human stroke cohort with extensive single-cell proteome analyses, we confirmed that older stroke patients display a similar precocious accumulation of blood CD62Llo neutrophil subset, worse reperfusion and outcome. Our results demonstrate how age-related alterations in the process of neutrophil differentiation and release from the bone marrow have a relevant pathogenic role in the major cerebrovascular disorder affecting the world population, that unleash emergency granulopoiesis.

overall_design: 16 samples of circulating CD62L low neutrophils collected from young and aged mice in basal conditions and 24h after MCAo

first: Marco

last: Bacigaluppi

first: Giorgia

last: Gullotta

first: Donatella

last: De Feo


title: Altered granulopoiesis aggravates stroke in the elderly.


title: Age-induced alterations of granulopoiesis generate atypical neutrophils that aggravate stroke pathology [scRNA-Seq 1]

summary: Stroke in aging leads to a dysregulated emergency granulopoiesis impacting neurological outcome.

overall_design: scRNAseq on FACS sorted blood myeloid cells of young and aged mice after experimental stroke


title: ChIP-seq of HTT protein in mouse cortex following HTT knockdown

first: Amol

last: Shetty

overall_design: Four-month-old male HttQ111/+  and age-matched Htt+/+ mice underwent unilateral intracerebroventricular injection of 500ug pan-huntingtin antisense oligonucleotide (Ionis #444652) or received no treatment.  Fresh-frozen cortical tissue ipsilateral to the injection was collected for ChIP at four weeks post injection.  For each ChIP preparation, chromatin DNA was prepared using ipsilateral cortical tissue from three mice.  Tissue was transferred to a glass dounce on ice and homogenized in cold PBS with protease inhibitors.  High-resolution X-ChIP-seq was performed as described (Skene and Henikoff, 2015), with slight modifications. IPs were performed using Abcam Anti-huntingtin antibody EPR5526 (#ab109115). ChIP-Seq library preparation and sequencing reactions were conducted at GENEWIZ, Inc. (South Plainfield, NJ, USA) using NEB NextUltra DNA Library Preparation kit following the manufacturer’s recommendations (Illumina, San Diego, CA, USA). Sequencing was performed using 2x150 Paired End (PE) configuration. Sequencing reads were aligned to the mouse genome (mm9) using HISAT2. Aligned reads from the four ChIP libraries were down-sampled to the size of the smallest sequencing library using samtools view -s. Aligned reads from the Input genomic DNA of all four samples were merged into a single control BAM file. Peak-calling was then performed with MACS2.2, scaling to the size of the input control library. The final set of reproducible peaks was obtained using the dba() function in the DiffBind R package, retaining peaks that were reproducible at FDR < 0.01 in at least two samples and excluding artifactual blacklist regions from ENCODE

first: Jeff

last: Carroll

first: Seth

last: Ament

first: Jocelynn

last: Pearl

last: Cantle


title: ChIP-seq of  HttQ111/+ and wildtype mice


title: MiR-431 attenuates synaptic plasticity and memory deficits in APPswe/PS1dE9 mice

city: nanjing

first: jianwei

last: ge

address: zhongshan road

institute: nanjing university

summary: Synaptic plasticity impairment plays a critical role in the pathogenesis of Alzheimer’s disease (AD), and emerging evidence has shown that microRNAs (miRNAs) are alternative biomarkers and therapeutic targets for synaptic dysfunctions in AD. In this study, we found that the level of miR-431 was downregulated in the plasma of amnestic mild cognitive impairment (aMCI) and AD patients. In addition, it was decreased in the hippocampus and plasma of APPswe/PS1dE9 (APP/PS1) mice. Lentivirus mediated miR-431 overexpression in the hippocampus CA1 ameliorated synaptic plasticity and memory deficits of APP/PS1 mice, while it didn't affect the Aβ levels. Smad4 was identified as a target of miR-431, and Smad4 knockdown modulated the expression of synaptic proteins including SAP102, and protected against synaptic plasticity and memory dysfunctions in APP/PS1 mice. Furthermore, Smad4 overexpression reversed the protective effects of miR-431, indicating that miR-431 attenuated synaptic impairment at least partially by Smad4 inhibition. Thus, these results indicated that miR-431/Smad4 might be a potential therapeutic target for AD treatment.

overall_design: Smad4 is a transcription factor,we did a cut&tag assay to find the target of smad4.

first: J

last: Ge

first: Z

last: Xue

first: S

last: Shu

first: X

last: Zhu


title: Transcriptomic analysis of neuroblastoma cells in response to stable over-expression of small peptide encoded by hepatocyte nuclear factor 4 alpha antisense RNA 1 (HNF4A-AS1)

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

summary: Neuroblastoma (NB), a malignant embryonic tumor arising from primitive neural crest cells, accounts for more than 7% of malignancies and around 15% of cancer-related mortality in childhood. Better elucidating the mechanisms of tumorigenesis and aggressiveness is important for improving the therapeutic efficiencies of NB. We identified a small 51-amino acid peptide (sPEP1) encoded by hepatocyte nuclear factor 4 alpha antisense RNA 1 (HNF4A-AS1) in NB cells treated by serum deprivation. To investigate the mechanisms underlying the oncogenic functions of sPEP1, we employed the Illumina HiSeq X Ten as a discovery platform to analyze the transcriptome profiling changes of human SH-SY5Y cells in response to stable over-expression of sPEP1. The results showed that stable over-expression of sPEP1 led to altered expression of 2543 human mRNAs, including 2457 up-regulated genes and 86 down-regulated genes. Then we found the possible roles of these differentially regulated mRNAs in selected pathways including stemness, senescence, invasion, and metastasis by Bioinformatic analysis. Furthermore, we validated the RNA-seq results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to sPEP1 over-expression in human NB cells, and these findings will help us understand the pathogenesis of NB.

overall_design: Total RNA of cells stably transfected with empty vector or sORF1 was extracted using the TRIzol® reagent according to the manufacturer's instructions. RNA concentration was measured using a Qubit® RNA Assay Kit with a Qubit® 2.0 Fluorometer (Life Technologies, Inc.), and integrity was assessed using the RNA Nano 6000 Assay Kit with a Bioanalyzer 2100 system (Agilent Technologies, CA). Library preparation and transcriptome sequencing on an Illumina HiSeq X Ten platform were performed by Novogene Bioinformatics Technology Co., Ltd. (Beijing, China), and 100 bp paired-end reads were generated. HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.

first: Tong

last: Qiangsong

first: Zheng

last: Liduan


title: Expression data from SUN2 downstream

city: Nanchang

first: Yi

last: Sang

state: Jiangxi

address: No.128,Xiangshan North Road

institute: Nanchang University

summary: SAD1/UNC84 domain protein-2(SUN2) is a member of the inner nuclear membrane LINC (linker of nucleoskeleton and cytoskeleton) complex, which maintains nuclear structure by connecting the nuclear lamina to the cytoskeleton. SUN2 is located at the inner nuclear membrane, where it extends into the perinuclear space via its C-terminal SUN domain and interacting with the nuclear lamina through its nucleoplasmic N-terminal domain. SUN2 might serve as a potential therapeutic target in cancer . Hsieh TH et al. showed that SUN2 inhibits cell proliferation and tumor malignancy both in vitro and in vivo and plays a tumor suppressor gene in central nervous system embryonal tumors. SUN2 are decreased in breast tumor tissues compared with mammary epithelial tissues. Our group has previously reported that SUN2 suppresses the Warburg effect by repressing the expression of GLUT1 and LDAH in lung cancer cells. These data suggest that the function of SUN2 is different in various cancers. However, the role of SUN2 in colon cancer remains unclear.In this study, we used the microarray to indentify the dnownstream of SUN2 in HCT116 after knocking down SUN2.

overall_design: scr and shSUN2-1 were for RNA extraction and hybridization on Affymetrix microarrays.

first: Lijuan

last: Liu


title: Defining prepubertal primate spermatogonial stem cells to address fertility preservation in prepubertal boys

city: San Antonio

first: Brian

middle: P.

last: Hermann

state: TX

address: 1 UTSA Circle

department: Department of Biology

institute: University of Texas at San Antonio

summary: Antineoplastic treatments for cancer and other non-malignant disorders can result in male long-term or permanent infertility by ablating spermatogonial stem cells (SSCs). Preserving the future fertility of prepubertal patients faced with this prospect cannot rely on sperm banking. SSC transplantation using testicular tissue harvested before sterilizing treatment is a promising approach for restoring fertility, but lack of exclusive biomarkers which can unequivocally identify prepubertal SSCs in any primate species limits the therapeutic potential. To address this, we performed single-cell RNA-seq on unselected testis cells from immature baboons and macaques and compared these cells with published data from pre-pubertal human germ cells functionally-defined mouse SSCs. We found discrete groups of human spermatogonia while baboon and rhesus spermatogonia appeared less heterogenous. Cross-species analysis revealed cell types analogous to human SSCs in baboon and rhesus germ cells, but comparison with mouse SSCs revealed significant differences with primate SSCs. Indeed, a core component of a human SSC gene expression signature was conserved in baboon and rhesus spermatogonia and absent from mouse SSCs. These results further resolve the identity of pre-pubertal human SSCs and define novel pathways that could be leveraged for advancing their selection and propagation in vitro.

sample_organism:
Macaca mulatta
Papio anubis

platform_organism:
Macaca mulatta
Papio anubis

overall_design: Single-cell transcriptomes of testicular cells from two immature baboons (aged 15 and 20 months) along with two rhesus monkeys (newborn and 26 months old) were analyzed.

first: Singh

last: Anukriti

first: Sean

last: Vargas

middle: P


title: Genomic adaptation underlies nutrient-driven reprogramming in malaria parasite [RNA-Seq]

city: Stockholm

first: Sherwin

last: Chan

address: Solnavagen 9

country: Sweden

institute: Karolinska Institutet

summary: We aimed to simultaneously characterize the dynamics of the codon and anti-codon pools during the intraerythrocytic developmental cycle

overall_design: Standard RNA-seq was performed on rings, trophozoites and schizonts with 3 replicates each, the codon composition in the samples were then estimated by codon content of each gene weighed by the expression level

first: Qian

last: Li


title: Genomic adaptation underlies nutrient-driven reprogramming in malaria parasite [PolySeq]

summary: We aimed to compare the polysome profiles of parasites upon acute amino acid starvation (6 hours of total depletion)

overall_design: Polysome profiling was performed on parasites (36hpi) either being grown in complete medium or in total amino acid depleted medium for 6 hours. Three experimental replicates performed.


title: Genomic adaptation underlies nutrient-driven reprogramming in malaria parasite [tRNA-Seq starvation]

type: Non-coding RNA profiling by high throughput sequencing

summary: We aimed to characterize the change in anti-codon pool upon acute amio acid depletion (6 hours of total depletion)

overall_design: TGIRT-tRNAseq was performed on trophozoites (36hpi) after culturing in complete/ amino acid deficient medium for 6 hours, a positive control group includes growing in amino acid deficient medium with 70nM halofuginone


title: Transcriptomic profile of ANGPTL3-deficient HepG2 cells

city: New York

first: Michael

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

summary: Cardiovascular disease is a leading cause of death worldwide, and inhibition of the hepatically secreted protein ANGPTL3 has emerged as an effective treatment for lowering low-density lipoprotein cholesterol (LDL), the cardinal risk factor for coronary artery disease (CAD). In this study, we examine the effects of complete genetic deficiency of ANGPTL3 on the hepatocyte transcriptome using a HepG2 cell culture model with the ANGPTL3 locus "knocked out" (KO) via CRISPR-Cas9.

overall_design: Wild type (WT) and ANGPTL3-knockout (KO) HepG2 cells were exposed to either vehicle control (fatty acid-free BSA) or 200uM oleic acid (conjugated to fatty acid-free BSA) in serum-free media for 12hr before sample collection.

first: Kendall

last: Burks


title: Transcriptional Landscape of Cottont Roots in Response to Salt Stress at Single-cell Resolution

city: Anyang

first: Pengtao

address: Huanghe River Avenue

institute: Anyang Institute of Technology

summary: Increasing soil salinization has led to severe losses of plant yield and quality. Researching the formation of plant salt tolerance and the molecular mechanism of the salt stress response is therefore urgent. We here take advantage of recent progress in single-cell transcriptomics technology to systematically analyze plant roots response to salt stress, and 57,185 high-quality cells were totally obtained from 5-day-old lateral root tips of Gossypium arboreum under natural growth and different salt-treatment conditions. Eleven cell types with an array of novel marker genes were identified and confirmed with RNA in situ hybridization. Pseudotime analysis on epidermal and root hair cells indicated the differentiation trajectory, and differential root-type cells responding to salt stress resulted in more epidermal and less endodermal cells. Abundant differentially expressed genes (DEGs) were found to be engaged in glycometabolism, reactive oxygen species hemeostasis, and phosphatidylinositol and MAKP signal pathways through functional enrichment analyses. Some candidate DEGs related with transcription factors and plant hormones responding to salt stress were also screened, which requires further functional verification to reveal the regulatory model of the plant roots response to salt stress. Combined with bulk RNA-seq data, a common DEG (Ga08G2497) annotated as Aldo-keto reductase-1 (AKR1) was selected to perform virus-induced gene silencing verification, and the silencing of GaAKR1 gene in G. arboreum resulted in severe stress-susceptibility phenotype, shorter root length, and less number of lateral roots. Physiological and biochemical detection also demonstrated that GaAKR1-silenced plants suffered more serious oxidative damages and, indicating that GaAKR1 might participates in salt tolerance of cotton by oxidation-reduction process. For the first time, we characterized a transcriptional atlas of plant roots under salt stress at a single-cell resolution, which explored the cellular heterogeneity, differential root-type cells, and differentiation trajectory, while providing valuable insights into the molecular mechanism underlying stress tolerance in plants.

overall_design: After being sterilized with 0.1% HgCl2 for 15 min, the full-grained seeds of G. arboreum SXY1 were rinsed with deionized water no less than three times and then germinated on ½ Murashige and Skoog (MS) solid medium with 15-g glucose and 2.6 g/L phytagel, adjusted to pH 5.7, and grown in an illumination incubator at 28°C/light for 16 h and 25°C/dark for 8 h. Subsequently, 5-day-old cotton seedlings were uniformly collected and randomly separated into four groups, which were differentially immersed into 40 mL MS liquid medium for only 0.5 h (natural growth control), MS liquid medium with 100 mM NaCl solution for 0.5 h (salt1) and 1 h (salt2), and 150 mM NaCl solution for 0.5 h (salt3). Two biological replications were conducted to ensure the statistical significance of this study, and numerous lateral roots were separately collected for further protoplast dissociation.

first: Qiankun

first: Yangyang

last: wei

first: Chaozhu

last: Xing


title: Osteoblast-intrinsic defect in glucose metabolism impairs bone formation in type II diabetic male mice.

city: Phildelphia

first: Fanxin

last: Long

state: Pennsylvania

address: Civc center blvd 3501

institute: Children's Hospital of Philadelphia

summary: Skeletal fragility is associated with type 2 diabetes mellitus (T2D), but the underlying mechanism is not well understood. Here, in a mouse model for youth-onset T2D, we show that both trabecular and cortical bone mass are reduced due to diminished osteoblast activity. Stable isotope tracing in vivo with 13C-glucose demonstrates that both glycolysis and glucose fueling of the TCA cycle are impaired in diabetic bones. Similarly, Seahorse assays show suppression of both glycolysis and oxidative phosphorylation by diabetes in bone marrow mesenchymal cells as a whole, whereas single-cell RNA sequencing reveals distinct modes of metabolic dysregulation among the subpopulations. Metformin not only promotes glycolysis and osteoblast differentiation in vitro, but also improves bone mass in diabetic mice. Finally, osteoblast-specific overexpression of either Hif1a, a general inducer of glycolysis, or Pfkfb3 which stimulates a specific step in glycolysis, averts bone loss in T2D mice. The study identifies osteoblast-intrinsic defects in glucose metabolism as an underlying cause of diabetic osteopenia, which may be targeted therapeutically.

overall_design: Examination of the metabolic alteration of bone marrow stromal cells (T2D vs CTRL)

first: Fangfang

last: Song


title: Comparative transcriptomics analysis of monocytes of heathy human subjects before and after a dietary oxalate load

city: Birmingham

first: Tanecia

last: Mitchell

state: AL

address: 720 20th Street South, 816E

department: Urology

institute: University of Alabama at Birmingham

summary: Next gen RNA Seq analysis was performed to study the effect of oxalate load on the transcriptome of monocytes in healthy human subjects. Healthy subjects consumed a fruit and vegetable smoothie containing high amount of oxalate. Blood was collected from them before and 5 hrs after consumption of the smoothie. Monocytes were purified from the blood and RNA Sequencing was performed by Illumina NextSeq 500 platform.  Differential gene expression analysis was performed using DESeq2 considering fold change > + 2.0 with a q value of < 0.05. 1197 genes were found to be differentially expressed which were used for pathway and functional analysis using Ingenuity software.

overall_design: ComparativeRNA Sequence analysis of Monocytes pre- and post-oxalate load

first: Parveen

last: Kumar

first: David

last: Crossman


title: Genomic adaptation underlies nutrient-driven reprogramming in malaria parasite [tRNA-Seq time series]

overall_design: TGIRT-tRNAseq was performed on rings, trophozoites and schizonts with 3 replicates each, the anti-codon composition in the samples were then estimated from the read counts, charged level of each tRNA was estimated from a separate library with RNA pretreated with 50mM sodium periodate, pH4.8


title: Influenza defective interfering virus promotes multiciliated cell differentiation and reduces the inflammatory response in mice

city: Bethesda

first: Matthew

last: Chung

state: MD

address: 50 South Dr

institute: NIAID (National Institute of Allergy and Infectious Diseases)

summary: Influenza defective interfering (DI) viruses have long been considered promising antiviral candidates because of their ability to interfere with replication-competent viruses and to induce antiviral immunity. However, the mechanisms underlying DI-mediated antiviral immunity have not been extensively explored. Here, we demonstrated interferon (IFN) independent protection conferred by influenza DI virus against homologous virus infection in mice deficient in type I and III IFN signaling. By integrating transcriptional and post-transcriptional regulatory data we identified unique host signatures in response to DI co-infection. DI-treated mice exhibited reduced viral transcription, less intense inflammatory and innate immune responses, and primed multiciliated cell differentiation in their lungs at an early stage of infection, even in the absence of type I or III IFNs. This increased multiciliogenesis could also be detected at the protein level by immunofluorescence staining of lung tissue from DI-treated mice. Overall, our study provides mechanistic insight into the protection mediated by DIs, implying a unifying theme involving inflammation and multiciliogenesis in maintaining respiratory homeostasis, and reveals their IFN-independent antiviral activity.

sample_organism: Influenza A virus (A/Puerto Rico/8/1934(H1N1))

overall_design: The firs Dataset consists of a bulk RNA-seq dataset containing 36 libraries generated with NEBNext Ultra II RNA library prep kit and poly(A) mRNA magnetic isolation module, a miRNA-seq dataset containing 36 libraries generated with QIAseq miRNA library kit, and a viral genome sequencing dataset containing 52 libraries generated from multi-segment reverse-transcription PCR (M-RT-PCR) products followed by library preparation with Nextera XT DNA library prep kit. This second dataset consists of 31 libraries generated with NEBNext Ultra II RNA library prep kit and poly(A) mRNA magnetic isolation module from the first in vivo study presented in the manuscript.

first: Chang

last: Wang

first: Rebekah

last: Honce

first: Mirella

last: Salvatore

first: Daniela

last: Chow

first: Davide

last: Randazzo

first: Jianjun

last: Yang

first: Nicholas

last: Twells

first: Lara

last: Mahal

first: Stacey

last: Schultz-Cherry

first: Elodie

last: Ghedin


title: G-protein mutants RNA-seq analysis of salt resonse in Arabidopsis and Marchantia

city: Sinagpore

first: Daisuke

last: Urano

address: 1 Research Link

country: Singapore

institute: Temasek Life Science Laboratory

summary: Purpose: To understand the dynamic salt-sress response in G-prtoein mutants in Arabidopsis and Marchantia

sample_organism:
Marchantia polymorpha
Arabidopsis thaliana
Oryza sativa Japonica Group

overall_design: 7-day old Arabidopiss seedlings , rice seedlings and Marchantia gemmalings were subjected to  100 mM NaCl  for 0, 2 and 24  hr, 2-3  biological replicates

first: Ting-Ying

last: Wu


title: Adrenergic signaling stimulates body-wide stem cell activation for limb regeneration (ATAC-Seq)

status: Public on May 13 2023

city: Cambridge

first: Jessica

last: Whited

state: MA

address: 7 Divintiy Street, Sherman Fairchild - Whited Lab

institute: Harvard University

summary: In axolotls, stem cells are systemically prompted to re-enter the cell cycle upon amputation. We sought to identify whether the proliferating cells of the systemically-activated limbs are epigenetically different from those of homeostatic limbs. identify which cells drive systemic-activation response in the limbs distant to the amputation.

overall_design: We dissociated homeostatic or systemically-activated limbs at 14 days post-amputation, and sorted them by their DNA content using FACS. We then performed bulk ATAC sequencing of the dividing, 4C population.

first: Steven

last: Blair

middle: L


title: Insights into promoter chromatin remodeling from the structure of ISW1a complex bound to the dinucleosome

city: Beijing

first: Pengjing

last: Hu

state: Beijing

address: 30 Shuangqing Rd, Haidian District

department: School of Life Science

institute: Tsinghua University

summary: Nucleosomes, the basic repeating units of chromatin, form evenly spaced arrays inside the cell. Chromatin remodelers alter the positions of nucleosomes, and are vital in regulating chromatin organization and gene expression. Here we report the cryoEM structure of the chromatin remodeler ISW1a complex bound to the dinucleosome. Both subunits of the complex recognize one nucleosome. The motor subunit binds at the canonical position of the nucleosome, with two arginine anchors recognizing the acidic patch. The DNA-binding module interacts with the entry linker DNA at the nucleosome edge, consistent with the protein ruler model in nucleosome spacing. The Ioc3 subunit recognizes the disk face of the adjacent nucleosome, being important for the spacing activity in vitro, and for chromatin organization in vivo. Together, our findings illustrate a new mode of chromatin remodeling in the context of higher-order chromatin

overall_design: MNase-seq in Saccharomyces cerevisiae. Compare nucleosome shift between WT-mutant(dIoc3, dAP, dH4), with an addition pair of WT-WT control group. Two biological replicates were sampled for each group.

first: Lifei

last: Li

first: Kangjing

last: Chen

first: Youyang

last: Sia

first: Youpi

last: Ye

first: Zhucheng


title: Adrenergic signaling stimulates body-wide stem cell activation for limb regeneration (4N RNA-Seq)

summary: In axolotls, stem cells are systemically prompted to re-enter the cell cycle upon amputation. We sought to identify which cells drive systemic-activation response in the limbs distant to the amputation.

overall_design: We dissociated homeostatic or systemically-activated limbs at 14 days post-amputation, and sorted them by their DNA content using FACS. We then performed single-cell RNA sequencing of the dividing, 4C population using 10X genomics.


title: Mechanistic toxicometabolomic studies of a model PPARα agonist on human pluripotent stem cell-derived liver organoids

first: Deepak

last: Mishra

address: 77 Massachusetts Avenue

department: Biological Engineering

institute: MIT

summary: Ectopic expression of Gata6 leads to differentiation of hiPSCs. We used scRNA-seq to analyze diversity of differentiated lineages from D0 to D8.

overall_design: Gata6 was induced to be expressed D0-D5 in mTeSR+ media prior to removal of inducer and transfer to APEL2 media.

first: Ron

last: Weiss


title: SPRK1 shRNA and overexpression followed by RNA-seq in glioblastoma cells

city: Campinas

first: Pedro

last: Cruz

address: Av Candido Rondon 400

country: Brazil

institute: UNICAMP

summary: SRPK1 is an SR (serine-arginine) protein kinase with an emerging role as a therapeutic target. SRPK1 phosphorylates the SR family of core spliceosomal components and accessory splicing factors, representing a pivotal regulator of splicing events in human cells. Because alternative splicing of mRNAs in the nervous system occurs at high frequency, the imbalance of mRNA isoforms can affect the function of important neural proteins. We used this RNA-seq dataset to classify splicing events upon genetic modulation of SRPK1, in glioblastoma cells.

overall_design: We performed transient transfection of the SRPK1 protein kinase for overexpression and knockdown conditions, in T98G glioblastoma cells and untreated cells, described here as NT. We performed 2 biological replicates of each condition.

middle: R

first: Katlin

middle: B

last: Massirer


title: Effect of degradation of IGFRIL/PTBP1 in HepG2 cells

first: Chengzhi

last: Gao

address: Taiping Road

department: Genetics & Integrative Omics

institute: Beijing Institute of Radiation Medicine

summary: To investigate the effect of IGFRIL/PTBP1 in HCC, we established HepG2 cell lines in which IGFRIL/PTBP1 mRNA has been degraded using siRNA.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HepG2 cells and its knockdown derivatives(si-IGFRIL and si-PTBP1).

first: Pengbo

last: Cao


title: siIGF2BP3 regulated genes in lung cancer cell

city: Yangzhou

first: Xiaolin

last: Wang

address: No98，Nantong West Road

institute: Department of Thoracic Surgery

summary: To investigate the global genes regulated by siIGF2BP3 high-throughput mRNA sequencing (RNA-Seq) was performed to compare the expression profile between  PC3 cells transfected with control siRNA or siIGF2BP3 siRNA.

overall_design: RNA-seq was performed in PC3 cells after control siRNA or siIGF2BP3 siRNA transfection


title: R-loop landscapes in yeast meiosis

status: Public on May 14 2023

first: Wei

address: 1st Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Meiotic recombination is initiated by the Spo11-dependent programmed DNA double-strand breaks (DSBs) that are preferentially concentrated within genomic regions known as hotspots, but the factor(s) which specify the positions for meiotic DSB hotspots remain unclear. Here, we show that the frequency and distribution of R-loops, a type of functional chromatin structure comprising single-stranded DNA and a DNA:RNA hybrid, change dramatically throughout meiosis. We detected the formation of multiple de novo R-loops in the pachytene stage, and found they co-localize with meiotic DSB hotspots. We further show that transcription-replication head-on collisions could promote R-loop formation during meiosis, and apparently direct the initiation of meiotic DSB formation. Furthermore, the hotspots can be eliminated by reverse the direction of either transcription or replication, and reconstituted by reverse both of their direction. Our study reveals that R-loops may play dual roles in meiotic recombination. In addition to participation in meiotic DSB processing, some meiotic DSB hotspots may be originated from the transcription-replication head-on collisions during meiotic DNA replication.

overall_design: Detection of R-loops by using ssDRIP-seq in yeast meiosis.

first: Chao

last: Liu

last: Xu

first: Liying

first: Zhuo

last: Yang

first: Qianwen

last: Sun


title: METTL3 regulated genes in HCC cell

city: Shanghai

first: Yinghao

last: Shen

address: 180 Fenlin Road

institute: Zhongshan Hospital

summary: To investigate the global genes regulated by METTL3 high-throughput mRNA sequencing (RNA-Seq) was performed to compare the expression profile between  Huh7cells transfected with control siRNA or METTL3 siRNA.

overall_design: RNA-seq was performed in Huh7 cells after control siRNA or METTL3 siRNA transfection


title: Effect of depletion of IGFRIL in HepG2 cells

summary: To demonstrate that IGFRIL is the cognate RNA of PTBP1, we established HepG2 cell lines in which IGFRIL gene has been depleted.

overall_design: Comparative analysis of CLIP-seq data for HepG2 cells and its IGFRIL-depleted derivatives.


title: Atypical Neurogenesis, Astrogliosis, and Excessive Hilar Interneuron Loss Are Associated with the Development of Post-Traumatic Epilepsy

city: Blacksburg

first: Michelle

middle: Lynne

last: Olsen

state: VA

address: 970 Washington Street SW

department: School of Neuroscience

institute: Virginia Tech

summary: We aimed to identify moleucalr sgnatures of astrocytes islaoted from the hippocampus in sham or CCI injured mice with or without spontaneous recurrent seizures

overall_design: Utilizing the murine unilateral focal control cortical impact (CCI) injury, we evaluated seizure onset using 24/7 EEG video analysis at 2-4 months post-injury. Isolation of region-specific astrocytes and RNA-seq was performed to determine differential gene expression in PTE+ vs. PTE- that may comport with the epileptogenic process

last: Theus


title: Adrenergic signaling stimulates body-wide stem cell activation for limb regeneration (2N RNA-Seq)

first: Jessica

last: Whited

summary: In axolotls, stem cells are systemically prompted to re-enter the cell cycle upon amputation. We sought to identify how the cells surrounding the systemically activated cells respond to an amputation.

overall_design: We dissociated homeostatic or systemically-activated limbs at 14 days post-amputation, and sorted them by their DNA content using FACS. We then performed single-cell RNA sequencing of the dividing, 2C population using 10X genomics.

first: Steven

last: Blair


title: Methanol fixation is the method of choice for droplet-based single-cell transcriptomics of neural cells

city: L'Hospitalet de Llobregat

first: Mireya

last: Plass

state: Barcelona

address: Feixa Llarga s/n, Pavelló de Govern,

country: Spain

institute: IDIBELL

summary: Single-cell transcriptomics methods have become very popular to study the cellular composition of organs and tissues and characterize the expression profiles of the individual cells that compose them. The main critical step for single-cell transcriptomics methods is sample preparation. Several methods have been developed to preserve cells after sample dissociation to uncouple sample handling from library preparation. Yet, the suitability of these methods depends on the types of cells to be processed. In this project, we perform a systematic comparison of preservation methods for droplet-based single-cell RNA-seq (scRNA-seq) on human neural progenitor cell populations derived from induced pluripotent stem cells (iPSCs) and highlight their strengths and weaknesses. We compared the cellular composition and expression profile of single-cell suspensions from fresh NPCs with that of NPCs preserved with Dimethyl Sulfoxide (DMSO), Methanol, vivoPHIX and Acetil-methanol (ACME). Our results show that while DMSO provides the highest cell quality in terms of RNA molecules and genes detected per cell. Yet, it strongly affects the cellular composition and the expression profile of the resulting datasets. In contrast, methanol fixed samples display a cellular composition like that of fresh samples while providing a good cell quality and smaller expression biases. Taken together, our results show that methanol fixation is the method of choice for performing droplet-based single-cell transcriptomics experiments on neural cell populations.

overall_design: We perform a systematic comparison of preservation methods for droplet-based single-cell RNA-seq (scRNA-seq) on human neural progenitor cell populations derived from induced pluripotent stem cells (iPSCs) and highlight their strengths and weaknesses. We compared the cellular composition and expression profile of single-cell suspensions from fresh NPCs with that of NPCs preserved with Dimethyl Sulfoxide (DMSO), Methanol, vivoPHIX and Acetil-methanol (ACME). Our results show that while DMSO provides the highest cell quality in terms of RNA molecules and genes detected per cell. Yet, it strongly affects the cellular composition and the expression profile of the resulting datasets.


title: The Role of Uridine Glucuronosyl transferase 2B28 (UGT2B28) in Prostate Cancer Progression [day30]

city: Houston

first: Danthasinghe

middle: Badrajee

last: Piyarathna

state: United States

address: One Baylor Plaza

institute: Baylor College of Medicine

summary:
To understand the effect of UGT2B28 on tumor growth, we generated lentiviral-mediated UGT2B28 knockdown and rescue (by overexpressing UGT2B28  in the knockdown background) in LAPC4 cells.
These engineered cells were then subcutaneously injected in athymic nude mice with pre-implanted testosterone pellets. We then performed transcriptomics on the xenograft tumors upon resection at ~30 days

overall_design: Comparative gene expression profiling analysis of RNA-seq data for LAPC4 control (NT), LAPC4 KD (2B28 knockdown), and LAPC4 rescue (overexpression of 2B28 in KD background)

first: Anindita

last: Ravindran

middle: W

last: Badrajee Piyarathna

first: Sreekumar

last: Arun


title: MAITs in HCC

status: Public on May 12 2023

first: Tim

middle: F.

last: Greten

address: 10 Center Drive, Building 10

department: National Cancer Institute (NCI)

institute: National Institutes of Health

summary: Here we investigate the role of mucosal-associated invariant T (MAIT) cells in human and murine hepatocellular carcinoma (HCC). We isolated immune cells of syngeneic HCC cell line RIL-175 tumor-bearing or tumor-free livers and applied FACS sorting (CD45+ leukocytes) prior to 10X genomics based scRNA-seq. This is a complimentary dataset to the human scRNA-seq (deposited through dbGaP), highly multiplexed immunofluorescence microscopy using CODEX technology (deposited through TCIA) of paired patient samples.

overall_design: Experimental setup: 7 weeks old female C57BL/6 mice were injected intrahepatically with syngeneic HCC cell line RIL-175 or left tumor-free. At d28 mice were sacrificed and liver and tumor-infiltrating MNCs were isolated after in vivo digestion. CD45+ sorted cells were subsequently subjected to single-cell RNA-sequencing.

first: Benjamin

last: Ruf

first: Kimia

last: Dadkhah

first: Matthias

last: Bruhns


title: Effects of hunger on neuronal histone modifications slow aging in Drosophila

city: Ann Arbor

first: Scott

last: Pletcher

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

summary:
To determine how dietary BCAAs modulate transcriptional networks in the brain, we designed three diets of varying BCAA concentrations (low BCAA, reference diet, and high BCAA).
We performed transcriptional profiling of brains using RNA-seq after flies had been on one of three BCAA diets for one week.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for brains of flies on reference diets, low BCAA, or high BCAA diets.

first: Yang

last: Lyu

first: Kristina

middle: J

last: Weaver


title: Next-generation sequencing of lncRNA expression in cerebral ischemia mouse

city: Wuhan

first: Qiong

last: Yuan

address: Huangjiahu Road 2#

institute: Wuhan University of Science and Technology

summary:
This study aimed to explore the differential expression profiles of lncRNAs of brain between the sham group and cerebral ischemia mouse.
Methods: In the present study, focal transient cerebral ischemia was induced by transient middle cerebral artery occlusion (tMCAO) in mice. LncRNA profiles of brain tissues in IS and controls were generated by high-throughput sequencing. The sequence reads that passed quality filters were analyzed at the transcript isoform level with an Illumina HiSeqTM 2500. qRT-PCR validation was performed using SYBR Green assays.
Results: The results showed that between the sham group and I/R group, 249 lncRNAs were upregulated and 5 lncRNAs were downregulated (fold change≥2, P < 0.05, treat >1). Bioinformatic analysis was done on the identified deregulated genes through gene ontology (GO) analysis, KEGG pathway analysis and network analysis. The bioinformatics analysis of lncRNAs and mRNAs profiles in the ischemic hemisphere of adult mice provides a new perspective in the neuroprotective effects of celastrol, particularly with regards to ischemic stroke.

overall_design: LncRNAs and mRNAs profiles in two groups of mice, including sham group, tMCAO group for ischemia 1h/reperfusion 6h.

first: Xiamin

last: Hu

first: Zhijun

last: Yu

first: Chunxiang

last: Zhang


title: Effect of overexpression of ZBED3 on gene expression in HHL-5 hepatocytes

city: Wanzhou

first: he

middle: xiao

last: luo

state: Chongqing

address: No. 165 Xincheng Road

institute: Chongqing university

summary:
To investigate the regulatory function of ZBED3 in NAFLD, we established a ZBED3-overexpressing HHL-5 cell line treated with FFAs.
We then performed gene expression profiling using RNA-seq data from 2 different cells treated with the same concentration of FFAs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HHL-5 cells (ZBED3-OE) treated with FFAs.

first: Xiaohe

last: Luo

first: Linxin

last: Chen


title: Trancriptomic analysis of hematopoietic stem cells (HSCs) from mice expressing wild-type, Knock-In, knock-down, knock-out and 36N SNP variants of GFI1.

city: Luebeck

first: Pradeep

middle: Kumar

last: Patnana

state: Schleswig-Holstein

address: Ratzeburger Allee 160

country: Germany

institute: Universitätsklinikum Schleswig-Holstein

summary: GFI1 is a transcriptional repressor that plays an essential role in HSCs development, lymphoid and myeloid differentiation and Acute Myeloid Leukemia (AML) pathogenesis. Low expression of Gfi1 leads to poor prognosis in AML patients and is associated with less overall survival in murine AML models. In the current study, we show that mice with a low level or loss of GFI1 expression resulted in significantly fewer HSCs compared to normal GFI1 expression. We also show that, in a competitive transplantation setup involving cells expressing low and normal GFI1 levels, HSCs with a low level of GFI1 expression reconstituted the bone marrow (BM) including the HSCs, progenitors and differentiated cells. In contrast, HSCs with the complete loss of GFI1 failed to regenerate BM in competition with cells expressing normal GFI1 levels. To further investigate the molecular changes, we performed RNAseq analysis in HSCs derived from wildtype (GFI1-KI), low-level (GFI1-KD), loss (Gfi1-KO) and Gfi1 mutant (GFI1-36N) mice. In the pathway analysis, we observed a significant upregulation of cell-cycle-related pathways in HSCs derived from mice expressing low-level and mutant variant (36N) of GFI1., Strikingly, these pathways are significantly downregulated in the HSCs of GFI1-KO mice.

overall_design: In the current study, we performed RNAseq analysis with HSCs isolated from five different mouse models. Gfi1-WT mice that express murine Gfi1, GFI1- KI mice, that express human GFI1 in murine locus, GFI1-KD mice that express 10-20% of human GFI1 gene, Gfi1-KO mice that show the complete absence of Gfi1 and GFI1-36N mice expressing mutant human GFI1-36N variant in the murine locus. The HSCs were FACS sorted and RNA was isolated immediately.

first: Cyrus

last: Khandanpour

first: Xiaoqing

last: Xie

middle: K

first: Daria

last: Frank

first: Axel

last: Künstner


title: A method for increasing the robustness of stable feature selection for biomarker discovery in molecular medicine developed using serum small extracellular vesicle associated miRNAs and the Barrett’s oesophagus disease spectrum

city: Bedford Park

first: George

last: Mayne

state: SA

address: Room 3D213, Dept of Surgery, Flinders Medical Center

department: Surgery

country: Australia

institute: Flinders University of South Australia

summary: The biomarker development field within molecular medicine remains limited by the methods that are available for building predictive models. We developed an efficient method for conservatively estimating confidence intervals for the cross validation derived prediction errors of biomarker models. This new method was investigated for its ability to improve the capacity of our previously developed method, StaVarSel, for selecting stable biomarkers. Compared with the standard cross validation method StaVarSel markedly improved the estimated generalisable predictive capacity of serum miRNA biomarkers for the detection of disease states that are at increased risk of progressing to oesophageal adenocarcinoma. The incorporation of our new method for conservatively estimating confidence intervals into StaVarSel resulted in the selection of less complex models with increased stability and improved or similar predictive capacities. The methods developed in this study have the potential to improve progress from biomarker discovery to biomarker driven translational research.

overall_design:
Controls (n=14, all male). This group of patients had a visibly normal oesophageal mucosa at endoscopy.
Non-dysplastic Barrett’s oesophagus (NDB; n=21, all male). This group of patients had endoscopically visible Barrett’s oesophagus which was confirmed by histology to be negative for dysplasia.
Barrett’s oesophagus with high grade dysplasia (HGD; n=19, all male). This group of patients had a histological confirmation of high-grade dysplasia within the Barrett’s oesophagus segment. In one patient, the presence of T1a cancer was also noted on the histology report.

>>>Submitter states: NOTE that we are unable to submit raw data files due to institutional human ethics privacy constraints. <<<

middle: C

first: Richard

last: Woodman

first: David

middle: I

last: Watson

first: Tim

last: Bright

first: Susan

last: Gan

first: Reginald

middle: V

last: Lord

first: Michael

last: Bourke

first: Angelique

last: Levert-Mignon

first: Isabell

last: Bastian

first: Tanya

last: Irvine

first: Ann

last: Schloithe

first: Marian

last: Martin

first: Lorraine

last: Sheehan-Hennessy

first: Damian

last: Hussey


title: Effect of pirfenidone on serum-stimulated human lung fibroblasts

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

state: CA

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

summary: Idiopathic pulmonary fibrosis (IPF) is an incurable lung disease with a poor prognosis. Fibroblasts and myofibroblasts are the key cells in the fibrotic process. Pirfenidone was approved as an anti-fibrotic drug for IPF treatment as it is able to slow disease progression. The mechanisms by which the drug acts on fibroblasts are not clear. Therefore, this study aims to examine the effects of pirfenidone on the human lung fibroblast (HLF) transcriptome in vitro.

overall_design: Three human lung fibroblast (HLF) samples (denoted N1, PF2, PF3) were plated at 200K cells/well and starved with serum free DMEM medium (SFM) overnight. Cells were then stimulated with 20% FBS+/- 1mM pirfenidone for another 24 hours. RNA was isolated from using the Qiagen RNeasy protocol with on-column DNase digestion and submitted for RNA sequencing.

first: Hsiao-Yen

last: Ma

middle: A

first: Ning

last: Ding


title: INTERCELLULAR HIF1alpha REPROGAMS MAMMARY PROGENITORS AND MYELOID IMMUNE EVASION TO DRIVE HIGH-RISK BREAST LESIONS

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: The origin of breast cancer, whether primary or recurrent,is unknown. Here, we show that invasive breast cancer cells under conditions of hypoxia release small extracellular vesicles (sEV) that disrupt the differentiation hierarchy of the normal mammary epithelium, expand stem and luminal progenitor cells, and induce atypical ductal hyperplasia, cellular proliferation, and intraepithelial neoplasia. This is accompanied by systemic immunosuppression with increased myeloid cell release of the “alarmin”, S100A9, and multiple oncogenic traits of EMT, sustained angiogenesis, and local and disseminated luminal cell invasion, in vivo. When applied on the genetic background of a driver oncogene (MMTV-PyMT), hypoxic sEV accelerate bilateral breast cancer onset and progression. Mechanistically, genetic or pharmacologic targeting of hypoxia-inducible factor-1 (HIF1) packaged in hypoxic sEV or homozygous deletion of S100A9 normalizes mammary gland differentiation, restores T cell function and prevents atypical hyperplasia. The transcriptome of sEV-induced mammary gland lesions resembles luminal breast cancer, and detection of HIF1 in plasma circulating sEV from luminal breast cancer patients correlates with clinical recurrence. Therefore, a pleiotropic sEV-HIF1 signaling axis drives local and systemic mechanisms of mammary gland transformation at high risk for full-blown, multifocal breast cancer. This pathway may provide a readily accessible biomarker of luminal breast cancer progression.

overall_design: RNAseq in control and exosome normoxia or hypoxia conditions

first: Irene

last: Bertolini

first: Dario

last: Altieri


title: Bisphenol B and bisphenol AF exposure enhances uterine diseases risks in mouse

city: Taiyuan

first: Xiaoyun

last: Wu

state: Shanxi

address: Wucheng Road 92, Xiaodian District

institute: Shanxi University

summary:
Bisphenol A (BPA) analogs, bisphenol B (BPB) and bisphenol AF (BPAF) have been widely detected in the environment and human products with increasing frequency. However, uterine health risks caused by BPBBisphenol A (BPA) analogs, bisphenol B (BPB) and bisphenol AF (BPAF) have been widely detected in the environment and human products with increasing frequency. However, uterine health risks caused by BPB and BPAF exposure need to be further elucidated. The study aimed to explore whether BPB or BPAF exposure will induce adverse outcomes in uterus.
We then performed gene expression profiling using data obtained from mouse uterus exposed to BPB and BPAF at 28 days.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from mouse uterus (control group, 28-day BPB exposure group, and 28-day BPAF exposure group).

first: Xiaowen

last: Yang

first: Yuchai

last: Tian

first: Pengchong

last: Xu

first: Huifeng

last: Yue

last: Sang


title: Rewiring of master transcription factor cistrome during high-grade serous ovarian cancer development

city: San Antonio

first: Kate

last: Lawrenson

address: 7703 Floyd Curl Dr.

institute: Cedars Sinai Medical Center

summary: The transcription factors MECOM, PAX8, SOX17 and WT1 are candidate master regulators of high-grade serous ‘ovarian’ cancer (HGSC), yet their cooperative role in the hypothesized tissue of origin, the fallopian tube secretory epithelium (FTSEC) is unknown. We generated 26 epigenome (CUT&TAG, CUT&RUN, ATAC-seq and HiC) data sets and 24 profiles of RNA-seq transcription factor knock-down followed by RNA sequencing in FTSEC and HGSC models to define binding sites and gene sets regulated by these factors in cis and trans. This revealed that MECOM, PAX8, SOX17 and WT1 are lineage-enriched, super-enhancer associated master regulators whose cooperative DNA-binding patterns and target genes are re-wired during tumor development. All four TFs were indispensable for HGSC clonogenicity and survival but only depletion of PAX8 and WT1 impaired FTSEC cell survival. These four TFs were pharmacologically inhibited by transcriptional inhibitors only in HGSCs but not in FTSECs. Collectively, our data highlights that tumor-specific epigenetic remodeling is tightly related to MECOM, PAX8, SOX17 and WT1 activity and these transcription factors are targetable in a tumor-specific manner through transcriptional inhibitors.

overall_design: CUT&RUN or CUT&TAG of H3K27ac, H3K27me3, MECOM, PAX8 and SOX17 for cell lines and primary ex vivo cultures. ATAC-seq of cell lines.

first: Robbin

last: Nameki

first: Pak

middle: H

last: Yu


title: Effects of short-term boron deficiency on gene expression in Pyrus betulaefolia Bunge roots

first: Tao

last: Chen

state: Jiangsu

address: 48 Wenhui East Road

department: School of Horticulture and Plant Protection

institute: Yangzhou University

summary: To investigate  the possible molecular mechanisms of boron deficiency tolerance in roots, we explored the internal changes of the gene expession of Pyrus betulaefolia Bunge roots after 24 hours boron deficiency

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of  Pyrus betulaefolia Bunge roots under 24 hours boron deficiency

first: Xiao

last: Liu

first: Jiabei

last: Cai


title: MACROPHAGE CD5L IS A NOVEL TARGET FOR CANCER IMMUNOTHERAPY

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

summary: Tumor associated macrophages (TAMs) can acquire an immunosuppressive, M2 polarization phenotype, thereby promoting tumor growth and protecting it from chemo or immuno-therapy. Since TAMs are plastic cells, their selective reprogramming presents an attractive therapeutic strategy. CD5L is a macrophage glycoprotein that controls key mechanisms in inflammatory responses and promotes M2 polarization. Here we report that CD5L TAMs expression in lung adenocarcinoma correlates with poor outcome. Additionally, cancer cell CMs induced macrophage M2 polarization and enhanced CD5L expression. We have raised a novel monoclonal antibody (mAb), RImAb, that specifically binds to human and mouse CD5L and blocks its M2 polarizing activity. RImAb administration reduced tumor growth in a mouse subcutaneous syngeneic model of lung cancer and modified the tumor microenvironment, altering intratumoral immune cell population profile, decreasing vascularity, and increasing the inflammatory milieu. The present study reveals a key function for CD5L protein in modulating macrophage activity and its interactions within the TME. Targeting CD5L with a mAb, was able to reduce tumor growth and modulate the TME, thus representing a promising approach to cancer immunotherapy.

overall_design: RNA-seq from CD45+CD11b+Ly6GlowLy6C+ cells were processed in control samples (n=3) and treated with RImAb (n=4).

first: M

last: Sarrias

first: C

last: Martori

first: L

last: Sanchez-Moral

first: T

last: Paul


title: Prediction of on-target and off-target activity of CRISPR-Cas13dguide RNAs using deep learning

city: New York

first: Hans-Hermann

last: Wessels

address: 101 Avenue of the Americas

institute: New York Genome Center

summary: Transcriptome engineering applications in living cells with RNA-targeting CRISPR effectors depend on accurate prediction of on-target activity and off-target avoidance. Here, we design and test ~200,000 RfxCas13d guide RNAs targeting essential genes in human cells with systematically-designed mismatches, insertions and deletions (indels). We find that mismatches and indels have a position- and context-dependent impact on Cas13d activity, and mismatches that result in G:U wobble pairings are better tolerated than other single-base mismatches. Using this large-scale dataset, we train a convolutional neural network that we term TIGER (Targeted Inhibition of Gene Expression via gRNA design) to predict efficacy from guide sequence and context. TIGER outperforms existing models at predicting on- and off-target activity on our dataset and published datasets. We show that TIGER scoring combined with specific mismatches yields the first general framework to modulate transcript expression, enabling use of RNA-targeting CRISPRs to precisely control gene dosage.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Evaluation of RfxCas13d guide RNAs for On-target and Off-target activity.

first: Andrew

last: Stirn

first: Alejandro

last: Méndez-Mancilla

first: Eric

last: Kim

first: Sydney

last: Hart

first: David

last: Knowles

first: Neville

middle: E

last: Sanjana


title: Highly efficient and multiplexed transcriptome profiling of cardiotoxicity induced by tyrosine kinase inhibitors

city: Beijing

first: Huan

last: Wang

address: Peking University Health Science Center, No. 38 Xueyuan Road, Haidian District

department: Basic Medical Sciences

institute: Peking University

summary: Tyrosine kinase inhibitors (TKIs) are anti-cancer therapeutics used in long-term treatment. However, many of them cause cardiotoxicity with limited cure. We aim to define molecular mechanisms of cardiotoxicity that can be targeted for oncocardiology treatment. Eight TKIs with different levels of cardiotoxicity were selected and transcriptome responses of human cardiomyocytes to them at varying doses and times were profiled using a high throughput RNAseq technique. Transcriptome changes are classified into 7 clusters with mainly single-drug clusters. Drug-specific effects on the transcriptome dominate over dose-, time- or toxicity-dependent effects. Two clusters with three TKIs (afatinib, ponatinib and sorafenib) have the top enriched pathway as the endoplasmic reticulum stress. These TKIs cause an increase in reactive oxygen species, lipid peroxidation, or calcium, and induce biased endoplasmic reticulum stress on the PERK and the IRE1α pathway. Inhibiting either PERK or IRE1α blocks expression of cardiomyocyte injury and pro-inflammatory markers. Our data contain rich information about stress responses of human cardiomyocytes to specific TKIs, representing potential molecular mechanisms of cardiotoxicity. ER stress-induced inflammation is a promising therapeutic target to mitigate ponatinib- and sorafenib-induced cardiotoxicity

overall_design: Comparative transcriptome of human cardiomyocytes treated with 8 FDA-approved TKIs. For 2 of the TKIs (Crizotinib and Ponatinib), treatments were done with 0,316µM at day 1, 3 and 5, as well as 1 and 3.16 µM at day 1. For 6 of the TKIs (Afatinib, Dasatinib, Gefitinib,  Nilotinib, Ponatinib, Sorafenib and Sunitinib), treatments were done with 3.16 µM at day 1, 3 and 5, as well as 1 and 10 µM at day 1. Controls were cells treated with DMSO (0.1%) for 1, 3 or 5 days. Each treatments were done in triplicate.

first: Peter

last: Sorger

first: Sarah

last: Boswell


title: The SNP rs755622 is associated with immune activation in Glioblastoma

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

institute: CLEVELAND CLINIC LERNER COM-CWRU

summary: Intratumoral heterogeneity is a defining hallmark of glioblastoma, driving drug resistant and ultimately recurrence. Many somatic drivers of microenvironmental change have been shown to affect this heterogeneity and ultimately treatment response. However, little is known about how germline mutations effect the tumoral microenvironment. Here, we find that the single-nucleotide polymorphism (SNP) rs755622 in promoter of the cytokine macrophage migration inhibitory factor (MIF), is associated with increased leukocyte infiltration in glioblastoma. Furthermore, we identified an association between rs755622 and lactotransferrin expression, which could also be used as a biomarker for immune-infiltrated tumors. These findings demonstrate that a germline SNP in the promoter region of MIF may impact the immune microenvironment and further reveals a link between lactotransferrin and immune activation.

overall_design: We demonstrate that patients with the MIF SNP rs755622 have an increase in lactotransferrin (LTF) expression and increased immune microenvironment signaling

first: Tyler

last: Alban

first: Justin

middle: D

last: Lathia


title: M1BP RNAi during Drosophila flight myogenesis: Analyses at 0h APF stage

city: Marseille

last: Saurin

address: Campus de Luminy

country: France

institute: IBDM / CNRS

summary: Oxidative metabolism is the predominant energy source for muscle contraction. How this is transcriptionally regulated during muscle development to accommodate different metabolic requirements and muscle types is largely unknown. We show that the formation of mitochondria cristae harbouring the respiratory chain is concomitant with a large-scale transcriptional upregulation of genes linked with oxidative phosphorylation (OXPHOS) during the middle of Drosophila flight muscle development. We further demonstrate using high-resolution imaging, transcriptomic and biochemical analyses that Motif-1-binding protein (M1BP) transcriptionally regulates the expression of genes encoding critical components for OXPHOS complex assembly and integrity. In the absence of M1BP, mitochondrial respiratory complexes are improperly assembled and aggregate in the mitochondrial matrix, triggering a strong protein quality control response. Together, this study provides the first insight into the transcriptional regulation of oxidative metabolism during Drosophila myogenesis and identifies M1BP as a novel player in this process.

overall_design: Differential gene expression analyses of M1BP RNAi in late larval (0h APF) wing disc associated myoblasts

first: Gabreila

last: Poliacikova

first: Marine

last: Barthez

first: Thomas

last: Rival

first: Aïcha

last: Aouane

first: Nuno

middle: M

last: Luis

first: Fabrice

last: Richard

first: Nicolas

last: Brouilly

first: Frank

last: Schnorrer

first: Corine

last: Maurel-Zaffran

first: Yacine

last: Graba


title: A woody plant degrading pathogen effector targets host glucose signaling protein VvRHIP1 to promote virulence

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

summary: Lasiodiplodia theobromae is one of the causal agents of Grapevine trunk diseases, which becomes a tremendous threat to the grapevine production worldwide. Plant pathogens secrete diverse effectors to suppress host immune responses or regulate the host metabolism to promote diseases. Our results suggest that L. theobromae LtCre1 targets host VvRHIP1 to manipulate the sugar signaling pathway, through disrupting the association of VvRHIP1 and VvRGS1 complex.

overall_design: Total RNA was isolated from N. benthamiana plant tissue using a TransZol Plant RNA Kit (TransGen Biotech, Beijing, China). The wild type seedings were used as control and samples grown under normal condition was collected for two biological replicates. The cDNA libraries were generated using NEBNext? Ultra? RNA Library Prep Kit for (Illumina, USA) according to manufacturer's recommendations. Then the libraries were sequenced using an Illumina Hiseq platform (Illumina, USA) and 150 bp paired-end reads were produced. Clean reads were filtered by removing reads containing ploy-N, reads containing adapter, and low-quality reads from the raw data. The filtered clean reads were aligned to the N. benthamiana reference genome using Hisat2 v2.0.4 with default parameters. The expression level for each transcript was normalized and estimated using the fragments per kilobases per million reads (FPKM) method (Trapnell et al., 2010). The differential expression analysis was determined using the DESeq R package (1.18.0) with default parameters (P-value <0.05; log2 (fold change) >2 or log2 (fold change) < -2).  Gene Ontology (GO) terms for all differentially expressed genes was identified by the GOseq R package. The KEGG enrichment analysis of differential expression genes was performed using KOBAS software with default parameters.

first: Qikai

last: Xing


title: The secretome of irradiated peripheral blood mononuclear cells attenuates activation of mast cells and basophils

city: Vienna

first: Martin

last: Direder

state: Vienna

address: Lazarettgasse 14

department: Orthopedic and Trauma Surgery

country: Austria

institute: Medical University Vienna

summary: Effect of PBMCsec on the transcriptional profile of dermal mast cells were investigated in a dataset of PBMCsec-treated female Balb/c mice dorsal skin.

overall_design: Single cell RNA-sequencing gene expression comparison of mouse dorsal skin subcutaneously injected with PBMCsec or vehicle control. Single-cell suspension from four samples per condition were prepared using MACS Miltenyi Whole Skin Dissociation Kit (Miltenyi). Libraries were generated using Chromium Next GEM Single Cell 3´GEM, Library & Gel Bead Kit v3.1, Chromium Nexxt GEM Chip G Single Cell Kit and Single Index Kit T Set A (all 19x Genomics, Pleasanton, CA, USA).

first: Maria

last: Laggner

first: Gabriela

last: Sánchez Acosta

first: Claudia

last: Kitzmüller

first: Dragan

last: Copic

first: Florian

last: Gruber

first: Lukas

last: Altenburger

first: Vera

last: Vorstandlechner

first: Alfred

last: Gugerell

first: Katharina

last: Klas

first: Daniel

last: Bormann

first: Anja

last: Peterbauer

first: Akira

last: Shibuya

first: Barbara

last: Bohle

first: Hendrik

last: Ankersmit

first: Michael

last: Mildner


title: CRISPR screening in human primordial germ cell-like cells specification

first: Youngsun

last: Hwang

address: 3800 Spruce Street Old Vet Quad 220E

institute: University of Pennsylvania

summary: Although molecular studies on the human reproduction are arising, mechanisms underlying human primordial germ cell (PGC) development have remained largely unknown. Here, we conducted custom CRISPR screening to identify a subset of key genes for acquisition and maintenance of PGC fate in humans, combined with in vitro system of hPGC-like cells (hPGCLCs). Among crucial candidates by screen analysis, we characterize AKT coactivator, TCL1A, as a progressive role in hPGCLC development. A mutant TCL1A downregulated gene expression related to translational control, followed by reduced global protein synthesis and proliferation consequently via depressing AKT-mTOR signaling pathway. Our study provides novel regulators critical to hPGCLC development and demonstrate the importance of translational control in human reproduction.

overall_design: hiPSCs, iMeLCs, hPGCLCs, from wild-type and TCL1A knockout, were used in this study.

first: Kotaro

last: Sasaki

first: Young

middle: S


title: The pathogenesis of common Gjb2 mutation associated with human hereditary deafness in mice

city: Shanghai

first: Qing

last: Li

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

summary: Mutations in GJB2 (Gap junction protein beta 2) are the most common genetic cause of non-syndromic hereditary deafness in humans, especially the 35delG and 235delC mutations. Owing to the homozygous-lethal of Gjb2 mutation in mice, there are currently no perfect mouse models carrying Gjb2 mutation to mimic human hereditary deafness and unveil the pathogenesis. Here, we first constructed heterozygous mutant mice, Gjb2+/35delG and Gjb2+/235delC, through androgenic haploid embryonic stem cells (AG-haESCs) mediated semi-cloning technology, which showed normal hearing function at P28. Furthermore, a homozygous mutant mouse model, Gjb235delG/35delG, was generated via enhanced tetraploid embryo complementation, which exhibited profound hearing loss like human patients at P14. Mechanism analysis showed that Gjb2 35delG disrupts the formation of intercellular gap junction channel and tunnel of Corti, and hair cell mechanotransduction, rather than the development of hair cells. Collectively, our study provides ideal mouse models for understanding the pathogenic mechanism and opens up a new avenue for investigating the treatment for DFNB1A-related hereditary deafness.

overall_design: The cochleae of wild-type and Gjb2 35delG/35delG mice were carefully collected and surgically divided into three equal sections, including the apical, middle, and basal turns.

first: Yilai

last: Shu

first: Jinsong


title: Beadchip technology to detect DNA methylation in the mouse faithfully recapitulates whole genome bisulfite sequencing

city: Durham

first: Elizabeth

last: Martin

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary: DNA methylation data generated by the Illumina Mouse Methylation Beadchip for comparison to WGBS

overall_design: Contained in the dataset are reads from 6 unique male C57B6/J mice, 6 unique female C57B6/J mice, 6 C3H/HeJ male mice and 6 C3H/HeJ female mice.

first: Paul

last: Wade


title: Spatial transcriptomics: The effect of consecutive slices data integration on accurate cell type annotation and clustering

city: Gdansk

first: Jakub

last: Mieczkowski

address: Debinki 12

country: Poland

institute: Medical University of Gdansk

summary: In 10X Genomics Visium Spatial Gene Expression (ST), the resolution for distinguishing neighboring cells can be improved using data integration with single-cell/single-nuclei transcriptomics profiles. Besides, depending on the cell type and tissue, nuclei size may vary significantly to an extent that it may exceed the thickness of tissue slices. This may jeopardize capturing full transcriptomics profile of single slice due to the improper/incomplete incision of nuclei during cryosectioning process and this may cause drawbacks in downstream analysis.   To monitor the probable consequences, we monitored the effect of consecutive slices data integration (CSDI) on improvement of cell type clustering and annotation through transferring cell labels from a single-nuclei transcriptomics dataset to ST. To do so, two consecutive slices from the orbitofrontal neocortex and temporal neocortex of two post mortem brain samples were obtained and their spatial transcriptomics profiles were retrieved using 10x Genomics Visium Spatial Gene Expression protocol.     Using CSDI, not only the number of identified clusters were increased and the inconsistency between the pattern of clusters in consecutive slices was resolved, but the layered-structure of gray matter was unveiled. Besides, only after CSDI the transferred annotations from single-nuclei transcriptomics to ST could match the microscopic results.  CSDI can improve the ST clustering and cell type annotation by providing the full signals coming from all cell types of single slice of tissue. The codes in R programming language are publicly available at https://github.com/ElyasMo/ST_snRNA-seq

overall_design: Four pairs of consecutive slices from Orbitofrontal and Temporal neocortex of post mortem brain samples

first: Elyas

last: Mohammadi

first: Katarzyna

last: Chojnowska

first: Michał

last: Bieńkowski

first: Anna

last: Kostecka

first: Koczkowska

last: Magdalena

first: Żmijewski

last: Michał

first: Jąkalski

last: Marcin

first: Inglesson

first: Hyman

last: Bradley

first: Filipowicz

last: Natalia

first: Olszewski

last: Paweł

first: Davies

last: Hanna

first: Wierzbicka

last: Justyna

first: Jan

last: Dumanski

first: Arkadiusz

last: Piotrowski


title: Rewiring of master transcription factor cistrome during high-grade serous ovarian cancer development [RNA-seq]

first: Kate

last: Lawrenson

summary: NOT PROVIDED; REQUESTED

overall_design: One fallopian tube secretory epithelial cell line  (FT246) and one high-grade serous ovarian cancer cell line (KURAMOCHI) were knocked down with siRNAs for two scrambled controls, MECOM,PAX8,SOX17 and WT1

first: Robbin

last: Nameki


title: Effect of LRP1 deletion in vascular mural cells and APOE gentotype on gene expression in mouse brains

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary:
To investigate the apoE isoform-dependent role of vascular mural cell (VMC)-LRP1, we generated VMC-specific LRP1 knockout mice (smLrp1-/-), followed by breeding these mice with either APOE3-targeted replacement (TR) or APOE4-TR mice
We then performed gene expression profiling analysis using data obtained from RNA-seq of cortical samples from 4 different mouse models

overall_design: Comparative gene expression profiling analysis of RNA-seq data for VMC-LRP1 deificency in the presenc eof apoE3 or apoE4

first: Takahisa

last: Kanekiyo


title: Systematic Identification of CRISPR-mediated Off-target Effects by CROss-seq

city: GuangZhou

first: Yan

last: Li

state: GuangDong

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

institute: Sun Yat-sen University

summary: We developed CROss-seq, a versatile, efficient and cost-effective method for genome-wide off-target profiling in multiple genome editing systems. Purpose: CRISPR-mediated genome editors have been widely deployed in basic research and therapeutic applications, yet the targeting specificity of these editors is still the major concern. Method to examine the genome-wide off-target effects of these editors remains lagging behind. Methods:  in vivo CROss-seq, the transfected cells are labeled with N3-kethoxal for 45 minutes; in vitro CROss-seq, the genomic DNA are incubated with N3-kethoxal for 2 hours. The treated gDNA are processed with biotin click reaction, fragmentation, adapter ligation, and pull-down steps. The purified libraries were sequenced on Illumina HiSeq X Ten platform to generate paired-end reads. Results: Through CROss-seq we successfully both in vivo and in vitro to evaluate the off-target effects of CRISPR-Cas9 nuclease, base editors and prime editor. The in vivo assay was more specific while in vitro assay was more sensitive, highlighting the necessity of coupling in vivo and in vitro assays to achieve a comprehensive and precise assessment of the off-target effects. CROss-seq also revealed chromatin accessibility plays an important role in the off-target activity of the CRISPR-based editing. In addition, we identified limited genome-wide off-target sites of BE and PE in vivo, indicating that both editors were highly specific to target site.

overall_design: CROss-seq utilized a high-specificity ssDNA capturing strategy, enables genome-wide profiling of on-target and off-target activity of CRISPR-mediated genome editors at the whole-genome level. We applied CROss-seq to off-target evaluation in HEK293T cells for Cas9, ABE7.10, ABE8e, BE3, BE4max and PE2, with several frequently used sgRNAs: “HBG1/2”, “HEK293 site 2”, and “HEK293 site 3”.

first: Guan-Zheng

last: Luo


title: C-type lectin receptor expression is a hallmark of neutrophils infiltrating the skin in epidermolysis bulls acquisita.

status: Public on May 11 2023

city: Chicago

first: Kyle

last: Amber

state: Illinois

address: 1735 W Harrison St. Lab 741

institute: Rush University Medical Center

summary: Characterization of neutrophil activation from blood to blister in experimental epidermolysis bullosa acquisita: C-type lectin receptors are dispensable in inducing disease.

overall_design: Mice aged 6-8 weeks were used for the experiments (n=3 / cohort). Mice were treated with thrice weekly injections of 250ug of antigen affinity purified vWFA2-COL7 IgG or control rabbit IgG for 2 weeks. Tissue harvesting was subsequently performed after this 2 week period. Single cell suspensions of whole blood (WB) cells or ear skin cells were pooled per cohort.